GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Algoriphagus aquaeductus T4

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_111393797.1 CLV31_RS14820 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_003253485.1:WP_111393797.1
          Length = 379

 Score =  303 bits (777), Expect = 4e-87
 Identities = 170/378 (44%), Positives = 234/378 (61%), Gaps = 5/378 (1%)

Query: 36  ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95
           +LTEE   + E  R  A  E+ P  I+ D    FP        DLG L  +V  +Y G G
Sbjct: 4   QLTEEHLAVQEAAREFAQSELLPGVIDRDSEAKFPHEQIKKMGDLGFLGMMVDPKYNGGG 63

Query: 96  MDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMT 153
           MD  ++ + +EE+ K+ AS ++ +    + ++   L+  GS   K+KYL R      ++ 
Sbjct: 64  MDTISYVIAMEELSKIDASASVSMSVN-NSLVCWGLEKYGSEEQKQKYLTRLAT-GEILG 121

Query: 154 AFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGM 213
           AF  +EP AGSD  + +T A   GD YV+NG K +ITNGS A +  V A TD SKG KG+
Sbjct: 122 AFCLSEPEAGSDATSQRTSAEWNGDHYVLNGTKNWITNGSTASVYLVIAQTDASKGHKGI 181

Query: 214 STFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSI 273
           S F+VE+G  G + G  E K+G+RG     L F D++VPAEN +GEEG GF + M  L+ 
Sbjct: 182 SVFLVEKGWEGFVIGKKEDKLGIRGSDTHSLMFTDVKVPAENRIGEEGFGFTFAMETLNG 241

Query: 274 NRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRK 333
            R+  A+QA+GIA GA E A+ +++ER+ FGKPI+    IQF +ADMAT++EAARLLV K
Sbjct: 242 GRIGIAAQALGIASGAYELALAYSKERKAFGKPISQHQAIQFKLADMATQIEAARLLVYK 301

Query: 334 ATTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQ 393
           A  L D  +        MAK +AS+ AM VT +AVQV GG GY++EY VER+MR+AK+TQ
Sbjct: 302 AAWLKDQGEDYAH-ASAMAKLYASEVAMNVTVEAVQVHGGYGYVKEYHVERLMRDAKITQ 360

Query: 394 IYTGTNQITRMVTGRSLL 411
           IY GT++I R+V  R +L
Sbjct: 361 IYEGTSEIQRIVISRGIL 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: 364
Number of extensions: 14
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: 379
Length adjustment: 31
Effective length of query: 383
Effective length of database: 348
Effective search space:   133284
Effective search space used:   133284
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