GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Burkholderia phytofirmans PsJN

Align FAA hydrolase family protein (characterized, see rationale)
to candidate BPHYT_RS28740 BPHYT_RS28740 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase

Query= uniprot:A0A2E7P912
         (281 letters)



>FitnessBrowser__BFirm:BPHYT_RS28740
          Length = 296

 Score =  360 bits (925), Expect = e-104
 Identities = 171/279 (61%), Positives = 210/279 (75%), Gaps = 1/279 (0%)

Query: 1   MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEGS 60
           M+L+R+G  GQE PG++D SG IRDLS  + D++G  +   +L K+ +LDL+ LP VE  
Sbjct: 1   MRLVRFGLPGQEHPGIIDSSGAIRDLSGIVSDIDGTTVSPVALAKLGELDLDRLPLVEAG 60

Query: 61  PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKK 120
            R+GACVGN+   +CIGLNY+DHAAE++ PIP EPVVFNK T ++ GPND V +P  ++K
Sbjct: 61  TRLGACVGNVRNLVCIGLNYSDHAAETDTPIPREPVVFNKHTGSISGPNDPVILPADAQK 120

Query: 121 TDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180
            DWEVELGVVIGK    IDE DA+ HVAGYC+ NDVSER YQ+ER G W KGK   +F P
Sbjct: 121 LDWEVELGVVIGKPAWQIDEADALEHVAGYCLANDVSERAYQLEREGQWTKGKSGFSFAP 180

Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240
           +GPWLVTRDE+ DPQ L +WL+V+G R Q GNT TMIF +AHIV+YLSRFM L  GDVI 
Sbjct: 181 LGPWLVTRDEIPDPQVLDLWLDVNGTRRQTGNTRTMIFNIAHIVAYLSRFMPLMAGDVII 240

Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQKTI 279
           TGTPPGVG+G KP  V+L+AG TM LG  GLGEQ QK +
Sbjct: 241 TGTPPGVGLGQKP-PVFLKAGDTMTLGGSGLGEQSQKVV 278


Lambda     K      H
   0.316    0.138    0.419 

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: 361
Number of extensions: 14
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: 281
Length of database: 296
Length adjustment: 26
Effective length of query: 255
Effective length of database: 270
Effective search space:    68850
Effective search space used:    68850
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: 42 (22.0 bits)
S2: 48 (23.1 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