GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02031 SMc02031 permease
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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