GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltP in Azospirillum brasilense Sp245

Align Proton/sodium-glutamate symport protein; Glutamate-aspartate carrier protein (characterized)
to candidate AZOBR_RS21140 AZOBR_RS21140 C4-dicarboxylate ABC transporter

Query= SwissProt::P24943
         (421 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS21140 AZOBR_RS21140
           C4-dicarboxylate ABC transporter
          Length = 433

 Score =  389 bits (999), Expect = e-113
 Identities = 188/417 (45%), Positives = 292/417 (70%), Gaps = 12/417 (2%)

Query: 6   LAWQIFIGLILGIIVGAIFYGNPKVATYLQPIGDIFLRLIKMIVIPIVISSLVVGVASVG 65
           L  Q+   + +GI++G  +   P +A  ++P+GD+F+++IKM++ PIV  ++V G++S+G
Sbjct: 16  LTVQVLTAITIGILLGHFY---PALAVQMKPLGDVFIKMIKMVIGPIVFLTVVTGISSIG 72

Query: 66  DLKKLGKLGGKTIIYFEIITTIAIVVGLLAANIFQPGTGVNMK--SLEKTDIQSYVDTTN 123
           D+KK+GK+GGK I+YFEI+TT A+ +GLL  N+ +PG+G+N++  SL+   +  Y     
Sbjct: 73  DMKKVGKVGGKAILYFEIVTTFALGLGLLVVNLVKPGSGMNIQAGSLKADAVAKYA---T 129

Query: 124 EVQHHSMVETFVNIVPKNIFESLTKGDMLPIIFFSVMFGLGVAAIGEKGKPVLQFFQGTA 183
           E Q+H+ ++  VNIVP N+  +  KGDML I+FF+V+FG+ ++A+G+KGK V   F+  +
Sbjct: 130 EAQNHTTIDFLVNIVPDNVIGAFVKGDMLQILFFAVIFGVALSAMGQKGKVVEDMFEKVS 189

Query: 184 EAMFYVTNQIMKFAPFGVFALIGVTVSKFGVESLIPLSKLVIVVYATMVFFIFVVLGGVA 243
            A+F V   +M+ AP G F  +  T+ K+GV SL  L +L+  VY TM  F+FVVLG +A
Sbjct: 190 HALFGVIGILMRVAPLGAFGAMSFTIGKYGVSSLTSLGQLMAAVYITMALFVFVVLGSIA 249

Query: 244 KLFGINIFHIIKILKDELILAYSTASSETVLPKIMEKMENFGCPKAITSFVIPTGYSFNL 303
           +L+  ++   ++ +KDEL++   T+SSE+VLP++MEKM+ FGC K +   VIPTGYSFNL
Sbjct: 250 RLYNFSLLTFLRYIKDELLIVLGTSSSESVLPRMMEKMQKFGCSKHVVGLVIPTGYSFNL 309

Query: 304 DGSTLYQALAAIFIAQLYGIDMPISQQISLLLVLMVTSKGIAGVPGVSFVVLLATLGTVG 363
           DG+++Y ++AAIFIAQ + ID+ I QQ+++L +LM+TSKG A V G  FV L ATL   G
Sbjct: 310 DGTSIYLSMAAIFIAQAFNIDLTIWQQLTILGLLMLTSKGAAAVTGGGFVTLAATLSATG 369

Query: 364 -IPIEGLAFIAGIDRILDMARTAVNVIGNSLAAIIMSKWEGQYNEEKGKQYIAQLQQ 419
            +PIEGLA + G+DR +  AR   N+IGN +A I+++K EG+++E K    +A+ Q+
Sbjct: 370 HLPIEGLALLLGVDRFMSEARAITNLIGNGVATIVVAKMEGEFDESKA---VAEYQE 423


Lambda     K      H
   0.326    0.143    0.404 

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: 465
Number of extensions: 20
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: 433
Length adjustment: 32
Effective length of query: 389
Effective length of database: 401
Effective search space:   155989
Effective search space used:   155989
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