GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proW in Desulfovibrio vulgaris Hildenborough

Align Glycine betaine/proline betaine transport system permease protein ProW (characterized)
to candidate 207785 DVU2298 glycine/betaine/L-proline ABC transporter, permease protein

Query= SwissProt::P14176
         (354 letters)



>lcl|MicrobesOnline__882:207785 DVU2298 glycine/betaine/L-proline
           ABC transporter, permease protein
          Length = 283

 Score =  221 bits (562), Expect = 2e-62
 Identities = 124/271 (45%), Positives = 166/271 (61%), Gaps = 1/271 (0%)

Query: 62  IPLDSWVTEGIDWVVTHFRPVFQGVRVPVDYILNGFQQLLLGMPAPVAIIVFALIAWQIS 121
           IPL +W+    D +V       +         ++  + LL  +P    I V AL+AW+ +
Sbjct: 9   IPLGAWLEAFTDNMVEWCSGATRAFSTVAGNGIDMLESLLGSIPPWAFIPVVALLAWRAT 68

Query: 122 GV-GMGVATLVSLIAIGAIGAWSQAMVTLALVLTALLFCIVIGLPLGIWLARSPRAAKII 180
              G+G   L+    I  +G W   M T+ALVL A    +V G+PLGI  A +    K++
Sbjct: 69  RKPGIGAFALLGFGLIWNLGLWEATMSTIALVLVATALAVVTGVPLGIAAAVNVTVRKVL 128

Query: 181 RPLLDAMQTTPAFVYLVPIVMLFGIGNVPGVVVTIIFALPPIIRLTILGINQVPADLIEA 240
            P+LD MQT PAFVYL+P +  FG+G V  V  T++FA+PP IR T LGI QVP DL+E 
Sbjct: 129 MPVLDLMQTMPAFVYLIPAIPFFGLGKVAAVFATVVFAMPPAIRFTCLGIRQVPDDLVEC 188

Query: 241 SRSFGASPRQMLFKVQLPLAMPTIMAGVNQTLMLALSMVVIASMIAVGGLGQMVLRGIGR 300
           + +FG S  Q L K++LPLA PTI+AGVNQT+MLALSMVVIA+MI   GLG  V + I R
Sbjct: 189 AEAFGTSRWQRLVKLELPLAAPTILAGVNQTIMLALSMVVIAAMIGARGLGGEVWKAIQR 248

Query: 301 LDMGLATVGGVGIVILAIILDRLTQAVGRDS 331
           L++G     G+GIVI+AI LDR+ Q +GR S
Sbjct: 249 LELGSGFEAGIGIVIVAICLDRVLQHIGRRS 279


Lambda     K      H
   0.326    0.141    0.435 

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: 316
Number of extensions: 21
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: 354
Length of database: 283
Length adjustment: 27
Effective length of query: 327
Effective length of database: 256
Effective search space:    83712
Effective search space used:    83712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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