Supplementary tables for the paper

"Alignment of protein sequences by their profiles."

Marc A. Marti-Renom, M.S. Madhusudhan and Andej Sali

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Testing and Training reference sets. The reference alignments are pairwise, structure-based alignments. They were extracted from our comprehensive database of pairwise structure-based alignments, DBAli. The alignments in DBAli were calculated by superposing all pairs of proteins of known structure in the Protein Data Bank (Feb. 1999) that are classified into the same H class in the CATH database, using the program CE. There are 33,920 such alignments with a Z-score higher than 3.8. They cover the entire spectrum of sequence and structure similarities.
First, 387 alignments were extracted from DBAli by requiring up to 40% sequence identity, at least 100 aligned residues, at least 50% of the residues aligned, and at least 90% of one chain spanned by the first and last aligned residue. Second, structure pairs that did not have at least 50% of the residues in the shorter chain aligned by MAMMOTH were also eliminated, resulting in the final set of 300 reference alignments. These 300 alignments were randomly divided into the training and testing sets of 100 and 200 alignments, respectively. The training set of alignments was used to optimize the gap initiation and gap extension penalties for all of our alignment protocols and the parameter s for the two posterior substitution matrix protocols, while the testing set was used to assess the performance of all examined alignment methods. The PDB chain identifiers, chain lengths, percentage sequence identities, RMSD’s for the aligned Cα atoms, average percentages of the aligned Cα atoms, and percentages of structurally equivalent residues are listed separately for the training and testing alignments.

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Testing set of pairs of structures Chain A Chain B % Seq. Id. RMSD 1qfeA 1rlcL 4.38 3.79 3adk 1nstA 4.74 3.34 1barA 1xyfA 4.84 1.84 1f6yA 1reqA 6.20 3.81 1dioA 1qfeA 6.25 2.95 1ez3A 1fewA 6.61 2.39 1dioA 1d9eA 6.67 3.30 1qfeA 1dxeA 6.76 3.15 1qfeA 1ald 6.91 3.84 1nsj 1reqA 7.32 3.16 