GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ch1CoA in Azospirillum brasilense Sp245

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate AZOBR_RS22310 AZOBR_RS22310 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS22310 AZOBR_RS22310
           isovaleryl-CoA dehydrogenase
          Length = 390

 Score =  251 bits (641), Expect = 2e-71
 Identities = 155/376 (41%), Positives = 212/376 (56%), Gaps = 5/376 (1%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           L E   +  D VR  A  EIAPRA E+D  + FP      F  LG+L       YGG  M
Sbjct: 13  LGESADMLRDTVRSFAADEIAPRAAEIDRTNEFPNELWRKFGDLGVLGITAEEEYGGAGM 72

Query: 64  GVLTLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTA 121
           G L   + +EE+ R  AS  L   A ++  +  I   G+ E K RYL +  +GE   + A
Sbjct: 73  GYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIRKNGTAEQKTRYLPKLISGEH--IGA 130

Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181
           LA +EP AGSD+++MK RA +QGD+YV+NG K +ITNG  AD +VVYA TD   G +GI+
Sbjct: 131 LAMSEPNAGSDVVSMKLRAEKQGDRYVLNGTKMWITNGPDADTLVVYAKTDVNAGPRGIT 190

Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241
           AF++EK   G    +   K+GMRGS   EL FE+ EVP ENI+G  G G   LM  L   
Sbjct: 191 AFLIEKSFKGFSVAQKLDKLGMRGSNTGELVFEDCEVPEENILGGVGRGVNVLMSGLDYE 250

Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301
           R   A   +GI Q  +D+ V +  DR QFG+PI     +Q  +ADM T + A++      
Sbjct: 251 RAVLAGGPLGIMQACMDVVVPYLHDRKQFGQPIGEFQLMQGKLADMYTIMNAAKAYVYAV 310

Query: 302 AELLDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQI 361
           A+  D G+  A    + A   A++ A  +  +A+Q LGG+GY+ E    R++RDAKL +I
Sbjct: 311 AKACDRGE-TARKDAAGAILFAAEKATWMALEAIQTLGGNGYINEYPTGRLLRDAKLYEI 369

Query: 362 YTGTNQITRMVTGRAL 377
             GT++I RM+ GR L
Sbjct: 370 GAGTSEIRRMLIGREL 385


Lambda     K      H
   0.319    0.134    0.371 

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: 330
Number of extensions: 13
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: 380
Length of database: 390
Length adjustment: 30
Effective length of query: 350
Effective length of database: 360
Effective search space:   126000
Effective search space used:   126000
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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