GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Shewanella loihica PV-4

Align Sodium:dicarboxylate symporter (characterized, see rationale)
to candidate 5208231 Shew_0743 sodium:dicarboxylate symporter (RefSeq)

Query= uniprot:A1S570
         (437 letters)



>FitnessBrowser__PV4:5208231
          Length = 433

 Score =  360 bits (924), Expect = e-104
 Identities = 190/406 (46%), Positives = 269/406 (66%), Gaps = 13/406 (3%)

Query: 14  KILIGMGAGILIGLLLRNFFGGSEWVQDYITEGFFHVIGTIFINSLKMLVVPLVFISLVC 73
           +ILIGM  GI  GL L     G + V           IGT+F+N++KML+VPLVF SL+ 
Sbjct: 25  QILIGMLLGICAGLGL-----GEQAV-------LLKPIGTLFVNTIKMLIVPLVFCSLIV 72

Query: 74  GTCSLSEPSKLGRLGGKTLAFYLFTTAIALVVAISAAVLVQPG-NASLASESMQYSAKEA 132
           G  S+ + +K+GR+G K+ AFYL TT+IA+ + ++   ++QPG   ++ S     + KE 
Sbjct: 73  GVTSMQDTAKMGRIGFKSFAFYLGTTSIAITLGLAVGHIMQPGAGLAMTSAESHNAVKEV 132

Query: 133 PSLADVLINIVPSNPMKALSEGNMLQIIIFAVIFGFAISHIGERGRRVAALFDDLNEVIM 192
           PS+ + LINIVP+NP+ AL+ G +LQ+I+FAV  G A+  IG+ G+    +F+ L E + 
Sbjct: 133 PSIMETLINIVPTNPIAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMY 192

Query: 193 RVVTLIMQLAPYGVFALMGKLALTLGMETLESVIKYFMLVLVVLLFHGFVVYPTLLKLFS 252
           ++  ++M+LAPYGVF LM  +A   GM+ L  +IK  + V +    H    Y  +L   +
Sbjct: 193 KLTDMVMKLAPYGVFGLMAWVAGEYGMDMLMPLIKVILAVYIGCALHIIGFYSLVLTFVA 252

Query: 253 GLSPLMFIRKMRDVQLFAFSTASSNATLPVTMEASEHRLGADNKVASFTLPLGATINMDG 312
            L+P+ F + + +    A++T+SS  TLP +M+ +   LG + K++SF LPLG TINMDG
Sbjct: 253 KLNPMQFFKGISNALAVAYTTSSSAGTLPASMKCASESLGINKKISSFVLPLGTTINMDG 312

Query: 313 TAIMQGVATVFIAQVFGIDLTITDYAMVVMTATLASIGTAGVPGVGLVMLAMVLNQVGLP 372
           TA+ QGV  +F+AQ FGIDLT  DY  +++TATLASIGTAGVPG GLVML +VL  VGLP
Sbjct: 313 TALYQGVTALFVAQAFGIDLTWVDYITIILTATLASIGTAGVPGAGLVMLTLVLTTVGLP 372

Query: 373 VEGIALILGVDRMLDMVRTAVNVTGDTVATVVIAKSEGALNEAVFN 418
           +EG+A+I G+DR+LDM RT VNV+GD VAT VIAKSE  L+   +N
Sbjct: 373 LEGVAIIAGIDRILDMARTVVNVSGDLVATTVIAKSEDELDLEHYN 418


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: 426
Number of extensions: 12
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: 433
Length adjustment: 32
Effective length of query: 405
Effective length of database: 401
Effective search space:   162405
Effective search space used:   162405
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