GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Shewanella oneidensis MR-1

Align ATPase (characterized, see rationale)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__MR1:202699
          Length = 376

 Score =  152 bits (384), Expect = 1e-41
 Identities = 92/238 (38%), Positives = 135/238 (56%), Gaps = 9/238 (3%)

Query: 27  VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86
           + K +G QFQAL  ++L +Q GE++ ++GPSGSGK+T LR +  LE    G I    H  
Sbjct: 8   ISKKFG-QFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHI----HFG 62

Query: 87  SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQV---RRWPVAQAEATARQLLE 143
           + D   +    + VG VFQ + LF H+TV  N+      +   +R   A+ +     LLE
Sbjct: 63  NRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLLE 122

Query: 144 RVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDL 203
            V++   A +YP QLSGGQ+QR+A+ARALA QP +LL DEP  ALD ++ +E+   +R L
Sbjct: 123 MVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRSL 182

Query: 204 ASE-GMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260
             E   T +  TH+   A E++DRVV+M++G I +   P   +  P S     FL  +
Sbjct: 183 HDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGNV 240


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: 259
Number of extensions: 7
Number of successful extensions: 4
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: 376
Length adjustment: 27
Effective length of query: 234
Effective length of database: 349
Effective search space:    81666
Effective search space used:    81666
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: 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:

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