GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltP in Shewanella amazonensis SB2B

Align Na+/H+ dicarboxylate symporter (characterized, see rationale)
to candidate 6936881 Sama_1055 sodium:dicarboxylate symporter (RefSeq)

Query= uniprot:L0GT47
         (419 letters)



>FitnessBrowser__SB2B:6936881
          Length = 417

 Score =  381 bits (979), Expect = e-110
 Identities = 192/401 (47%), Positives = 274/401 (68%), Gaps = 3/401 (0%)

Query: 11  LRLLVRLPLWQQILIGLALGVAAGMAFGADAQLLAPIGTLFLNAIKMLIVPLVFVSLVAG 70
           ++ L ++P WQ++L G ALG+  G+  G  A +L P+G LF+ AIKML+ PLV  ++V  
Sbjct: 3   IQTLNKIPFWQKVLAGFALGILTGVLLGESATVLKPLGDLFIAAIKMLVAPLVLCAIVVS 62

Query: 71  ITSMQDSAKLGRISLKTIAIYLVTTAFAVSIGLLFGALFSPGEGMNMVASGNEQAKQAPS 130
           ITS+  S+ L R+S KT+A++++T   A  IGL  G+ F  G  M + AS   + +  P 
Sbjct: 63  ITSLGSSSNLKRLSFKTLALFMLTGTLASLIGLAVGSSFDMGGSMQL-ASTEVRERVVPG 121

Query: 131 LVSILVGLVPANPVTAFAEGNILQIIVFAIALGVSINLIGERGAPAVRLFDALAETFYKL 190
              +L+ ++P NP  +   G +LQIIVFA  +G++IN +GE+  P  ++FDA AE  ++L
Sbjct: 122 FAQVLLDMIPVNPFASLTNGKVLQIIVFAALVGIAINAVGEKAEPLKKVFDAGAEVMFQL 181

Query: 191 TDLVMRVAPIGVFALTAGVVGSHGAEVLLPLAGVIGVIYLASIAHVLLVYGGLLGLLARL 250
           T +V+++ PIGVF L A VVG +G   LLPL   I  IY+A++ H++ VYGGL+   ARL
Sbjct: 182 TRMVLKLTPIGVFGLMAWVVGEYGLSTLLPLGKFIIAIYVAALIHIVFVYGGLVKFAARL 241

Query: 251 NPLRFFQGIAPALAVAFSTSSSSGTLPVSIECARKNLGVSEGVAGFVLPVGATINMDGT- 309
           +PL+FF+   PA  VAFST+SS GTLPV+ +CA +++GVS+  + FVLP+GAT+NMDG  
Sbjct: 242 SPLQFFRKAMPAQLVAFSTASSFGTLPVTTKCA-ESMGVSKRYSAFVLPMGATMNMDGCG 300

Query: 310 AIYQGVLALFIAQAFGIDLSAGQYAMIILTATLASIGTAGIPGAGLIMLGLVLTAAGLPL 369
            IY  + A+FIAQ +GI L    Y +I +TAT+AS+GTAG+PG+ ++ML + L   GLPL
Sbjct: 301 GIYPAIAAIFIAQIYGIPLDMTDYMLIAVTATVASVGTAGVPGSAMVMLTVTLGVVGLPL 360

Query: 370 EGVALIAGIDRILDMARTTVNVAGDLMTTTLVGRSEQELDR 410
           EG+A IA IDR++DM RT  NV GD+MT  +VG SE ELDR
Sbjct: 361 EGIAFIAAIDRVIDMIRTCTNVTGDMMTAVVVGNSEGELDR 401


Lambda     K      H
   0.324    0.140    0.386 

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: 518
Number of extensions: 22
Number of successful extensions: 4
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: 419
Length of database: 417
Length adjustment: 32
Effective length of query: 387
Effective length of database: 385
Effective search space:   148995
Effective search space used:   148995
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: 41 (22.0 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