GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Pseudomonas fluorescens FW300-N2E3

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate AO353_19350 AO353_19350 2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_19350
          Length = 270

 Score =  107 bits (268), Expect = 2e-28
 Identities = 85/280 (30%), Positives = 136/280 (48%), Gaps = 29/280 (10%)

Query: 1   MPYAAVNGTELHYRIDGERHGNAPWIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGH 60
           MP+A ++G  LHY +D    G  P ++L+ S   D +MWAPQ+ ALS+H RV+  D  GH
Sbjct: 1   MPFATIDGQLLHY-VD---QGTGPVVLLAGSYLWDQAMWAPQIVALSQHHRVIAVDLWGH 56

Query: 61  GHS-EAPKGPYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVAL 119
           G S   P+G  +++     VL L+D L I R    GLS+GG+ GV LA     R+  + L
Sbjct: 57  GESGPLPEGMTSLDDQARQVLALLDHLDIDRVTLVGLSVGGMWGVRLALSAPQRLNGLVL 116

Query: 120 CNTAARIGSPEV----WVPRAVKARTEGMHA--LADAVLPRWF-------TADYMEREPV 166
            +T   +  PE+    +     +    G+ +  L D V+P +F       +A Y +    
Sbjct: 117 MDTYVGV-EPELTRQYYFSLFKQIEDSGVISPQLLDIVVPIFFRPGIDPQSALYQDFRAR 175

Query: 167 VLAM----IRDVFVHTDKEGYASNCEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQG 222
           + A+    +R+  V   +  +  +       +L PE        L++ G  D    P + 
Sbjct: 176 LAALPPERLRESIVPMGRITFGRDDLLPRLGELNPET------TLLMCGDQDKPRPPLET 229

Query: 223 RELAQAIAGARYVELDASHISNIERADAFTKTVVDFLTEQ 262
           RE+A+ I     +  +A HISN+E  +  TK ++ FL E+
Sbjct: 230 REMAELIGCPYLLVPEAGHISNLENPEFVTKALLKFLAER 269


Lambda     K      H
   0.320    0.134    0.402 

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: 169
Number of extensions: 12
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: 263
Length of database: 270
Length adjustment: 25
Effective length of query: 238
Effective length of database: 245
Effective search space:    58310
Effective search space used:    58310
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 (21.8 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