GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Azospirillum brasilense Sp245

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AZOBR_RS26485 AZOBR_RS26485 enoyl-CoA hydratase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__azobra:AZOBR_RS26485
          Length = 262

 Score =  179 bits (455), Expect = 4e-50
 Identities = 107/253 (42%), Positives = 146/253 (57%), Gaps = 3/253 (1%)

Query: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFAAG 64
           IL    G VGL+T+NRP  LNAL+   + EL  AL E ++DD +  IVVTG+ E+AF AG
Sbjct: 7   ILTSRDGAVGLITINRPTTLNALDVPTLLELERALGELESDDGVHVIVVTGAGERAFVAG 66

Query: 65  ADIGMMSTYTYMDVYK--GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFA 122
            DI  + +   +  Y    + + R +    +  KP IAAV G+ALGGG EL +  DI  A
Sbjct: 67  GDIADLDSRQGLAHYLDFAEVVHRVFRRFETCDKPTIAAVNGWALGGGTELVLSLDIRIA 126

Query: 123 ADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIP 182
           ADTAKFG PEI LG+ PGAGGTQR+ R +   +A +L  T     AAEA   GLV+R +P
Sbjct: 127 ADTAKFGLPEINLGLFPGAGGTQRILRQIPPCRARELVFTGDQFTAAEAVAWGLVNRAVP 186

Query: 183 AASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHSLFATEDQKE 242
            A L+ EA+A A  IA      + + K ++    E  L   + +E+ +   +  ++D  E
Sbjct: 187 KADLMAEAMATAQKIAAKSPLILKLTKRTLRHGAEMPLGASLAYEQAMIGLVLDSQDAHE 246

Query: 243 GMAAFVEKRKPVF 255
           G  AF+EKRK  F
Sbjct: 247 GCRAFLEKRKAAF 259


Lambda     K      H
   0.321    0.134    0.380 

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: 178
Number of extensions: 7
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: 258
Length of database: 262
Length adjustment: 24
Effective length of query: 234
Effective length of database: 238
Effective search space:    55692
Effective search space used:    55692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 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