GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacH in Paraburkholderia bryophila 376MFSha3.1

Align Xylose/arabinose import permease protein XacH (characterized, see rationale)
to candidate H281DRAFT_00167 H281DRAFT_00167 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= uniprot:D4GP36
         (317 letters)



>FitnessBrowser__Burk376:H281DRAFT_00167
          Length = 312

 Score =  144 bits (363), Expect = 3e-39
 Identities = 89/279 (31%), Positives = 145/279 (51%), Gaps = 19/279 (6%)

Query: 42  PFVLMSIA-VYGGTGYNFAISFTDYEGLGT----PDYSTLDLEMYAQALSSDAFIAAAQN 96
           P V++S+  VYG       I+ T Y  L      P Y  + L+ Y +   +D F  +A N
Sbjct: 36  PSVVISLVFVYG------FIAITGYLSLSNSRLMPRYEFVGLDRYRELFDNDVFWTSAAN 89

Query: 97  NLVLLVGFTTICLVLGLFLAILLDHGIRFSEKFQTVYLLPMSLSFVVTAQLWLWMFNVES 156
                + F  IC+ LGLFLAILLD  IR     + V+L PM+LSF+VT   W W+     
Sbjct: 90  LGWFGIPFIGICIGLGLFLAILLDQQIRNEGALRAVFLYPMALSFIVTGTAWQWIMTPSI 149

Query: 157 GILNLVV----TTLGFNPVDWLGNPSIALGAVILALIWQFSGYTMVVYLAGLQSIPDDQF 212
           G+  +      T+  F+   WLG+P  A+  V++A +WQ +G+ M ++LAGL+ +  + F
Sbjct: 150 GLEKVFHDWGWTSFSFS---WLGDPDKAIFCVVIAAVWQSTGFVMALFLAGLRGVDGEIF 206

Query: 213 EAARVDGASITRTYLRIIVPQLKEASVSAAVVLMVFALKAFTFLYALVGRYRPPNGTDIL 272
           +AA++DGA++   Y +I++P ++    S  ++L    +K F  + AL     P   + + 
Sbjct: 207 KAAQMDGANLPTIYRKIVIPSMRPVFFSVLLILCHITIKTFDLVVALTAG-GPGTSSSLP 265

Query: 273 ATLMVRRAFKFGEWAYSAAIATMLLIMALGVIGPYLYYQ 311
           A  M   +F  G+    AA + M+L   + V+ P +Y +
Sbjct: 266 AIFMYTFSFNRGQLGVGAASSMMMLATVVAVLVPLMYLE 304


Lambda     K      H
   0.326    0.140    0.424 

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: 245
Number of extensions: 13
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: 317
Length of database: 312
Length adjustment: 27
Effective length of query: 290
Effective length of database: 285
Effective search space:    82650
Effective search space used:    82650
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 (21.6 bits)
S2: 48 (23.1 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