GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpP in Phaeobacter inhibens BS107

Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate GFF508 PGA1_c05200 putative ABC transporter, inner membrane component

Query= TCDB::G3LHZ0
         (288 letters)



>lcl|FitnessBrowser__Phaeo:GFF508 PGA1_c05200 putative ABC
           transporter, inner membrane component
          Length = 287

 Score =  437 bits (1124), Expect = e-127
 Identities = 212/286 (74%), Positives = 244/286 (85%), Gaps = 1/286 (0%)

Query: 3   KTWNNKAWFLVLPVLLLVAFSAVIPLMTVVNYSVQDTFGNNEFFWAGTDWFVQTLHSDRF 62
           KT N KAWF VLPVLLLVAF+A+IP+MTVVNYSVQ+TFG+N FFW G DWF Q L SDRF
Sbjct: 2   KTENQKAWFFVLPVLLLVAFNALIPMMTVVNYSVQETFGDNVFFWQGLDWFQQILRSDRF 61

Query: 63  WESLQRNLLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNVVGTIWQV 122
             +L R  +F+F+IL +EIPLGI IAL+MP+ G  VPVCLVLMALP+LIPWNVVG +W +
Sbjct: 62  HAALGRQFMFTFLILIIEIPLGIAIALSMPRKGFWVPVCLVLMALPMLIPWNVVGAMWNI 121

Query: 123 FGRVDIGLLGHTLE-AIGLDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDA 181
           F   DIGLLG+ L   +G++Y+  +DPI AWVT+I MDVWHWTSLVVLL YAGLVSIPDA
Sbjct: 122 FTLPDIGLLGYFLNHTLGINYDMTQDPIAAWVTIITMDVWHWTSLVVLLSYAGLVSIPDA 181

Query: 182 YYQAAKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTF 241
           YYQAAKIDGAS W+VFR+IQLPKMK VL IA+LLRFMDSF IYTEPFV+TGGGPGNSTT 
Sbjct: 182 YYQAAKIDGASNWAVFRFIQLPKMKTVLTIAILLRFMDSFNIYTEPFVLTGGGPGNSTTL 241

Query: 242 LSIDLVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTVMTSSDEN 287
           LSIDLVK+A+GQFDLGPAAAMS+IYF I LL+SW+FYTVMT  D+N
Sbjct: 242 LSIDLVKIALGQFDLGPAAAMSLIYFAITLLVSWLFYTVMTKDDQN 287


Lambda     K      H
   0.329    0.143    0.464 

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: 366
Number of extensions: 13
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: 288
Length of database: 287
Length adjustment: 26
Effective length of query: 262
Effective length of database: 261
Effective search space:    68382
Effective search space used:    68382
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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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