GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Shewanella loihica PV-4

Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)

Query= TCDB::P73721
         (252 letters)



>FitnessBrowser__PV4:5208351
          Length = 342

 Score =  144 bits (363), Expect = 2e-39
 Identities = 80/242 (33%), Positives = 137/242 (56%), Gaps = 7/242 (2%)

Query: 9   ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68
           ++ +Q+  ++    +LRG+   ++  ++ +++GPSGCGK+T L+ +  L+PIS GR+ + 
Sbjct: 4   LTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRISIN 63

Query: 69  GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRAL 128
           G  LSG    +  +   R  VGM+FQ + LFPHLTV +N+L   + + +          L
Sbjct: 64  GRLLSGP---ETFVPSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQARLGEML 120

Query: 129 TYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL-N 187
             +   GLG +   YP +LSGGQ+QRV+IAR L  +PE+LL DEP S +D ++ GE++  
Sbjct: 121 ALVKLEGLGGR---YPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVE 177

Query: 188 VMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLS 247
           + + L + G++   VTH    A   ++++  F  G I + G    ++  P    +  FL 
Sbjct: 178 IREILKQRGVSAVFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFLG 237

Query: 248 RI 249
           ++
Sbjct: 238 QV 239


Lambda     K      H
   0.321    0.139    0.397 

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: 239
Number of extensions: 6
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: 252
Length of database: 342
Length adjustment: 26
Effective length of query: 226
Effective length of database: 316
Effective search space:    71416
Effective search space used:    71416
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