Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__SynE:Synpcc7942_0626 Length = 619 Score = 214 bits (546), Expect = 7e-60 Identities = 173/558 (31%), Positives = 266/558 (47%), Gaps = 53/558 (9%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+ +S+ + H + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAK-EFNTIAVDDGIAMGHGGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--I 185 SR++IA S ++ + DA + + CDKI PG++M ALR ++P +FV GGPM +G I Sbjct: 96 SRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRL-NIPAVFVSGGPMEAGKVI 154 Query: 186 SNKEK-----ADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 N E+ D A+ + + E++ E + + G+C+ TAN+ L E +GL Sbjct: 155 LNGEERHLDLVDAMVVAADDRESDEDVATIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLV------NSIVAL 294 LPG + R L EA + +L KQ + E V RS+ N+I Sbjct: 215 LPGNGSLLATHGDRKELFLEAGRLAVKLAKQ--YYEQDDESVLPRSIASFKAFENAICLD 272 Query: 295 HATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGM 353 A GGSTN LH+ A A AG+ T +D+ LS +P L V P+ K + AGG+ Sbjct: 273 IAMGGSTNTVLHLLAAAHEAGVDFTMKDIDRLSRKIPNLCKVAPSTQKYHMEDVHRAGGV 332 Query: 354 AFLIRELLEAGLLHEDVNTVAGRGL-------------------SRY--------TQEPF 386 ++ EL AGLLH +V TV L SRY TQE F Sbjct: 333 IAILGELDRAGLLHREVPTVHSPSLGAALDQWDINRETATEEAKSRYLAAPGGVPTQEAF 392 Query: 387 LDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIV 444 + + W ++ + +R + A+S +GGL V+ GNL ++K + V + Sbjct: 393 SQSKR--WTALDLDR-ENGCIRDIEHAYSQDGGLAVLYGNLAEQGCIVKTAGVDENILVF 449 Query: 445 EAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFK 503 PAVV + Q + + G +++ V ++R++GPR GM E+ T +L + G Sbjct: 450 SGPAVVCESQDEAVNWILNGRVKEGDVVLIRYEGPRGGPGMQEMLYPTSYL-KSKGLGKA 508 Query: 504 VALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFA 563 AL+TDGR SG + + HVSPEA GG +A V GD I +D + L V +E A Sbjct: 509 CALITDGRFSGGTSGLSIG-HVSPEAAEGGLIALVEQGDRIEIDIPNRRIHLAVSEEELA 567 Query: 564 AREPAKGLLGNNVGSGRE 581 R A G+ + ++ Sbjct: 568 HRRAAMEARGDQAWTPKD 585 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: 924 Number of extensions: 50 Number of successful extensions: 9 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: 619 Length adjustment: 37 Effective length of query: 571 Effective length of database: 582 Effective search space: 332322 Effective search space used: 332322 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