Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate AZOBR_RS01620 AZOBR_RS01620 putative oxidoreductase subunit with NAD(P)-binding domain and ferridoxin-like domain
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__azobra:AZOBR_RS01620 Length = 478 Score = 349 bits (895), Expect = e-100 Identities = 196/484 (40%), Positives = 269/484 (55%), Gaps = 36/484 (7%) Query: 6 PVTELTPDFRGRAEEALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELGNRIKAG 65 P T P+ A +AL+D +L+ +A + +R A E E LR+ G +K Sbjct: 3 PTTHAFPE---NARKALSDERLQKVLAIAPAGFVNRRKQAADRLPEFEDLRDQGRDLKNH 59 Query: 66 ALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEME 125 L+ L LE E K+ E G VHW T +EA + GI V KGKSM+SEE+ Sbjct: 60 VLANLDTYLEAFEGKVIEQGGHVHWCRTDQEARDAILGICRKVGAKTVTKGKSMISEEIG 119 Query: 126 MNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFH----DKLGEPE 181 +NDYL G+ +E+D+GEYI+QL E PSHII PA H + V F D + Sbjct: 120 INDYLEANGLTPIETDLGEYIIQLRREPPSHIIAPAFHLSKADVEGTFRQAHTDLPADRV 179 Query: 182 TEDVNQLIQIGRRTLRRKFMEADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIA 241 ++ LI R+ LRRKF +ADVG++G N +AETG+ ++V NEGNG ++ P VH+ Sbjct: 180 LDEPKVLIAEARQVLRRKFQQADVGITGANIMVAETGSTVIVTNEGNGDLTQILPRVHVV 239 Query: 242 VTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVLLDNG 301 + I+KVVP L D ++ LL RSA GQ + Y +GPR+P +LDGPEE H+VLLDNG Sbjct: 240 IATIDKVVPTLEDAALVLRLLARSATGQEASAYTTFSTGPRRPGDLDGPEEFHVVLLDNG 299 Query: 302 RTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVP 361 R+ A + + L CIRCGACMNHCPVY VGGH YG VYPGPIG ++ P + G+ + Sbjct: 300 RS-ALLGTEFQDVLRCIRCGACMNHCPVYGSVGGHAYGWVYPGPIGSVMQPALLGVKEAG 358 Query: 362 DHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQPQQVKGGGAKYSRTERWIWRG 421 P+AS+ CG C VCP++IP+P++++ R++ + QP ++ G A +W G Sbjct: 359 HLPNASTFCGRCEAVCPMRIPLPKMMRHWREKEFEQNLQPAAMRRGLA--------LW-G 409 Query: 422 WQMLNTRPALYRSFLWAATRF--RALAPKKAGP-----------WTENHSAPVPARRSLH 468 W RPALY AATR RAL G WT + P P ++ Sbjct: 410 W--FARRPALYH----AATRMAVRALGALGRGKGRFASLPLAQGWTRHRDMPAPEGKTFQ 463 Query: 469 DLAA 472 + A Sbjct: 464 QMWA 467 Lambda K H 0.317 0.135 0.403 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: 598 Number of extensions: 28 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: 483 Length of database: 478 Length adjustment: 34 Effective length of query: 449 Effective length of database: 444 Effective search space: 199356 Effective search space used: 199356 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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