Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate Pf1N1B4_1188 Predicted L-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF
Query= uniprot:B2TBY8 (464 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1188 Length = 484 Score = 276 bits (707), Expect = 8e-79 Identities = 171/444 (38%), Positives = 236/444 (53%), Gaps = 36/444 (8%) Query: 31 LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEH 90 L KR A E E +R L + ++ LS L LEQ NGVTVHWA T +E Sbjct: 40 LMSKRAASFSDAFEREHLRVLGNAVRARALSKLPDLLEQLEQNLTRNGVTVHWAETVDEA 99 Query: 91 NALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHM 150 N +V I+ ++K KSM+++E +M L +GI +E+D+GE I QLDH+ PSH+ Sbjct: 100 NGIVLSIIRAHEARQVIKGKSMVSEEMEMNHVLAAQGIECLESDMGEFIVQLDHEKPSHI 159 Query: 151 VVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVA 210 ++PA+HK VA LF +G + D+ L + R R F E G++G NFAVA Sbjct: 160 IMPAIHKNAGQVASLFHDKLGVE-YTKDVDQLIQIGRKVLRQKFF-EADIGVSGVNFAVA 217 Query: 211 ETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYT 270 ETGT+++ NEGN +S VPP+HIA GIEK++ + D+ + +L+RSALG PIT Y Sbjct: 218 ETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVENLRDVVPLLSLLTRSALGQPITTYV 277 Query: 271 SHFRAPRP------GTEMHFILVDHGRSERLAMEDFWYSLKCIRCGACMNTCPVYRRSGG 324 + PR E+H +L+D+GRS+ A + +L CIRCGACMN CPVY R GG Sbjct: 278 NMISGPRKEHELDGPQEVHLVLLDNGRSQAFADSELRQTLNCIRCGACMNHCPVYTRIGG 337 Query: 325 LSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIA 383 +YG Y GPIG II P L + P AS+L G+C VCPVKI I + + R Sbjct: 338 HAYGEVYPGPIGKIITPHMVGLAKVPDHPSASSLCGACGEVCPVKIPIPALLRRLR---E 394 Query: 384 ERHEVPFVKQEVLKMAG---------------RLLASPTLYRATVSSMGSALRRLPNFVL 428 E + P +V++ G +L +SPTLYR + LR L Sbjct: 395 ENVKAPDSPHQVMRGQGSKYSRKERFIWNAWAKLNSSPTLYR-LFGFFATRLRAL----- 448 Query: 429 YNPLNI--WGKQRELPEAPKLTFH 450 P N+ W + P+ + H Sbjct: 449 -TPSNVGPWTQNHSAPKPAARSLH 471 Lambda K H 0.320 0.133 0.406 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: 487 Number of extensions: 22 Number of successful extensions: 6 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: 464 Length of database: 484 Length adjustment: 33 Effective length of query: 431 Effective length of database: 451 Effective search space: 194381 Effective search space used: 194381 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: 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