GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Marinobacter adhaerens HP15

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate GFF3115 HP15_3058 leucine/isoleucine/valine transporter ATP-binding subunit

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Marino:GFF3115
          Length = 251

 Score =  250 bits (639), Expect = 2e-71
 Identities = 127/258 (49%), Positives = 186/258 (72%), Gaps = 9/258 (3%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +L+V++LSM+FGGL+A+++ S + +  +I ++IGPNGAGKTTVFNC++GFYKPT G I F
Sbjct: 1   MLEVQNLSMRFGGLLAVDEVSLDVQEHEIVSIIGPNGAGKTTVFNCMSGFYKPTGGKILF 60

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTIL 133
             K      ++  PD++I++   V RTFQ++RLFS +TV+ENLLVAQH  L   +   I 
Sbjct: 61  EGKE-----VQGKPDYKISRLGMV-RTFQHVRLFSQMTVVENLLVAQHRHL---NTNLIS 111

Query: 134 GLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELL 193
           GLI    Y+++  ++++ A +WL++  L+D A+  AG+L YG QRRLEIAR M T P+LL
Sbjct: 112 GLIQTPSYRKKEQKSLDRAAYWLDRVGLLDMANREAGNLAYGQQRRLEIARCMVTEPKLL 171

Query: 194 CLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISD 253
            LDEPAAGLNP E+  LN L+ S++ +   S++LIEHDMS+VM+ISD + V+  G+ ++ 
Sbjct: 172 MLDEPAAGLNPAETKELNQLIISLKEDYNVSVVLIEHDMSLVMDISDRINVINQGRPLAS 231

Query: 254 GTPDHVKNDPRVIAAYLG 271
           GTP+ ++ +  VI AYLG
Sbjct: 232 GTPEEIRQNDDVIKAYLG 249


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: 223
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: 292
Length of database: 251
Length adjustment: 25
Effective length of query: 267
Effective length of database: 226
Effective search space:    60342
Effective search space used:    60342
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 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