1qfeA 1nsj 7.35 2.91 1dxeA 1f61A 7.59 3.17 2asr 1occC 7.81 2.73 1fioA 1dn1B 7.82 3.23 1cb8A 1qazA 7.97 4.01 1qfeA 1f6yA 8.02 2.76 1nal1 1qtwA 8.07 3.72 1rpxA 1dioA 8.17 2.83 1dtyA 1b9hA 8.17 3.38 1czfA 1tsp 8.43 2.98 1bs2A 1a8h 8.50 2.94 1dorB 1nal1 8.52 3.07 1pii 1dxeA 8.70 2.84 1aw1B 1dosA 8.73 3.86 1fq0A 1qrqA 8.78 3.22 1nsj 2reqB 8.78 3.11 5rubB 1thfD 8.98 2.97 1cqqA 1cu1A 9.09 2.82 1dxeA 1rpxA 9.13 2.97 1wkd 1qfeA 9.21 3.52 2mnr 1dorB 9.35 4.00 1ak1 1qgoA 9.38 3.13 1de5A 1a0cA 9.47 3.22 1fq0A 1pscA 9.50 3.74 1dae 1nipA 9.59 3.01 1a80 1fq0A 9.76 3.24 1nal1 1fq0A 9.80 2.61 1qhtA 1noyA 10.00 3.11 1nal1 1ezwA 10.09 3.17 1dxeA 1fq0A 10.11 3.12 2ercA 1eizA 10.12 3.13 1nal1 1aw1B 10.60 3.20 1mpf 1a0tP 10.73 3.29 2thiA 1anf 10.86 3.63 1aw1B 1f6yA 11.06 3.44 1cu1A 7lprA 11.11 2.52 1fohB 1qq2A 11.11 3.12 1dfoA 1b9hA 11.20 3.12 1vjs 1bvzA 11.23 3.39 1fq0A 2tpsA 11.28 2.62 1igs 1ad1B 11.28 2.69 1udrB 1qo0D 11.30 2.39 1b9hA 1qgnA 11.36 2.92 4kbpB 1qhwA 11.37 2.89 2tpsA 1nal1 11.37 2.67 1nksF 1nipA 11.40 3.10 1ad1B 1qr7B 11.52 3.08 1noyA 1tgoA 11.54 3.27 1qgxA 1fpkA 11.58 3.01 1cj0A 1b9hA 11.89 2.93 1fts 1dae 12.09 2.74 1eokA 1d2kA 12.10 2.59 1dfoA 1bs0A 12.21 2.88 1dfoA 1elqA 12.29 2.81 1qgnA 1dfoA 12.32 2.84 1dqyA 1broA 12.36 2.98 1fofA 1skf 12.45 3.35 1d2fB 1cj0A 12.50 3.84 1nzyA 1tyfB 12.50 2.48 1qlwA 1auoA 12.50 2.89 1aw1B 1fq0A 12.56 3.04 1edt 1ctn 12.60 3.05 1chmA 1xgmA 12.61 2.29 1b5l 1evsA 12.75 2.52 1c3qA 1bx4A 12.76 3.35 1aw1B 1ald 12.86 3.10 1c0aA 12asA 12.97 2.57 1ad1B 1dioA 13.22 3.59 1b9hA 1bs0A 13.29 2.75 1b3uA 1ibrB 13.40 4.00 1jud 1fezA 13.43 3.36 1a9nA 1d0bA 13.55 3.49 1d9eA 1fq0A 13.57 3.07 1igs 1fq0A 13.72 2.65 1amoA 4nll 13.77 2.85 1plq 1dmlA 13.83 3.65 1ad1B 2tpsA 13.88 2.55 1qj2C 1fiqB 13.88 2.49 1gal 3cox 14.03 3.20 1cj0A 1qgnA 14.04 2.96 2hrvA 1cu1A 14.29 2.49 1b54 1qu4D 14.35 3.08 1ahuA 1f0xA 14.37 3.82 1eut 1czvA 14.48 2.38 1dubA 1tyfB 14.54 3.18 1rkd 1c3qA 14.63 3.03 1ez0C 1ad3A 14.72 2.71 1vpt 1eizA 14.86 2.74 2tmdA 1f6mA 15.03 3.42 1gtxA 2gsaA 15.29 2.17 1cqqA 2hrvA 15.38 2.47 1d9eA 1de5A 15.38 3.90 1ad1B 1qfeA 15.48 2.84 1qu4D 1sftB 15.49 3.81 1aj6 1b62A 15.62 2.64 1qrrA 1a4uA 15.88 2.54 1itg 1bco 15.94 2.56 3adk 1gky 16.13 2.94 1havA 2hrvA 