To : ALL Subj: Next post The next post is to Jesse Hornbacher. He has asked me for referen

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From: Martin Goldberg 4 Jun 94 17:24 To : ALL Subj: Next post The next post is to Jesse Hornbacher. He has asked me for references that in many species Hemoglobin is very similar and that, in particular, the similarity rate between humans and chimps is 98%. What I have done, instead, is to run a similarity search using human hemoglobin as a match criterion and searched the entire Genbank data base. What is in the post is the reply to my inquiry. I will commnet on it as I post it. Technically, those that understand computers will likely understand it more than others as it relies on some algorithms to do these matchings. John P. is now posting in here and at one point told me that he had written some of these types of programs. --- msgedsq 2.1 * Origin: Welcome to the lab. Now roll up your sleeve. (1:124/4115.221) From: Martin Goldberg 4 Jun 94 17:27 To : Jesse Hornbach Subj: Hemoglobin You asked for this data, and here it is. I will explain as we go along.... This is a representation of the best matches. I asked for 80 of the best ones or we would have gotten too much background. The scores show how many matches of how many are perfect matches. Remember that a semi conservative substitution is not counted as a miss or a hit, although it is almost the same thing as an exact match. Score Init1 Initn < 2 33 33:================= 4 5 5:=== 6 18 18:========= 8 60 60:============================== 10 307 307:================================================== 12 534 534:================================================== 14 691 691:================================================== 16 2298 2298:================================================== 18 3161 3161:================================================== 20 5391 5391:================================================== 22 6375 6375:================================================== 24 4620 4620:================================================== 26 3732 3732:================================================== 28 2927 2874:================================================== 30 2047 1929:================================================== 32 1251 1133:================================================== 34 776 700:================================================== 36 456 458:================================================== 38 288 333:================================================== 40 189 252:================================================== 42 133 187:================================================== 44 68 106:==================================++++++++++++++++ 46 36 76:==================++++++++++++++++++++ 48 31 53:================+++++++++++ 50 25 54:=============++++++++++++++ 52 11 21:======+++++ 54 8 29:====+++++++++++ 56 2 20:=+++++++++ 58 2 8:=+++ 60 0 3:++ 62 1 4:=+ 64 4 6:==+ 66 0 5:+++ 68 0 2:+ 70 4 2:=- 72 0 0: 74 1 0:- 76 1 0:- 78 1 1:= 80 0 0: 80 513 519:================================================== mean initn score: 20.9 (3.94) mean init1 score: 20.9 (3.94) The "="'s are exact matches ofr the lineup....the "+"'s are semi conservative subs and the "-"'s are misses. The best scores are: init1 initn opt.. Sw:Hba_Human P01922 HEMOGLOBIN ALPHA CHAIN. 2/94 655 655 655 Sw:Hba_Gorgo P01923 HEMOGLOBIN ALPHA CHAIN. 7/86 654 654 654 Sw:Hba_Preen P01924 HEMOGLOBIN ALPHA CHAIN. 7/86 653 653 653 Sw:Hba_Ponpy P06635 HEMOGLOBIN ALPHA CHAIN. 2/91 649 649 649 Sw:Hba_Macas P21766 HEMOGLOBIN ALPHA-1, ALPHA-2, AND ALP... 648 648 648 Sw:Hba_Macfa P21767 HEMOGLOBIN ALPHA-A, ALPHA-Q, ALPHA-R... 647 647 647 Sw:Hba_Macmu P01925 HEMOGLOBIN ALPHA CHAIN. 5/91 646 646 646 Sw:Hba_Cerae P01926 HEMOGLOBIN ALPHA CHAIN. 7/86 646 646 646 Sw:Hba_Sagfu P01929 HEMOGLOBIN ALPHA CHAIN. 7/86 646 646 646 Sw:Hba_Macne P19002 HEMOGLOBIN ALPHA-1, ALPHA-2, AND ALP... 645 645 645 Sw:Hba_Macsi P21768 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 645 645 645 Sw:Hba_Macsp P07402 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 644 644 644 Sw:Hba_Calar P18972 HEMOGLOBIN ALPHA CHAIN. 