GapMind for catabolism of small carbon sources

 

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

Align GlpQ, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3609748 Dshi_3131 binding-protein-dependent transport systems inner membrane component (RefSeq)

Query= TCDB::G3LHZ1
         (273 letters)



>FitnessBrowser__Dino:3609748
          Length = 265

 Score =  410 bits (1053), Expect = e-119
 Identities = 195/260 (75%), Positives = 225/260 (86%)

Query: 14  LVPTIYIIFLILPIYWLINMSFKENSEITGAFSLWPTNPTLRNYTVIFTDPSWYNGYINS 73
           L+P  YI+FL+LPIYWL+ MSFK  +EI   F+L+P   TL +Y  IFTDP+WY GYINS
Sbjct: 6   LIPIFYILFLMLPIYWLVTMSFKTTNEILAGFTLFPQTFTLDSYITIFTDPTWYWGYINS 65

Query: 74  IIYVVMNTVISVAAALPAAYAFSRYRFLGDKHLFFWLLTNRMAPPAVFALPFFQLYSAFG 133
           IIYV +NTV+SVA ALPAAYAFSRYRFLGDK LFFWLLTNRMAP AVFALPFFQLYS+  
Sbjct: 66  IIYVSLNTVLSVAVALPAAYAFSRYRFLGDKQLFFWLLTNRMAPAAVFALPFFQLYSSVK 125

Query: 134 LIDTHIAVALAHCLFNVPLAVWILEGFMSGVPKEIDETAYIDGYSFPRFFIKIFIPLIAS 193
           + DTH+AVALAH LFNVPLAVWILEGFM  +PKE+DETAY+DGYSFPRFFIKIF+P I +
Sbjct: 126 IFDTHLAVALAHTLFNVPLAVWILEGFMRSIPKELDETAYVDGYSFPRFFIKIFLPNIGA 185

Query: 194 GVGVAGFFCFMFSWVELLLARTLTTTAAKPISAIMTRTVSASGMDWGVLAAAGVLTIIPG 253
           GVGVA FFCFMFSWVE+LLA+TLT   AKPI+A+MTRT S++G + G+LAAAG LTIIPG
Sbjct: 186 GVGVAAFFCFMFSWVEMLLAKTLTAVEAKPIAAVMTRTASSAGYELGLLAAAGTLTIIPG 245

Query: 254 ALVIYFVRNYIAKGFALGRV 273
           A+VIYFVRNYIA+GFA+GRV
Sbjct: 246 AIVIYFVRNYIARGFAMGRV 265


Lambda     K      H
   0.330    0.142    0.456 

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: 359
Number of extensions: 6
Number of successful extensions: 1
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: 273
Length of database: 265
Length adjustment: 25
Effective length of query: 248
Effective length of database: 240
Effective search space:    59520
Effective search space used:    59520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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