GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Burkholderia phytofirmans PsJN

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BPHYT_RS28020 BPHYT_RS28020 enoyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__BFirm:BPHYT_RS28020
          Length = 272

 Score =  145 bits (367), Expect = 6e-40
 Identities = 97/254 (38%), Positives = 141/254 (55%), Gaps = 5/254 (1%)

Query: 1   MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFF 59
           M EL  +    V  LTL RP A NA     L+QL   +E    +  +   VITG+  +FF
Sbjct: 1   MIELDYADDGAVAQLTLKRPPA-NAFTPEGLLQLQQTVERLNGEARVRAIVITGDGPKFF 59

Query: 60  AAGADLNEMAE--KDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVV 117
           +AGADLN  A+  +++A T        +  LQ     +IAA+NGYA+G G E AL CD+ 
Sbjct: 60  SAGADLNTFADGNREVARTAAARFGAAFETLQNARPVVIAAINGYAMGGGLECALACDIR 119

Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177
           +A ++A   LPE  +G++P   GTQ L   VG+  A +M+L+GE + A  A + GLV +V
Sbjct: 120 IAEQHALLALPETAVGLLPCGCGTQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEV 179

Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQE-VALQAGLAQERQLFTLLAATED 236
                  + AL +A+++A  SP A+  +K  + Q +  V   A LA ER+ F  L    D
Sbjct: 180 VEKGAARDAALVMAARVATLSPQAVGFSKTLIHQGRSGVPRAAALALERERFVDLFDGAD 239

Query: 237 RHEGISAFLQKRTP 250
           + EG++AFL+KR P
Sbjct: 240 QREGVNAFLEKRPP 253


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: 124
Number of extensions: 6
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: 255
Length of database: 272
Length adjustment: 25
Effective length of query: 230
Effective length of database: 247
Effective search space:    56810
Effective search space used:    56810
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.

Links

Downloads

Related tools

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