Align Iron-sulfur cluster-binding oxidoreductase, CCG domain pair-containing, putative benzoyl-CoA reductase electron transfer protein (characterized, see rationale)
to candidate Echvi_0731 Echvi_0731 Fe-S oxidoreductase
Query= uniprot:Q39TW0 (387 letters) >FitnessBrowser__Cola:Echvi_0731 Length = 264 Score = 187 bits (476), Expect = 2e-52 Identities = 96/242 (39%), Positives = 145/242 (59%), Gaps = 5/242 (2%) Query: 146 EGMELLYFTGCYLSYDPRMRKVAAATAAILNKAGVDFGILGSKESCCGESIRKTGNEELF 205 E E+L++ GC S+D R + V A ILNK GV F +LG +E+C G+ R+ GNE LF Sbjct: 17 ESPEILFWVGCAGSFDDRYKAVTQAFVKILNKVGVSFAVLGPEETCTGDPARRAGNEFLF 76 Query: 206 KRLAKENIKQFIDNGVTKILVSSPHCYHTFVNEYPEFKVNFEVVFISQYIGQLINEGRLQ 265 + A NI+ V K++ + PHC++T NEYP +EV+ SQ++ LIN+G++ Sbjct: 77 QMQAVANIQVMNGYNVKKVVTACPHCFNTIKNEYPALGGEYEVIHHSQFLQSLINDGKIV 136 Query: 266 IT--GEF-AKKVTYHDPCYLGRHNGIYDEPRQVLQQVPGLELLEMADNRESSLCCGGGGG 322 + GEF KK+T+HD CYLGR N +Y+ PR++++ + +EL+EM R LCCG GG Sbjct: 137 MKGGGEFKGKKITFHDSCYLGRANNVYEAPREIIKAL-DVELVEMKRCRTKGLCCGAGGA 195 Query: 323 RIWME-TPKEERFADLRIRQAVDVGATVLATSCPYCITNFTDSSLDLADHEKVEVKDLAE 381 +++ E P + R +A+ GA+ +A CP+C+T D + V+V DLAE Sbjct: 196 QMFKEPEPGNKDINVERTEEALGTGASAIAVGCPFCLTMMADGVKNKEKESDVKVVDLAE 255 Query: 382 II 383 +I Sbjct: 256 LI 257 Lambda K H 0.320 0.139 0.427 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 322 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 387 Length of database: 264 Length adjustment: 28 Effective length of query: 359 Effective length of database: 236 Effective search space: 84724 Effective search space used: 84724 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory