GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Limnohabitans curvus MWH-C5

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG

Query= SwissProt::P0C0Y5
         (267 letters)



>NCBI__GCF_003063475.1:WP_108358580.1
          Length = 255

 Score =  123 bits (309), Expect = 3e-33
 Identities = 80/260 (30%), Positives = 136/260 (52%), Gaps = 9/260 (3%)

Query: 7   TKHESLLDQLSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKE 66
           T H S   +L  +GKV ++TGA+  +G+G+  A   A  GA V +    +A   +E VK+
Sbjct: 3   TNHNSQAQRL--QGKVSLITGAA--QGIGLATALKFAREGAIVIVCDVKQA-AVDEAVKQ 57

Query: 67  LEKTYGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWN 126
            +   G +A  +   V   +  +  VK V+  FG+ID  + NAG T D+ +   ++E ++
Sbjct: 58  CQ-ALGAQALGFVVDVTQRDMVDATVKAVLDKFGRIDVLVNNAGITQDARLQKMTLEQFD 116

Query: 127 HVVQVDLNGTFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMA 186
            V+ V+L G FHCA+AV      +G+G ++  +S+ G   NF   QT+Y   K G I   
Sbjct: 117 RVIDVNLRGVFHCAQAVTEAMVAQGSGVILNASSVVGIYGNF--GQTNYAATKFGVIGFT 174

Query: 187 RSLANEWRDFA-RVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYF 245
           ++ + E      RVN+++PG+I T +   +P++        +P+ R G  +++   Y + 
Sbjct: 175 KTWSRELGPKGIRVNAVAPGFIQTPILSTIPEKVIHEMTDRVPLKRLGQPEDIANVYAFL 234

Query: 246 ASDASTYTTGADLLIDGGYT 265
           ASD + Y  G  + + GG T
Sbjct: 235 ASDEAAYINGTVIEVAGGLT 254


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: 162
Number of extensions: 9
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: 267
Length of database: 255
Length adjustment: 25
Effective length of query: 242
Effective length of database: 230
Effective search space:    55660
Effective search space used:    55660
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