GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Pseudomonas litoralis 2SM5

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_090271761.1 BLU11_RS01725 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_900105005.1:WP_090271761.1
          Length = 236

 Score = 91.3 bits (225), Expect = 2e-23
 Identities = 76/252 (30%), Positives = 124/252 (49%), Gaps = 27/252 (10%)

Query: 9   MSDDTLLKVEHLSMKFGG-----LMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGF 63
           MSDD +L++E +   F          ++D      RG++TALIGP+G+GK+T+ N I   
Sbjct: 1   MSDD-VLRLERIGKIFNQGTPLESTVLHDIDLRLGRGELTALIGPSGSGKSTLLNLIGLL 59

Query: 64  YKPTMGMITFNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNK 123
             P+ G +    +  +    +      +  +A +   FQ   L S  +VLEN+L+     
Sbjct: 60  DVPSAGELYLQGQPTRDS--DDATRTHLRNQA-LGFVFQFHHLISAFSVLENVLMP---- 112

Query: 124 LMKASGYTILGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIA 183
           L+  SG             R + EAI+LAR  L +  L   AD    ++  G Q+R+ IA
Sbjct: 113 LIIRSG-------------RPSTEAIDLARGLLREVGLEKMADKKPTEISGGQQQRVAIA 159

Query: 184 RAMCTGPELLCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVV 243
           RA+ T P LL  DEP   L+ + + ++  L + I ++ G SIL++ HD  +       V 
Sbjct: 160 RALITRPPLLLADEPTGNLDTKTAESVFDLFRRINSQFGCSILVVTHDPRLAASCPRTVQ 219

Query: 244 VLEYGQKISDGT 255
           +++ G+ +SD T
Sbjct: 220 LVD-GRIVSDET 230


Lambda     K      H
   0.318    0.136    0.386 

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: 162
Number of extensions: 9
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: 292
Length of database: 236
Length adjustment: 25
Effective length of query: 267
Effective length of database: 211
Effective search space:    56337
Effective search space used:    56337
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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