Align Iron-sulfur cluster-binding protein, putative (characterized, see rationale)
to candidate AZOBR_RS14960 AZOBR_RS14960 formate dehydrogenase subunit alpha
Query= uniprot:Q39TW6 (218 letters) >FitnessBrowser__azobra:AZOBR_RS14960 Length = 938 Score = 105 bits (263), Expect = 2e-27 Identities = 73/239 (30%), Positives = 112/239 (46%), Gaps = 40/239 (16%) Query: 4 INLQIDGKEVVATEGMTILDAAKSVGISIPTLCHHEKLEPYGGCRICTVEVE-VRGWPKL 62 + L IDG+ V EG +++ AA GI++P LC + L+ YG CR+C VE+E RG P Sbjct: 19 VTLDIDGRTVTVPEGTSVMRAAMEAGITVPKLCATDMLDAYGSCRLCMVEIEGRRGTP-- 76 Query: 63 VAGCIYPVEKGLVVRTRNEKIDKIRKVLLEEMLAHAP---------DSEELKALAQEYGA 113 A C PV G+ V T+NE++ ++R+ ++E ++ P + EL+ +A G Sbjct: 77 -ASCTTPVAPGMKVHTQNERLGRLRRGVMELYISDHPLDCLTCPTNGNCELQDMAGAVGL 135 Query: 114 DRDRF----EKH---------------PSFCIHCGLCVRYCAEIKKKNAVGFVDRGSNRE 154 R+ E H PS CI C CVR C E++ A+ RG + + Sbjct: 136 RNVRYGYEGENHRAAVKDESNPYFTFDPSKCIVCSRCVRACGEVQGTFALTIDGRGFDSK 195 Query: 155 IS--FIPEIAAKECWDCKECFPLCPTSALQAAYVLAGALMTPPEEA---HSGGCGCSCS 208 +S + + EC C C CPT+ L ++ + PE + CG CS Sbjct: 196 VSPGALEQFMDSECVSCGACVQACPTATLTEKSLIE---LGQPEHSVITTCAYCGVGCS 251 Lambda K H 0.320 0.137 0.432 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: 476 Number of extensions: 26 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: 218 Length of database: 938 Length adjustment: 32 Effective length of query: 186 Effective length of database: 906 Effective search space: 168516 Effective search space used: 168516 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