GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Erythrobacter marinus HWDM-33

Align L-iditol 2-dehydrogenase; EC 1.1.1.14 (characterized)
to candidate WP_047094432.1 AAV99_RS12695 NAD(P)-dependent alcohol dehydrogenase

Query= CharProtDB::CH_000596
         (353 letters)



>NCBI__GCF_001013305.1:WP_047094432.1
          Length = 354

 Score =  158 bits (400), Expect = 2e-43
 Identities = 122/358 (34%), Positives = 179/358 (50%), Gaps = 23/358 (6%)

Query: 9   MKAAVMHNTREIKIETLPVPDINHDEVLIKVMAVGICGSDLHYYTNGRIGNYVVEKPFIL 68
           MKAA+      I +   PVPD+   + L+K+    ICG+D+H       G Y VEK   +
Sbjct: 1   MKAAIFVEPGRIVLGEKPVPDVGPLDALMKITTTTICGTDVHILK----GEYPVEKGLTV 56

Query: 69  GHECAGEIAAVGSSVDQFKVGDRV---AVEPGVT-----CGRCEAC--KEGR-YNLCPDV 117
           GHE  G I  +GS+V  F  G RV   A+ P  T     CG    C  +EG  +      
Sbjct: 57  GHEPVGRIEKLGSAVYGFTEGQRVIAGAITPSGTSTASLCGFHAQCGGQEGHGWKAIGGW 116

Query: 118 QFLATPPVDGAFVQYIKMRQDFVFL--IPDSLSYEEAALI-EPFSVGIHAAARTKLQPGS 174
           +F  T  +DGA  +Y+ +      L  IPD LS E+  +  +  S G   A   K++ G 
Sbjct: 117 RFGNT--IDGAQAEYLLVPDAMANLAPIPDGLSDEQVLMCPDIMSTGFGGAESGKIRIGD 174

Query: 175 TIAIMGMGPVGLMAVAAAKAFGAGTIIVTDLEPLRLEAAKKMGATHIINIREQDALEEIK 234
           T+A+   GP+GL A A A   GA TII  +  P R+  +++MGATH+++  + D ++EI 
Sbjct: 175 TVAVFAQGPIGLFATAGAYMMGATTIIGVESIPARMAMSRQMGATHVVDFSKVDPVDEIM 234

Query: 235 TITNDRGVDVAWETAGNPAALQSALASVRRGGKLAIVGLPSQN-EIPLNV--PFIADNEI 291
            IT+ RGVDVA E  G  +  + AL  +R GG L+ +G+ S +  IP +     + DN I
Sbjct: 235 KITDGRGVDVAIEALGLQSTFEGALRVLRPGGTLSSLGVYSGDLTIPCDAFSAGLGDNHI 294

Query: 292 DIYGIFRYANTYPKGIEFLASGIVDTKHLVTDQYSLEQTQDAMERALQFKNECLKVMV 349
                        + +  +ASG +DTK LVT ++ L+   DA E     +   LKV +
Sbjct: 295 VTTLCPGGKERMRRLMATVASGRIDTKALVTHRFPLDSIVDAYELFANQRGGVLKVAI 352


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: 323
Number of extensions: 20
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: 354
Length adjustment: 29
Effective length of query: 324
Effective length of database: 325
Effective search space:   105300
Effective search space used:   105300
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