GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Xanthobacter autotrophicus Py2

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_000017645.1:WP_012116241.1
          Length = 390

 Score =  255 bits (652), Expect = 1e-72
 Identities = 152/386 (39%), Positives = 217/386 (56%), Gaps = 23/386 (5%)

Query: 36  ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95
           +L E   +L + VR+ +  EIAPRA EID  + FP         LGLL      EYGG+G
Sbjct: 12  DLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGGSG 71

Query: 96  MDITTFAMVLEEIGKVCASTALMLLAQADGMLS-IILDGSPALKEKYLPRF--GEKSTLM 152
           +      + +EEI +  AS  L   A ++  ++ I  +G+   K KYLP+   GE    +
Sbjct: 72  LGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEH---V 128

Query: 153 TAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKG 212
            A A +EPGAGSD+++M+TRA KKGD+Y++NG K +ITNG +A+ L V+A TDP+ G KG
Sbjct: 129 GALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKG 188

Query: 213 MSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALS 272
           M+ F+VER  PG        K+GMRG    EL F+D EVP EN++G  G+G   LM  L 
Sbjct: 189 MTAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLD 248

Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLV- 331
             R   A    GI Q  ++  + +  ER+QFG+PI     +Q  IADM   + A +  V 
Sbjct: 249 YERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVY 308

Query: 332 -------RKATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVER 384
                  R ATT  DA           A  +A++ A  +  +A+Q +GG+GY+ +Y   R
Sbjct: 309 AVAKACDRGATTREDAAG---------AILYAAEKATWMALEAIQTLGGNGYINDYPTGR 359

Query: 385 MMREAKLTQIYTGTNQITRMVTGRSL 410
           ++R+AKL +I  GT++I RM+ GR L
Sbjct: 360 LLRDAKLYEIGAGTSEIRRMLIGRQL 385


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: 385
Number of extensions: 15
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: 390
Length adjustment: 31
Effective length of query: 383
Effective length of database: 359
Effective search space:   137497
Effective search space used:   137497
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 Apr 09 2024. 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