Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate BPHYT_RS26970 BPHYT_RS26970 4Fe-4S ferredoxin
Query= uniprot:Q726S3 (717 letters) >FitnessBrowser__BFirm:BPHYT_RS26970 Length = 464 Score = 213 bits (542), Expect = 2e-59 Identities = 137/375 (36%), Positives = 193/375 (51%), Gaps = 15/375 (4%) Query: 28 DKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDTLYAQFKAEAEKRGVKVHLA 86 DK R R I E + E+A K+H N+ QF A AE GV VH A Sbjct: 25 DKRLWDLREKRDAQAHGIAEWETMRELASGIKEHTLSNLSQYLEQFAAAAEANGVTVHWA 84 Query: 87 RTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRH 146 TA E N ++ +I + +KSKSM +E + LE + V+ETDLGE I Q+ H Sbjct: 85 ATAEEHNALVHQIMSERGMTTLVKSKSMLTDECKMREYLEPRGITVMETDLGERIQQLDH 144 Query: 147 EGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFA-TADMGISG 204 + PSHMV+PA+H R VA+LF + + DI L + R R +F G++G Sbjct: 145 QDPSHMVVPAVHKLRADVAELFGRTIGTDPKNSDIHYLAESQRMNTRPYFVREKTAGMTG 204 Query: 205 ANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQ 264 NFAVAETGT+ + TNEGNA L +P +H+A G++KL+P + D +++L R+A G Sbjct: 205 CNFAVAETGTVVVCTNEGNADLSANVPPLHIASIGIEKLIPKVSDLGVFIRMLSRSALGS 264 Query: 265 AITSYVTWIGGANECEACVDGRKEMHIVFLDNGR--RALAEDPLFSQVLRCVRCGACANV 322 IT Y + EMH + +D+GR R ED +S L+C+RCGAC N Sbjct: 265 PITQYTSHFRAPRP-------GTEMHFILVDHGRSERLAMEDFWYS--LKCIRCGACMNT 315 Query: 323 CPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPRL 382 CPVYR GG G Y G IG I+ F + + + +N SC ++C I++ Sbjct: 316 CPVYRRSGGLSYGGTYSGPIGAIINPTFDLKRYSALPFASTLN-GSCTNVCPVKINIHEQ 374 Query: 383 IKEIRARLNEEEGMP 397 I + R + E +P Sbjct: 375 IYKWRTVIAERHEVP 389 Lambda K H 0.321 0.135 0.402 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: 674 Number of extensions: 35 Number of successful extensions: 4 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: 717 Length of database: 464 Length adjustment: 36 Effective length of query: 681 Effective length of database: 428 Effective search space: 291468 Effective search space used: 291468 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 (21.9 bits) S2: 53 (25.0 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