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_050655857.1 C1M55_RS09530 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_002893965.1:WP_050655857.1
          Length = 380

 Score =  238 bits (608), Expect = 2e-67
 Identities = 142/378 (37%), Positives = 213/378 (56%), Gaps = 13/378 (3%)

Query: 38  TEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGMD 97
           ++E + L+E+ R++A + +AP+  E ++   +P          GLLS   P E+GG    
Sbjct: 9   SQEARDLIELTRDVADKVLAPKVNEYEKAEKYPDGVFPALGQAGLLSLPYPEEFGGGDQP 68

Query: 98  ITTFAMVLEEIGKVCASTALMLLAQADGMLSIILDGSPALKEKYLPRFGEKSTLMTAFAA 157
              +  VLEEI    A+ A+ +   +     +   G+   K ++LP     +T+  A++ 
Sbjct: 69  YEVYLQVLEEIASRWAAVAVAVSVHSLSCFPLFTFGTDEQKNRWLPDMLGGNTI-GAYSL 127

Query: 158 TEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMSTFV 217
           +E  AGSD  A+  +A      Y +NG K +ITNG  AD   ++A T    G++G+S  +
Sbjct: 128 SEAQAGSDAAALSCKATPTDGGYRVNGSKAWITNGGKADFYNLFARTSDD-GSRGVSCLL 186

Query: 218 VERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSINRVF 277
           V++   GL +G  E+KMG+R  P +   ++D  +P E L+G+ G+G      AL   R+ 
Sbjct: 187 VDKDAEGLSFGKPEEKMGLRAVPTASANYDDAFIPEERLIGQRGQGLPIAFSALDSGRLG 246

Query: 278 CASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKATTL 337
            A+ AVGIAQGAL+ A+ + +ER+ FGK I     + F++ADMA  V++AR       T 
Sbjct: 247 IAAVAVGIAQGALDDAVAYAKERKAFGKRIIDHQGLGFVLADMAAAVDSAR------ATY 300

Query: 338 LDAKDKRGPLI-----GGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLT 392
           LDA  +R   +       +AK  A+D AMKVTTDAVQV GG GY Q++ VER MREAK+T
Sbjct: 301 LDAARRRDAGVPYSRNASVAKLVATDAAMKVTTDAVQVFGGYGYTQDFPVERYMREAKIT 360

Query: 393 QIYTGTNQITRMVTGRSL 410
           QI+ GTNQI R+V  R L
Sbjct: 361 QIFEGTNQIQRLVIARQL 378


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: 384
Number of extensions: 11
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: 380
Length adjustment: 31
Effective length of query: 383
Effective length of database: 349
Effective search space:   133667
Effective search space used:   133667
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