GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Dinoroseobacter shibae DFL-12

Align ATPase (characterized, see rationale)
to candidate 3608829 Dshi_2221 ABC transporter related (RefSeq)

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Dino:3608829
          Length = 259

 Score =  232 bits (592), Expect = 5e-66
 Identities = 125/248 (50%), Positives = 165/248 (66%), Gaps = 11/248 (4%)

Query: 21  MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80
           +I    + K YG   + L GVS+  +RG+VV ++G SGSGKST LR  N LE  QRG++ 
Sbjct: 8   VIEIRDLHKAYG-ALEVLKGVSIRAERGDVVSLIGSSGSGKSTLLRCCNLLEDSQRGDVL 66

Query: 81  IEGH----------RLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWP 130
             G           R   D++ +  IR  + MVFQQFNL+ H+T+L+N+M APV V   P
Sbjct: 67  FCGEPVTWTGSGLDRRPADKKQVIRIRTNLSMVFQQFNLWAHMTILENVMEAPVTVLGEP 126

Query: 131 VAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDP 190
             + EA AR LL++V I ++ D YP QLSGGQQQR AIAR LAM+P+ LLFDEPTSALDP
Sbjct: 127 PKEVEARARALLDKVGIGDKCDAYPAQLSGGQQQRAAIARGLAMEPKALLFDEPTSALDP 186

Query: 191 EMVREVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQS 250
           E+ +EV+ V++DLA+EG TML+ TH++  A +V+D VV +  G I EE PPD  F  P+S
Sbjct: 187 ELEQEVVKVIKDLAAEGRTMLIVTHDMRLAADVSDHVVFLHQGLIEEEGPPDILFGQPKS 246

Query: 251 DRAKQFLA 258
            R KQFL+
Sbjct: 247 ARLKQFLS 254


Lambda     K      H
   0.321    0.134    0.387 

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: 197
Number of extensions: 5
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: 261
Length of database: 259
Length adjustment: 24
Effective length of query: 237
Effective length of database: 235
Effective search space:    55695
Effective search space used:    55695
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 (21.9 bits)
S2: 47 (22.7 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:

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