Among the proteins that the resources determined to be neighbors, I decided to explore two in depth. The first is 3PRN, another bacterial porin. The second is a bit more interesting, functionally. Not suprisingly, 3PRN was found as a structural neighbor by all the resources. 2OMF is a protein found in mitocondrial membranes and used in ATP synthesis. 2OMF was found as a structural neighbor by only CATH, CE and FSSP. VAST failed to identify 2OMF as a structural neighbor.

SCOP classified the three proteins as being equally different (or at least all three diverged within the heirarchy at the same time). All three proteins were classified in the same family ( Porin), but 2POR was in the protein domain for Rhodobacter capsulatus, 3PRN was in the protein domain for Rhodopseudomonas blastica, and 2OMF was in the protein domain for E. Coli.

CATH, CE, and FSSP all found 2POR more similar to 3PRN than to 2OMF. CATH found all three proteins to be in the same homologous superfamily (Integral membrane protein porin: 2.40.160.10), but 3PRN and 2POR were also in the same sequence family (2.40.160.10.2).

CE and FSSP both found the RMSD between 2POR and 3PRN to be less than the RMSD between 2POR and 2OMF. Both resources also aligned a greater percentage of the residues in the protein when comparing 2POR and 3PRN. The table below compares the results of CE, FSSP, and VAST:

Comparison of RMSDs and Sequence Alignment of 3PRN and 2OMF with 2POR

	3PRN RMSD	2OMF RMSD	3PRN Sequence Alignment	2OMF Sequence Alignment
CE	2.7	3.0	259/289	265/340
FSSP	2.5	2.7	254/289	262/340
VAST	3.1	--	255/289	--

The sequence alignment below between 2POR, 3PRN, and 2OMF (from CE) indicates that 2POR is slightly more similar to 3PRN, but it's still well aligned with 2OMF. Considering how long ago in evolution bacteria and mitocondria diverged, the similarity is striking.

2POR:_ 1/2 EVKLSGDARMGVMYNGD------D--------WNFSSRSRVLFTMSGTTD-SGLEFGASF 3PRN:_ 1/2 MISLNGYGRFGLQYVEDRGVGLED--------TIISSRLRINIVGTTETD-QGVTFGAKL 2OMF:_ 11/12 -VDLYGKAVGL-HYFSK------GNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWE 2POR:_ 46/47 KAH--------------ESVGAETGEDGTVFLSGA---FGKIEMGDALGASEALF-G-DL 3PRN:_ 52/53 RMQWDDGDAFAG-----TAGNAA-----QFWTSYN---GVTVSVGNVDTAFDSVALT-YD 2OMF:_ 63/64 YNFQGNNSEGADAQTGNK-------TRLAFAGLKYADVGSFDYGR-NYGVVYDAL-GYTD 2POR:_ 87/88 YEVGYTDLDDRGGNDIPY-----LTGDERLT--------AEDNPVLLYTYSAG------A 3PRN:_ 98/99 SEMGYEWSS---FGDAQS-----SFFAY--NSKYDASGALDNYNGIAVTYSIS------G 2OMF:_ 114/115 MLPE--------FGGDTAYSDDFFVGRV---------------GGVATYRNSNFFGLVDG 2POR:_ 128/129 FSVAASMSDGKVGETSE--DD-------AQEMAVAAAYTFGNYTVGLGYEKI---DSPD- 3PRN:_ 142/143 VNLYLSYVDPD--QTVDSSLV-------TEEFGIAADWSNDMISLAAAYTTDAGGIV--- 2OMF:_ 151/152 LNFAVQYLGKNE--------RDTARRSNGDGVGGSISYEYEGFGIVGAYGAA---DRTNL 2POR:_ 175/176 -TALM----ADMEQLELAAIAK-FGATNVKAYYADGELDRDFARAVFDLTPVAAAATAVD 3PRN:_ 190/191 ----------DNDIAFVGAAYKFNDAGTVGLNWYDNGLST-------------------A 2OMF:_ 200/201 QEAQPLGNGKKAEQWATGLKYD-ANNIYLAANYGETRNA--TPITNKFTNTS---GFANK 2POR:_ 229/230 HKAYGLSVDSTFGA-TTVGGYVQVLDID------TIDDVTYYGLGASYDLGGGASIVGGI 3PRN:_ 221/222 GDQVTLYGNYAFGA-TTVRAYVSDIDR--------AGADTAYGIGADYQFAEGVKVSGSV 2OMF:_ 254/255 TQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDY 2POR:_ 282/283 ADNDLPN-------SDMVADLGVKFKF 3PRN:_ 272/273 QSGFA---------NETVADVGVRFDF 2OMF:_ 314/315 IINQIDSDNKLGVGSDDTVAVGIVYQF