GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Lacinutrix algicola AKS293

Align ABC transporter for D-glucosamine, ATPase component (characterized)
to candidate WP_055437631.1 ASC41_RS15790 ABC transporter ATP-binding protein

Query= reanno::pseudo3_N2E3:AO353_21725
         (265 letters)



>NCBI__GCF_001418085.1:WP_055437631.1
          Length = 220

 Score =  134 bits (337), Expect = 2e-36
 Identities = 87/227 (38%), Positives = 135/227 (59%), Gaps = 12/227 (5%)

Query: 15  LLEIRDLHKQYGPLEVLKGVDLTMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQILL 74
           +++  ++HK Y  L VLKGV++ +++G VV+++GSSG+GKTTLL+ +  L+         
Sbjct: 1   MIKAENIHKYYDDLHVLKGVNVHIKKGEVVSIVGSSGAGKTTLLQILGTLDTISK----T 56

Query: 75  DGESIGYHEVNGKRVRH-SEKVIAQHR-AMTGMAFQQFNLFPHLTALQNVTLGLLKVKKL 132
           D  S+    +NGK +   SEK +A+ R    G  FQ   L P  TA++NV +    +KK 
Sbjct: 57  DDSSL---IINGKNISSLSEKQLAKFRNEHIGFIFQFHQLLPEFTAIENVCIPAF-IKKT 112

Query: 133 HKDEAVVLAEKWLERVGLLERRDHYPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALD 192
            K EA   A++ L+ +GL  R +H P +LSGG+QQRVA+ARA+  NPSL+  DE +  LD
Sbjct: 113 PKAEATKRAKELLDFLGLSHRYNHKPNELSGGEQQRVAVARALINNPSLIFADEPSGNLD 172

Query: 193 PELVGEVLSVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRI 238
            E    + S+   L ++ G T ++VTH    A +++D+ + M  G I
Sbjct: 173 SESAENLHSLFFKLRDEFGQTFVIVTHNEELA-DLADRKLVMVDGVI 218


Lambda     K      H
   0.319    0.135    0.379 

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: 120
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: 265
Length of database: 220
Length adjustment: 23
Effective length of query: 242
Effective length of database: 197
Effective search space:    47674
Effective search space used:    47674
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 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