Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF3355 HP15_3297 binding-protein-dependent transport systems inner membrane component
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Marino:GFF3355 Length = 344 Score = 218 bits (555), Expect = 1e-61 Identities = 112/238 (47%), Positives = 166/238 (69%), Gaps = 8/238 (3%) Query: 43 IEWILRGL-------PWWLVILAFMALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQT 95 + W L G PWW+VI +A+ ++ W L L V + + + +D MQT Sbjct: 95 LSWFLDGALYAMLNTPWWIVIPLLLAVVYVVTKSWKLMLFVGGSIVLLAFIDHYDYAMQT 154 Query: 96 LALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKV 155 LA++ + + V++GVP+GI +A+S ++ + +PVLD++QT+P FVYLIP + LF + + Sbjct: 155 LAIIFVCAFLCVLLGVPIGIAMARSNSLQRMIIPVLDMLQTLPPFVYLIPLIFLFSVTES 214 Query: 156 PAI-LATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLATPTIMAG 214 +A I+YA+ P+IRLT+LGIR VD +V+EAA AFG +P Q L+ V++PLA P IMAG Sbjct: 215 KLYGIAIILYAIVPVIRLTNLGIRLVDKDVIEAADAFGMTPRQKLYKVQIPLALPNIMAG 274 Query: 215 LNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLDRITQ 272 +NQTIMM+L+MVV+AS++ A GLG VL GI+ L++G GL +G+GIVILAV+LDR+T+ Sbjct: 275 VNQTIMMSLAMVVIASLVSAPGLGVLVLRGIRNLELGVGLVSGLGIVILAVILDRVTK 332 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: 324 Number of extensions: 14 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: 344 Length adjustment: 27 Effective length of query: 258 Effective length of database: 317 Effective search space: 81786 Effective search space used: 81786 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