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_RS11560 BWI76_RS11560 oxidoreductase

Query= BRENDA::F2YCN5
         (340 letters)



>FitnessBrowser__Koxy:BWI76_RS11560
          Length = 327

 Score =  179 bits (454), Expect = 9e-50
 Identities = 112/313 (35%), Positives = 173/313 (55%), Gaps = 17/313 (5%)

Query: 14  ISIKGIDKSATRVALGTWAIGGW-MWGGTDD-DASIKTIHRAIDLGINIIDTAPAYGRGH 71
           I +   D   +R+ LGTWAIGG   W G  D    I TI  A   GIN+IDTAP Y  G+
Sbjct: 4   IPLGSTDIRLSRMGLGTWAIGGGPAWNGDLDLRICIDTIIEAHRCGINLIDTAPGYNFGN 63

Query: 72  AEEVVGKAIKG-QRDNLIIATKVGLDWTLTP-------DQSMRRNSSASRIKKEIEDSLR 123
           +E +VG+A+K   R ++++ TK G+ W  T        D+ + +N +   I++E++ SL+
Sbjct: 64  SEVIVGQALKQLPRRDIVVETKCGIVWERTGSLFNKVGDRQLYKNLTPESIREEVDASLQ 123

Query: 124 RLGTDYIDLYQVHWPDP---LVPIEETATILEALRKEGKIRSIGVSNYSVQQMDEFKKYA 180
           RLG D ID+Y  HW        PI ET   L AL+KEGKIR+IG +N     + E+ K+ 
Sbjct: 124 RLGIDTIDIYMTHWQSVEPCFTPIAETVATLNALKKEGKIRAIGAANVDAGHIREYLKHG 183

Query: 181 ELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGLLSGRMTADRAFTGDDLRKT 240
           EL + Q+ Y++ +R ++ ++LP  ++N +VV  Y  L +GLLSG +T D  +     R  
Sbjct: 184 ELDIVQAKYSILDRALEAELLPLCQQNGIVVQVYSPLEQGLLSGTITRD--YVPGGARAN 241

Query: 241 DPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLEQGPTLALW-GACKPEQIDG 299
              FQ+      +  +E+ + L  E Y  ++ ALA+ W+L+Q   + L  GA  PEQ+  
Sbjct: 242 KVWFQRENMLRVIDMLEQWQPLC-EKYRCAIPALALAWILKQSDLITLLSGATAPEQVRE 300

Query: 300 IDEVFGWQISDED 312
             +     ++D+D
Sbjct: 301 NIDALTIALTDDD 313


Lambda     K      H
   0.317    0.136    0.407 

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: 264
Number of extensions: 14
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: 340
Length of database: 327
Length adjustment: 28
Effective length of query: 312
Effective length of database: 299
Effective search space:    93288
Effective search space used:    93288
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: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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