GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Sphingomonas koreensis DSMZ 15582

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ga0059261_2803 Ga0059261_2803 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Korea:Ga0059261_2803
          Length = 266

 Score =  145 bits (366), Expect = 8e-40
 Identities = 89/261 (34%), Positives = 143/261 (54%), Gaps = 9/261 (3%)

Query: 4   LIVSRQQRVLLLTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNARFFAAGA 63
           L   R+  +L+LT++ PA RNAL+  L   LV     A  D S+S  ++TG    F AG 
Sbjct: 6   LKAEREGPILILTIDDPATRNALSPELTRALVAACAEANADMSVSCVILTGAGDVFCAGG 65

Query: 64  DLNEMAEK--DLAATLNDTRPQLWARLQAFNK-------PLIAAVNGYALGAGCELALLC 114
           ++ +M  +    A    + R    A +Q   +       P IAAVNG A+GAG + A +C
Sbjct: 66  NIKDMYARANHFAGNAAEIRRTYQAGVQTIARALYDLEVPSIAAVNGAAMGAGMDFATMC 125

Query: 115 DVVVAGENARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLV 174
            + +A E A+F    I LG+   AGG   L R++G S A+++ L+G++I A +A + GLV
Sbjct: 126 TMRIASERAKFAESFIKLGLTSAAGGAWFLNRAIGASAAAELALTGDTIDAARALEIGLV 185

Query: 175 SDVFPSDLTLEYALQLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLLAAT 234
           S V P    L+ A  LA ++ARH   +++   + LR+S  + L A L     +  ++  T
Sbjct: 186 SGVVPHAALLDEARALAKRIARHPAHSIRLNTRLLRESARLDLSAALEIASAMQAVVQQT 245

Query: 235 EDRHEGISAFLQKRTPDFKGR 255
           +D++E ++A ++KR P +KG+
Sbjct: 246 DDQYEAVAAAVEKRPPAYKGK 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: 97
Number of extensions: 3
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: 255
Length of database: 266
Length adjustment: 24
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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