GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livM in Pseudomonas stutzeri RCH2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1060 Psest_1093 ABC-type branched-chain amino acid transport system, permease component

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__psRCH2:GFF1060
          Length = 335

 Score =  106 bits (264), Expect = 1e-27
 Identities = 82/275 (29%), Positives = 125/275 (45%), Gaps = 31/275 (11%)

Query: 37  LLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHT 96
           L + L A   N+++GYAGLL  G+ AF+A G Y+   M S +             +GL T
Sbjct: 56  LCFALFACAFNLLLGYAGLLSFGHAAFFATGGYITGYMLSSY-------------SGLST 102

Query: 97  SLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGP 156
            L I+     L +   G + G   ++ +G Y A++TL   +++  F   +  P   T G 
Sbjct: 103 ELGIL--AGTLASTVLGGLFGMLAIRRQGIYFAMITLALAQLV--FFVFVQAP--FTGGE 156

Query: 157 KGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAW 216
            GL  +    +FGL           D+ +    YY  L + V+   I  R   S  G+  
Sbjct: 157 NGLQGVPRGHLFGL----------VDMKNNMAMYYFVLAVFVLGFAIIQRTIHSPYGQVL 206

Query: 217 MAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIV 276
            AIRE+E  A ++G N    KLLAF + A+  G++GA         S        S  ++
Sbjct: 207 KAIRENEPRAVSLGYNVDRHKLLAFVISAALAGLAGATKTVVFQLASLTDAHWHMSGEVI 266

Query: 277 AMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311
            M +LGG+G I G ++GA ++  L   L    GPL
Sbjct: 267 LMTLLGGVGTILGPLVGATVVVTLQSSLS--NGPL 299


Lambda     K      H
   0.328    0.144    0.430 

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: 292
Number of extensions: 20
Number of successful extensions: 4
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: 358
Length of database: 335
Length adjustment: 29
Effective length of query: 329
Effective length of database: 306
Effective search space:   100674
Effective search space used:   100674
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: 49 (23.5 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