GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Azospirillum brasilense Sp245

Align proton/sodium-glutamate symport protein GltT (characterized)
to candidate AZOBR_RS28110 AZOBR_RS28110 C4-dicarboxylate ABC transporter

Query= CharProtDB::CH_088342
         (421 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS28110 AZOBR_RS28110
           C4-dicarboxylate ABC transporter
          Length = 457

 Score =  295 bits (756), Expect = 1e-84
 Identities = 149/406 (36%), Positives = 251/406 (61%), Gaps = 9/406 (2%)

Query: 6   LAWQIFIGLILGIIVGAIFYGNPKVAAYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65
           L +Q+ +GL LGI+ G  +   P + A L+P+GD F++L+KM++ P+V  ++V G+ S+ 
Sbjct: 22  LYFQVVVGLTLGILAGHFW---PDLGASLKPLGDGFVKLVKMMIAPVVFCTIVSGITSLN 78

Query: 66  DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGAGVNMK--SLEKTDIQSYVDTTN 123
           D +++GK   K++  F  +T  A+++GL A  I +PG G+++   SL+ T    Y     
Sbjct: 79  DTREIGKTLVKSMALFYALTVAALLIGLAAVMIIEPGVGMHVSAASLDPTVAARYAKQAA 138

Query: 124 EVQHHSMVETFVNIVPKNIFESLSTGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183
            V     V   ++I+P + F + + G++LP++  SV+ G G+  +G+ G+PV+Q  +  +
Sbjct: 139 PVGFTDFV---LHIIPHSFFGAFAEGEVLPVLLISVLVGFGLTRVGKAGEPVVQGIESFS 195

Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMLFFIFAVLGGVA 243
             +F     IMK AP G F  +  TV K+G++S+  L  L++  Y     F+  V+G +A
Sbjct: 196 HVLFAAFGFIMKLAPIGAFGAMAFTVGKYGIDSIGSLGLLILTFYVACGVFLMVVIGTLA 255

Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPRIMDKMEKFGCPKAITSFVIPTGYSFNL 303
           +L G +++ +++  ++EL++   T+SSE VLPR++ K+E  GC K ++  V+P GYSFNL
Sbjct: 256 RLHGFSLWKVLRYFREELLIVLGTSSSEPVLPRVLQKLEALGCKKGVSGLVLPMGYSFNL 315

Query: 304 DGSTLYQALAAIFIAQLYGIDMSVSQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTV- 362
           DG+ +Y  LA++FIAQ   I +S  Q  ++L V+++TSKG AGV G  FV L+ATL  + 
Sbjct: 316 DGTAIYLTLASLFIAQACDIHLSGGQIFAMLGVMLLTSKGAAGVTGSGFVALVATLTVMP 375

Query: 363 GIPVEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEE 408
            +PV G+A + GIDR +  AR   ++I N +A+I++S WE   + E
Sbjct: 376 DLPVAGVALLVGIDRFMSEARALTSIISNCVASIVVSIWENACDRE 421


Lambda     K      H
   0.326    0.143    0.402 

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: 416
Number of extensions: 17
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: 421
Length of database: 457
Length adjustment: 32
Effective length of query: 389
Effective length of database: 425
Effective search space:   165325
Effective search space used:   165325
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 (21.6 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 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