GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Oceanisphaera arctica V1-41

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate WP_104485805.1 UN63_RS05650 dicarboxylate/amino acid:cation symporter

Query= uniprot:A1S570
         (437 letters)



>NCBI__GCF_002936955.1:WP_104485805.1
          Length = 442

 Score =  518 bits (1333), Expect = e-151
 Identities = 255/427 (59%), Positives = 332/427 (77%), Gaps = 4/427 (0%)

Query: 8   KIGLTGKILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLV 67
           K+ LT K+L+GM  GI+ G + R   G   +VQ+Y+  G   V G IFI SLKMLVVPL+
Sbjct: 7   KLSLTSKVLLGMSLGIVAGFIFRTLLGEVAFVQEYVVNGLLQVGGEIFIASLKMLVVPLI 66

Query: 68  FISLVCGTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPGNASLASESMQY 127
           F+SLVCGT SL + S LGRLGGKTLAFYL TTAIA+ +A+    L +PG+    + +  +
Sbjct: 67  FVSLVCGTSSLKDLSTLGRLGGKTLAFYLVTTAIAISLALLMGNLFKPGDGVDLTAATTF 126

Query: 128 SAKEAPSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDL 187
           + KEAPSL DV++ + P+NP+ ++++GN LQII+FAV+FG AIS  G+ G R+AA+F D 
Sbjct: 127 ATKEAPSLGDVIVGMFPTNPINSMAQGNTLQIIVFAVLFGIAISLAGKPGERIAAMFGDF 186

Query: 188 NEVIMRVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTL 247
           NEVIM++VTL+M +APYGVF LM +L  +LG++ + ++++YF+++   LL HG V Y  +
Sbjct: 187 NEVIMKLVTLLMNVAPYGVFCLMAQLFTSLGLDAIVNLMEYFLVLAGTLLLHGLVTYSIM 246

Query: 248 LKLFSGLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGAT 307
            + F+GL+PL F++KM D  +FAFSTASSNAT+PVTME +  R+G DNKVA+FT+PLGAT
Sbjct: 247 FRAFTGLNPLTFLKKMEDAVMFAFSTASSNATIPVTMETATRRMGVDNKVAAFTVPLGAT 306

Query: 308 INMDGTAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLN 367
           INMDGTAIMQGVAT FIAQ F IDLT  DY MV+MTATLAS+GTAGVPGVGL+MLAMVLN
Sbjct: 307 INMDGTAIMQGVATAFIAQAFNIDLTFNDYLMVIMTATLASVGTAGVPGVGLIMLAMVLN 366

Query: 368 QVGLPVEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFNDPKAGKTAG 427
           QVGLPVEGIALI+GVDR+LDM+RTAVN+TGD+V T ++ KSEGA++ A FN+P AGK   
Sbjct: 367 QVGLPVEGIALIIGVDRLLDMIRTAVNITGDSVVTCIVGKSEGAMDVARFNNPNAGKR-- 424

Query: 428 SFDAEVH 434
             + E+H
Sbjct: 425 --EEEIH 429


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: 517
Number of extensions: 20
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: 437
Length of database: 442
Length adjustment: 32
Effective length of query: 405
Effective length of database: 410
Effective search space:   166050
Effective search space used:   166050
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 24 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