GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Rhodococcus qingshengii djl-6-2

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_003939784.1 C1M55_RS25280 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_002893965.1:WP_003939784.1
          Length = 385

 Score =  319 bits (818), Expect = 8e-92
 Identities = 169/375 (45%), Positives = 235/375 (62%), Gaps = 2/375 (0%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L EE   L   +R L+ +EIAP A ++DEN  FP  A       G  +  VP  Y G G 
Sbjct: 12  LNEEHDELRAAIRGLSEKEIAPYAKDVDENARFPEEALTALNASGFNAIHVPEAYDGQGA 71

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFA 156
           D     +V+EE+ +VC S++L+      G + +IL GS  LK K LP        M ++A
Sbjct: 72  DSVATCIVIEEVARVCGSSSLIPAVNKLGTMGLILKGSEELKSKVLPDLVNGG--MASYA 129

Query: 157 ATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTF 216
            +E  AGSD  +M+TRA   GD +++NG KC+ITNG  +   TV A TDP KGA G+S+F
Sbjct: 130 LSEREAGSDAASMRTRAKADGDDWILNGSKCWITNGGKSTWYTVMAVTDPDKGANGISSF 189

Query: 217 VVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRV 276
           +V +   G + G  EKK+G++G P +EL+FE+  +P + ++GE G GF   +  L   R 
Sbjct: 190 MVHKDDEGFVVGPKEKKLGIKGSPTAELYFENCRIPGDRIIGEPGTGFKTALETLDHTRP 249

Query: 277 FCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATT 336
              +QAVG+AQGAL+ A+ +T++R+QFGK I+    +QFM+ADMA +VEAARL+V  +  
Sbjct: 250 TIGAQAVGLAQGALDAALAYTKDRKQFGKSISDFQAVQFMLADMAMKVEAARLMVYTSAA 309

Query: 337 LLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQIYT 396
             +  +K    I   AK FASD AM+VTTDAVQ+ GG+GY  ++ VERMMR+AK+TQIY 
Sbjct: 310 RAERGEKNLGFISAAAKCFASDVAMEVTTDAVQLFGGAGYTTDFPVERMMRDAKITQIYE 369

Query: 397 GTNQITRMVTGRSLL 411
           GTNQI R+V  R+LL
Sbjct: 370 GTNQIQRVVMSRALL 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: 393
Number of extensions: 17
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: 414
Length of database: 385
Length adjustment: 31
Effective length of query: 383
Effective length of database: 354
Effective search space:   135582
Effective search space used:   135582
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