GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Pseudomonas stutzeri RCH2

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate GFF1351 Psest_1386 Na+/H+-dicarboxylate symporters

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__psRCH2:GFF1351
          Length = 409

 Score =  275 bits (704), Expect = 1e-78
 Identities = 154/403 (38%), Positives = 242/403 (60%), Gaps = 14/403 (3%)

Query: 14  KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFH---VIGTIFINSLKMLVVPLVFIS 70
           +ILI    G+ IG L      G+      + EG  +   + G+IFI  LKM+++PL+F S
Sbjct: 7   QILIAACLGVAIGWLT-----GTLPTDAPVREGVLYASTLAGSIFIGLLKMVLIPLIFTS 61

Query: 71  LVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG---NASLASESMQY 127
           +V G  +L    ++ R+ G  L ++  TT+ A++VA+ AA L +PG   +  L +E+M  
Sbjct: 62  IVVGVANLQAHHQVHRVWGGALVYFTLTTSAAMLVALVAANLFKPGAGLSLDLFAEAMND 121

Query: 128 SAKEAPSLADVLINIVPS---NPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALF 184
                 +L +  ++   +   NP  AL+ G++L +++FA+  G A+   G+R R +  + 
Sbjct: 122 FEARQLTLPEFFLHFFANLFQNPFAALANGSILAVVVFAMFIGIALVAGGDRYRNILVVL 181

Query: 185 DDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVY 244
            +  E++MR+++ IM+LAP G+ AL+ KL     +  L +V  +  LV    LFHG VV 
Sbjct: 182 QEFLELMMRIISWIMRLAPLGILALLIKLVAEQDVALLSAVGGFIALVFATTLFHGTVVL 241

Query: 245 PTLLKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPL 304
           P +L L +G SPL F R  R+  + AF+T+SS ATLP+++  +E  L     +A F LPL
Sbjct: 242 PGILFLATGKSPLWFFRGTREALITAFATSSSAATLPISLRCAEDNLKVRPGIAGFVLPL 301

Query: 305 GATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAM 364
           GAT+NMDGTA+ +  A +F+A + GI+L++   A+V  TA +AS G  G+P  G+V + M
Sbjct: 302 GATMNMDGTALYEAAAALFVANLMGIELSLAQQAVVFFTAMIASTGAPGIPSAGMVTMVM 361

Query: 365 VLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAK 407
           VL  VGLP E +A++L +DR+LD VRTAVNV GD + +VV+ +
Sbjct: 362 VLQAVGLPAEAVAILLPIDRLLDTVRTAVNVEGDIIGSVVVQR 404


Lambda     K      H
   0.325    0.139    0.388 

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: 356
Number of extensions: 19
Number of successful extensions: 2
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: 437
Length of database: 409
Length adjustment: 32
Effective length of query: 405
Effective length of database: 377
Effective search space:   152685
Effective search space used:   152685
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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