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; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate AZOBR_RS17455 AZOBR_RS17455 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS17455 AZOBR_RS17455 acyl-CoA
           dehydrogenase
          Length = 387

 Score =  208 bits (529), Expect = 3e-58
 Identities = 128/362 (35%), Positives = 197/362 (54%), Gaps = 19/362 (5%)

Query: 63  IDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDITTFAMVLEEIGKVCASTALMLLAQ 122
           IDE   +P    D     G ++ L+P EYGG+G+ +T  ++++EEI +   ++      Q
Sbjct: 31  IDEERGYPEAFVDALTKAGWMAALIPEEYGGSGLGLTEASVIMEEINRSGGNSGACH-GQ 89

Query: 123 ADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVI 182
              M +++  GS   + +YLP+       + +   TEP  G+D   +KTRA KKGD+YVI
Sbjct: 90  MYNMNTLVRHGSEEQRRRYLPKIAAGELRLQSMGVTEPTTGTDTTRIKTRAEKKGDRYVI 149

Query: 183 NGQKCFITNGSVADILTVWAYTDP----SKGAKGMSTFVVERGTPGLIYGHNEKKMGMRG 238
           NGQK +I+    +D++ + A T P     K ++GMS F+V+      I    +K M ++ 
Sbjct: 150 NGQKVWISRVQHSDLMILLARTTPLDQVRKKSEGMSIFIVD------IKEAMQKGMTVQP 203

Query: 239 CPN------SELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVFCASQAVGIAQGALER 292
             N      +ELFF++LE+PAENL+GEEG+GF Y++  L+  RV  A++ +G     +++
Sbjct: 204 IRNMVNHETNELFFDNLEIPAENLIGEEGQGFKYILTGLNAERVLIAAECIGDGYWFIDK 263

Query: 293 AMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTLLDAKDKRGPLIGGMA 352
              +TR+R+ FG+PIA    +QF IA+   EVEAA L+  +A  L DA +  G     MA
Sbjct: 264 VCDYTRDRQVFGRPIAQNQGVQFPIAESFIEVEAANLMRFEACRLYDAGEPCGAQ-ANMA 322

Query: 353 KTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIY-TGTNQITRMVTGRSLL 411
           K  A+  + +     +Q  GG G+  EY VER  RE +L Q+    TN I   V    L 
Sbjct: 323 KYLAAKASWEAANACLQFHGGFGFASEYDVERKFRETRLYQVAPVSTNLILAYVAEHVLD 382

Query: 412 FP 413
            P
Sbjct: 383 LP 384


Lambda     K      H
   0.318    0.133    0.375 

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: 344
Number of extensions: 18
Number of successful extensions: 4
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: 414
Length of database: 387
Length adjustment: 31
Effective length of query: 383
Effective length of database: 356
Effective search space:   136348
Effective search space used:   136348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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