GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltL in Marinomonas arctica 328

Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_111609155.1 DK187_RS20495 amino acid ABC transporter ATP-binding protein

Query= TCDB::P48243
         (242 letters)



>NCBI__GCF_003259225.1:WP_111609155.1
          Length = 242

 Score =  259 bits (662), Expect = 3e-74
 Identities = 131/240 (54%), Positives = 170/240 (70%)

Query: 1   MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60
           ++ +  V KY+GD H L  IDL I  G+VV ++G SGSGKSTL R IN LE  +EG I +
Sbjct: 3   LVNLHQVHKYYGDHHVLKGIDLVIKAGEVVSIIGKSGSGKSTLLRCINGLEQYQEGGITV 62

Query: 61  DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120
           DGK +  E   +  L   VGM+FQ+FNLFPH+T+ +NV LAP  V K  K+EAE  A ++
Sbjct: 63  DGKEVTTEDIQVRRLALSVGMIFQNFNLFPHMTVGENVMLAPTIVLKKSKAEAEATARAM 122

Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180
           LE+VG+A + D YP +LSGGQQQRVAIARALAM+PK++L DE TSALDPE+V EVL V+ 
Sbjct: 123 LEKVGLAEKFDSYPEKLSGGQQQRVAIARALAMSPKVLLCDEITSALDPELVGEVLKVLE 182

Query: 181 SLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLGKIL 240
            LAKEG+T+V VTHEM FAR    RV+FM  G + E  +P +  +NP++D  K F+G +L
Sbjct: 183 QLAKEGITLVLVTHEMNFARDVGSRVVFMHQGKVWEQGDPKTVLSNPQTDELKQFMGAVL 242


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: 181
Number of extensions: 3
Number of successful extensions: 1
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: 242
Length adjustment: 23
Effective length of query: 219
Effective length of database: 219
Effective search space:    47961
Effective search space used:    47961
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.

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