GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Pseudomonas simiae WCS417

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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