GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Caulobacter crescentus NA1000

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate CCNA_01892 CCNA_01892 short chain dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__Caulo:CCNA_01892
          Length = 546

 Score =  130 bits (327), Expect = 6e-35
 Identities = 87/263 (33%), Positives = 128/263 (48%), Gaps = 17/263 (6%)

Query: 1   MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60
           M+ K   +V LVTG    IG A   R A  G  + + D N   +E+A       G +  +
Sbjct: 26  MTSKAQSRVVLVTGGADGIGWAACQRFARAGDQVLVADRN---VERARERADSLGPDHHA 82

Query: 61  YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQ-DYPSDDFARVLTINVTG 119
              DV+SE  +    + + R+FG++D L NNAG          D  +++ AR+  INVTG
Sbjct: 83  IAMDVSSEAQIREGFEQLHREFGRLDVLVNNAGVTDPQPTATLDQTAEEVARLQAINVTG 142

Query: 120 AFHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179
           AF   +   R MI Q +G I+N AS AG+       +Y  SK A+I+LT T A + A   
Sbjct: 143 AFLAAREAGRLMIEQGHGAIINLASGAGLVALAKRTSYSASKAAVISLTRTLACEWAAKG 202

Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239
           +RVNA+ PGY        + V+ Q   G      DP +V    +  +P+ R G+  E+  
Sbjct: 203 VRVNAVLPGYTR-----TQMVQDQIDAG----LLDPSIV----LSRIPLGRMGEPEEMAE 249

Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262
              FL  D +S++ G  L + GG
Sbjct: 250 GAFFLASDAASYVVGATLVVDGG 272



 Score = 96.7 bits (239), Expect = 9e-25
 Identities = 67/255 (26%), Positives = 114/255 (44%), Gaps = 18/255 (7%)

Query: 8   KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67
           +V  +TG G  IG          G  + +++ + E  +    ++ ++ +  ++ + DV +
Sbjct: 296 RVSAITGGGRGIGRCVVDLFHAAGDRLLVIERDAEGAKALAEALGDEHIVVQADITDVAA 355

Query: 68  EEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKAV 127
            EA      +    +G++D L NNAG    F P  +  + DF  V  +N +G     KA 
Sbjct: 356 VEAAFAQAQA---RWGRLDVLINNAGAADVFKPSLEQTAQDFTSVYDLNFSGPLATAKAA 412

Query: 128 SRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAISP 187
           +R M     G IVN  S+AG+   P   AY  +K A+  ++ + A + A   IRVN ++P
Sbjct: 413 ARLM--SQGGVIVNLGSIAGLGALPQRNAYCAAKAAVTMMSRSLACEWASAGIRVNTVAP 470

Query: 188 GYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLGD 247
           GY+      E    L  K          +    ++    P+ R GD  E+   +AFL   
Sbjct: 471 GYI------ETPAVLALKSAG-------RAQFDKIRRRAPIGRLGDPMEVARTIAFLASP 517

Query: 248 DSSFMTGVNLPIAGG 262
            +S++ G  L + GG
Sbjct: 518 AASYVAGATLTVDGG 532


Lambda     K      H
   0.318    0.135    0.384 

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: 309
Number of extensions: 12
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 262
Length of database: 546
Length adjustment: 30
Effective length of query: 232
Effective length of database: 516
Effective search space:   119712
Effective search space used:   119712
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: 50 (23.9 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