Align 4Fe-4S ferredoxin-type domain-containing protein (characterized, see rationale)
to candidate Echvi_1568 Echvi_1568 Uncharacterized conserved protein containing a ferredoxin-like domain
Query= uniprot:B2TBY8 (464 letters) >FitnessBrowser__Cola:Echvi_1568 Length = 457 Score = 492 bits (1266), Expect = e-143 Identities = 243/451 (53%), Positives = 313/451 (69%), Gaps = 1/451 (0%) Query: 7 HAKAAGAFIGKTEHVAFHDKRLWDLREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQY 66 HA+ A AFI +HD+ LW +R RD A GI EWET+R+ AS K + LS+L + Sbjct: 6 HAEEAAAFIKDDARTHWHDETLWHVRSNRDRSAQGIPEWETLRDTASATKNYVLSHLGEL 65 Query: 67 LEQFAAAAEANGVTVHWAATAEEHNALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPR 126 LEQF A A+ANGV V WA +EHN V++I+ E ++ +VKSKS+LT+EC + YLE + Sbjct: 66 LEQFEANAKANGVEVLWARDDKEHNEHVYRILQENKVSNIVKSKSILTEECGLNHYLEKK 125 Query: 127 GITVMETDLGERIQQLDHQDPSHMVVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQ 186 G V++TDLGERI Q Q PSH+V+PA+H + D+ E+F IGT SD +YL E+ Sbjct: 126 GYDVVDTDLGERIIQFAKQTPSHIVLPAIHLKKQDIGEIFHDHIGTKKGASDPNYLTEAA 185 Query: 187 RMNTRPYFVREKTAGMTGCNFAVAETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPK 246 R + R FV E A +TG NF +AETG VVCTNEGNAD+ ++ +HIA +GIEKLIP+ Sbjct: 186 RQHLRKKFV-EANAAITGVNFGIAETGGFVVCTNEGNADMGTHLADVHIACMGIEKLIPR 244 Query: 247 VSDLGVFIRMLSRSALGSPITQYTSHFRAPRPGTEMHFILVDHGRSERLAMEDFWYSLKC 306 +DLGVF+R+L+RSA G IT Y+SHF P G +++ ILVD+GR+ +L EDF SLKC Sbjct: 245 AADLGVFLRLLARSATGQSITNYSSHFHRPAKGKKLYIILVDNGRTAQLGREDFKNSLKC 304 Query: 307 IRCGACMNTCPVYRRSGGLSYGGTYSGPIGAIINPTFDLKRYSALPFASTLNGSCTNVCP 366 IRCGACMNTCP+YRRSGG SY T GPIG+I++P DLK+YS LPFASTL GSC++VCP Sbjct: 305 IRCGACMNTCPIYRRSGGHSYNYTVPGPIGSILSPGRDLKQYSTLPFASTLCGSCSDVCP 364 Query: 367 VKINIHEQIYKWRTVIAERHEVPFVKQEVLKMAGRLLASPTLYRATVSSMGSALRRLPNF 426 VKINIHEQ+YKWR VI E V KQ +K+AG P LY +AL+ P Sbjct: 365 VKINIHEQLYKWRQVITENTNVDKSKQLSMKVAGMTFGKPVLYDLAGKMARTALKITPKS 424 Query: 427 VLYNPLNIWGKQRELPEAPKLTFHAWYKKNR 457 ++Y+ LN+WGK R+LPE PK +F W+KKNR Sbjct: 425 LVYSSLNVWGKHRDLPEVPKESFKEWFKKNR 455 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: 545 Number of extensions: 19 Number of successful extensions: 3 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: 457 Length adjustment: 33 Effective length of query: 431 Effective length of database: 424 Effective search space: 182744 Effective search space used: 182744 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