GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Sinorhizobium meliloti 1021

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate SM_b20115 SM_b20115 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Smeli:SM_b20115
          Length = 573

 Score =  207 bits (526), Expect = 1e-57
 Identities = 159/518 (30%), Positives = 265/518 (51%), Gaps = 48/518 (9%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME-LSL 126
           +AI+++++D+   H  ++H  + +K+ + +       AGG P      +  E+ ++  ++
Sbjct: 41  IAILNTWSDLNPCHAHFKHRIDDVKRGVLQ-------AGGFPVELPVQSLSESSLKPTTM 93

Query: 127 PSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS 186
             R  +A+     L  +  D A+++G CDK  P L+MGA+  G LP IF+P GPM  G  
Sbjct: 94  LYRNFLAMEAEELLRGHPIDGAVLMGGCDKTTPALVMGAISAG-LPMIFLPSGPMLRGHY 152

Query: 187 NKEK----ADVRQRYAEGKA---TREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
             E     +D  + + E +A   T E+ +  E     S G C  +GTA+T   + E +GL
Sbjct: 153 KGEHLGSGSDAWKYWDERRAGTITDEQWIGVEEGIARSYGHCMTFGTASTMTAIAESLGL 212

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG--EIVDERSLVNSIVALHAT 297
            LPGAS +         ++    +++  +  +      +G  +I+ E+S+ N+     AT
Sbjct: 213 TLPGASSIPAADANHIRMSTRCGRRIVEMVHEK-----LGPEKIITEKSVANASAVAMAT 267

Query: 298 GGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADI-NHFQAAGGMAFL 356
           G STN  +H+ A+A+ AG+ LT +D+  +S   P ++++ P+GK  +   F  AGG+  L
Sbjct: 268 GCSTNAVVHLIAMARRAGVPLTLEDLDGISRTTPVIANIRPSGKQYLMEDFYYAGGLRAL 327

Query: 357 IRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSP 416
           + E+ E  LLH D  TV+G  L    +   + N               +++RP++     
Sbjct: 328 MAEMKE--LLHLDAMTVSGFPLGATLEGAEVHNS--------------DVIRPLSNPIYH 371

Query: 417 EGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELE--KDFVA 472
           EG L V++GNL     V+K SA   + ++ E PA+VF    ++  A    +L+   D V 
Sbjct: 372 EGSLAVLKGNLAPDGCVVKPSACEERLRVHEGPALVFDSYPEMKAAIDDEDLDVTPDHVL 431

Query: 473 VMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVAL-VTDGRMSGASGKIPAAIHVSPEAQ 530
           ++R  GP+   GMPE   M P    +  +G++  L ++D RMSG S      +HV+PE+ 
Sbjct: 432 ILRNAGPKGGPGMPEWG-MLPIPKKILKQGYRDMLRISDARMSGTSYGA-CILHVAPESH 489

Query: 531 VGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPA 568
           VGG L+ VR GDIIRVD    T+++ VD +  A R  A
Sbjct: 490 VGGPLSLVRTGDIIRVDVANRTIDMLVDEEILAMRRAA 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: 795
Number of extensions: 47
Number of successful extensions: 8
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: 573
Length adjustment: 37
Effective length of query: 571
Effective length of database: 536
Effective search space:   306056
Effective search space used:   306056
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