GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Lutibaculum baratangense AMV1

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_023430324.1 N177_RS00865 zinc-binding dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_000496075.1:WP_023430324.1
          Length = 388

 Score =  187 bits (476), Expect = 3e-52
 Identities = 111/361 (30%), Positives = 180/361 (49%), Gaps = 17/361 (4%)

Query: 5   VPQNMKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRI----GNY 60
           +P+ MKA V+ +  ++ +   PVP     EVL+++ AV IC +DL    NG      G  
Sbjct: 15  IPETMKAWVLGDPDQLTLTEKPVPSPKRAEVLVRIDAVAICATDLEIIHNGPPAMIQGGA 74

Query: 61  VVEKPFILGHECAGEIAAVGSSVDQFKVGDRVAVEPGVTCGRCEACKEGRYNLCPDVQFL 120
              K F  GHE  G + A+G  VD++ +GDRV VE    CG+C+ C++G Y  C +    
Sbjct: 75  PFNKNFTPGHEYMGTVVALGEGVDEYTIGDRVTVEIHAGCGQCKRCRQGMYTSCHNYGLN 134

Query: 121 ATP----------PVDGAFVQYIKMRQDFVFLIPDSLSYEEAALIEPFSVGIHAAARTK- 169
                          DG F +Y     + +  +PD +S EEA L+      ++       
Sbjct: 135 YGDRNKGHRANGFTTDGGFAEYAVNNINTLVHVPDDMSDEEATLVVTAGTAMYGLTELGG 194

Query: 170 LQPGSTIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDA 229
           L  G ++ + G GP+GL+ VA AKA GA  +I+T     RLE  KK+GA H IN+R ++A
Sbjct: 195 LVAGESVVVTGPGPIGLLGVAVAKALGAQPVILTGTRDNRLEMGKKLGADHTINVRNENA 254

Query: 230 LEEIKTITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQNEIPLNVPFIADN 289
           +E ++ I   +GVD   E +G   A+  A   V RGG++ +   P +  +P++V ++  N
Sbjct: 255 VERVREIMGGKGVDYVVECSGASNAVNEAAQMVNRGGRICLAAFPHE-AVPVDVAYLVRN 313

Query: 290 EIDIYGIFRYANTYP-KGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVM 348
            I +YGI     +   +   F+     D   + T  + +   + A++ A +   + +KV+
Sbjct: 314 NIYVYGIRGEGKSATHRAAAFMEQKRFDATLIHTHTFPMGDLETALKYARERIEDAIKVV 373

Query: 349 V 349
           V
Sbjct: 374 V 374


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: 315
Number of extensions: 17
Number of successful extensions: 5
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: 388
Length adjustment: 30
Effective length of query: 323
Effective length of database: 358
Effective search space:   115634
Effective search space used:   115634
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