GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Marinobacter adhaerens HP15

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Marino:GFF4159
          Length = 269

 Score =  189 bits (479), Expect = 6e-53
 Identities = 102/245 (41%), Positives = 152/245 (62%), Gaps = 8/245 (3%)

Query: 9   QPLLQVNGVETYYG-NIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICG-----SPQ 62
           + LL+++ +E  Y  +++ L G+ + V KG IV+L+G+NGAGKST + ++ G       +
Sbjct: 2   EALLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGE 61

Query: 63  ARTGSVVFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGA-GLDNLK-HFA 120
              G V F G+D+  +P   + R  +    EGRR+F  +TV ENL      L   K   +
Sbjct: 62  VTAGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLS 121

Query: 121 EDVEKIFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVK 180
           +  E ++  FPRLKER  Q  G LSGGEQQML++GRAL+A+P L++LDEPSLGLAPL+V+
Sbjct: 122 DSYELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVE 181

Query: 181 GIFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAA 240
            IF  + ++N  +G  + LVEQNA  +L ++   Y+M NGK+ + G   +L AN +V+  
Sbjct: 182 EIFTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEF 241

Query: 241 YLEGG 245
           YL  G
Sbjct: 242 YLGVG 246


Lambda     K      H
   0.320    0.137    0.387 

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: 190
Number of extensions: 8
Number of successful extensions: 3
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: 247
Length of database: 269
Length adjustment: 24
Effective length of query: 223
Effective length of database: 245
Effective search space:    54635
Effective search space used:    54635
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (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