Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 16238 b2130 predicted transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Keio:16238 Length = 385 Score = 102 bits (255), Expect = 1e-26 Identities = 65/197 (32%), Positives = 104/197 (52%), Gaps = 16/197 (8%) Query: 90 DLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPS---FVYLIPA 146 D Q L L+ A + ++VIGVP+GI S + +L+V+QT+PS F LI Sbjct: 175 DALAQHLTLLFGAVLPALVIGVPLGIWCYFSTARQGAIFSLLNVIQTVPSVALFGLLIAP 234 Query: 147 LM-------------LFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193 L + G G PA++A ++YA+ PL+R +G+ Q+ +V+E+A A G Sbjct: 235 LAALVTAFPWLGTLGIAGTGMTPALIALVLYALLPLVRGVVVGLNQIPRDVLESARAMGM 294 Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253 S Q V+LPLA P + L ++ + M V+A++IGA G G V G+ + + Sbjct: 295 SGAQRFLHVQLPLALPVFLRSLRVVMVQTVGMAVIAALIGAGGFGALVFQGLLSSAIDLV 354 Query: 254 LEAGIGIVILAVVLDRI 270 L I +++LAV+ D + Sbjct: 355 LLGVIPVIVLAVLTDAL 371 Lambda K H 0.327 0.142 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: 332 Number of extensions: 19 Number of successful extensions: 2 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: 285 Length of database: 385 Length adjustment: 28 Effective length of query: 257 Effective length of database: 357 Effective search space: 91749 Effective search space used: 91749 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: 49 (23.5 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