Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF2247 PGA1_c22790 glycine betaine transport system permease protein
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Phaeo:GFF2247 Length = 342 Score = 217 bits (553), Expect = 3e-61 Identities = 107/229 (46%), Positives = 168/229 (73%), Gaps = 1/229 (0%) Query: 45 WILRGLPWWLVILAFMALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATI 104 W+ +PW++++ +A++ +SR +T+ V + + ++ +D+ MQTL+++ + T Sbjct: 101 WLFEAMPWFIMVPLLVAISWYASRSRPVTIFVAVSIMLLALVDHYDVAMQTLSIIFVCTT 160 Query: 105 VSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAI-LATII 163 +SV+ GVP+GI ++KS ++ +P+LD++QT+P+FVYLIP + LF + + +A I+ Sbjct: 161 ISVLFGVPIGIAMSKSDRLQKSVVPLLDLLQTLPTFVYLIPLIFLFSVTESKLYGIAIIL 220 Query: 164 YAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMAL 223 YA+ P+IRLTDLGIR VD +V+EAA AFG + Q L V+LPLA P IMAG+NQTIMM+L Sbjct: 221 YAIVPVIRLTDLGIRLVDQDVIEAANAFGMNDRQKLMRVQLPLALPNIMAGINQTIMMSL 280 Query: 224 SMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDRITQ 272 +MVV+AS++ A GLG VL GI+ L++G G+ AGIGIV+LAV+LDR+++ Sbjct: 281 AMVVIASLVSAPGLGVNVLRGIRNLELGVGIVAGIGIVLLAVILDRVSK 329 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: 304 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: 342 Length adjustment: 27 Effective length of query: 258 Effective length of database: 315 Effective search space: 81270 Effective search space used: 81270 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: 48 (23.1 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