GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Sphingomonas koreensis DSMZ 15582

Align Glyoxylate reductase; EC 1.1.1.26 (characterized)
to candidate Ga0059261_2669 Ga0059261_2669 Lactate dehydrogenase and related dehydrogenases

Query= SwissProt::Q9C4M5
         (331 letters)



>FitnessBrowser__Korea:Ga0059261_2669
          Length = 318

 Score =  244 bits (624), Expect = 2e-69
 Identities = 137/317 (43%), Positives = 187/317 (58%), Gaps = 7/317 (2%)

Query: 2   KPKVFITRQIPENGIKMIEKFYEIELWKDPKAPPRGVLLEKVREVDALVTLVTDKVDKE- 60
           +P++ +TR+ PE     +   Y++   +   +     L + +RE DAL   VTD++ ++ 
Sbjct: 3   RPRILLTRRWPEAVEARLAARYDVTRNETDMSMDAAALAQAMREHDALCPTVTDRITRDV 62

Query: 61  LLENAPKLKIIAQYAVGYDNIDIEEATKRGIYVTNTPGVLTDATADLAFALLLAVARRIV 120
           +L    + +II  Y  G+++ID++ A + GI VTNTP VLTDATAD+A  L+L   RR  
Sbjct: 63  ILTEGRRARIIGNYGAGFEHIDLDAAREAGIAVTNTPDVLTDATADIAMTLILMATRRAG 122

Query: 121 EADAFVRSGEWKKSEVGWHPLMFLGYGLKGKTLGIVGFGRIGQALAKRAKGFGMKIIYYS 180
           E +  +R+GEW     GW P   LG  L+GK LG+VG+GRI +A+A RAK FGMKI  +S
Sbjct: 123 EGERELRAGEW----TGWRPTHLLGRSLRGKVLGLVGYGRIARAVADRAKAFGMKIAVHS 178

Query: 181 RTRKPEAEEEIGAEYVDFETLLKESDFISLHVPLTKETYHMIGEKELKLMKPNAILINTS 240
           R+R  +  E     +   ++LL  +D +SLH P    T HMI    L  MK +A+L+NT 
Sbjct: 179 RSRAEDVPET--DYHASLQSLLSIADVVSLHAPGGAATRHMIDAAALSAMKRDAVLVNTG 236

Query: 241 RGAVVDTNALIKALKEGWIAGAGLDVFEEEPYYNEELFKLKNVVLAPHIGSATHEAREGM 300
           RG ++D  AL +ALK G IA AGLDV+E EP     L  L N VL PH GSAT E RE M
Sbjct: 237 RGTLIDEAALAEALKVGTIAAAGLDVYEREPAVEAALIDLPNAVLLPHFGSATLETREAM 296

Query: 301 AELVAKNLIAFAKGEIP 317
              VA NL AF  G  P
Sbjct: 297 GMKVADNLDAFFAGHEP 313


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: 249
Number of extensions: 10
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: 318
Length adjustment: 28
Effective length of query: 303
Effective length of database: 290
Effective search space:    87870
Effective search space used:    87870
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.

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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