GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztA in Magnetovibrio blakemorei MV-1

Align BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_069956932.1 BEN30_RS03095 amino acid ABC transporter substrate-binding protein

Query= TCDB::Q52663
         (338 letters)



>NCBI__GCF_001746755.1:WP_069956932.1
          Length = 327

 Score =  368 bits (944), Expect = e-106
 Identities = 179/326 (54%), Positives = 231/326 (70%), Gaps = 1/326 (0%)

Query: 13  AALVAGAASASTLDDVKARGQLICGSNPGLTGFAAPDANGVYQGFDVAVCKAVAAAVLGD 72
           A ++A +A A TL+DV ARG L CG N GL GF+  D  G + G DV VC+AVAAAVLGD
Sbjct: 3   ATMIATSAFAGTLEDVTARGTLSCGVNTGLPGFSLQDDKGNWTGIDVDVCRAVAAAVLGD 62

Query: 73  PMKVKYVPLTGETRFTALASGEVDVLVRNSTWTFSRDTELALDFVAVNYYDGQGFMVNKS 132
             KV++VPLT + RFTAL SGE+D+L RN+TWT +RDT L L+F  VNYYDGQGF+V K+
Sbjct: 63  ATKVRFVPLTAKERFTALQSGEIDMLSRNTTWTHTRDTSLGLNFAGVNYYDGQGFLVQKA 122

Query: 133 LGVSSAKELDGATICVQTGTTTEMNLADFFKANNMTYTPVNIADDAEGQQKFAAGACDSY 192
           LGV SAKELDGA++C+Q GTTTE+NLAD+F+ N M Y+ V      + ++ F A  CD  
Sbjct: 123 LGVKSAKELDGASVCIQAGTTTELNLADYFRLNGMKYSAVVYDTSDQTREGFEAARCDIL 182

Query: 193 TTDASGLASSRATLPNAADIVILPEIISKEPLGPVVRHGDNNWGDIVRWSFYALVAAEEY 252
           T+D S L + R+ + +    V+LPE+ISKEPLGPVVR GD+ W +IV+W+ YA V AEE 
Sbjct: 183 TSDQSQLYAIRSKMADPTSAVVLPEVISKEPLGPVVRQGDDAWFNIVKWTLYAQVNAEEM 242

Query: 253 GITKANLEEVAASTQNPEIRRLLGLEGDMGKKIGLDNDFAKRAILASGNYGEVFEANIGA 312
           G+T AN  E+  +  +P ++RLLG EGD G K+G+  D+A   +   GNYGE+FE N+G 
Sbjct: 243 GVTSANAMEMKTAA-DPNVKRLLGTEGDAGAKLGISADWAYNVVSQVGNYGEMFERNVGL 301

Query: 313 STSIGLARGLNAQWTQGGLMYAPPFR 338
            T + +ARGLNA W  GGL YAPP R
Sbjct: 302 KTPLAIARGLNALWNNGGLQYAPPIR 327


Lambda     K      H
   0.316    0.132    0.384 

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: 334
Number of extensions: 9
Number of successful extensions: 2
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: 338
Length of database: 327
Length adjustment: 28
Effective length of query: 310
Effective length of database: 299
Effective search space:    92690
Effective search space used:    92690
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 (21.6 bits)
S2: 49 (23.5 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