GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Sulfurivirga caldicuralii DSM 17737

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_200770547.1 BUQ81_RS04135 dicarboxylate/amino acid:cation symporter

Query= uniprot:A1S570
         (437 letters)



>NCBI__GCF_900141795.1:WP_200770547.1
          Length = 422

 Score =  286 bits (732), Expect = 9e-82
 Identities = 160/415 (38%), Positives = 252/415 (60%), Gaps = 18/415 (4%)

Query: 8   KIGLTGKILIGMGAGILIGLLLRN--FFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVP 65
           K+ L  +IL+ +   +L+G L        G  W+  Y        IGT+F+N+LKM+VVP
Sbjct: 2   KLALHWQILLALALAVLMGWLTGTDATILGVHWIAIY------DFIGTLFLNALKMVVVP 55

Query: 66  LVFISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNAS-----L 120
           LV  +++ G  S++     GRLG KTL +YL T+AIA+++ I+   L+QPG +      +
Sbjct: 56  LVMAAIITGMASIARQGGFGRLGLKTLGYYLMTSAIAILIGITLVNLIQPGVSDNPPPQI 115

Query: 121 ASESM---QYSAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERG 177
           A+++    +   ++   +A+V + ++P+N ++A +E  ML +I F+++FG+ +  I    
Sbjct: 116 AADTQLQQKLEGRDIGDIAEVFLRMIPTNIVEAAAETQMLGLIFFSLLFGYFMMKIQTPY 175

Query: 178 RRVAALF-DDLNEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVL 236
           R     F   + EV+M++   +M+ AP GVF L+       G +   ++  +F+ V++ L
Sbjct: 176 RDTLYNFWQGVFEVMMQITEWVMKFAPLGVFGLVAASVARTGFDQFANLALFFITVVLAL 235

Query: 237 LFHGFVVYPTLLKLFSGL-SPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADN 295
             H FVV P +L+   G+ +P    + M    L AFST+SS +TLPVT+E  E   G  N
Sbjct: 236 GIHFFVVMPLILRFIGGVRNPWKHYKVMLPAILTAFSTSSSASTLPVTIECVERGAGVPN 295

Query: 296 KVASFTLPLGATINMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVP 355
           +++ F LPLGAT+NMDGTA+ + VA +FIAQ+FG+ L +T   M+++ A L SIG AG+P
Sbjct: 296 RISGFVLPLGATVNMDGTALYEAVAALFIAQLFGVHLDVTQQFMIIVIALLTSIGVAGIP 355

Query: 356 GVGLVMLAMVLNQVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEG 410
              LV ++++L  VGLP E I L+L VDR+LDM+RT VN+  D+V  VVIA+SEG
Sbjct: 356 SASLVAISIILVSVGLPAEAIGLLLVVDRLLDMMRTTVNIFSDSVGAVVIARSEG 410


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: 381
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: 437
Length of database: 422
Length adjustment: 32
Effective length of query: 405
Effective length of database: 390
Effective search space:   157950
Effective search space used:   157950
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 Apr 09 2024. 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