Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate GFF924 Psest_0953 iron-sulfur cluster-binding protein
Query= uniprot:B2TBY8 (464 letters) >FitnessBrowser__psRCH2:GFF924 Length = 486 Score = 283 bits (725), Expect = 7e-81 Identities = 176/441 (39%), Positives = 240/441 (54%), Gaps = 30/441 (6%) Query: 31 LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWAATAEEH 90 L KR E E +RE+ + I+ LS L + LE+ NGV VHWA T EE Sbjct: 44 LMTKRAVAFSDADERERLREMGNRIRARALSKLPELLERLETNLTRNGVNVHWAETVEEA 103 Query: 91 NALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDHQDPSHM 150 N +V +I ++K KSM+++E +M +LE GI +E+D+GE I QLDH+ PSH+ Sbjct: 104 NNIVLEIARAHEARQVIKGKSMVSEEMEMNHFLEGHGIECLESDMGEYIVQLDHEKPSHI 163 Query: 151 VVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTRPYFVREKTAGMTGCNFAVA 210 ++PA+HK VA LF +G + D+ L + R R F E G++G NFAVA Sbjct: 164 IMPAIHKNAGQVASLFHEKLGVE-YTKDVDQLIQIGRRTLRQKFF-EADIGVSGVNFAVA 221 Query: 211 ETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGSPITQYT 270 ETGT+++ NEGN +S VPP+HIA GIEK++ + D+ + +L+RSALG PIT Y Sbjct: 222 ETGTLLLVENEGNGRMSTGVPPVHIAVTGIEKVVENLRDVVPLLSLLTRSALGQPITTYV 281 Query: 271 SHFRAPRPGTEM------HFILVDHGRSERLAMEDFWYSLKCIRCGACMNTCPVYRRSGG 324 + +PR E+ H IL+D+GRS+ A + +L CIRCGACMN CPVY R GG Sbjct: 282 NMISSPRKADELDGPQEVHLILLDNGRSQAFADSELRQTLNCIRCGACMNHCPVYTRVGG 341 Query: 325 LSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNVCPVKINIHEQIYKWRTVIA 383 +YG Y GPIG II P L + P AS+L G+C VCPVKI I + + R Sbjct: 342 HTYGEVYPGPIGKIITPHMVGLDKVPDHPSASSLCGACGEVCPVKIPIPSILRRLREENI 401 Query: 384 ERHEVP----------FVKQEVLKMAG-RLL-ASPTLYRATVSSMGSALRRLPNFVLYNP 431 + + P + K+E L AG RLL +PTLYR + LR L P Sbjct: 402 KAPDDPHKVMRGQGSKYSKKERLMWAGWRLLNTNPTLYR-VFGFFATRLRGL------TP 454 Query: 432 LNI--WGKQRELPEAPKLTFH 450 NI W + P+ + H Sbjct: 455 SNIGPWTQNHSAPKPAARSLH 475 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: 525 Number of extensions: 27 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: 464 Length of database: 486 Length adjustment: 33 Effective length of query: 431 Effective length of database: 453 Effective search space: 195243 Effective search space used: 195243 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