Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_955 Length = 619 Score = 209 bits (531), Expect = 4e-58 Identities = 181/595 (30%), Positives = 274/595 (46%), Gaps = 68/595 (11%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+V+S+ + H + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SR++IA S ++ + DA + + CDKI PG++M A+R ++P IFV GGPM +G Sbjct: 96 SRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPVIFVSGGPMEAGKTR 154 Query: 185 ----------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLM 234 + D A+ + ++ E E + + G+C+ TAN+ L Sbjct: 155 LANPVTKVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFTANSMNCLT 214 Query: 235 EVMGLHLPGASFVNPYTPLRDALTHEAAQQVTRLTKQ---SGNFTPIGEIVDERSLVNSI 291 E +GL LPG V R+ L A +++ L KQ + + V ++ N++ Sbjct: 215 EALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEQDDERVLPRSVGFKAFENAM 274 Query: 292 VALHATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAA 350 A GGSTN LH+ AIA A I T D+ LS VVP L V PN K I A Sbjct: 275 TLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVHRA 334 Query: 351 GGMAFLIRELLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLV----------WRDGPI- 399 GG+ ++ EL AG LH DV TV T + LD +V + GP Sbjct: 335 GGIMAILGELDRAGKLHTDVPTV-----HTATLKDALDQWDIVRTQDEAVRTFYMAGPAG 389 Query: 400 -------------ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQ 440 SLD E +R AFS EGGL V+ GN+ V+K + V Sbjct: 390 VPTQVAFSQATRWPSLDLDRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDES 449 Query: 441 HQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQD 499 + E A V + Q + A +++ V ++R++GP+ GM E+ T ++ + Sbjct: 450 ILVFEGTAHVTESQDEAVANILADKVQAGDVVIVRYEGPKGGPGMQEMLYPTSYI-KSKG 508 Query: 500 RGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDA 559 G AL+TDGR SG + + H SPEA GGA+ V++GD IR+D T+ + V Sbjct: 509 LGKACALLTDGRFSGGTSGLSIG-HCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSD 567 Query: 560 DEFAAREPAKGLLG--------NNVGSGRELFGFMRMAFSSAEQGASAFTSALEN 606 +E A R A+ G V + + + + M SA++GA S LE+ Sbjct: 568 EELAKRREAQNAKGWKPAQPRPRKVSAALKAYAKLVM---SADKGAVRDLSLLED 619 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: 869 Number of extensions: 50 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 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