Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate AO353_05710 AO353_05710 (Fe-S)-binding protein
Query= uniprot:B2TBY8 (464 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05710 Length = 484 Score = 279 bits (713), Expect = 2e-79 Identities = 175/461 (37%), Positives = 242/461 (52%), Gaps = 40/461 (8%) Query: 20 HVAFHDKRLWD--------LREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFA 71 H A DK+L + L KR A E E +R L + I+ LS L LEQ Sbjct: 21 HEALGDKQLRNNFRSAMDSLMAKRAASFSDAFEREHLRALGNAIRARALSKLPDLLEQLE 80 Query: 72 AAAEANGVTVHWAATAEEHNALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVM 131 NGVTVHWA T +E N +V I+ ++K KSM+++E +M L +G+ + Sbjct: 81 QNLTRNGVTVHWAETVDEANGIVLSIIRAHEARQVIKGKSMVSEEMEMNHVLAEQGVECL 140 Query: 132 ETDLGERIQQLDHQDPSHMVVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTR 191 E+D+GE I QLDH+ PSH+++PA+HK VA LF +G + D+ L + R R Sbjct: 141 ESDMGEFIVQLDHEKPSHIIMPAIHKNAGQVASLFHDKLGVE-YTKDVDQLIQIGRKVLR 199 Query: 192 PYFVREKTAGMTGCNFAVAETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLG 251 F E G++G NFAVAETGT+++ NEGN +S VPP+HIA GIEK++ + D+ Sbjct: 200 QKFF-EADIGVSGVNFAVAETGTLLLVENEGNGRMSTTVPPVHIAVTGIEKVVENLRDVV 258 Query: 252 VFIRMLSRSALGSPITQYTSHFRAPRPG------TEMHFILVDHGRSERLAMEDFWYSLK 305 + +L+RSALG PIT Y + PR E+H +L+D+GRS+ A + +L Sbjct: 259 PLLSLLTRSALGQPITTYVNMISGPRKAHELDGPQEVHLVLLDNGRSQAFADSELRQTLN 318 Query: 306 CIRCGACMNTCPVYRRSGGLSYGGTYSGPIGAIINP-TFDLKRYSALPFASTLNGSCTNV 364 CIRCGACMN CPVY R GG +YG Y GPIG II P L + P AS+L G+C V Sbjct: 319 CIRCGACMNHCPVYTRIGGHAYGEVYPGPIGKIITPHLVGLAKVPDHPSASSLCGACGEV 378 Query: 365 CPVKINIHEQIYKWRTVIAERHEVPFVKQEVLKMAG---------------RLLASPTLY 409 CPVKI I + + R E + P +V++ G +L +SPTLY Sbjct: 379 CPVKIPIPALLRRLR---EENVKAPDSPHQVMRGQGSKYSRKERFIWNAWAKLNSSPTLY 435 Query: 410 RATVSSMGSALRRLPNFVLYNPLNIWGKQRELPEAPKLTFH 450 R + LR L N + W + P+ + H Sbjct: 436 R-LFGFFATRLRALTP----NNIGPWTQNHSAPKPAARSLH 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: 23 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