GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Flavobacterium beibuense F44-8

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_035136158.1 Q763_RS16555 ABC transporter ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>NCBI__GCF_000769915.1:WP_035136158.1
          Length = 234

 Score =  148 bits (373), Expect = 1e-40
 Identities = 85/227 (37%), Positives = 133/227 (58%), Gaps = 16/227 (7%)

Query: 1   MIKMTGVQKYFG----DFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEG 56
           MIK+  + K F     +  AL DI +E+ +G+ V ++G SG GKSTL   +  L++   G
Sbjct: 1   MIKIENLSKVFRTEEVETKALNDISIEVKKGEFVTIMGASGCGKSTLLNIVGLLDSASGG 60

Query: 57  TIEIDGKVLPEEGKGLANL------RADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKK 110
           +     K+L  E  GL+        + ++G VFQ+FNL   L++ DN+ L P+    +  
Sbjct: 61  SY----KLLDREINGLSESEKAKVRKENIGFVFQNFNLIDELSVYDNIEL-PLIYNNVPS 115

Query: 111 SEAEKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPE 170
            E +K    + ER+GI+++   YP QLSGGQQQR A+ARAL  NPKI+L DEPT  LD +
Sbjct: 116 GERKKRVEEIAERLGISHRLKHYPQQLSGGQQQRAAVARALVNNPKIILADEPTGNLDSK 175

Query: 171 MVNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVED 217
             NEV++++  L   G T++ VTH   +    + + ++M DG+I+++
Sbjct: 176 NGNEVMELLTDLHANGATILMVTHS-EYDASFSQKTIYMKDGMILKE 221


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: 122
Number of extensions: 6
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: 242
Length of database: 234
Length adjustment: 23
Effective length of query: 219
Effective length of database: 211
Effective search space:    46209
Effective search space used:    46209
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