GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praD in Shewanella halifaxensis HAW-EB4

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate WP_012277179.1 SHAL_RS10920 2-keto-4-pentenoate hydratase

Query= BRENDA::B0VXM8
         (267 letters)



>NCBI__GCF_000019185.1:WP_012277179.1
          Length = 271

 Score =  170 bits (430), Expect = 3e-47
 Identities = 103/265 (38%), Positives = 149/265 (56%), Gaps = 8/265 (3%)

Query: 4   TVKVSLYRKFAELLNEAEREKREVARITEEVPDLSAEEAYKIQEELIKIKTNSGHRIIGP 63
           T   SL    AE L  A R+   +  ++E    L+ ++AY+I    ++ + N G ++IG 
Sbjct: 8   TTNSSLIEMHAEELLLALRKGEAITPLSERTTSLTIDDAYQISRLCLQQRENDGEQLIGK 67

Query: 64  KMGLTSQAKMAQMKVKEPIYGYLFDYMFVPSGGAIHMSE--LIHPKVEVEIAFILGEDLE 121
           K+G+TS A    + V +P +G+L + M   +G  I +S+  LI PK E EIAF L EDL 
Sbjct: 68  KIGVTSLAVQQMLNVHQPDFGFLTNSMHFNNGDCISLSKAKLIQPKAEGEIAFCLKEDLH 127

Query: 122 GPHVTSTQVLSATKYVAPALEIIDSRYQDFTFTLPDVIADNASSSRVVIGNTMTPIHSLK 181
           GP VT+  VL AT +VAP  EI+DSR +D+  ++ D +ADNAS    VIG+T TP     
Sbjct: 128 GPGVTAQDVLDATLWVAPCFEIVDSRIEDWRISIVDTVADNASCGVFVIGDTHTP----P 183

Query: 182 TDLDLIGAALYI--NGELKACGAGAAVFNHPANSVAVLANMLARKGERLKAGDIILTGGI 239
            ++DL  A + I  N +    G G+AV  HPA +VA L N L   G   K G+IIL+G +
Sbjct: 184 REIDLAEAQMEIKKNSQFAGSGLGSAVQGHPAQAVAWLTNTLGEYGIPFKKGEIILSGAL 243

Query: 240 TEAIQLSAGDTVIGQLDQLGDVSLS 264
              I   +GD    +++ LG  S+S
Sbjct: 244 APLIVAQSGDKFTMEIEGLGSCSIS 268


Lambda     K      H
   0.316    0.134    0.364 

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: 178
Number of extensions: 10
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: 267
Length of database: 271
Length adjustment: 25
Effective length of query: 242
Effective length of database: 246
Effective search space:    59532
Effective search space used:    59532
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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