GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Klebsiella michiganensis M5al

Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate BWI76_RS19345 BWI76_RS19345 D-arabinitol 4-dehydrogenase

Query= BRENDA::O08355
         (493 letters)



>FitnessBrowser__Koxy:BWI76_RS19345
          Length = 455

 Score =  229 bits (584), Expect = 2e-64
 Identities = 134/399 (33%), Positives = 211/399 (52%), Gaps = 6/399 (1%)

Query: 31  HIGVGGFHRAHQAYYTDALMNTGEGLDWSICGVGLRSEDRKARDDLAGQDYLFTLYELGD 90
           HIG+G FHRAHQA+Y   L+ +G+   W I    +R++  +    LA Q   + L  +  
Sbjct: 9   HIGLGSFHRAHQAWYLHRLIASGDKR-WHIAAGNIRNDAEQVVQALAAQGGRYVLETVSP 67

Query: 91  TDDTEVRVIGSISDMLLAEDSAQALIDKLASPEIRIVSLTITEGGYCIDDSNGEFMAHLP 150
             + E   I SI  +L  +   Q LI++ A+P+ ++++ T+TEGGY ++  + +     P
Sbjct: 68  EGEREYEEITSIQKLLPWQAGLQPLINEGANPQTKVIAFTVTEGGYYLNTRH-QLETSNP 126

Query: 151 QIQHDLAHPSSPKTVFGFICAALTQRRAAGIPAFTVMSCDNLPHNGAVTRKALLAFAALH 210
            +Q DLA     KT++G +   L +R A      T+++CDN+ HNG      ++ F  L 
Sbjct: 127 DLQADLA--GECKTIYGTLARILEKRMADNAGPLTLLNCDNVRHNGERFHDGMVEFLQLT 184

Query: 211 NAE-LHDWIKAHVSFPNAMVDRITPMTSTAHRLQLHDEHGIDDAWPVVCEPFVQWVLEDK 269
             + + DW+  + + PN MVDRITP  +     ++  + GIDD  PV+ E F+QWV+E+ 
Sbjct: 185 GKQAVIDWMAVNTTCPNTMVDRITPRPAADLPARIKAQTGIDDKAPVMGETFIQWVVENN 244

Query: 270 FVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNGSHLALTYLGFLKGYRFVHETMNDPLFVA 329
           F + RP  E VGV+    V PYEE KI +LN SH  + + G L G +++HE+       A
Sbjct: 245 FRDERPKLEAVGVEMVASVIPYEEAKIRILNASHSCIAWAGTLIGQQYIHESTLTDFIYA 304

Query: 330 YMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDRFSNQAIADQLERVCSDGSSKFPKFTVPT 389
               Y+  DV P L    GIDL  Y+  ++ RF+N  I D  +RV +DG SK P    PT
Sbjct: 305 IADRYVTEDVIPCLGD-NGIDLPTYRDVVLKRFTNPYIQDTNQRVAADGFSKIPAMIAPT 363

Query: 390 INRLIADGRETERAALVVAAWALYLKGVDENGVSYTIPD 428
           +      G   E  A++ A + ++++   +  + Y   D
Sbjct: 364 LQECYQRGVRPEATAMLPALFFVFMEQWHKGTLPYQYQD 402


Lambda     K      H
   0.321    0.137    0.414 

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: 560
Number of extensions: 33
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: 493
Length of database: 455
Length adjustment: 33
Effective length of query: 460
Effective length of database: 422
Effective search space:   194120
Effective search space used:   194120
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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