GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Dinoroseobacter shibae DFL-12

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 3608199 Dshi_1604 Enoyl-CoA hydratase/isomerase (RefSeq)

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Dino:3608199
          Length = 264

 Score =  124 bits (311), Expect = 2e-33
 Identities = 86/257 (33%), Positives = 132/257 (51%), Gaps = 9/257 (3%)

Query: 4   LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63
           L+ S    +  LTLN P + N L++A+L  L  +++  A D +  V V+ G  R F AG 
Sbjct: 6   LLRSDADGIATLTLNAPQSLNVLSDAMLAALQAQIDTLAEDRTTRVVVLRGAGRAFCAGH 65

Query: 64  DLNEM-----AEKDLAAT---LNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCD 115
           DL EM     +E   AA    L D   ++   LQA  +P+IA V+G A  AGC+L    D
Sbjct: 66  DLKEMTAARQSEDGGAAAFKDLFDRCARMMMGLQALPQPVIAQVHGIATAAGCQLVATAD 125

Query: 116 VVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVS 175
           + VA E ARFG+  + +G+         L R++ +  A +++ +GE I AQ+AQ  GLV+
Sbjct: 126 MAVAAEGARFGVNGVNIGLFCSTPMVA-LSRNIPRKQAFELLTTGEMIEAQKAQALGLVN 184

Query: 176 DVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATE 235
            V P++        LA+K+A      +   K+A  +  +++L    A    +     A  
Sbjct: 185 RVVPTEDLEAETNALATKVAEKRGAVVAIGKRAFYEQSQMSLADAYAFTGNVMVKNMALR 244

Query: 236 DRHEGISAFLQKRTPDF 252
           D  EGI+AFL KR P++
Sbjct: 245 DTEEGIAAFLDKRPPNW 261


Lambda     K      H
   0.318    0.130    0.356 

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: 112
Number of extensions: 7
Number of successful extensions: 2
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: 255
Length of database: 264
Length adjustment: 24
Effective length of query: 231
Effective length of database: 240
Effective search space:    55440
Effective search space used:    55440
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 (21.8 bits)
S2: 47 (22.7 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