Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMa1467 SMa1467 inner-membrane permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Smeli:SMa1467 Length = 220 Score = 105 bits (262), Expect = 9e-28 Identities = 62/195 (31%), Positives = 110/195 (56%), Gaps = 7/195 (3%) Query: 79 LLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMP 138 +++ + ++G T++ ++++ +A +++ VP+G+ + +S+ + L + +M T+P Sbjct: 7 IIDNLDIIGT--RTIEHISIVFLAVGIAIATAVPIGVAITQSKSTADTVLYLASMMITVP 64 Query: 139 S---FVYLIPALMLFG--LGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGG 193 S F +IP L G +G VPA++A I+Y+ P+IR T I VD + EAA G Sbjct: 65 SIALFGLMIPLLSPIGHGIGYVPAVVAVILYSQLPIIRNTYTAITNVDPALREAAKGMGM 124 Query: 194 SPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKG 253 S Q L VE+PLA P IMAG+ ++M + + +A+ IGA GLG + GI D + Sbjct: 125 STWQRLRQVEIPLAIPVIMAGVRTAVVMNIGVTAIAAYIGAGGLGTFISRGISQSDPRQL 184 Query: 254 LEAGIGIVILAVVLD 268 + + + +LA+ D Sbjct: 185 VTGALAVSLLAIAAD 199 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: 175 Number of extensions: 10 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: 220 Length adjustment: 24 Effective length of query: 261 Effective length of database: 196 Effective search space: 51156 Effective search space used: 51156 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