GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Dinoroseobacter shibae DFL-12

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate 3608348 Dshi_1750 acyl-CoA dehydrogenase domain protein (RefSeq)

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Dino:3608348
          Length = 381

 Score =  232 bits (592), Expect = 1e-65
 Identities = 137/377 (36%), Positives = 206/377 (54%), Gaps = 6/377 (1%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L+EEQ  + +M R+     IAP A+  +++ + P       A LG     V  E GG+G+
Sbjct: 5   LSEEQSAIFDMARDFGAENIAPHALAWEKDGTIPKTLWPELAALGFGGLYVTEESGGSGL 64

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD--GSPALKEKYLPRFGEKSTLMTA 154
                 +V E +   C S A  L      M + +LD  GS  +K ++LP      T+ + 
Sbjct: 65  SRLDATLVFEALSMACPSVAAFL--SIHNMCAAMLDKFGSDDVKARFLPPALTMETVFS- 121

Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214
           +  TEPG+GSD  A+KTRA +  + Y + G K FI+ G  +D   V A T    G +G+S
Sbjct: 122 YCLTEPGSGSDAAALKTRAERTNEGYRLTGTKAFISGGGYSDAYIVMARTGED-GPRGIS 180

Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274
           + +VE G PGL +G  E KMG R  P  ++  +D  VPA NL+GEEG GF Y M  L   
Sbjct: 181 SLIVEDGAPGLSFGGLEDKMGWRAQPTRQVQLDDCAVPAANLLGEEGAGFRYAMMGLDGG 240

Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334
           R+  A+ ++G AQ AL+  + +  ER  FGKPI     +QF +AD   E++AAR+ +R+A
Sbjct: 241 RLNIAACSLGAAQAALDATVAYMGERRAFGKPIDQFQALQFRLADAEIELQAARVFLRQA 300

Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394
              LD           MAK F ++   +V    +Q+ GG GY+ +Y +E+++R+ ++ QI
Sbjct: 301 AWKLDQGAPDATTHCAMAKKFVTEAGSRVADQCLQLHGGYGYLADYGIEKLVRDLRVHQI 360

Query: 395 YTGTNQITRMVTGRSLL 411
             GTN+I R++T R+LL
Sbjct: 361 LEGTNEIMRLLTARALL 377


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: 322
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: 381
Length adjustment: 31
Effective length of query: 383
Effective length of database: 350
Effective search space:   134050
Effective search space used:   134050
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 17 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