GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xyrA in Herbaspirillum seropedicae SmR1

Align D-xylose reductase (EC 1.1.1.307) (characterized)
to candidate HSERO_RS16785 HSERO_RS16785 aldo/keto reductase

Query= BRENDA::F2YCN5
         (340 letters)



>FitnessBrowser__HerbieS:HSERO_RS16785
          Length = 335

 Score =  162 bits (410), Expect = 1e-44
 Identities = 96/282 (34%), Positives = 157/282 (55%), Gaps = 2/282 (0%)

Query: 42  DDDASIKTIHRAIDLGINIIDTAPAYGRGHAEEVVGKAIKGQRDNLIIATKVGLDWTLTP 101
           DD  S+ TI RA++LGIN++DTA  YG    EE++G+AIKG+RD   IATK G+    + 
Sbjct: 37  DDAESLATIDRALELGINLLDTADMYGPYTNEELLGRAIKGRRDKFFIATKFGIRRDPSD 96

Query: 102 DQSMRRNSSASRIKKEIEDSLRRLGTDYIDLYQVHWPDPLVPIEETATILEALRKEGKIR 161
             +   + S + I++ +E SL+RLG + IDLY  H  DP  PIE T  +L  L + GKIR
Sbjct: 97  PGARGVDGSPAYIRQAVEGSLKRLGVETIDLYYQHRIDPATPIEVTMGVLADLVQAGKIR 156

Query: 162 SIGVSNYSVQQMDEFKKYAELAVSQSPYNLFEREIDKDILPYAKKNDLVVLGYGALCRGL 221
            IG+S  S   ++   +   +   QS Y+L+ R+ + ++L   +   +  + Y  L RG 
Sbjct: 157 YIGLSEASAATLERAHRVHPVTALQSEYSLWTRDPEAEVLAACRTLGIGFVAYSPLGRGF 216

Query: 222 LSGRMTADRAFTGDDLRKTDPKFQKPRFEHYLAAVEELKKLAKEHYNKSVLALAIRWMLE 281
           L+G +        DD R+++P+FQ   F   L   E++K++A +H   +   LA+ W++ 
Sbjct: 217 LTGAIQRFEDLAEDDFRRSNPRFQGENFARNLQLAEKVKEMAGQH-GCTPSQLALAWVMA 275

Query: 282 QGPTLA-LWGACKPEQIDGIDEVFGWQISDEDLKQIDAILAK 322
           Q P +  + G  +   ++      G +++ EDL+ +DAI  +
Sbjct: 276 QDPHIVPIPGTKRRRYLEDNAGSVGVKLAPEDLQALDAIFPR 317


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: 291
Number of extensions: 17
Number of successful extensions: 2
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: 335
Length adjustment: 28
Effective length of query: 312
Effective length of database: 307
Effective search space:    95784
Effective search space used:    95784
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.

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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