Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF5138 PS417_26320 ABC transporter permease
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__WCS417:GFF5138 Length = 281 Score = 212 bits (540), Expect = 7e-60 Identities = 121/267 (45%), Positives = 173/267 (64%), Gaps = 10/267 (3%) Query: 11 RAPVNDFIQALV---TNYGW-VFKAISGVILKAVLFIEWILRGLPWW--LVILAFMALAC 64 + P+ +I A V T +G F AI+ + I + L W+ L ++ +AL Sbjct: 6 KIPLGQYIAAFVEWLTQHGANYFDAIASTL---ETMIHGVTFALTWFNPLALIGLIALLA 62 Query: 65 RS-SRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVV 123 R+W LT+ V A + LG W TM+TLA +L AT+V VVIGVP+GI+ A + Sbjct: 63 HFIQRKWGLTVFVIASFLLILNLGYWQETMETLAQVLFATLVCVVIGVPLGIVAAHKPMF 122 Query: 124 RNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAE 183 + PVLD+MQT+P+FVYLIP L LFGLG VP +++T+++A+ IRLT LGIR V E Sbjct: 123 YTMMRPVLDLMQTVPTFVYLIPTLTLFGLGVVPGLISTVVFAIAAPIRLTYLGIRDVPQE 182 Query: 184 VVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLN 243 +++A AFG S Q+L +ELP A P+I AG+ Q IM++LSMVV+A+++GA GLG+ V+N Sbjct: 183 LMDAGKAFGCSRRQLLSRIELPHAMPSIAAGITQCIMLSLSMVVIAALVGADGLGKPVVN 242 Query: 244 GIQTLDVGKGLEAGIGIVILAVVLDRI 270 + T D+ G EAG+ IV+LA++LDRI Sbjct: 243 ALNTADIALGFEAGLAIVLLAIMLDRI 269 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: 249 Number of extensions: 10 Number of successful extensions: 1 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: 281 Length adjustment: 26 Effective length of query: 259 Effective length of database: 255 Effective search space: 66045 Effective search space used: 66045 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: 47 (22.7 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