GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Geotalea uraniireducens Rf4

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate WP_011940340.1 GURA_RS17985 aldo/keto reductase

Query= BRENDA::F2YCN5
         (340 letters)



>NCBI__GCF_000016745.1:WP_011940340.1
          Length = 328

 Score =  154 bits (390), Expect = 2e-42
 Identities = 98/290 (33%), Positives = 157/290 (54%), Gaps = 7/290 (2%)

Query: 38  WGGTDDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDW 97
           +G +D+  SI TI+RAIDLG+ ++DTA  YG    EE++G+AI+G+R  +++ATK G+  
Sbjct: 27  YGQSDEAESIATINRAIDLGVTLLDTADMYGPFTNEELLGRAIRGRRSQVVLATKFGILR 86

Query: 98  TLTPDQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKE 157
           T  P  S         +    + SL+RLG D+IDLY  H  DP VPIEET   +  L   
Sbjct: 87  TSDP-TSRGVCGRPDYVLTSCDSSLKRLGVDHIDLYYQHRVDPDVPIEETMGAMADLVTA 145

Query: 158 GKIRSIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGAL 217
           GK+R +G+S      +        +   QS Y+L+ R+ + ++LP  ++  + ++ Y  L
Sbjct: 146 GKVRYLGLSEAKPAIIRRAHAVHPVTALQSEYSLWTRDPEDEVLPTLRELGIGLVAYSPL 205

Query: 218 CRGLLSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLA--LA 275
            RG L+G++ +   F  DD R+  P+FQ   F   L  VE ++ +A     K + A  LA
Sbjct: 206 GRGFLTGQIKSFDDFAADDYRRNSPRFQGENFTKNLELVERVRAIAA---RKEITAGQLA 262

Query: 276 IRWMLEQGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAKNI 324
           + W+L QG  +  + G  + + ++         IS+ +L +IDA L K +
Sbjct: 263 LAWVLAQGNDIVPIPGTKRRKYLEENIAATTVSISESELAEIDAALPKGV 312


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: 277
Number of extensions: 16
Number of successful extensions: 3
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: 328
Length adjustment: 28
Effective length of query: 312
Effective length of database: 300
Effective search space:    93600
Effective search space used:    93600
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 Apr 09 2024. 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