GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Sphingomonas koreensis DSMZ 15582

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate Ga0059261_4052 Ga0059261_4052 Acyl-CoA dehydrogenases

Query= SwissProt::Q2LQN9
         (414 letters)



>FitnessBrowser__Korea:Ga0059261_4052
          Length = 385

 Score =  234 bits (597), Expect = 3e-66
 Identities = 149/383 (38%), Positives = 212/383 (55%), Gaps = 18/383 (4%)

Query: 37  LTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARD----LFADLGLLSPLVPVEYG 92
           L+E  +++ +  +  A   I P A +ID    FP   RD       +LGL    V  E+G
Sbjct: 10  LSETAEMIRDTTQRFAKERIEPLAAKIDAEDWFP---RDELWTAMGELGLHGITVDEEFG 66

Query: 93  GTGMDITTFAMVLEEIGKVCASTALMLLAQADGMLSIILD-GSPALKEKYLPRF--GEKS 149
           G G+      +  EE+ +  AS  L   A ++  ++ I    SPA K KYLPR   GE  
Sbjct: 67  GLGLGYLEHVIACEEVSRASASIGLSYGAHSNLCVNQISRWASPAQKAKYLPRLISGEH- 125

Query: 150 TLMTAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKG 209
             + + A +E GAGSD+++MK RA  KGD+YV+NG K +ITN + AD L V+A T   +G
Sbjct: 126 --VGSLAMSEAGAGSDVVSMKLRAEHKGDRYVLNGTKFWITNAAYADTLVVYAKT--GEG 181

Query: 210 AKGMSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMG 269
           ++G++TF++E+  PG   G    KMGMRG P +EL F+D EVP EN++G    G   LM 
Sbjct: 182 SRGITTFLIEKDMPGFSIGQKIDKMGMRGSPTAELVFDDCEVPEENVMGPLNGGVGVLMS 241

Query: 270 ALSINRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARL 329
            L   R   A   +GI Q  L+  + + RER+QFG+ I     +Q  +ADM   + +AR 
Sbjct: 242 GLDYERTVLAGIQLGIMQACLDVVLPYLRERKQFGQAIGSFQLMQAKVADMYVALNSARA 301

Query: 330 LVRKATTLLDA-KDKRGPLIGGMAKTFASDTAMKVTTDAVQVMGGSGYMQEYQVERMMRE 388
            V       DA K  R    G  A   AS+ A +V  +AVQ +GG+GY +++ VER +R+
Sbjct: 302 YVYAVAQACDAGKTTRFDAAG--AILLASENAFRVAGEAVQALGGAGYTKDWPVERFLRD 359

Query: 389 AKLTQIYTGTNQITRMVTGRSLL 411
           AKL  I  GTN+I RM+ GR L+
Sbjct: 360 AKLLDIGAGTNEIRRMLIGRELI 382


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: 332
Number of extensions: 21
Number of successful extensions: 6
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: 385
Length adjustment: 31
Effective length of query: 383
Effective length of database: 354
Effective search space:   135582
Effective search space used:   135582
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.

Links

Downloads

Related tools

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