GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Sphingomonas koreensis DSMZ 15582

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate Ga0059261_3350 Ga0059261_3350 Na+/H+-dicarboxylate symporters

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__Korea:Ga0059261_3350
          Length = 436

 Score =  272 bits (696), Expect = 1e-77
 Identities = 147/404 (36%), Positives = 238/404 (58%), Gaps = 16/404 (3%)

Query: 24  LIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVCGTCSLSEPSK 83
           ++G L+     G  W     +  +   IG +F+  ++MLVVPLVF+++  G  +L++P +
Sbjct: 35  ILGALVLGAIAGVAWGPGATSIAW---IGELFVRLIRMLVVPLVFLTIAAGVAALADPKR 91

Query: 84  LGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQYSAKEAPSLADVLINIV 143
           LG +G KTLA Y+FTT +A+   +  A L+ PG  +  ++++  +    P  A + + I+
Sbjct: 92  LGSIGVKTLAMYVFTTTLAVTTGLIVATLIGPGIGASFADAVPRAMGTPPDTARMFMEII 151

Query: 144 PSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLNEVIMRVVTLIMQLAP 203
           P NP+ A+++G  L +I FA++ G  +   G+    V A  +  ++V++++V  +M+ AP
Sbjct: 152 PDNPVGAMADGKTLSVIFFAILVGAGVIAAGKGAEPVRAFLNGASDVMLKIVGFVMETAP 211

Query: 204 YGVFALMGKLALTLGMETLESVIKYFMLV-----LVVLLFHGFVVYPTLLKLFSGLSPLM 258
           +GVFAL+  +  T G  +  +++K  + V     +V LL HG +V    ++L + LSPL 
Sbjct: 212 FGVFALIAVVMGTSGPASFLAILKLAICVVAGSAVVTLLIHGLIV----VRLMAWLSPLP 267

Query: 259 FIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATINMDGTAIMQG 318
           F R + D  +  FST+SS+ATLPV +  +++ LG    VAS  LPLGATI MDG A+   
Sbjct: 268 FFRGIADAIMVGFSTSSSSATLPVAIRVAQNNLGISKPVASTVLPLGATIGMDGAAMYVA 327

Query: 319 VATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLPVEGIAL 378
           + T+F AQ FG+DLT  DY ++  T T+ ++G A VP   L +LA VL+ +G+  E  AL
Sbjct: 328 MLTLFSAQAFGLDLTWADYLVIAATTTIVAMGVAPVPSGSLFVLAAVLHAIGITPEQTAL 387

Query: 379 ILG----VDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFN 418
           ++G     DR+LDM RT  NVT D      +A+ EG ++  V+N
Sbjct: 388 VVGFVLPFDRILDMTRTVPNVTSDLAIATAVARWEGEMDVTVYN 431


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: 396
Number of extensions: 12
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: 437
Length of database: 436
Length adjustment: 32
Effective length of query: 405
Effective length of database: 404
Effective search space:   163620
Effective search space used:   163620
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: 51 (24.3 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