GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Caulobacter crescentus NA1000

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate CCNA_02929 CCNA_02929 sorbitol dehydrogenase

Query= BRENDA::B2ZRE3
         (347 letters)



>lcl|FitnessBrowser__Caulo:CCNA_02929 CCNA_02929 sorbitol
           dehydrogenase
          Length = 346

 Score =  259 bits (662), Expect = 7e-74
 Identities = 148/346 (42%), Positives = 206/346 (59%), Gaps = 6/346 (1%)

Query: 1   MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGK-IPVLPGSVLGH 59
           M+A+ +     V  + ++ P  Q   DA+V+V    ICGSDLH+YHG       G  +GH
Sbjct: 1   MKALRYHGARDVRYESMDDPTPQSDRDAIVQVTACSICGSDLHIYHGHGFSEDLGFCVGH 60

Query: 60  EFVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCERGGVYGYGPMFGNLQ 119
           E VG+V  VG G+Q L+ GD V+ P  + CG C  C       CE G    YG +   LQ
Sbjct: 61  EAVGEVVEVGRGVQRLKVGDKVMLPAAVGCGRCRSCLSGVIQTCENGQGACYG-LSARLQ 119

Query: 120 GAQAEILRVPFSNVNLRKLPPNLSPERAIFAGDILSTAYGGLIQGQLRPGDSVAVIGAGP 179
           G+QAE +RVP +++N   +P  +S ++A+   D L+TA+ G    ++RPG SVAVIG GP
Sbjct: 120 GSQAEAVRVPAADMNAVPVPDGVSMDQALMMTDALATAWFGARNAEVRPGASVAVIGLGP 179

Query: 180 VGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPINAEQENPVRRVRSETNDEGPDL 239
           +GLMA+E A V+GA  + AID +P R   A   GAI ++ ++   + RVR +T   G D 
Sbjct: 180 IGLMAVESAYVMGAHVVYAIDPLPARRALAEEAGAIALHPDEA--LARVREDTKGRGLDC 237

Query: 240 VLEAVGGAATLSLALEMVRPGGRVSAVGVDNAPSFPFPLASGLVKDLTFRIGLANVHLYI 299
           V+EAVGG AT+  AL +VRP G VS +GV  A  F FPL       LTFR+G  +V   +
Sbjct: 238 VIEAVGGEATVDAALRLVRPRGVVSVIGVQQAKRFAFPLERAFGAGLTFRVGTCSVPEEL 297

Query: 300 DAVLALLASGRLQPERIVSHYLPLEEAPRGYELFDRKE--ALKVLL 343
            A+  L+ SGRL+PE+ +SH LPL + P  Y LF+ +E  ALK++L
Sbjct: 298 PALFPLVRSGRLRPEKYISHRLPLSDGPEAYRLFESREAGALKMVL 343


Lambda     K      H
   0.321    0.141    0.420 

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: 354
Number of extensions: 16
Number of successful extensions: 4
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: 347
Length of database: 346
Length adjustment: 29
Effective length of query: 318
Effective length of database: 317
Effective search space:   100806
Effective search space used:   100806
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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