GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malG in Phaeobacter inhibens BS107

Align ABC-type maltose transporter (subunit 2/3) (EC 7.5.2.1) (characterized)
to candidate GFF1303 PGA1_c13190 ABC transporter permease protein

Query= BRENDA::P68183
         (296 letters)



>FitnessBrowser__Phaeo:GFF1303
          Length = 276

 Score = 98.2 bits (243), Expect = 2e-25
 Identities = 80/269 (29%), Positives = 127/269 (47%), Gaps = 16/269 (5%)

Query: 27  IMFPLLMVVAISLRQGNFATGSLIPEQISWDHWKLALGFSVEQADGRITPPPFPVLLWLW 86
           I FP+L  +  S +    A     P    +  W L   +SV Q            + +LW
Sbjct: 24  IFFPILWTILTSFKTEAQAISD--PPVFLFFDWTLE-NYSVVQERS-------DYMRFLW 73

Query: 87  NSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYALFDR 146
           NSV +AG S I  + ++   A++ A +       +L  ML  +M PAV  L  +Y LF +
Sbjct: 74  NSVIIAGGSTILGIIIAVPAAWSMAFVPSKRTKDILLWMLSTKMLPAVGVLYPIYILFIK 133

Query: 147 LGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAALDGATPWQAFRLV 206
           +G     +  N  G V+   L  + + VW +  YF+ I   + EAA +DGAT  +    V
Sbjct: 134 MG-----LLDNRFGLVVVLMLINLPIIVWMLYTYFKEIPGEILEAARMDGATLKEEILYV 188

Query: 207 LLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWGDFAAA 266
           L P+++P +A   +L+ I A  E    +L L    +  L   +  Y +P+   +   +AA
Sbjct: 189 LTPMAIPGIASTLLLNIILAWNEA-FWTLNLTAAKAAPLTAFIASYSSPEGLFYAKLSAA 247

Query: 267 AVMSALPITIVFLLAQRWLVNGLTAGGVK 295
           + M+  PI I+   +Q+ LV+GLT G VK
Sbjct: 248 STMAIAPILILGWFSQKQLVSGLTFGAVK 276


Lambda     K      H
   0.328    0.141    0.435 

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: 236
Number of extensions: 15
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: 296
Length of database: 276
Length adjustment: 26
Effective length of query: 270
Effective length of database: 250
Effective search space:    67500
Effective search space used:    67500
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 (21.8 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