GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ch1CoA in Sinorhizobium meliloti 1021

Align cyclohex-1-ene-1-carbonyl-CoA dehydrogenase (EC 1.3.8.10) (characterized)
to candidate SM_b21121 SM_b21121 isovaleryl-CoA dehydrogenase

Query= BRENDA::Q39QF5
         (380 letters)



>FitnessBrowser__Smeli:SM_b21121
          Length = 387

 Score =  243 bits (619), Expect = 9e-69
 Identities = 152/382 (39%), Positives = 212/382 (55%), Gaps = 17/382 (4%)

Query: 4   LTEEQKLTLDMVRDVATREIAPRALELDEKSLFPEYARDLFAKLGLLNPLLPAAYGGTEM 63
           L EE       VR  A+  IAP A + D  + FP        +LGLL      A+GG  +
Sbjct: 10  LGEEIDALRASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGL 69

Query: 64  GVLTLALILEELGRVCASTALLLIAQTDGMLPIIH-GGSPELKERYLRRF-AGESTLLTA 121
           G L   + +EE+ R  AS  L   A ++  +  I+  G P  K RYL +  +GE   + A
Sbjct: 70  GYLAHCVAMEEISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEH--VGA 127

Query: 122 LAATEPAAGSDLLAMKTRAVRQGDKYVINGQKCFITNGSVADVIVVYAYTDPEKGSKGIS 181
           LA +EP AGSD+++MK +A ++GD+YV+NG K +ITNG  ADV+VVYA TDP  G +GI+
Sbjct: 128 LAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGIT 187

Query: 182 AFVVEKGTPGLVYGRNESKMGMRGSINSELFFENMEVPAENIIGAEGTGFANLMQTLSTN 241
           AF+VEK  PG   G+   K+GMRGS  SEL F + EVP EN++G  G G   LM  L   
Sbjct: 188 AFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYE 247

Query: 242 RVFCAAQAVGIAQGALDIAVRHTQDRVQFGKPIAHLAPVQFMVADMATAVEASRLLTRKA 301
           RV  +A  +GI    LD+ V +  +R QFG+PI     +Q  +ADM   + A+R      
Sbjct: 248 RVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAV 307

Query: 302 AELLDDGDKK------AVLYGSMAKTMASDTAMRVTTDAVQVLGGSGYMKENGVERMMRD 355
           A   D G+         +LY       A++ A  +  +A+Q LGG+GY  +    R++RD
Sbjct: 308 AAACDRGETARKDAAGCILY-------AAEKATAMALEAIQALGGNGYTNDYPAGRLLRD 360

Query: 356 AKLTQIYTGTNQITRMVTGRAL 377
           AKL +I  GT++I RM+ GR L
Sbjct: 361 AKLYEIGAGTSEIRRMLIGREL 382


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: 324
Number of extensions: 15
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: 380
Length of database: 387
Length adjustment: 30
Effective length of query: 350
Effective length of database: 357
Effective search space:   124950
Effective search space used:   124950
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 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