GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Pseudomonas stutzeri RCH2

Align ATPase (characterized, see rationale)
to candidate GFF16 Psest_0016 ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__psRCH2:GFF16
          Length = 278

 Score =  226 bits (576), Expect = 4e-64
 Identities = 125/272 (45%), Positives = 171/272 (62%), Gaps = 20/272 (7%)

Query: 1   MTPLGRQPEPVTAIASAPETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSG 60
           + P  +QPE         + ++   GV K YG +   L G+ L ++ GE V ++GPSGSG
Sbjct: 11  LNPTPQQPEQA-------QPLVRFAGVTKRYG-ELTVLDGLDLQIEEGEKVAIIGPSGSG 62

Query: 61  KSTFLRTLNALESHQRGEIWIEGHRLSH-----------DRRDIATIRQEVGMVFQQFNL 109
           KST LR L  LE    G I ++G  L+H           + R +  +R +VGMVFQ FNL
Sbjct: 63  KSTLLRVLMTLEGIDEGVIEVDGEPLTHMPDASGQLVPANARHLRRVRGKVGMVFQSFNL 122

Query: 110 FPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVAIA 169
           FPH+  LQN+M APVQV     A+A   A +LL  V + ++ + +P QLSGGQQQRVAIA
Sbjct: 123 FPHMNALQNVMEAPVQVLGLSKAEARGRAEELLAMVGLEDKLEHFPAQLSGGQQQRVAIA 182

Query: 170 RALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTMLVATHEVGFAREVADRVV 228
           RALAM+P+++LFDE TSALDPE+  EVL+V+R L  +  +TML+ TH++GFARE ADRV 
Sbjct: 183 RALAMRPKVMLFDEVTSALDPELCGEVLNVIRRLGEAHNLTMLMVTHQMGFAREFADRVC 242

Query: 229 LMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260
               G+I E+  PD  F  PQ +R ++FL+ +
Sbjct: 243 FFHQGRIHEQGSPDELFNNPQEERTREFLSAV 274


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: 230
Number of extensions: 12
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: 261
Length of database: 278
Length adjustment: 25
Effective length of query: 236
Effective length of database: 253
Effective search space:    59708
Effective search space used:    59708
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