GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Corynebacterium deserti GIMN1.010

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_053546284.1 CDES_RS13820 S-(hydroxymethyl)mycothiol dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_001277995.1:WP_053546284.1
          Length = 368

 Score =  132 bits (331), Expect = 2e-35
 Identities = 91/293 (31%), Positives = 146/293 (49%), Gaps = 37/293 (12%)

Query: 27  VPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFILGHECAGEIAAVGSSVDQF 86
           +PD    +V++K+ + G+C +DL Y    R G+   E PF+LGHE AG +  VG +V   
Sbjct: 24  IPDPGPHDVIVKIQSTGVCHTDLAY----RDGDISDEFPFLLGHESAGVVETVGDAVTHV 79

Query: 87  KVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFLA-----------TPPVD-GAFVQYIK 134
           +VGD V +     CG C AC++G    C +    +           TP +  G+F +   
Sbjct: 80  EVGDFVVLNWRAVCGECRACRKGDLEYCFNTHNASKKMTLTDGTELTPALGIGSFAEKTL 139

Query: 135 MRQDFVFLI-PDSLSYEEAALIEPFSVGIHAAART-KLQPGSTIAIMGMGPVGLMAVAAA 192
           + +     + PD+       L      G+ +A  T +++ G ++A+ G+G VG+ AVA A
Sbjct: 140 VHEGQCTKVNPDADPAAAGLLGCGIMAGLGSAVNTGEVKRGESVAVFGLGGVGMAAVAGA 199

Query: 193 KAFGAGTIIVTDLEPLRLEAAKKMGATHIINIRE-------QDALEEIKTITNDRGVDVA 245
           K  GA TII  D++  +LE AK+ GATH+I+  +        +  ++++ IT+  G DVA
Sbjct: 200 KIAGATTIIAVDIDAKKLEWAKEFGATHVIDSSQLSGEGENSEVAQKVREITDGFGTDVA 259

Query: 246 WETAGNPAALQSALASVRRGGKLAIVGLP---SQNEIPLNVPFIADNEIDIYG 295
            +  G     Q A  S    G++ +VG+P   S+ E+P          ID YG
Sbjct: 260 IDAVGIMPTWQQAFYSRDHAGRMVMVGVPNLTSRIEVP---------AIDFYG 303


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: 324
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: 368
Length adjustment: 29
Effective length of query: 324
Effective length of database: 339
Effective search space:   109836
Effective search space used:   109836
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