11/90 643 643 643 Sw:Hba_Atege P01927 HEMOGLOBIN ALPHA CHAIN. 4/90 642 642 642 Sw:Hba_Cebap P01928 HEMOGLOBIN ALPHA CHAIN. 7/86 641 641 641 Sw:Hba_Cebca P07421 HEMOGLOBIN ALPHA CHAIN. 4/88 641 641 641 Sw:Hba_Certo P01933 HEMOGLOBIN ALPHA CHAIN. 11/90 635 635 635 Sw:Hba_Colba P01930 HEMOGLOBIN ALPHA CHAIN. 7/86 634 634 634 Sw:Hba_Mansp P08258 HEMOGLOBIN ALPHA-I AND ALPHA-II CHAI... 633 633 633 Sw:Hba_Nycco P01937 HEMOGLOBIN ALPHA CHAIN. 7/86 629 629 629 Sw:Hba_Cynsp P11753 HEMOGLOBIN ALPHA CHAIN. 10/89 628 628 628 Sw:Hba_Lorta P01938 HEMOGLOBIN ALPHA CHAIN. 5/92 627 627 627 Sw:Hba3_Gorgo P01934 HEMOGLOBIN ALPHA-3 CHAIN. 7/86 627 627 627 Sw:Hba_Myove P11757 HEMOGLOBIN ALPHA CHAIN. 10/89 626 626 626 Sw:Hba_Tarba P01940 HEMOGLOBIN ALPHA CHAIN. 7/86 626 626 626 Sw:Hba_Papcy P01931 HEMOGLOBIN ALPHA CHAIN. 11/88 625 625 625 Sw:Hba_Thege P01932 HEMOGLOBIN ALPHA CHAIN. 7/86 625 625 625 Sw:Hba3_Pantr P01935 HEMOGLOBIN ALPHA-3 CHAIN. 5/91 625 625 625 Sw:Hba2_Galcr P01939 HEMOGLOBIN ALPHA-B CHAIN (ALPHA-II)... 624 624 624 Sw:Hba_Rouae P01956 HEMOGLOBIN ALPHA CHAIN. 7/86 623 623 623 Sw:Hba1_Galcr P14259 HEMOGLOBIN ALPHA-A CHAIN (ALPHA-I).... 621 621 621 Sw:Hba_Pteal P14389 HEMOGLOBIN ALPHA CHAIN. 5/91 619 619 619 Sw:Hba_Marma P08852 HEMOGLOBIN ALPHA CHAIN. 11/88 619 619 619 Sw:Hba_Spepa P11750 HEMOGLOBIN ALPHA CHAIN. 11/90 617 617 617 Sw:Hba_Tapge P28780 HEMOGLOBIN ALPHA CHAIN. 12/92 616 616 616 Sw:Hba_Antpa P14387 HEMOGLOBIN ALPHA CHAIN. 1/90 616 616 616 Sw:Hba_Turtr P18978 HEMOGLOBIN ALPHA CHAIN. 11/90 615 615 615 Sw:Hba_Horse P01958 HEMOGLOBIN ALPHA CHAINS (SLOW AND FA... 614 614 614 Sw:Hba_Speci P09420 HEMOGLOBIN ALPHA CHAIN. 3/89 613 613 613 Sw:Hba_Macca P09839 HEMOGLOBIN ALPHA CHAIN. 1/90 612 612 612 Sw:Hba_Speto P07403 HEMOGLOBIN ALPHA CHAIN. 4/90 612 612 612 Sw:Hba_Ctegu P20854 HEMOGLOBIN ALPHA CHAIN. 11/91 611 611 611 Sw:Hba_Ptepo P14390 HEMOGLOBIN ALPHA CHAIN. 5/91 611 611 611 Sw:Hba_Phyca P09904 HEMOGLOBIN ALPHA CHAIN. 11/90 610 610 610 Sw:Hba_Cersi P01963 HEMOGLOBIN ALPHA CHAIN. 7/86 609 609 609 Sw:Hba_Tapte P01962 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 608 608 608 Sw:Hba_Hipam P19015 HEMOGLOBIN ALPHA CHAIN. 11/90 608 608 608 Sw:Hba_Rabit P01948 HEMOGLOBIN ALPHA-1 AND ALPHA-2 CHAIN... 608 608 608 Sw:Hba1_Tadbr P11755 HEMOGLOBIN ALPHA-1 CHAIN. 10/89 608 608 608 Sw:Hba_Rhiun P09906 HEMOGLOBIN ALPHA CHAIN. 3/89 607 607 607 Notice that all the hits that were made were for hemoglobin. As you can see, the human matched the human for a perfect score. As we go down the list you can see that they line up less and less. the top of the list are the simians and the apes. At the bottom are things like rabbits and the like. I will show the actual matches... Hemo Sw:Hba_Human DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE) DT 01-FEB-1994 (REL. 28, LAST ANNOTATION UPDATE) DE HEMOGLOBIN ALPHA CHAIN. . . . SCORES Init1: 655 Initn: 655 Opt: 655 100.0% identity in 141 aa overlap ^^^^^^ 10 20 30 40 50 60 Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Hba_Hu VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK 10 20 30 40 50 60 70 80 90 100 110 120 Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Hba_Hu KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA 70 80 90 100 110 120 130 140 Hemo VHASLDKFLASVSTVLTSKYR ||||||||||||||||||||| Hba_Hu VHASLDKFLASVSTVLTSKYR 130 140 Top line labeled "HEMO" is my sequence of Hemoglobin submitted. Bottom is the target sequence. Obviously it matches 100%. No one could argue, but this is how the computer works. Hemo Sw:Hba_Gorgo ID HBA_GORGO STANDARD; PRT; 141 AA. AC P01923; DT 21-JUL-1986 (REL. 01, CREATED) DT 21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE) DT 21-JUL-1986 (REL. 01, LAST ANNOTATION UPDATE) DE HEMOGLOBIN ALPHA CHAIN. . . . SCORES Init1: 654 Initn: 654 Opt: 654 99.3% identity in 141 aa overlap ^^^^^ Gorilla. 