GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Sphingomonas koreensis DSMZ 15582

Align ATPase (characterized, see rationale)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Korea:Ga0059261_3874
          Length = 243

 Score =  135 bits (341), Expect = 6e-37
 Identities = 88/211 (41%), Positives = 123/211 (58%), Gaps = 7/211 (3%)

Query: 36  QALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGH---RLSHDRRD 92
           Q L GVS++V  GE+ +++GPSG GKST L  L+ L    +GE+   G+   R+    RD
Sbjct: 26  QILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQGEVDALGNPICRMKAGARD 85

Query: 93  IATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQAD 152
              +    G VFQ FNLF  LT  + +    +Q  +   A+A   AR  LE V +  +  
Sbjct: 86  AFRLAN-TGFVFQGFNLFNALTAEEQVAYV-LQCMKVKPAEARQRARAALEAVGLGPRMR 143

Query: 153 KYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTML 211
             P +LSGG++QRVAIARALA QPRIL  DEPTSALD      V+ ++RD+A ++G  +L
Sbjct: 144 LRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHAVIALLRDIAHNQGAAVL 203

Query: 212 VATHEVGFAREVADRVVLMADGQIVEEAPPD 242
             TH+       ADR++ M DG+I+ +  PD
Sbjct: 204 CVTHDPRLL-SFADRIIHMEDGRIIRDERPD 233


Lambda     K      H
   0.321    0.134    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: 156
Number of extensions: 10
Number of successful extensions: 4
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: 261
Length of database: 243
Length adjustment: 24
Effective length of query: 237
Effective length of database: 219
Effective search space:    51903
Effective search space used:    51903
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 (21.9 bits)
S2: 46 (22.3 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