GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

Align 3-hydroxybutyryl-CoA dehydratase; EC 4.2.1.55 (characterized)
to candidate GFF3794 PGA1_262p01980 putative enoyl-CoA hydratase

Query= CharProtDB::CH_091794
         (261 letters)



>FitnessBrowser__Phaeo:GFF3794
          Length = 263

 Score =  190 bits (482), Expect = 3e-53
 Identities = 106/255 (41%), Positives = 148/255 (58%), Gaps = 4/255 (1%)

Query: 6   VILEKEGKVAVVTINRPKALNALNSDTLKEMDYVIGEIENDSEVLAVILTGAGEKSFVAG 65
           +  E+ G VAV+T+NRP+ LNALN  T   +  ++  IE D  + A+ILTGAGE++F AG
Sbjct: 5   ITYERNGAVAVLTLNRPEKLNALNYATNDCLLSLLNAIEIDPSIRAIILTGAGERAFSAG 64

Query: 66  ADISEMKEMNTI----EGRKFGILGNKVFRRLELLEKPVIAAVNGFALGGGCEIAMSCDI 121
            DI E  E          R F   G  +  RLE  +KP+IAAVNG A GGGCEI  +  +
Sbjct: 65  GDIHEFTESVKAGVDEAVRDFCKRGQTMTARLEAFQKPIIAAVNGIAFGGGCEITEAVHL 124

Query: 122 RIASSNARFGQPEVGLGITPGFGGTQRLSRLVGMGMAKQLIFTAQNIKADEALRIGLVNK 181
            +AS  A F +PE+ +GI P FGGTQRL RL G   A +L+ T     A  A  +GLVN+
Sbjct: 125 AVASERAMFAKPEINIGIPPTFGGTQRLPRLAGRKRALELLLTGDTFSAQRACEMGLVNR 184

Query: 182 VVEPSELMNTAKEIANKIVSNAPVAVKLSKQAINRGMQCDIDTALAFESEAFGECFSTED 241
           +V   ELM  A ++A++I+ ++P+A      A+ RG+   ID  L  E E F    +T+D
Sbjct: 185 IVPHDELMPAAFDLADRIIRHSPLAASRIITAVTRGINTTIDEGLLIEREQFARMAATKD 244

Query: 242 QKDAMTAFIEKRKIE 256
             + + A+I +R  E
Sbjct: 245 VHEGLGAWIARRTPE 259


Lambda     K      H
   0.317    0.134    0.365 

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: 183
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: 261
Length of database: 263
Length adjustment: 25
Effective length of query: 236
Effective length of database: 238
Effective search space:    56168
Effective search space used:    56168
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 (21.6 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