16.15 2.69 1qu0A 1c4rE 16.18 1.90 3minA 1mioB 16.27 2.80 1bci 2isdA 16.39 2.44 1taq 1a76 16.41 3.62 1ldcA 1dorB 16.42 3.07 1eizA 2admA 16.48 3.20 2pueA 1bykA 16.60 1.76 1chmA 1mat 16.88 1.97 1ciu 1vjs 17.09 3.06 1dcnB 1c3cA 17.21 2.63 1rpt 1ihp 17.59 3.15 12asA 1b8aA 17.67 2.63 1smpA 1kuh 17.69 2.62 1xgmA 1a16 17.70 1.85 1d9eA 1nsj 17.73 3.15 1dm0L 1tcs 17.83 2.65 1qr7B 1d9eA 17.93 2.35 1gnwA 1eemA 18.04 1.96 1dpe 1rkm 18.09 3.51 1ar1B 1fftB 18.61 1.82 1ttpB 1oasA 18.67 2.29 1nal1 1thfD 18.72 2.64 1ag8A 1ez0C 18.74 2.14 1qgiA 1chkA 18.94 2.53 1cqxA 1qfjA 19.46 3.26 1dil 1eut 19.60 2.27 1ad1B 1d9eA 19.67 3.06 1d0bA 1yrgA 19.79 2.82 1c3cA 1fuoA 19.85 2.88 1dfjI 1yrgA 19.88 2.46 1tdj 1oasA 19.93 1.89 1eemA 1gsdB 20.00 2.95 1havA 1cqqA 20.11 2.27 1uok 1ciu 20.12 2.59 1lrv 1b3uA 20.46 3.40 1dgd 1gtxA 20.47 2.05 1bw9A 1ch6A 20.48 2.36 1occC 1fftC 20.65 1.65 1xel 1db3A 20.73 2.31 1bqg 1fhuA 20.85 2.75 1mat 1bn5 20.97 1.92 1ahn 1amoA 21.05 2.44 1fbl 1kuh 21.54 2.66 1dfjI 1d0bA 21.88 2.59 1daaA 1et0A 22.05 1.90 1imaA 1qgxA 22.05 2.00 1ciu 2aaa 22.51 2.18 1db3A 1bxkA 22.84 2.12 1whsB 1ivyA 22.92 1.00 1ovaA 1sek 23.58 1.82 1eur 1sll 23.58 1.99 7ahlA 1pvl 23.90 1.75 1gpmA 1qdlB 24.10 1.94 1whsB 1cpy 24.31 2.04 1ipsB 1dcs 24.91 2.60 1b5fA 1fknA 25.00 1.92 1dar 1dpfA 25.00 2.29 2reb 1cr2A 25.00 2.75 1tlfC 2pueA 25.37 1.72 1dxy 1psdA 25.63 2.29 1psdA 1gdhA 25.63 1.99 4tf4B 1nbcA 25.87 2.10 1lyaD 1fknA 26.25 2.18 1gdoB 1ct9A 26.84 2.00 1fiqC 1alo 27.42 1.87 1ac5 1cpy 27.83 2.40 2shpA 1yptA 27.91 2.53 1iov 1ehiA 28.71 1.86 4mhtA 1dctA 28.94 1.95 1reqA 1cb7A 29.13 1.62 1cpy 1ivyA 29.64 1.86 2plc 2isdA 29.77 4.05 1d2kA 1ctn 29.95 1.50 1xgmA 1mat 30.29 1.53 1ag8A 1euhA 30.56 1.51 1whsA 1cpy 30.68 2.37 1ahsB 1bvp4 30.95 1.19 1au1B 1b5l 31.13 2.19 1agrE 1emuA 32.00 1.54 1atiA 1qf6A 32.14 2.16 1ahuA 1diiA 32.68 1.33 1hrdA 1gtmA 33.49 1.89 1ciy 1dlc 33.62 1.92 1kobB 1a06 34.50 2.05 1froA 1fa6B 36.00 1.78 1etu 1dar 37.21 2.33 1tcs 1apgA 37.70 1.35 1larA 1pty 38.69 1.68 1alo 1qj2A 38.85 1.13 1alo 1fiqA 38.93 1.17 1eepA 1dorB 39.29 2.74

