GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Snodgrassella alvi wkB2

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_025331133.1 SALWKB2_RS07905 zinc-dependent alcohol dehydrogenase family protein

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_000600005.1:WP_025331133.1
          Length = 356

 Score =  134 bits (337), Expect = 4e-36
 Identities = 105/357 (29%), Positives = 168/357 (47%), Gaps = 19/357 (5%)

Query: 9   MKAAVMHNTREIKIETLPVPDI-NHDEVLIKVMAVGICGSDLHYYT--NGRIGNYVVEKP 65
           MKA V +   +I+ E    P I    + +I++    ICG+DL  +   N  I    ++K 
Sbjct: 1   MKAMVYYGAGDIRFEERTKPVIIEPTDAIIRLTRTTICGTDLGIWKGKNPEIEQTAIQKD 60

Query: 66  F-----ILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQ-F 119
                 ILGHE  G I   GS+V  FK GD+V +     CG CE C++  Y  C     +
Sbjct: 61  GQFNGRILGHEGIGIIEETGSAVKNFKKGDKVIISCVSRCGTCENCQKQLYAHCQSGGGW 120

Query: 120 LATPPVDGAFVQYIK--MRQDFVFLIPDSLSYEEAALIEPFSVGIH--AAARTKLQPGST 175
           +    +DG   +Y++     + ++ +P +L+ + A L+       H        ++PG T
Sbjct: 121 IMGYMIDGTQAEYVRTPFADNSLYRLPANLNEDVAVLLSDALPTAHEIGVQYGDVKPGDT 180

Query: 176 IAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKT 235
           +AI+G GPVG+  +  A+ +    II+ D++  RL  AK++GAT IIN   +DA+  +  
Sbjct: 181 VAIVGAGPVGMSCLLTAQLYSPSQIIMIDMDDNRLHMAKELGATQIINSASEDAVARVLE 240

Query: 236 ITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYG 295
            T  RGVD A E  G  A        V+ GG LA VG+  Q+ +   +  +    + I  
Sbjct: 241 YTGGRGVDCAMEAVGLEATWNICQRVVKEGGHLANVGVHGQS-VNFELEKLWIKNLTITT 299

Query: 296 IFRYANTYPKGIEFLASGIVDTKHLVTDQY---SLEQTQDAMERALQFKNECLKVMV 349
               ANT    ++   SG +  + L T  +    LE+  D  + A   K   +KV++
Sbjct: 300 GLVNANTTGMLLKTCCSGKLPMEKLATHHFHFNELEKAYDVFKHAADEK--AMKVII 354


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: 296
Number of extensions: 19
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: 353
Length of database: 356
Length adjustment: 29
Effective length of query: 324
Effective length of database: 327
Effective search space:   105948
Effective search space used:   105948
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 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