GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Echinicola vietnamensis KMM 6221, DSM 17526

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Cola:Echvi_2055
          Length = 561

 Score =  210 bits (535), Expect = 1e-58
 Identities = 165/528 (31%), Positives = 247/528 (46%), Gaps = 50/528 (9%)

Query: 48  GVAGCGSEDKHSLRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGG 107
           GVA CG E        N  N+ + S              F E IK +  +    G F   
Sbjct: 41  GVASCGYES-------NPCNMHLNS--------------FAEDIKASTNQADLSG-FIFN 78

Query: 108 TPAMCDGVTQGEAGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALR 167
           T  + DG + G +GM  SLPSREVIA S    +  + FD  + +  CDK +PG++MG LR
Sbjct: 79  TIGISDGQSMGTSGMRYSLPSREVIADSIESFILGHSFDGVVTIPGCDKNMPGVVMGMLR 138

Query: 168 FGHLPTIFVPGGPMPSGISNKEKADVRQRYA------EGKATREELLESEMKSYHSPGTC 221
               P I V GG + SG    EK ++   +        G+ + E+ +     +    G C
Sbjct: 139 VNR-PGIMVFGGTIRSGNYKGEKLNIVSAFEAYGKKINGQISDEDYMGVIKNACPGAGAC 197

Query: 222 TFYGTANTNQLLMEVMGLHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQ--SGNFTPIG 279
               TANT    +E MGL LP   F + Y P       E  + + +  KQ  + +  P  
Sbjct: 198 GGMYTANTMSSAIEAMGLSLP---FSSSY-PATSKEKREECKNIGKYIKQLLALDIKP-K 252

Query: 280 EIVDERSLVNSIVALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN 339
           +I+ ++SL N++    A GGSTN  LH+ AIA+ AGI  T +D   ++   P L    P+
Sbjct: 253 DIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETPVLGDFKPS 312

Query: 340 GKADINHFQAAGGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPI 399
           GK  +      GG+   ++  L  GLLH D  TV G+ ++   ++  +D         P+
Sbjct: 313 GKFMMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLED--ID---------PV 361

Query: 400 ESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLAD 459
           +   E+++ P+     P G L V+ GNL            + +     A VF D+     
Sbjct: 362 KPSKESVIHPLDNPIKPSGHLCVLHGNLAPEGAVAKISGKEGKSFTGTAKVFDDEPSANA 421

Query: 460 AFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGK 518
           A K  E++K  V V+R+ GP+   GMPE+ K T  + +    G  VAL+TDGR SG +  
Sbjct: 422 AMKNKEIQKGDVVVIRYVGPKGGPGMPEMLKPTSII-IGAGLGSDVALITDGRFSGGTHG 480

Query: 519 IPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAARE 566
                HV+PEA +GG +  ++DGD+I +D     + + V   EFA R+
Sbjct: 481 FVVG-HVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERK 527


Lambda     K      H
   0.318    0.134    0.386 

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: 830
Number of extensions: 52
Number of successful extensions: 7
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: 608
Length of database: 561
Length adjustment: 36
Effective length of query: 572
Effective length of database: 525
Effective search space:   300300
Effective search space used:   300300
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: 53 (25.0 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