GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iatP in Sinorhizobium meliloti 1021

Align Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized)
to candidate SMc02031 SMc02031 permease

Query= TCDB::B8H230
         (332 letters)



>FitnessBrowser__Smeli:SMc02031
          Length = 349

 Score =  235 bits (600), Expect = 1e-66
 Identities = 132/311 (42%), Positives = 187/311 (60%), Gaps = 11/311 (3%)

Query: 29  ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88
           ++ L+LL+A    A   FLT  N  N+  + +   I+AVG TFVIL GGID++V ++ A 
Sbjct: 33  LIALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILTGGIDLSVAAIAAL 92

Query: 89  ASIAAAYVVTAV-----VGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLG 143
           ++   A ++T       +  G     +A+L+  LIG+A G + G  ++   +P FI TLG
Sbjct: 93  SASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGWLISKFKIPDFIATLG 152

Query: 144 GMTVWRGATLLLNDGGPISGFN------DAYRWWGSGEILFLPVPVVIFALVAAAGHVAL 197
            MT +RGA LL+ DG P+  FN      ++  W G G++  +PV  +I  L AAAG   L
Sbjct: 153 TMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVSALIALLCAAAGWYVL 212

Query: 198 RYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAG 257
           RYT  GR +YAVGGN  AA  SG+++       YAI G LA ++G +L  RL SA A+  
Sbjct: 213 RYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAGIILVGRLNSANALMA 272

Query: 258 TGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLII 317
            G ELR IASVVIGG +L GG GGV G+++GA +IGVL NGL +L V+ + Q++  G++I
Sbjct: 273 DGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLLDVSPFWQRIAQGVVI 332

Query: 318 VAAVAFDHYAR 328
           V  V FD + R
Sbjct: 333 VVVVIFDQWRR 343


Lambda     K      H
   0.325    0.140    0.413 

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: 315
Number of extensions: 26
Number of successful extensions: 3
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: 332
Length of database: 349
Length adjustment: 28
Effective length of query: 304
Effective length of database: 321
Effective search space:    97584
Effective search space used:    97584
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: 49 (23.5 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