10 20 30 40 50 60 Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK ||||||||||||||||||||||:||||||||||||||||||||||||||||||||||||| Hba_Go VLSPADKTNVKAAWGKVGAHAGDYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK 10 20 30 40 50 60 70 80 90 100 110 120 Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Hba_Go KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA 70 80 90 100 110 120 130 140 Hemo VHASLDKFLASVSTVLTSKYR ||||||||||||||||||||| Hba_Go VHASLDKFLASVSTVLTSKYR 130 140 SCORES Init1: 653 Initn: 653 Opt: 653 97.9% identity in 141 aa overlap ^^^^^ One of the simians... 10 20 30 40 50 60 Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK ||||||||||||||||||:|:||||||||||||||||||||||||||||||||||||||| Hba_Pr VLSPADKTNVKAAWGKVGGHGGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK 10 20 30 40 50 60 70 80 90 100 110 120 Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA |||||||||||||||||:|||||||||||||||||||||||||||||||||||||||||| Hba_Pr KVADALTNAVAHVDDMPHALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA 70 80 90 100 110 120 130 140 Hemo VHASLDKFLASVSTVLTSKYR ||||||||||||||||||||| Hba_Pr VHASLDKFLASVSTVLTSKYR 130 140 If you look carefully at the last two comparisons, you can see where the differences occur. There is no more reason to list all the matches here. I will list the similarities 97.9% identity in 141 aa overlap 97.2% identity in 141 aa overlap 97.2% identity in 141 aa overlap 96.5% identity in 141 aa overlap 96.5% identity in 141 aa overlap 96.5% identity in 141 aa overlap 96.5% identity in 141 aa overlap 96.5% identity in 141 aa overlap 96.5% identity in 141 aa overlap 95.7% identity in 141 aa overlap 95.7% identity in 141 aa overlap 92.9% identity in 141 aa overlap 93.6% identity in 141 aa overlap 93.6% identity in 141 aa overlap 90.1% identity in 141 aa overlap 92.9% identity in 141 aa overlap 89.4% identity in 141 aa overlap 90.8% identity in 141 aa overlap 91.5% identity in 141 aa overlap 92.2% identity in 141 aa overlap 91.5% identity in 141 aa overlap 88.7% identity in 141 aa overlap 92.2% identity in 141 aa overlap 90.1% identity in 141 aa overlap 92.2% identity in 141 aa overlap 87.2% identity in 141 aa overlap 90.8% identity in 141 aa overlap 90.8% identity in 141 aa overlap 90.1% identity in 141 aa overlap 90.1% identity in 141 aa overlap 83.7% identity in 141 aa overlap 87.9% identity in 141 aa overlap 90.1% identity in 141 aa overlap 89.4% identity in 141 aa overlap ID HBA_MACCA STANDARD; PRT; 141 AA. AC P09839; DT 01-MAR-1989 (REL. 10, CREATED) DT 01-MAR-1989 (REL. 10, LAST SEQUENCE UPDATE) DT 01-JAN-1990 (REL. 13, LAST ANNOTATION UPDATE) DE HEMOGLOBIN ALPHA CHAIN. . . . SCORES Init1: 612 Initn: 612 Opt: 612 10 20 30 40 50 60 Hemo VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK |||:|||:||||||:|||::||||||||||||||||||||||||||||:||||||||||| Hba_Ma VLSAADKGNVKAAWDKVGGQAGEYGAEALERMFLSFPTTKTYFPHFDLAHGSAQVKGHGK 10 20 30 40 50 60 70 80 90 100 110 120 Hemo KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA ||||||||||:|:||:|:||||||||||:|||||||||||||||||||||:| ||||||| Hba_Ma KVADALTNAVGHMDDLPGALSALSDLHAYKLRVDPVNFKLLSHCLLVTLASHHPAEFTPA 70 80 90 100 110 120 130 140 Hemo VHASLDKFLASVSTVLTSKYR :|||||||:|||||||||||| Hba_Ma IHASLDKFFASVSTVLTSKYR 130 140 This is the last one. You can see that there are more differences in it fromt he first one, but then rabbits are somewhat more removed from humans than chimps. The point of all of this is to whow you that relatedness occurs on a molecular level. I can look at the DNA of any animal and tell how far removed it is from another by getting the sequence of the DNA and showing base pair differences. A single pair difference is enough. This makes much more logical sense to me thatn believing in a fairy story that sounds as if some kid made it up. --- msgedsq 2.1 * Origin: Welcome to the lab. Now roll up your sleeve. (1:124/4115.221)

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