Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_037456692.1 N825_RS21145 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_000576635.1:WP_037456692.1 Length = 571 Score = 186 bits (472), Expect = 2e-51 Identities = 151/513 (29%), Positives = 247/513 (48%), Gaps = 45/513 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGME-LSL 126 + I ++++++ + + E IKK + E AGG P ++ GE+ M ++ Sbjct: 41 IGICNTFSELTPCNAHFRQLIEHIKKGVLE-------AGGVPFEFPVLSCGESNMRPTAM 93 Query: 127 PSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS 186 R + ++ ++ N D +++ CDK P L+MGA LP+I + GGPM +G Sbjct: 94 LFRNLASMDVEESIRANPIDGVVLMAGCDKTTPSLLMGAASCD-LPSIVISGGPMLNGKF 152 Query: 187 NKEK----ADVRQRYAE----GKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMG 238 + DV R++E G +R + L +E SPG C GTA+T + E +G Sbjct: 153 RGQDIGSGTDV-WRFSEEVRAGVMSRADFLAAENAMSRSPGHCMTMGTASTMASMAEALG 211 Query: 239 LHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATG 298 + LPG + R L +++ + + + I+ + N++ A G Sbjct: 212 VALPGNAAYPAVDAHRARLARMTGRRIVGMVDED---LRLSHILTRDAFANAVKVNGAIG 268 Query: 299 GSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIR 358 GSTN +H+ AIA G + T D + VPT+ ++ P+G+ + F AGG+ L++ Sbjct: 269 GSTNAVVHLLAIAGRVGTEFTLDDWDRWGQGVPTILNLMPSGRYLMEDFCYAGGLPALMK 328 Query: 359 ELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEG 418 E+ AGLL D TV+GR + + E+ + +++RP+A+A EG Sbjct: 329 EI--AGLLKLDAPTVSGRTVGENIE--------------AAENFNPDVIRPMAQALVAEG 372 Query: 419 GLRVMEGNLG--RGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKD--FVAVM 474 G+ V++GNL ++K SA + E AVVF +D +L+ D V V+ Sbjct: 373 GIAVLKGNLAPDGAIIKPSAASPHLMRHEGRAVVFDTIEDYKRKVDDPDLDIDETCVMVL 432 Query: 475 RFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEAQVG 532 R GP+ GM E+ M +L+ + ++D RMSG A G + +H +PEA +G Sbjct: 433 RNCGPKGYPGMAEVGNMALPRKLLEKGVRDMVRISDARMSGTAFGTV--ILHTAPEAAIG 490 Query: 533 GALARVRDGDIIRVDGVKGTLELKVDADEFAAR 565 G LA V DGDII VD T+ L+V +E R Sbjct: 491 GTLALVADGDIIAVDVAARTIHLRVSDEELERR 523 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: 831 Number of extensions: 37 Number of successful extensions: 6 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: 571 Length adjustment: 37 Effective length of query: 571 Effective length of database: 534 Effective search space: 304914 Effective search space used: 304914 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 24 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