GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS28110
          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:

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