GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Pseudomonas fluorescens FW300-N2C3

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO356_26645 AO356_26645 crotonase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_26645
          Length = 267

 Score =  116 bits (291), Expect = 4e-31
 Identities = 81/255 (31%), Positives = 127/255 (49%), Gaps = 11/255 (4%)

Query: 3   ELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAG 62
           E+ VSR++  ++L  NR A  N ++     +L    EA      + V V+      F++G
Sbjct: 20  EVDVSRERADIIL--NR-APLNVISMGQRDELRQVFEALDAHKGVRVIVLRSVGEHFSSG 76

Query: 63  ADLNEMAEKDLAATLNDTRPQLW--ARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAG 120
            D+    E    A+        W  A      KP+I A  GY  G G EL+L CD  +A 
Sbjct: 77  GDIKGFLE----ASPEHVSKLAWNVAAPARCEKPVIVANRGYTFGVGFELSLACDFRIAS 132

Query: 121 ENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFPS 180
           +  R+ LPE  LG +PG+GG+ RL + +G +    MV+  + IT  QA   G+ ++V P 
Sbjct: 133 QTTRYALPEQNLGQIPGSGGSARLQKIIGITRTKHMVMRAKRITGDQAYAWGIATEVVP- 191

Query: 181 DLTLEYALQ-LASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAATEDRHE 239
           D  LE  +  L  ++ R SPLA + AK+ +  +++  L   +  E   ++ L +++D  E
Sbjct: 192 DTELESTVDALVDELRRFSPLAQRTAKKLINDNEDAPLTVAIEMEGHCYSRLRSSKDFKE 251

Query: 240 GISAFLQKRTPDFKG 254
           G+ AF  KRT  F G
Sbjct: 252 GVEAFHSKRTAVFIG 266


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: 101
Number of extensions: 5
Number of successful extensions: 1
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: 267
Length adjustment: 25
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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