GapMind for catabolism of small carbon sources

 

Alignments for a candidate for potA in Streptococcus oralis 7747

Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate WP_000590982.1 HK29_RS06510 amino acid ABC transporter ATP-binding protein

Query= TCDB::P31134
         (377 letters)



>NCBI__GCF_000382825.1:WP_000590982.1
          Length = 247

 Score =  162 bits (409), Expect = 1e-44
 Identities = 94/242 (38%), Positives = 137/242 (56%), Gaps = 9/242 (3%)

Query: 19  LLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIML 78
           +++I NL+KS+ GQ  +D ++L I KGE+ AL+G+SG GKST LR L   E P +G I +
Sbjct: 1   MIKISNLSKSFSGQTVLDHLNLDIQKGEVVALIGSSGAGKSTFLRSLNYLETPDSGSIQI 60

Query: 79  D--GVDLSQVP-----PYLRPINMMFQSYALFPHMTVEQNIAFGL-KQDKLPKAEIASRV 130
           D   VD S++         R ++M+FQ + LF   T   N+  GL    KL   E     
Sbjct: 61  DDFSVDFSKITQEEILALRRKLSMVFQQFNLFERRTALDNVKEGLVVVKKLSDQEATKIA 120

Query: 131 NEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQL 190
            E L  V + +     P  LSGGQ+QRVALAR+LA +P +LLLDEP  ALD +L   ++ 
Sbjct: 121 KEELAKVGLSDRENHYPRHLSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEK 180

Query: 191 EVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFI 250
            + D   + G T ++V+HD      +A +I  +++GK ++ G P+EI  HP    + EF 
Sbjct: 181 SIAD-AAKSGQTMILVSHDMSFVAQVADKILFLDKGKIIESGTPDEIIHHPKEERTKEFF 239

Query: 251 GS 252
            S
Sbjct: 240 AS 241


Lambda     K      H
   0.321    0.137    0.400 

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: 203
Number of extensions: 9
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: 377
Length of database: 247
Length adjustment: 27
Effective length of query: 350
Effective length of database: 220
Effective search space:    77000
Effective search space used:    77000
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: 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