GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Azospirillum brasilense Sp245

Align BadK (characterized)
to candidate AZOBR_RS18155 AZOBR_RS18155 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__azobra:AZOBR_RS18155
          Length = 248

 Score =  149 bits (376), Expect = 5e-41
 Identities = 100/252 (39%), Positives = 137/252 (54%), Gaps = 11/252 (4%)

Query: 12  GRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIASM 70
           G V  ITL+RP  LNA+   +   L  A+   +ADD I  +V+ G   RAF  G+DI  +
Sbjct: 3   GFVATITLDRPQKLNAVTPEMAAQLVAAVARCNADDDIRCVVLTGAGPRAFCCGSDIREL 62

Query: 71  AAWSYSDVYGSNFITRNWE----TIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSA 126
                 D Y + +  RN E     IR +RKP +AAV G A+GGG E A++CDI IA  +A
Sbjct: 63  ------DRYDTAWNFRNREDYCDAIRGLRKPSIAAVNGYAFGGGLETAMSCDIRIASENA 116

Query: 127 KFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRL 186
           +F  PEIKLG + G G    L  +IG + A  M L+  P+ A++A  +GLVS VV  DRL
Sbjct: 117 QFGAPEIKLGWIGGGGVAAFLSHSIGTSNAAMMILTGDPIPADKALAWGLVSEVVPADRL 176

Query: 187 RDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQA 246
                 +A  +A+ +  A    K +L  A    + + I +ER      FA+ADA EG  A
Sbjct: 177 LARAQEIAAIVASRAPIAAETAKLNLKAAHTMPVEKAIEYERDLQTICFATADAAEGRAA 236

Query: 247 FLEKRAPCFSHR 258
           F EKR+P F  +
Sbjct: 237 FKEKRSPVFRRK 248


Lambda     K      H
   0.321    0.135    0.389 

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: 116
Number of extensions: 7
Number of successful extensions: 2
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: 248
Length adjustment: 24
Effective length of query: 234
Effective length of database: 224
Effective search space:    52416
Effective search space used:    52416
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: 46 (22.3 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