Align Iron-sulfur cluster binding protein (characterized, see rationale)
to candidate BPHYT_RS26970 BPHYT_RS26970 4Fe-4S ferredoxin
Query= uniprot:E4PLR6 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS26970 Length = 464 Score = 289 bits (739), Expect = 2e-82 Identities = 169/404 (41%), Positives = 232/404 (57%), Gaps = 18/404 (4%) Query: 1 MSQRIPVTELTPDFRGRAEE-ALADGQLRNNFRVAMDSLMTKRANAFPDADEREGLRELG 59 MS RI + F G+ E A D +L + L KR E E +REL Sbjct: 1 MSNRIDHAKAAGAFIGKTEHVAFHDKRLWD--------LREKRDAQAHGIAEWETMRELA 52 Query: 60 NRIKAGALSRLPDLLEQLEQKLTENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSM 119 + IK LS L LEQ NGV VHWA T EE N+LVH I+ R + +VK KSM Sbjct: 53 SGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEHNALVHQIMSERGMTTLVKSKSM 112 Query: 120 VSEEMEMNDYLAERGVECLESDMGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLG- 178 +++E +M +YL RG+ +E+D+GE I QLD++ PSH+++PA+HK V++LF +G Sbjct: 113 LTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHMVVPAVHKLRADVAELFGRTIGT 172 Query: 179 EPETEDVNQLIQIGRRTLRRKFM-EADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPP 237 +P+ D++ L + R R F+ E G++G NFA+AETGT+++ NEGN +S PP Sbjct: 173 DPKNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVAETGTVVVCTNEGNADLSANVPP 232 Query: 238 VHIAVTGIEKVVPNLRDVVPLVSLLTRSALGQPITTYVNLISGPRKPDELDGPEEVHLVL 297 +HIA GIEK++P + D+ + +L+RSALG PIT Y + PR E+ H +L Sbjct: 233 LHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYTSHFRAPRPGTEM------HFIL 286 Query: 298 LDNGRTGAFADAQMRQTLNCIRCGACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGL 357 +D+GR+ A +L CIRCGACMN CPVY R GG +YG Y GPIG II P L Sbjct: 287 VDHGRSERLAMEDFWYSLKCIRCGACMNTCPVYRRSGGLSYGGTYSGPIGAIINPTF-DL 345 Query: 358 DKVPDHPSASSLCGACGEVCPVKIPIPELLQRLRQENVKNPEQP 401 + P AS+L G+C VCPVKI I E + + R + E P Sbjct: 346 KRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIAERHEVP 389 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: 513 Number of extensions: 19 Number of successful extensions: 5 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: 464 Length adjustment: 33 Effective length of query: 450 Effective length of database: 431 Effective search space: 193950 Effective search space used: 193950 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 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