GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Rhodobacter maris JA276

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_097070176.1 CRO22_RS10865 acyl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_900217815.1:WP_097070176.1
          Length = 381

 Score =  231 bits (589), Expect = 3e-65
 Identities = 132/377 (35%), Positives = 207/377 (54%), Gaps = 6/377 (1%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTGM 96
           L+EE + + EM +     EIAP A   +   + P       A LGL    V  E+GG+G+
Sbjct: 5   LSEESRAIFEMAQAFGQEEIAPHARAWEAAGTIPRALWAKVAALGLGGLYVSEEHGGSGL 64

Query: 97  DITTFAMVLEEIGKVCASTALMLLAQ--ADGMLSIILDGSPALKEKYLPRFGEKSTLMTA 154
                 +V E +   C S +  L       GM+     G+P LK+++LP+     T+ + 
Sbjct: 65  SRLDATLVFEALAMACPSVSAFLSIHNMCGGMIEKF--GAPDLKDRFLPKLCTMETVFS- 121

Query: 155 FAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKGMS 214
           +  TEPG+GSD  A++TRA      + +NG K FI+ G  +D       T    G KG+S
Sbjct: 122 YCLTEPGSGSDAAALRTRAEAVPQGWKLNGTKAFISGGGYSDAYITMVRTG-EPGPKGIS 180

Query: 215 TFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALSIN 274
           T +VE GTPGL +G  E KMG R  P +++ F+D  +PAENLVG  G+GF+Y M  L   
Sbjct: 181 TVIVEAGTPGLSFGAKEDKMGWRAQPTAQVQFDDCIIPAENLVGAPGRGFSYAMAGLDGG 240

Query: 275 RVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVRKA 334
           R+  A+ A+G AQ A+   + +  ER+ FG+ +     +QF +A+M  ++++AR+ +R+A
Sbjct: 241 RLNIAASALGGAQAAMNATLAYMGERKAFGQSLDQFQALQFRLAEMEVKLQSARIFLRQA 300

Query: 335 TTLLDAKDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMREAKLTQI 394
              LD           MAK + +D A  V    +Q+ GG GY+ +Y +E+++R+ ++ QI
Sbjct: 301 AWKLDQGAPDATKFCAMAKLYVTDAAFDVANQCLQLHGGYGYLADYGIEKILRDLRVHQI 360

Query: 395 YTGTNQITRMVTGRSLL 411
             GTN+I R++ GR++L
Sbjct: 361 LEGTNEIMRLIIGRAVL 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: 334
Number of extensions: 18
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: 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 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