GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pedobacter sp. GW460-11-11-14-LB5

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate CA265_RS08610 CA265_RS08610 alcohol dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>FitnessBrowser__Pedo557:CA265_RS08610
          Length = 339

 Score =  159 bits (403), Expect = 8e-44
 Identities = 98/325 (30%), Positives = 162/325 (49%), Gaps = 12/325 (3%)

Query: 28  PDINHDEVLIKVMAVGICGSDLHYYTNGR-IGNYVVEKPFILGHECAGEIAAVGSSVDQF 86
           P++  D  +IK+  +GICG+DLH +   +   NY    P +LGHE +GE+     + D F
Sbjct: 20  PELKKDHAIIKIKRIGICGTDLHAFEGTQPFFNY----PRVLGHELSGELVEADGA-DGF 74

Query: 87  KVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGAFVQYIKMRQDFVFLIPDS 146
           K+G+ V   P   CG C AC+  + N C  +Q      VDG   +Y+++      L  + 
Sbjct: 75  KIGEAVTFIPYFNCGECIACRMNKPNCCVKMQVCGVH-VDGGMREYLQVPSR-TLLHGEG 132

Query: 147 LSYEEAALIEPFSVGIHAAARTKLQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLE 206
           LSY+E AL+EP ++G H   R  +QPG  + ++G GP+GL  +  A+  GA  +I  D+ 
Sbjct: 133 LSYDELALVEPLAIGAHGVRRADVQPGEFVLVIGAGPIGLGTMEFARIAGA-NVIALDIN 191

Query: 207 PLRLEAAK-KMGATHIINIREQDALEEIKTITNDRGVDVAWETAGNPAALQSALASVRRG 265
             RL   K K+   H++N    D ++++  ITN     V  +  GN  A+ +A+  +  G
Sbjct: 192 EDRLAFCKDKLKVAHVVNALSPDVVQQLSDITNGDMPTVVIDATGNQKAINNAINYMAHG 251

Query: 266 GKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA-NTYPKGIEFLASGIVDTKHLVTDQ 324
            +  ++GL  + ++  N P     E  +          +   I+ + +G+V+  + +T Q
Sbjct: 252 ARFVLIGL-QKGDLIFNHPEFHKRESTLMSSRNATIEDFEHVIKSMKAGLVNPTNYITHQ 310

Query: 325 YSLEQTQDAMERALQFKNECLKVMV 349
              E  +D  E  L  KN  +K MV
Sbjct: 311 VQFEAVKDEFESWLDPKNGVIKAMV 335


Lambda     K      H
   0.320    0.137    0.401 

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: 285
Number of extensions: 13
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: 353
Length of database: 339
Length adjustment: 29
Effective length of query: 324
Effective length of database: 310
Effective search space:   100440
Effective search space used:   100440
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:

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