GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Paenisporosarcina indica PN2

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_075618903.1 GY23_RS09270 alcohol dehydrogenase catalytic domain-containing protein

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_001939075.1:WP_075618903.1
          Length = 339

 Score =  166 bits (421), Expect = 6e-46
 Identities = 102/330 (30%), Positives = 167/330 (50%), Gaps = 10/330 (3%)

Query: 9   MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68
           MK  +    + ++++ +  P +  DEVL+KV A G+CGS++  Y      N +   P ++
Sbjct: 1   MKTLLWTKAQVMEMQEIEKPAVKSDEVLVKVEAAGVCGSEIEGYLGH---NSLRVPPLVM 57

Query: 69  GHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLATPPVDGA 128
           GHE AG IA VGS+V    + DRV V P ++CG+C +C++G  NLC   Q +      G 
Sbjct: 58  GHEFAGTIAEVGSAVKHIAMNDRVVVNPLISCGKCGSCRKGYENLCETRQIIGIHR-PGG 116

Query: 129 FVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAART-KLQPGSTIAIMGMGPVGLM 187
           F +Y+ +    ++ IPDSL +  A+L EP +  + A  R     P + + + G G +GL+
Sbjct: 117 FAEYVAVPASCIWPIPDSLDFITASLTEPLACSLRATKRAMAANPFANVVVYGAGAIGLL 176

Query: 188 AVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIKTITNDRGVDVAWE 247
           +   A+  GA  +I+ D+   RLE  +  G  H +   + D   ++  I  +RGVDV  +
Sbjct: 177 SALVAQMMGASNVIIFDINEKRLETVRNSGIEHALLSNDPDLKNKLAEIVGERGVDVIID 236

Query: 248 TAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADNEIDIYGIFRYA-NTYPKG 306
            AG       A+  +  GG +  +GL   +E P+ V     +EI     F Y    + + 
Sbjct: 237 AAGFVPTRLQAIEIINYGGTIMNIGL-GVDETPIPVNVQIRSEITFLASFCYTKQDFYEA 295

Query: 307 IEFLASGIVDTKHLVTDQY-SLEQTQDAME 335
           +E L SG +  KH V  +  +LE+   A +
Sbjct: 296 LEVLKSGKI--KHDVWSEIRTLEEGDGAFQ 323


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: 281
Number of extensions: 14
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 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