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_048058439.1 MMARC5_RS02070 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU3
         (247 letters)



>NCBI__GCF_000016125.1:WP_048058439.1
          Length = 253

 Score = 99.8 bits (247), Expect = 5e-26
 Identities = 75/240 (31%), Positives = 124/240 (51%), Gaps = 18/240 (7%)

Query: 11  LLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVF 70
           ++ V+GVE  Y +   L  V   V KGE+VS++G NGAGKSTL+  I      + G++  
Sbjct: 2   IVSVDGVEFKYKSTEILKDVKFEVKKGEVVSILGINGAGKSTLIKCINKILPPKKGTITI 61

Query: 71  EGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK--------HFAED 122
           E  D+ +M   ++A+ ++   P+ R     MTV + L +G    ++K           E+
Sbjct: 62  ENLDVNKMDRLDLAK-KVGYVPQ-RSNGNYMTVFDALLLGR-KPHIKWEISQKDIEITEN 118

Query: 123 VEKIFTLFPRLKERHAQRG-GTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKG 181
           V K+  L     +++A R    LSGGE Q + IGR L+  PKL+LLDEP+  L       
Sbjct: 119 VLKLLDL-----DKYALRNTNELSGGELQKVIIGRVLVQEPKLILLDEPTNNLDLKNQLE 173

Query: 182 IFEAIRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAY 241
           +   ++ ++ +E +T  +V  +   ALR S +  ++ +GK+   G GKE++    +   Y
Sbjct: 174 VMRILKDVSVSENITSIIVMHDINLALRYSDKFLMLKDGKIFAEG-GKEIINTQNIVEVY 232


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: 161
Number of extensions: 9
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: 253
Length adjustment: 24
Effective length of query: 223
Effective length of database: 229
Effective search space:    51067
Effective search space used:    51067
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.

Links

Downloads

Related tools

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