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Proteins in Functional Cluster

Proteins in the Same Functional Cluster

When we say that a protein sequence X from organism org1 is a potential ortholog of a sequence Y from organism org2, we mean that
We compute a functional cluster by starting with a given ORF, adding all ptotential orthologs of the ORF that have the same (i.e., identical) function, gathering all proteins that connect to this set, and so forth. Each step involves gathering only potential orthologs with the same function.
Such a cluster is useful for locating recognizably homologous sequences that have maintained the same function, but it can be misleading; you need to remember that there may be many other sequences that are "closer" (by whatever similarity measure is being used) and do not have the same function. To properly understand what is going on, you need a phylogenetic tree of the related proteins. We offer this simple clustering mechanism, along with the "trimmed ortholog clusters", to give you some idea of what the relationships are in protein space; hopefully detailed trees will be generated during the next few years.
Function: LONG-CHAIN-FATTY-ACID--COA LIGASE (EC 6.2.1.3)
Length (aa) Alternative Names Location
 RAA00428 823 fadD Aquifex_aeolicus_691989_689521
 RAG48341 601 tg|AF0200 Archaeoglobus_fulgidus_175951_177753
 RAG50253 569 tg|AF1772 Archaeoglobus_fulgidus_1591628_1593334
 RBB00164 645 tg|BB0593 3615_612048_613982
 RBB00597 630 tg|BB0137 3615_137766_135877
 RBS01824 549 yngI BSUB9999_1955429_1953783
 RBS02850 560 lcfA BSUB9999_2919430_2917751
 RCE10267 618 F28F8.2 Z81071_20125_20409,Z81071_20459_20710,Z81071_20760_21421,Z81071_21466_21841,Z81071_22074_22190,Z81071_22238_22399
 RCY06372 636 slr1609 Synechocystis_487467_489374
 RDR02856 584 --- gdr_54_34275_36026
 REC01658 566 ydiD Escherichia_coli_K12_1781001_1782698
 REC05109 561 fadD Escherichia_coli_K12_1887770_1886088
 RHI00001 599 tg|HI0002 H.influenzae_625_2421
 RHI08067 562 sp|P46450 H.influenzae_409674_411359
 RML00425 300 --- B912_27036_27935
 RML00516 381 --- EMBL:L78813_26428_25286
 RMT04495 600 fadD15 MTBH37RV_2448158_2449957
 RMT04593 547 fadD35 MTBH37RV_2821594_2819954
 RNG00581 556 --- Contig249_1560_3227
 RNG01013 258 --- Contig292_3747_4520
 RNM01387 556 --- Contig254.1_6739_8406
 RNM01768 517 --- Contig267.0_6453_4903
 RPA00539 564 --- Contig48_151949_153640
 RPA06952 562 --- Contig50_145452_147137
 RPA06953 562 --- Contig50_143529_145214
 RPG00364 495 --- 141_1_1485
 RPG00996 557 --- 40_11527_13197
 RRC00290 630 --- M3_271672_273561
 RTH01137 548 MTH657 M.thermo_587291_585648
 RTP00336 656 TP0145 AE000520_165904_167871

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