GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Hydrogenophaga taeniospiralis CCUG 15921 NBRC 102512

Align Cyclohex-1-ene-1-carbonyl-CoA dehydrogenase; Ch1CoA; EC 1.3.8.10 (characterized)
to candidate WP_068170917.1 HTA01S_RS11035 isovaleryl-CoA dehydrogenase

Query= SwissProt::Q2LQN9
         (414 letters)



>NCBI__GCF_001592305.1:WP_068170917.1
          Length = 393

 Score =  238 bits (606), Expect = 3e-67
 Identities = 146/384 (38%), Positives = 214/384 (55%), Gaps = 14/384 (3%)

Query: 36  ELTEEQKLLMEMVRNLAVREIAPRAIEIDENHSFPVHARDLFADLGLLSPLVPVEYGGTG 95
           +L E+   L + VR  A  EIAPRA EID++  FP+       +LG+L   VP +YGG  
Sbjct: 10  QLGEDIDALRDAVREFAQAEIAPRAAEIDKSDQFPMDCWRKMGELGVLGITVPEQYGGAN 69

Query: 96  MDITTFAMVLEEIGKVCASTALMLLAQADGMLSII-LDGSPALKEKYLPRF--GEKSTLM 152
           M      + +EEI +  AS  L   A ++  ++ I  +G+ A K KYLP+   GE    +
Sbjct: 70  MGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNDAQKAKYLPKLISGEH---V 126

Query: 153 TAFAATEPGAGSDLLAMKTRAVKKGDKYVINGQKCFITNGSVADILTVWAYTDPSKGAKG 212
            A A +EPGAGSD+++MK +A  KG  Y++NG K +ITNG  AD L V+A ++P  GA+G
Sbjct: 127 GALAMSEPGAGSDVISMKLKAEDKGGYYLLNGNKMWITNGPDADTLVVYAKSEPEMGARG 186

Query: 213 MSTFVVERGTPGLIYGHNEKKMGMRGCPNSELFFEDLEVPAENLVGEEGKGFAYLMGALS 272
           ++ F++E+G PG        K+GMRG    EL F+++EVPA+N++G    G   LM  L 
Sbjct: 187 VTAFLIEKGMPGFSIAQKLDKLGMRGSHTGELVFQNVEVPAQNILGGLNMGAKVLMSGLD 246

Query: 273 INRVFCASQAVGIAQGALERAMQHTREREQFGKPIAHLTPIQFMIADMATEVEAARLLVR 332
             R       +GI Q  ++  + +  +R+QFG+ I     IQ  +ADM T ++AAR    
Sbjct: 247 YERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAARSFAY 306

Query: 333 KATTLLDAKDKRGPLIGGMAKTFASD---TAMKVT---TDAVQVMGGSGYMQEYQVERMM 386
                LD        +  + K  AS    TA K T    + VQ+ GG+GY+ EY + R+ 
Sbjct: 307 TVAKNLDLLGTEH--VRQVRKDCASVILWTAEKATWMAGEGVQIYGGNGYINEYPLGRLW 364

Query: 387 REAKLTQIYTGTNQITRMVTGRSL 410
           R+AKL +I  GT++I RM+ GR L
Sbjct: 365 RDAKLYEIGAGTSEIRRMLIGREL 388


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: 381
Number of extensions: 12
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: 393
Length adjustment: 31
Effective length of query: 383
Effective length of database: 362
Effective search space:   138646
Effective search space used:   138646
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 Apr 09 2024. 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