Align Histidine transport system permease protein HisQ (characterized)
to candidate AZOBR_RS19270 AZOBR_RS19270 sulfate transporter
Query= SwissProt::P0A2I9 (228 letters) >FitnessBrowser__azobra:AZOBR_RS19270 Length = 286 Score = 38.5 bits (88), Expect = 1e-07 Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 15/89 (16%) Query: 65 MLLIFYGLQIALNVVTDSLGIDQIDIDPMVAGIITLGFIYGAYFTETFRGAFMAVPKGHI 124 +L+ ++GL++A LGI I L FI + T + +P Sbjct: 137 LLMEWFGLRVAFT----PLGI-----------AIALTFIGLPFVVRTVQPILQDLPPEEE 181 Query: 125 EAATAFGFTHGQTFRRIMFPAMMRYALPG 153 EAA A G T Q FRR++FPA++ L G Sbjct: 182 EAAAALGATRWQAFRRVVFPALLPALLTG 210 Lambda K H 0.328 0.144 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: 154 Number of extensions: 11 Number of successful extensions: 1 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: 228 Length of database: 286 Length adjustment: 24 Effective length of query: 204 Effective length of database: 262 Effective search space: 53448 Effective search space used: 53448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 47 (22.7 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