GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Marinicella litoralis KMM 3900

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate WP_099018991.1 CCS90_RS07845 glucose 1-dehydrogenase

Query= SwissProt::P0C0Y5
         (267 letters)



>NCBI__GCF_002591915.1:WP_099018991.1
          Length = 250

 Score =  135 bits (339), Expect = 1e-36
 Identities = 88/249 (35%), Positives = 133/249 (53%), Gaps = 10/249 (4%)

Query: 19  KGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKAKAY 78
           + KVV++TGAS  +G+G   A   A  GA V ++  SR+Q   + V    K  G KA A 
Sbjct: 5   ENKVVLITGAS--RGIGEAIAHQFAAQGAQVIVS--SRSQEGIDAVANAIKQNGGKAGAI 60

Query: 79  KCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSG-ILDGSVEAWNHVVQVDLNGTF 137
            C      S + L+K  +  +GQ+D  I NA A    G +LD   EA    ++V++ G F
Sbjct: 61  TCHNGDKASRDGLIKQTIEQYGQLDVMINNAAANPYFGNVLDMGFEAIKKTIEVNIEGYF 120

Query: 138 HCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRDFA 197
           H ++  G   +++G G ++ T+S++G +A F   Q+ Y+ +KA  I M  S A E   F 
Sbjct: 121 HMSQLAGQQMRKQGAGVIINTSSVNGRVAGF--NQSLYSASKAAIISMTESFAKECAQFG 178

Query: 198 -RVNSISPGYIDTGLSDFVPKETQQLWHSM--IPMGRDGLAKELKGAYVYFASDASTYTT 254
            RVN++ PG  DT  +  + +    L   +  IP+GR    +E+  AY++ ASDA+ Y T
Sbjct: 179 IRVNAVLPGLTDTKFASALTQNEAMLKMILPQIPLGRIAQPEEIAPAYLFLASDAAKYIT 238

Query: 255 GADLLIDGG 263
           G  L IDGG
Sbjct: 239 GVSLPIDGG 247


Lambda     K      H
   0.316    0.131    0.383 

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: 144
Number of extensions: 6
Number of successful extensions: 3
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: 267
Length of database: 250
Length adjustment: 24
Effective length of query: 243
Effective length of database: 226
Effective search space:    54918
Effective search space used:    54918
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 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