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.
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:
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