GapMind for catabolism of small carbon sources

 

Aligments for a candidate for galdh in Caulobacter crescentus NA1000

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate CCNA_03495 CCNA_03495 D-beta-hydroxybutyrate dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03495 CCNA_03495
           D-beta-hydroxybutyrate dehydrogenase
          Length = 265

 Score =  124 bits (310), Expect = 3e-33
 Identities = 80/255 (31%), Positives = 127/255 (49%), Gaps = 8/255 (3%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDI-QGEKVEKVAAHWRE-QGADVVAIK 76
           L+ +V ++TG+  GIG A+    A+Q   +V++ + +   +E+  A   E  G +V+   
Sbjct: 7   LQGQVAIVTGSTSGIGHAMADALAAQGCNIVMNGLGEMNAIERARAEMAETHGVEVLYHG 66

Query: 77  ADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYG 136
           AD++R  ++  M R A    G +D+LVN AGV          E+ W    A++L  A++ 
Sbjct: 67  ADMTRPIEIADMVRAAKAEFGELDILVNNAGVQHVAPVEDFPEDKWDLIIAVNLSSAFHA 126

Query: 137 CKAVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVN 196
            KA +P M EQG G I+NIAS H     P    Y  AKHG++GLT+ + +E A  GI  N
Sbjct: 127 TKAAVPIMKEQGRGRIVNIASAHGLVASPFKSAYVAAKHGIMGLTKTVALEVAQHGITCN 186

Query: 197 AIAPGYIETQL------NVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASD 250
           AI PG+++T L      +     G ++    R       P ++     ++    ++L SD
Sbjct: 187 AICPGFVKTPLVEAQIADQAKARGISEEAVMRDVILASQPTKQFVTFDQLNGMLLYLVSD 246

Query: 251 EAPFINASCITIDGG 265
                N +   IDGG
Sbjct: 247 LGASANGAAYQIDGG 261


Lambda     K      H
   0.321    0.138    0.424 

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: 185
Number of extensions: 9
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: 272
Length of database: 265
Length adjustment: 25
Effective length of query: 247
Effective length of database: 240
Effective search space:    59280
Effective search space used:    59280
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 (21.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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