GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Klebsiella michiganensis M5al

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase

Query= BRENDA::P76082
         (255 letters)



>FitnessBrowser__Koxy:BWI76_RS20065
          Length = 285

 Score =  110 bits (276), Expect = 2e-29
 Identities = 82/245 (33%), Positives = 126/245 (51%), Gaps = 10/245 (4%)

Query: 15  LTLNRPAARNALNNALLMQLVNELEAAATDTSISVCVITGNA-RFFAAGADLNEMAE--- 70
           +T+NRP  RNA     + +++  L  A  D +I V V+TG   + F AG D     +   
Sbjct: 37  ITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKAFCAGGDQKVRGDYGG 96

Query: 71  -KDLAATLNDTRPQLWARLQAFNKPLIAAVNGYALGAGCELALLCDVVVAGENARFGLPE 129
            +D +   +        +++   KP++A V GY++G G  L ++CD+ +A ENA FG   
Sbjct: 97  YQDDSGVHHLNVLDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMCDLTIAAENAIFGQTG 156

Query: 130 ITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDVFP-SDLTLEYAL 188
             +G   G  G   + R VG+  A ++        AQQA   GLV+ V P +DL  E  +
Sbjct: 157 PKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPLADLEKE-TV 215

Query: 189 QLASKMARHSPLALQAAKQALRQSQEVALQAGLAQERQLFTLL-AATEDRHEGISAFLQK 247
           +   +M ++SP+AL+  K AL  + +   QAGL +     T+L   TE+  EG +AF QK
Sbjct: 216 RWCREMLQNSPMALRCLKAAL--NADCDGQAGLQELAGNATMLFYMTEEGQEGRNAFNQK 273

Query: 248 RTPDF 252
           R PDF
Sbjct: 274 RQPDF 278


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: 109
Number of extensions: 6
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: 285
Length adjustment: 25
Effective length of query: 230
Effective length of database: 260
Effective search space:    59800
Effective search space used:    59800
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