GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpD in Cupriavidus basilensis 4G11

Align 2-oxopent-4-enoate hydratase subunit (EC 4.2.1.80) (characterized)
to candidate RR42_RS32640 RR42_RS32640 4-oxalocrotonate decarboxylase

Query= metacyc::MONOMER-3403
         (222 letters)



>FitnessBrowser__Cup4G11:RR42_RS32640
          Length = 262

 Score =  158 bits (400), Expect = 8e-44
 Identities = 89/213 (41%), Positives = 127/213 (59%), Gaps = 1/213 (0%)

Query: 8   ELGDELYQAMVQRETVTPLTSRGFDISVEDAYHISLRMLERRLAAGERVIGKKIGVTSKA 67
           +L + L  A + RE V  +T    ++  EDAY I   +  R+ A G R+ G K+G+TS A
Sbjct: 10  QLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAGLKMGLTSFA 69

Query: 68  VQNMLGVHQPDFGYLTDAMVYNSGEAMPISEKLIQPRAEGEIAFILKKDLMGPGVTNADV 127
               +GV  P +G+LTD      G A+  +  LI P+ E EIAF+LK  L GPG    DV
Sbjct: 70  KMRQMGVTDPVYGFLTDYGACMDGGAIDTAS-LIHPKVEAEIAFVLKHPLKGPGCHIGDV 128

Query: 128 LAATECVIPCFEVVDSRIQDWKIKIQDTVADNASCGLFVLGDQAVSPRQVDLVTCGMLVE 187
           LAAT+ V+P  EV+DSR ++++  ++  +ADN S   FV+G    S   +DL   G+++E
Sbjct: 129 LAATDFVLPAVEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDLKNLGVVLE 188

Query: 188 KNGQLLSTGAGAAALGSPVNCVAWLANTLGHFG 220
           KNG++++T AGAA LG P + VA LAN LG  G
Sbjct: 189 KNGEVVATAAGAAVLGHPASSVAMLANMLGARG 221


Lambda     K      H
   0.319    0.136    0.395 

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: 119
Number of extensions: 7
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: 222
Length of database: 262
Length adjustment: 23
Effective length of query: 199
Effective length of database: 239
Effective search space:    47561
Effective search space used:    47561
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 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