GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Shewanella sp. ANA-3

Align Histidine transport ATP-binding protein HisP (characterized)
to candidate 7026313 Shewana3_3455 ABC transporter related (RefSeq)

Query= SwissProt::P02915
         (258 letters)



>FitnessBrowser__ANA3:7026313
          Length = 656

 Score =  145 bits (366), Expect = 2e-39
 Identities = 91/241 (37%), Positives = 144/241 (59%), Gaps = 17/241 (7%)

Query: 2   MSENKLHVIDLHKRYGGHE----VLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEK 57
           MS+  L V   ++ +   E    VLK ++L    G++++I+G+SGSGKST +  +  L+K
Sbjct: 1   MSKPLLEVSACYRSFQAGEQQLTVLKDINLSIARGEMVAIVGASGSGKSTLMNILGCLDK 60

Query: 58  PSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEA 117
           PS+G+  ++GQ+ +       Q+ V +  +LR  R     +FQ ++L   +  + NV E 
Sbjct: 61  PSKGSYFIDGQDTS-------QMDVDELAKLR--REHFGFIFQRYHLLGDLNAVGNV-EV 110

Query: 118 PIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLF 177
           P    G  + + RERA   L+++G+ ER   K P  LSGGQQQRVS+ARAL    DV+L 
Sbjct: 111 PAVYAGKDRLERRERAESLLSRLGLGERLDHK-PNQLSGGQQQRVSVARALMNGGDVILA 169

Query: 178 DEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGK-IEEEGD 236
           DEPT ALD     E++R++Q+L  EG+T+++VTH+M  A+H +  +I +  G  I +E +
Sbjct: 170 DEPTGALDSHSGEEMMRLLQELHREGQTIIIVTHDMHVAQH-ADRIIEIKDGVIISDEPN 228

Query: 237 P 237
           P
Sbjct: 229 P 229


Lambda     K      H
   0.319    0.136    0.383 

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: 337
Number of extensions: 15
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: 258
Length of database: 656
Length adjustment: 31
Effective length of query: 227
Effective length of database: 625
Effective search space:   141875
Effective search space used:   141875
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 (21.7 bits)
S2: 50 (23.9 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