GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Klebsiella michiganensis M5al

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate BWI76_RS05410 BWI76_RS05410 2,5-didehydrogluconate reductase B

Query= BRENDA::I7HD84
         (322 letters)



>FitnessBrowser__Koxy:BWI76_RS05410
          Length = 267

 Score =  143 bits (361), Expect = 4e-39
 Identities = 100/302 (33%), Positives = 146/302 (48%), Gaps = 51/302 (16%)

Query: 16  MPLVGFGCWKVSPEDAEATIYNAIKSGYRLIDGAADYGNEVEVGRGINKAIKEGIVTREE 75
           +P+ G G +++  +    ++  A++ GYR ID A  Y NE  VG+    AI E  V R E
Sbjct: 3   IPVFGLGTFRLKDDVVITSVKTALELGYRTIDTAQIYDNEAAVGQ----AIAESGVARNE 58

Query: 76  VFVVTKLWNTYHNKDRLRGAFDKQLKDLGLDYVDLYLIHFPVPLKYVDIDQAYPAGWYQP 135
           +F+ TK+W    NK++L  +  + L+ L  DYVDL LIH+P P   V +++         
Sbjct: 59  LFITTKIWIENLNKEKLIASLKESLQKLRTDYVDLTLIHWPSPNDAVAVEEF-------- 110

Query: 136 NKTEIEFEPSPMHECWREMEKLVENK---LARNIGISNFNVQLILDLLTYAKIKP-AVLQ 191
                             M  L+E K   L R IGISNF + L+   +     +  A  Q
Sbjct: 111 ------------------MAALLEAKKQGLTRQIGISNFTIPLMERAIAAVGAENIATNQ 152

Query: 192 VELHPYLQQSRMVAWVQSQGIHITAYS--SFGPASFVDLTTDGKTAAPLLEHSTIKEIAN 249
           +EL PYLQ  ++V W +  GIHIT+Y   ++G A               L+   I  IA 
Sbjct: 153 IELSPYLQNRKVVNWAREHGIHITSYMTLAYGKA---------------LKDEAIARIAA 197

Query: 250 KHNKTTGQVLLRWSTERNIAVIPKSTNQDRIKSNLDIFSWSLDKEDMDKIASLDKGLRFN 309
           K++ T  QV+L W+     AVIP ST ++ + SNL      LD++D   IA+LD   R  
Sbjct: 198 KYDATPAQVILAWAMGEGYAVIPSSTKRENLASNLKAQDLQLDEDDRQAIAALDCNDRLV 257

Query: 310 DP 311
            P
Sbjct: 258 SP 259


Lambda     K      H
   0.318    0.135    0.408 

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: 212
Number of extensions: 10
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: 322
Length of database: 267
Length adjustment: 26
Effective length of query: 296
Effective length of database: 241
Effective search space:    71336
Effective search space used:    71336
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 (21.7 bits)
S2: 48 (23.1 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