GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Novosphingobium fuchskuhlense FNE08-7

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_067911841.1 AQZ52_RS13795 crotonobetainyl-CoA hydratase

Query= BRENDA::P76082
         (255 letters)



>NCBI__GCF_001519075.1:WP_067911841.1
          Length = 259

 Score =  155 bits (391), Expect = 1e-42
 Identities = 100/262 (38%), Positives = 153/262 (58%), Gaps = 10/262 (3%)

Query: 1   MSELIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFA 60
           MS + + +Q  +L++TL+RP A NA++ A  ++L    +    D ++ V +ITG  RFF+
Sbjct: 1   MSAVKLDQQGGILIITLDRPKA-NAIDVATSLELHAAFKTLNDDPALRVGIITGTGRFFS 59

Query: 61  AGADLNEMAEKDLAATLNDTRPQLWARLQAF---NKPLIAAVNGYALGAGCELALLCDVV 117
           AG DL   A  D  A   D  P  +A L  +    KP+IAAVNG A+G G ELAL  D++
Sbjct: 60  AGWDLG--AANDGEAVDADHGPGGFAGLTEYFSLTKPVIAAVNGLAVGGGFELALAADLI 117

Query: 118 VAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177
           V  E A+F LPE  LG++P +GG  RL +++   LA +M+L+G  + A +A    LVS V
Sbjct: 118 VVSETAKFWLPEAQLGMLPDSGGLLRLPKAIPARLAREMILTGRRLDAAEALSLHLVSRV 177

Query: 178 FPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQ----LFTLLAA 233
              D  +  AL+LA+ +A+ +PLAL AA+  LR ++ + ++AG    R      +  +  
Sbjct: 178 TEPDALMACALELATTVAQSAPLALTAARDILRATEGMEVEAGYRLMRSGAIPAYQAMLQ 237

Query: 234 TEDRHEGISAFLQKRTPDFKGR 255
           ++D  EG  AF + R P++KGR
Sbjct: 238 SDDALEGPRAFGEGRAPEWKGR 259


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: 118
Number of extensions: 7
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: 259
Length adjustment: 24
Effective length of query: 231
Effective length of database: 235
Effective search space:    54285
Effective search space used:    54285
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 24 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