GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Herbaspirillum aquaticum IEH 4430

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_039790199.1 CEJ45_RS12595 isovaleryl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_002213425.1:WP_039790199.1
          Length = 394

 Score =  241 bits (615), Expect = 3e-68
 Identities = 146/378 (38%), Positives = 212/378 (56%), Gaps = 7/378 (1%)

Query: 39  EEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMDI 98
           E+   L E V   A  EIAPRA EID +  FP+       DLG+L   V  EYGG G+  
Sbjct: 13  EDIAALREAVAAFAQTEIAPRAAEIDRSDQFPMDLWKKLGDLGVLGITVGEEYGGAGLGY 72

Query: 99  TTFAMVLEEIGKVCASTALMLLAQADGMLSIIL-DGSPALKEKYLPRFGEKSTLMTAFAA 157
               + +EEI +  AS  L   A ++  ++ I  +G+   K KYLP+       + A A 
Sbjct: 73  LAHIIAMEEISRASASVGLSYGAHSNLCVNQIKRNGNEEQKRKYLPKL-ISGDFIGALAM 131

Query: 158 TEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFV 217
           +EP AGSD+++MK RA KKGD+YV+NG K +ITNG  AD+L V+A TD   GA+GM+ F+
Sbjct: 132 SEPNAGSDVVSMKLRADKKGDRYVLNGSKMWITNGPDADVLVVYAKTDLDAGARGMTAFL 191

Query: 218 VERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVF 277
           VE+G  G        K+GMRG    EL F+D EVP EN++G  G+G   LM  L   R  
Sbjct: 192 VEKGYKGFSVAQKLDKLGMRGSHTGELVFQDCEVPEENVLGGVGRGVNVLMSGLDFERSV 251

Query: 278 CASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAAR---LLVRKA 334
            +   +GI Q  ++  + +  +R+QFG+ I     +Q  +ADM + + A +     V +A
Sbjct: 252 LSGGPLGIMQACMDVVVPYVHDRKQFGQAIGEFQLMQGKLADMYSTMMACKAYVYAVGQA 311

Query: 335 TTLLDAKDKRGPLIGGMAKT--FASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392
               D+ DK   L    A    ++++ A  +  +A+Q +GG+GY+ EY V R+ R+AKL 
Sbjct: 312 CDRADSADKVRALRKDAAGAILYSAEKATWMAGEAIQSLGGNGYINEYPVGRLWRDAKLY 371

Query: 393 QIYTGTNQITRMVTGRSL 410
           +I  GT++I RM+ GR L
Sbjct: 372 EIGAGTSEIRRMLIGREL 389


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: 377
Number of extensions: 13
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: 394
Length adjustment: 31
Effective length of query: 383
Effective length of database: 363
Effective search space:   139029
Effective search space used:   139029
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 24 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