GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Methanococcus maripaludis C5

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_269208425.1 MMARC5_RS07475 amino acid ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000016125.1:WP_269208425.1
          Length = 240

 Score =  105 bits (261), Expect = 1e-27
 Identities = 70/213 (32%), Positives = 112/213 (52%), Gaps = 4/213 (1%)

Query: 27  LAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFEGRDITRMPTH-EIAR 85
           L GVD+ V KGE++ ++G +G+GKSTL+  I G  +   G + FEG DIT    +    R
Sbjct: 14  LKGVDLKVAKGEVLVIVGPSGSGKSTLLRCINGLEKITEGHMYFEGDDITDKKVNINKIR 73

Query: 86  LRIAQSPEGRRIFPRMTVLENLQMGAG--LDNLKHFAEDVEKIFTLFPRLKERHAQRGGT 143
            +I    +   +FP +TVL+N+       L   K  AE +         L+ +  Q    
Sbjct: 74  QKIGMVFQQFNLFPHLTVLDNITFAPRKVLKVSKKEAETLAMELLKKVGLEGKENQYPIQ 133

Query: 144 LSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKLNEAEGLTVFLVEQN 203
           LSGG+QQ ++I RAL  +P  +L DEP+  L P +VK + + +++L   EG+T+ +V   
Sbjct: 134 LSGGQQQRVAIARALAMKPDAMLFDEPTSALDPELVKEVLDVMKQL-AYEGMTMVVVTHE 192

Query: 204 AFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236
              A  +  R   + NG++   G   E+ +NP+
Sbjct: 193 MGFAKEVGDRLIFIDNGQILEDGDPAEIFSNPK 225


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: 166
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: 240
Length adjustment: 23
Effective length of query: 224
Effective length of database: 217
Effective search space:    48608
Effective search space used:    48608
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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