GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Sinorhizobium meliloti 1021

Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate SM_b20297 SM_b20297 permease

Query= uniprot:I7DRS6
         (467 letters)



>FitnessBrowser__Smeli:SM_b20297
          Length = 426

 Score =  284 bits (726), Expect = 5e-81
 Identities = 160/456 (35%), Positives = 255/456 (55%), Gaps = 36/456 (7%)

Query: 6   LFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFFIL 65
           LF     LL+ G+P+   L +++  ++L +  + L + AG    A    F LLA+PFFIL
Sbjct: 4   LFGGWFALLIAGMPVGFTLIVAALAYML-WQGTGL-NFAGQRMIAGLNSFPLLAVPFFIL 61

Query: 66  ASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIA 125
            +  M   GV  RI  F+ A VGH+ GGL    + A +LF+ +SGS+ A    +G + I 
Sbjct: 62  TAQLMNLSGVTERIFDFAKALVGHIRGGLGHVNIMASVLFSGMSGSAVADAAGLGQLEIK 121

Query: 126 GMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLM 185
            MR  GY ++F+  +   +  +G LIPPSI +VVY      S+G +FL G++PGL+    
Sbjct: 122 AMRDAGYDEQFSGSITAASAIIGPLIPPSIPLVVYGVIANTSIGGLFLGGIVPGLLCAAS 181

Query: 186 LMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAVA 245
           LM+ +YV+A  +N    +  G+  V ++  +A + L+   II+GGI+ G+F+PTEAA VA
Sbjct: 182 LMIMVYVIAWRRNYATAQRAGFRRVWSTFWHALLPLITPFIIIGGIFAGVFSPTEAAVVA 241

Query: 246 SVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALFE 305
           + YA F+   VYR++   K              L  +L +TV +                
Sbjct: 242 ASYALFLGVVVYREITFAK--------------LVTVLRETVSH---------------- 271

Query: 306 AGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQFM 365
               T  +  +I    +  +V+  EQVPQ +AT  L+    P+ FLI+VN++LL  G F+
Sbjct: 272 ----TAAVGLLIMGVSLFGYVIAREQVPQHVATFFLTYAEDPLTFLILVNLMLLALGTFI 327

Query: 366 EPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPMM 425
           E   +L+++ P++ P A++ G+DP+H G+++V N+ IG++TPP+G+ LFV S VA +P  
Sbjct: 328 EALAILLLIVPVLVPTALQFGVDPVHFGVMVVFNLMIGILTPPMGVALFVVSKVADIPFG 387

Query: 426 AVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMG 461
            + R  LP L  L V L++IT  P + T +P+ ++G
Sbjct: 388 VLARGILPLLIPLVVVLVLITIFPALVTFIPDQMLG 423


Lambda     K      H
   0.329    0.144    0.421 

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: 592
Number of extensions: 40
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 467
Length of database: 426
Length adjustment: 32
Effective length of query: 435
Effective length of database: 394
Effective search space:   171390
Effective search space used:   171390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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