GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Mesorhizobium ciceri WSM1271

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate YP_004139338.1 Mesci_0115 polar amino acid ABC transporter inner membrane subunit

Query= TCDB::Q52665
         (434 letters)



>NCBI__GCF_000185905.1:YP_004139338.1
          Length = 224

 Score =  108 bits (270), Expect = 2e-28
 Identities = 67/212 (31%), Positives = 116/212 (54%), Gaps = 14/212 (6%)

Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLL 285
           GFL  L++G+ +I + +P+G+ ++L R      ++ L+VG  +  R +P++ +L    +L
Sbjct: 23  GFLNTLLLGILSIGIGIPIGLGISLVRLYAPKPLRWLAVGYTDIFRALPVLVVL----IL 78

Query: 286 LQYFLP-PGTNFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQ 344
           + Y LP  G         V       +AY AEV R G+ ++PRGQ+EA+ ALGL +    
Sbjct: 79  IYYALPFLGIRLSSWASAVTAFAFIMSAYSAEVFRSGIESIPRGQFEASQALGLPFLLTL 138

Query: 345 RLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGLFDPLKGISNVVRSDMAWKGTYW--E 402
           R +++PQA+++ IP + S+ + +FKDT+L + V L + LK  +N        +  Y    
Sbjct: 139 RKVVLPQAIRVVIPPMTSNCVSMFKDTSLASTVALPELLKEATNA-------QSLYANPS 191

Query: 403 PYIFVALIFFLFNFSMSRYSMYLERKLKRDHR 434
           P I  AL++ +F + M R    LE + K + +
Sbjct: 192 PLIGAALVYLIFLWPMVRLVSLLEERFKTEKK 223


Lambda     K      H
   0.329    0.143    0.457 

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: 269
Number of extensions: 13
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: 434
Length of database: 224
Length adjustment: 27
Effective length of query: 407
Effective length of database: 197
Effective search space:    80179
Effective search space used:    80179
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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