GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Dinoroseobacter shibae DFL-12

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate 3609257 Dshi_2643 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding (RefSeq)

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__Dino:3609257
          Length = 316

 Score =  224 bits (570), Expect = 3e-63
 Identities = 124/321 (38%), Positives = 186/321 (57%), Gaps = 9/321 (2%)

Query: 4   KVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKELLE 63
           K+ I+R +PE  +      ++  L +  +      L   +R+ D ++  + D    E+  
Sbjct: 2   KLLISRPLPEAVLARARARFDCTLRETTQPMRAEELRGALRDYDLVLPTLGDAFSAEVFA 61

Query: 64  NAP--KLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIVE 121
           + P  + +++A + VGY++ID   A   G+ VTNTPG +TDATAD A  L+L  ARR  E
Sbjct: 62  DVPEPRARLLANFGVGYNHIDAVAARAAGVAVTNTPGAVTDATADTALTLILMAARRAGE 121

Query: 122 ADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAK-GFGMKIIYYS 180
            +  VR+G W     GWHP   LG  + GKTLG++G GRIGQA+A R   GFGM++++Y+
Sbjct: 122 GERLVRAGTW----TGWHPTQMLGLHVTGKTLGVIGMGRIGQAIAARCHHGFGMEVVFYN 177

Query: 181 RTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTS 240
           R+  P+  +    +      ++  +D + + VP   ET+H+IG +    M+P+A+ +N +
Sbjct: 178 RS--PKTPDLPARQLASVAEVMAAADIVVVAVPGGAETHHLIGAEAFAAMQPHAVFVNIA 235

Query: 241 RGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGM 300
           RG VVD  ALI AL+ G +  AGLDV+E EP   E L  ++NVVL PH+G+A  E RE M
Sbjct: 236 RGDVVDEAALIAALQAGQLGAAGLDVYEFEPAVPEALIGMENVVLLPHLGTAALEVREAM 295

Query: 301 AELVAKNLIAFAKGEIPPNLV 321
             +   NLIA A+G   PN V
Sbjct: 296 GHMALDNLIACAEGAPLPNPV 316


Lambda     K      H
   0.317    0.137    0.392 

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: 244
Number of extensions: 12
Number of successful extensions: 4
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: 316
Length adjustment: 28
Effective length of query: 303
Effective length of database: 288
Effective search space:    87264
Effective search space used:    87264
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: 48 (23.1 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