Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate AZOBR_RS15765 AZOBR_RS15765 osmoprotectant uptake system permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__azobra:AZOBR_RS15765 Length = 390 Score = 114 bits (284), Expect = 4e-30 Identities = 66/185 (35%), Positives = 102/185 (55%), Gaps = 13/185 (7%) Query: 97 ALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYL------------- 143 AL+ A + +++IGVP+GI +S V + PVL+V+QT+PS Sbjct: 187 ALVAAALVPTLLIGVPLGIAAQRSAAVGRLVFPVLNVVQTIPSIALFGLLLAPLSALAAA 246 Query: 144 IPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVE 203 P L + G+G VPA++A +Y++ P+ R T G+ V V EAA G +P QI + VE Sbjct: 247 FPGLGIGGVGPVPAVIALTLYSLLPIARNTAAGLAGVPEPVREAARGIGMTPRQIFWRVE 306 Query: 204 LPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVIL 263 PLA P +AGL T++ A+ + VA++IGA GLG + G+ + L + +++L Sbjct: 307 APLALPVFLAGLRITLVQAVGLAAVAALIGAGGLGAIMFQGLFANALDLVLLGAVPVILL 366 Query: 264 AVVLD 268 AV D Sbjct: 367 AVAAD 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: 298 Number of extensions: 23 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: 390 Length adjustment: 28 Effective length of query: 257 Effective length of database: 362 Effective search space: 93034 Effective search space used: 93034 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