GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Herbaspirillum seropedicae SmR1

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate HSERO_RS05485 HSERO_RS05485 phosphoesterase

Query= SwissProt::P0DOW0
         (331 letters)



>FitnessBrowser__HerbieS:HSERO_RS05485
          Length = 345

 Score =  114 bits (284), Expect = 5e-30
 Identities = 97/326 (29%), Positives = 151/326 (46%), Gaps = 22/326 (6%)

Query: 23  EPGWIALRVAGVGICGSELSGYL--GHNELR-KPPLVMGHEFSGVVEEVGHGVTNVKIGD 79
           +P  + ++V   GICGS+L  Y   G   +R K P+V+GHE SG + EVG  VT++  G 
Sbjct: 24  QPQQLKVKVKAGGICGSDLHYYHHGGFGVVRIKEPMVLGHEVSGQIAEVGTAVTDIAPGT 83

Query: 80  LVTANPLVTCGRCIHCLRGERQRCESRRIIGI-----DFPGAYAERVLVPSNQCYAVKDA 134
            +  +P   CG C +C  G++  C   R  G         GA+ + +++  +Q + V D 
Sbjct: 84  RIAISPSRPCGACKYCQEGKQNHCLDMRFYGSAMRTPHVQGAFRQEIIIERSQAHVVADH 143

Query: 135 I---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVDPN 191
           +   + A+ EPL+ A+ AV  A   VG   +V G G IG + V     +GA  + V D  
Sbjct: 144 VSDGEAAMAEPLSVALHAVRRAGPLVGKRVLVTGCGPIGALVVVAARRAGALEVVVTDVA 203

Query: 192 DERLKISQLWGA------TEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRRDSLNALIRG 245
              L+ +   GA       E    L A   D    +FD + +A G       +L AL   
Sbjct: 204 SMPLQAALQVGADSAINMAETPAALKAYAADK--GTFDVLFEASGNERALVGALEALRPQ 261

Query: 246 GRAVWIGLHEALTHLDGNQIVRDELEVRGSFCYTDDEFIRAVSLINSQKFLPVDRQWLDV 305
              V +GL   +     N +V  ELE RG+F +  +EF  AV L+N +K + V       
Sbjct: 262 AIIVQVGLGGDI-QFPANLLVGKELEWRGAFRF-HEEFAMAVELMN-RKLVDVKPLITAT 318

Query: 306 RSLEEGPAAFKELVNGSPFSKIILTF 331
             + +   AF+   + S   K+ ++F
Sbjct: 319 YPIAQAVEAFEIAGDRSRMMKVQISF 344


Lambda     K      H
   0.322    0.139    0.424 

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: 260
Number of extensions: 18
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: 331
Length of database: 345
Length adjustment: 28
Effective length of query: 303
Effective length of database: 317
Effective search space:    96051
Effective search space used:    96051
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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