Training set of pairs of structures Chain A Chain B % Seq. Id. RMSD 2mnr 1wkd 5.80 4.02 1a80 1bf6A 5.86 4.05 12asA 1qf6A 7.31 2.89 1evkA 12asA 7.34 3.09 5rubB 1qfeA 7.60 3.58 1wkd 1dxeA 7.79 3.11 1cb7B 1qfeA 8.06 3.00 1dioA 1f6yA 8.33 3.46 1plq 1b77A 8.48 3.59 1fq0A 1f6yA 8.54 3.11 1cm5A 1b8bA 8.55 3.03 1bmfD 1cbuC 8.72 2.88 1wba 1af9 9.41 2.49 1tyfB 1ef9A 9.58 2.49 1han 1cjxA 9.74 3.30 1dob 1f8rA 9.87 3.93 1b9hA 1d2fB 9.97 3.55 1cb7B 1d9eA 10.00 3.29 2hrvA 7lprA 10.45 2.57 1exfA 1cqqA 10.46 2.65 1zen 1ttpA 10.59 2.91 1dfoA 1b8gA 10.74 3.80 1noyA 1qqcA 11.02 3.28 1cb7B 1f6yA 11.16 3.00 1cqqA 1jxpA 11.19 2.75 1czvA 1gog 11.19 2.47 1c3d 1dceB 11.23 3.68 1aw1B 1nsj 11.28 2.96 5xinB 1de5A 11.33 3.17 1b78A 1ex2A 11.54 2.93 1nal1 1qfeA 12.22 2.99 1qprA 1b54 12.28 3.19 1qr7B 1f6yA 12.35 3.14 1pda 1gr2A 12.44 3.59 1d9vA 2thiA 12.70 2.98 1d9eA 1f6yA 13.28 3.40 1elqA 1cj0A 13.33 3.09 1qfeA 1d9eA 13.49 2.91 2pth 1cfzA 13.51 2.90 1jxpA 2hrvA 13.53 2.47 1dae 1ffh 13.79 2.42 1cj0A 1bs0A 13.95 2.89 1ebmA 1mpgA 14.91 3.19 1qqtA 1ile 15.01 3.10 1mat 1a16 15.02 3.31 1bg9 1bf2 15.14 2.84 1bvzA 1bg9 15.14 2.75 1qrrA 1db3A 15.20 2.43 2hvm 1e15A 15.38 3.13 1ad1B 1cb7B 15.77 3.07 1bg9 1ciu 16.42 2.74 1aw1B 1d9eA 16.46 3.32 1ad1B 1fq0A 16.58 2.58 1d9eA 1d3gA 16.60 3.78 1ez3A 1fioA 16.67 1.45 1dorB 1d3gA 16.72 3.48 1cy9A 1d6mA 16.88 3.58 1bavC 1qmuA 17.57 1.83 1ciu 1bplB 17.61 2.67 1b37A 1f8rA 17.66 2.95 1bmtA 1cb7A 18.11 1.81 1d0bA 1ds9A 18.18 3.68 1bw9A 1aup 18.21 2.47 1bvzA 2aaa 18.44 2.41 1tcs 1qi7A 18.93 2.23 1dtyA 1gtxA 18.96 2.63 1ck7A 1hxn 19.59 2.48 1ac5 1whsB 19.86 2.00 1jud 1cr6A 19.88 3.32 2pgi 1dqrA 19.91 2.03 1sll 1dil 20.86 2.76 1rkd 1bx4A 21.21 2.26 1dcqA 1myo 21.24 2.34 1a8h 1qqtA 21.64 2.24 1rnl 1srrC 21.67 2.14 3pte 1ei5A 22.12 2.65 1eepA 1dosA 22.67 3.05 1ekjA 1ddzA 22.68 2.38 1c0mA 1itg 22.73 2.07 1uok 1bvzA 23.96 2.21 1udrB 1rnl 24.14 2.12 2isdA 1ptd 24.45 3.83 1kbcA 1smpA 24.54 2.54 1sebH 1eu4A 25.67 1.94 1aup 1ch6A 25.73 1.87 1fknA 1psaB 26.40 2.20 1gph4 1gdoB 26.55 2.43 1ihp 1qfxA 27.39 2.34 1dubA 1nzyA 27.78 2.19 1gdoB 1ecfB 28.00 1.81 1ft1B 1dceB 30.10 1.92 1c8oA 3caaA 30.67 1.88 1atiA 1evkA 31.63 2.20 1a06 1tkiA 32.42 1.68 2pgd 1pgjA 32.62 1.54 1bx4A 1dgyA 34.34 1.35 1apyB 9gaaA 34.75 1.11 1dvpA 1elkA 35.04 1.79 1whsA 1ivyA 35.57 1.70 2fcbA 1f2qA 39.63 2.05

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