GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS21140
          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:

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