Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate HSERO_RS08540 HSERO_RS08540 choline ABC transporter permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__HerbieS:HSERO_RS08540 Length = 216 Score = 111 bits (278), Expect = 1e-29 Identities = 64/194 (32%), Positives = 114/194 (58%), Gaps = 5/194 (2%) Query: 88 IWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPS---FVYLI 144 I +LT+Q L L+ +A +++ IGVP+GIL+ + R + + + ++ T+PS F +I Sbjct: 14 ILELTLQHLKLVGIAVSLAIAIGVPLGILIVRVRWLAGPLMGLATIVLTLPSIALFGLMI 73 Query: 145 PALMLFG--LGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGV 202 P FG +G +PAI A +Y++ P++R T L + ++A + EA G + Q L V Sbjct: 74 PLFSKFGAGIGPLPAITAVFLYSLLPIMRNTYLALENIEAGIKEAGIGIGMTFWQRLRMV 133 Query: 203 ELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVI 262 +LPLA P I+ G+ ++M + ++ +A++IGA GLG +L+ I ++ K + + I + Sbjct: 134 DLPLAVPVILGGVRTAVVMNIGVMAIAAIIGAGGLGVLILHAISQSNMQKLVVGAVMISV 193 Query: 263 LAVVLDRITQGFGK 276 LA++ D + Q K Sbjct: 194 LAIIADTLLQRLQK 207 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: 211 Number of extensions: 17 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: 216 Length adjustment: 24 Effective length of query: 261 Effective length of database: 192 Effective search space: 50112 Effective search space used: 50112 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: 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