GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Novosphingobium fuchskuhlense FNE08-7

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_067913242.1 AQZ52_RS15945 ATP-binding cassette domain-containing protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_001519075.1:WP_067913242.1
          Length = 208

 Score = 92.4 bits (228), Expect = 7e-24
 Identities = 70/210 (33%), Positives = 99/210 (47%), Gaps = 25/210 (11%)

Query: 37  AKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITFNQKSGKQYLLERLPDFRITKEAR 96
           A  G ITAL+GP+GAGK++V   + G  +P  G I      G   L + L    +  EAR
Sbjct: 21  ASAGGITALVGPSGAGKSSVLEALAGLLRPEAGRIAV----GGTVLFDSLARVNLPPEAR 76

Query: 97  VART-FQNIRLFSGLTVLENLLVAQHNKLMKASGYTILGLIGVGPYKREAAEAIELARFW 155
                FQ++RLF    VL NLL  Q                 + P +R      E+A F 
Sbjct: 77  ACGVMFQDLRLFPHRRVLGNLLYGQR----------------LAPPERRFLSLEEVADF- 119

Query: 156 LEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAGLNPRESATLNALLK 215
           L+ A L+ R       L  G  +R+ I RA+ +GP  L +DEP   L+      + A+++
Sbjct: 120 LDIAPLLGRRPRT---LSGGEAQRVAIGRALLSGPRFLLMDEPLTALDDARREAIIAVIE 176

Query: 216 SIRAETGTSILLIEHDMSVVMEISDHVVVL 245
            IR E    ILL+ HD + V  ++D VV L
Sbjct: 177 RIRDELALPILLVSHDRADVARLADTVVEL 206


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: 156
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: 208
Length adjustment: 24
Effective length of query: 268
Effective length of database: 184
Effective search space:    49312
Effective search space used:    49312
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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