Align Uncharacterized protein (characterized, see rationale)
to candidate WP_043745482.1 AMB_RS20885 (Fe-S)-binding protein
Query= uniprot:B2TBW0 (256 letters) >NCBI__GCF_000009985.1:WP_043745482.1 Length = 249 Score = 146 bits (368), Expect = 5e-40 Identities = 91/244 (37%), Positives = 123/244 (50%), Gaps = 15/244 (6%) Query: 12 VALFIPCFIDAFYPEVGIATLELLERFGIQVDYPQEQTCCGQPMANSGAHAEAAGTERVF 71 V F C ID FYPE G+A +ELL+R G++V +P QTCCGQP N+G EA R+ Sbjct: 10 VYFFGTCLIDLFYPEAGLAGMELLQREGLKVVFPPNQTCCGQPARNNGYQDEARKVARLQ 69 Query: 72 ARNFAGYDYIVGPSASCIHHVREHLTAL----EQTDEVKKVRANAYELVEFLHDVVGARE 127 +F G IV PS SC ++ H + D A YEL EFL DV+G + Sbjct: 70 MDSFPGDWPIVVPSGSCAGMMKTHYPEMFEGTPDHDRAVAFSARVYELTEFLVDVLGVKL 129 Query: 128 FPWAEFPHRVGLHNSCSALRHLKEASISEVAGAPFSKPRTLLEGVKGIEFVKPARPDECC 187 + + H SC + R EA + E +P+ LL + + V+ R ECC Sbjct: 130 VDKGQ-KVTITWHPSCHSQR---EAGVVE-------QPKALLRQLTNVTLVENPREKECC 178 Query: 188 GFGGTFSVTEEPVSVRMGQDKVRDHLNAGAEYIVSGDMSCLMHQQGCAERMKADARFIHI 247 GFGG F+V + +S M DKV GA +VSGD CLM+ G AE+ + HI Sbjct: 179 GFGGAFAVRQAEISAAMVTDKVASIEETGATQVVSGDCGCLMNITGAAEKAAKGFKGRHI 238 Query: 248 AQVL 251 A+ + Sbjct: 239 AEFI 242 Lambda K H 0.323 0.137 0.422 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: 187 Number of extensions: 11 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: 256 Length of database: 249 Length adjustment: 24 Effective length of query: 232 Effective length of database: 225 Effective search space: 52200 Effective search space used: 52200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 46 (22.3 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