Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_007677372.1 BN137_RS05280 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_000319285.1:WP_007677372.1 Length = 616 Score = 220 bits (560), Expect = 2e-61 Identities = 172/551 (31%), Positives = 267/551 (48%), Gaps = 42/551 (7%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+V+S+ + H + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVVNSFTQFVPGHVHLRDLGKLVAEQIEAAGGVAK-EFNTIAVDDGIAMGHGGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SRE+IA S ++ + DA + + CDKI PG++M +LR ++P IFV GGPM +G Sbjct: 96 SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASLRL-NIPVIFVSGGPMEAGKTK 154 Query: 185 ----ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 I + D + A + E+ + E + + G+C+ TAN+ L E +GL Sbjct: 155 LSDQIIKLDLVDAMIQGANPHVSDEQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIG----EIVDERSLVNSIVALHA 296 PG + R L A +++ LTK+ + I + + N++ A Sbjct: 215 QPGNGSLLATHADRKDLFINAGKRIVSLTKRYYEQDDVSALPRNIASKAAFENAMTLDIA 274 Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAF 355 GGSTN LH+ A AQ A I T D+ LS VP L V P+ K + AGG+ Sbjct: 275 MGGSTNTVLHLLAAAQEAEIDFTMSDIDRLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIG 334 Query: 356 LIRELLEAGLLHEDVNTVAG----RGLSRYTQEPFLDNG-KLVWRDGPI----------- 399 ++ EL AGL++ DVN V G + L +Y D+ K ++R GP Sbjct: 335 ILGELDRAGLMNRDVNNVLGLTLPQTLEQYDVMLTQDSAVKEMFRAGPAGIRTTQAFSQS 394 Query: 400 ---ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVV 450 ++LD E +R + A+S +GGL V+ GN ++K + V + PA V Sbjct: 395 CRWDTLDDDRQEGCIRSLEHAYSQDGGLAVLYGNFAENGCIVKTAGVDEGSLVFRGPAKV 454 Query: 451 FQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTD 509 ++ Q D +A G++ V V+R++GP+ GM E+ T FL + G AL+TD Sbjct: 455 YESQDDAVEAILGGKVVAGDVVVIRYEGPKGGPGMQEMLYPTSFLKSM-GLGKACALITD 513 Query: 510 GRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAK 569 GR SG + + HVSPEA GG +A + DGD+I +D ++L+V + AAR A+ Sbjct: 514 GRFSGGTSGLSIG-HVSPEAASGGNIALIEDGDMIAIDIPNRGIQLEVSDQQLAARREAQ 572 Query: 570 GLLGNNVGSGR 580 G + + R Sbjct: 573 EARGADAWTPR 583 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: 917 Number of extensions: 41 Number of successful extensions: 10 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: 616 Length adjustment: 37 Effective length of query: 571 Effective length of database: 579 Effective search space: 330609 Effective search space used: 330609 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