GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Rhizobium leguminosarum bv. trifolii WSM1325

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate WP_012760746.1 RLEG_RS35160 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>NCBI__GCF_000023185.1:WP_012760746.1
          Length = 381

 Score =  252 bits (644), Expect = 1e-71
 Identities = 154/374 (41%), Positives = 214/374 (57%), Gaps = 9/374 (2%)

Query: 11  TLDMVRDVATR----EIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEMGVL 66
           T D +R+   R     IAP A+E+DE + FP         LGL    +   +GG  +G L
Sbjct: 9   TADAIRETTARFAADHIAPLAVEIDESNTFPRQLWPEMGALGLHGITVEEEFGGAGLGYL 68

Query: 67  TLALILEELGRVCASTALLLIAQTDGML-PIIHGGSPELKERYLRRF-AGESTLLTALAA 124
              + +EE+ R  AS  L   A ++  +  I    SPE K RYL +  +GE   + +LA 
Sbjct: 69  DHVVAMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRYLPKLISGEH--VGSLAM 126

Query: 125 TEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGISAFV 184
           +E  AGSD+++M+ RA ++GD+YV+NG K +ITN   ADV+VVYA TDP  G KGISA +
Sbjct: 127 SEVGAGSDVVSMRLRAEKKGDRYVLNGTKFWITNAPHADVLVVYAKTDPAAGPKGISALI 186

Query: 185 VEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTNRVF 244
           +EKG PG    +  SK+GMRGS  +EL FE+  VPAE ++G EG G   LM  L   R  
Sbjct: 187 IEKGLPGFGVSKKLSKLGMRGSDTAELVFEDCAVPAEALMGREGEGVKILMSGLDYERAV 246

Query: 245 CAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKAAEL 304
            A   +GI Q  LD+ + + +DR QFGK I     +Q  +ADM  A+ ++R      A  
Sbjct: 247 LAGGPLGIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYSVARA 306

Query: 305 LDDGDKKAVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRDAKLTQIYTG 364
            D G +      + A   AS+ A++V+ +A+Q LGG+GY KE  VER +RDAKL  I  G
Sbjct: 307 CDAG-RATRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDIGAG 365

Query: 365 TNQITRMVTGRALL 378
           TN+I R + GR L+
Sbjct: 366 TNEIRRYLIGRELI 379


Lambda     K      H
   0.319    0.134    0.371 

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: 328
Number of extensions: 11
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: 380
Length of database: 381
Length adjustment: 30
Effective length of query: 350
Effective length of database: 351
Effective search space:   122850
Effective search space used:   122850
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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