GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Ruegeria conchae TW15

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_010442787.1 G7G_RS0117695 isovaleryl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_000192475.1:WP_010442787.1
          Length = 387

 Score =  258 bits (658), Expect = 3e-73
 Identities = 151/377 (40%), Positives = 213/377 (56%), Gaps = 3/377 (0%)

Query: 36  ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95
           +L E+   L EMV   A   + P A EID +++FP        DLGLL   VP EYGG G
Sbjct: 9   DLGEDVNALREMVHRWAQERVKPMAAEIDASNAFPNELWKEMGDLGLLGVTVPEEYGGAG 68

Query: 96  MDITTFAMVLEEIGKVCASTALMLLAQADGMLSII-LDGSPALKEKYLPRFGEKSTLMTA 154
           M      + +EE+ +  AS +L   A ++  ++ I L+G+   K+KYLPR       + A
Sbjct: 69  MSYLAHTIAVEEVARASASVSLSYGAHSNLCVNQIKLNGTDEQKQKYLPRL-ISGDHVGA 127

Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214
            A +E  AGSD+++MK RA K+ D Y +NG K +ITNG  AD L V+A TDP  G+KG++
Sbjct: 128 LAMSESSAGSDVVSMKLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPEAGSKGIT 187

Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274
            F++E+   G     +  K+GMRG   +EL FED+EVP EN++GEEG+G A LM  L   
Sbjct: 188 AFLIEKEMKGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVAVLMSGLDYE 247

Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334
           RV  A    GI    L+  M +  ER+QFGKPI     +Q  IADM T + +AR  V + 
Sbjct: 248 RVVLAGIGTGIMAACLDEVMPYLAERKQFGKPIGSFQLMQGKIADMYTAMNSARAYVYEV 307

Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394
               D  D            +AS+ AM     AVQ +GG+G++ +  V R+ R+AKL +I
Sbjct: 308 AKACDRGDVTRQDAAACC-LYASEQAMVQAHQAVQALGGAGFLSDSPVSRIFRDAKLMEI 366

Query: 395 YTGTNQITRMVTGRSLL 411
             GT++I RM+ GR ++
Sbjct: 367 GAGTSEIRRMLIGREMM 383


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: 362
Number of extensions: 11
Number of successful extensions: 5
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 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