GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Sinorhizobium meliloti 1021

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate SM_b20297 SM_b20297 permease

Query= TCDB::P74224
         (445 letters)



>FitnessBrowser__Smeli:SM_b20297
          Length = 426

 Score =  198 bits (504), Expect = 2e-55
 Identities = 128/431 (29%), Positives = 214/431 (49%), Gaps = 17/431 (3%)

Query: 11  MFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFGIMANGTLLAI 70
           +F G    L  G PV F+L   A+ + +       +    L+   QR+   + +  LLA+
Sbjct: 4   LFGGWFALLIAGMPVGFTLIVAALAYML-------WQGTGLNFAGQRMIAGLNSFPLLAV 56

Query: 71  PFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAATVVAMG 130
           PFFI    ++  SG+ E++ +    ++GH+RGGL    I+   + +  +G   A    +G
Sbjct: 57  PFFILTAQLMNLSGVTERIFDFAKALVGHIRGGLGHVNIMASVLFSGMSGSAVADAAGLG 116

Query: 131 LISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIGSLLPGL 190
            + +  M   GY ++ +  +  AS  +G +IPPS+ L+V       S+G LF+G ++PGL
Sbjct: 117 QLEIKAMRDAGYDEQFSGSITAASAIIGPLIPPSIPLVVYGVIANTSIGGLFLGGIVPGL 176

Query: 191 MMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLPPLVLILLVLGSIFF 250
           + A S  + V +IAW + + A A  A  R +             L PL+   +++G IF 
Sbjct: 177 LCAASLMIMVYVIAW-RRNYATAQRAGFRRVWSTFWH------ALLPLITPFIIIGGIFA 229

Query: 251 GIASPTEAGAVGSIGAIALAHFNQR-LNWKALWEVCDATLRITSMVMLILLGSTAFSLVF 309
           G+ SPTEA  V +  A+ L     R + +  L  V   T+  T+ V L+++G + F  V 
Sbjct: 230 GVFSPTEAAVVAASYALFLGVVVYREITFAKLVTVLRETVSHTAAVGLLIMGVSLFGYVI 289

Query: 310 RGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLPLFKPVAEALNL 369
              +  + +           + FL +  + +  LG FI+   I  +++P+  P A    +
Sbjct: 290 AREQVPQHVATFFLTYAEDPLTFLILVNLMLLALGTFIEALAILLLIVPVLVPTALQFGV 349

Query: 370 DLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAVPFIGLQVLVLLLI 429
           D + +GV+V  NL    LTPP G ALF +  V  A +  G + RG +P +   V+VL+LI
Sbjct: 350 DPVHFGVMVVFNLMIGILTPPMGVALFVVSKV--ADIPFGVLARGILPLLIPLVVVLVLI 407

Query: 430 IIFPALINWLP 440
            IFPAL+ ++P
Sbjct: 408 TIFPALVTFIP 418


Lambda     K      H
   0.331    0.148    0.443 

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: 500
Number of extensions: 27
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: 445
Length of database: 426
Length adjustment: 32
Effective length of query: 413
Effective length of database: 394
Effective search space:   162722
Effective search space used:   162722
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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