Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_047213238.1 PATSB16_RS06380 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_001931675.1:WP_047213238.1 Length = 620 Score = 197 bits (502), Expect = 8e-55 Identities = 160/542 (29%), Positives = 254/542 (46%), Gaps = 45/542 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+V+S+ + H + K + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVVNSFTQFVPGHVHLRDLGALVAKQIEAAGGVAK-EFNTIAVDDGIAMGHGGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SRE+IA S ++ + DA + + CDKI PG++M A+R ++P +FV GGPM +G Sbjct: 96 SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGKVK 154 Query: 185 -------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVM 237 I+ + D + A+ K + E+ E E + + G+C+ TAN+ L E + Sbjct: 155 SPADGQVIAKIDLIDAMIKAADPKVSDAEIAEVERSACPTCGSCSGMFTANSMNCLTEAI 214 Query: 238 GLHLPGASFVNPYTPLRDALTHEAAQQVTRLTK---QSGNFTPIGEIVDERSLVNSIVAL 294 GL LPG + R L +A + V L + Q + + + + ++ + ++L Sbjct: 215 GLALPGNGTIVATHAWRRGLFEQAGRLVVDLCRRYYQEEDASVLPRSIATKAAFENAMSL 274 Query: 295 H-ATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGG 352 A GGSTN LH+ A AQ AG+ T D+ +S VP L V P+ K I AGG Sbjct: 275 DVAMGGSTNTVLHLLAAAQEAGVDFTMSDIDRISRRVPCLCKVAPSTDKYHIEDVHRAGG 334 Query: 353 MAFLIRELLEAGLLHEDVNTV----AGRGLSRYTQEPFL-DNGKLVWRDGP--------- 398 + ++ EL A LL +V G ++++ + + +R P Sbjct: 335 IMGILGELARAELLDLSCGSVHSGTLGEAIAKWDVAGEAGEEAQKFYRAAPGGIPTTVAF 394 Query: 399 -----IESLDEN----ILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAP 447 ++LD + +R A+S +GGL V+ GNL ++K + V + Sbjct: 395 SQEAVFDALDTDRNTGCIRSKQSAYSKDGGLAVLYGNLAEKGCIVKTAGVDESQWVFSGR 454 Query: 448 AVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVAL 506 A VF+ Q D +A ++ V V+R++GP+ GM E+ T +L + G AL Sbjct: 455 ARVFESQDDAVEAILGDKVVAGDVVVIRYEGPKGGPGMQEMLYPTSYLKS-KGLGKTCAL 513 Query: 507 VTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAARE 566 TDGR SG S + H SPEA GG + V +GD+I +D + + L V A+R Sbjct: 514 FTDGRFSGGSSGLVIG-HASPEAAEGGTIGLVEEGDVIEIDIPQRKMHLAVSDQVLASRR 572 Query: 567 PA 568 A Sbjct: 573 AA 574 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: 871 Number of extensions: 43 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 608 Length of database: 620 Length adjustment: 37 Effective length of query: 571 Effective length of database: 583 Effective search space: 332893 Effective search space used: 332893 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