Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_057508546.1 ABB28_RS10335 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_001431535.1:WP_057508546.1 Length = 611 Score = 202 bits (514), Expect = 3e-56 Identities = 180/583 (30%), Positives = 267/583 (45%), Gaps = 53/583 (9%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +AI +S+ + H + + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAIANSFTQFVPGHVHLKDLGQLVAREIEQAGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISN 187 SRE+IA S ++ + DA + + CDKI PG++M ALR +P IFV GGPM +G + Sbjct: 96 SREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRL-DIPVIFVSGGPMEAGKTK 154 Query: 188 KEK-----ADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242 + D A+ A+ E++ E E + + G+C+ TAN+ L E +GL LP Sbjct: 155 LSEHKLDLVDAMVIAADDSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLP 214 Query: 243 GASFVNPYTPLRDALTHEAAQQVTRLTK-----QSGNFTPIGEIVDERSLVNSIVALHAT 297 G R+ L A + + L + P G I + N++ A Sbjct: 215 GNGTTLATHADREMLFRRAGRVIVELCHRWYGGEDPRALPSG-IATAAAFGNAMTLDIAM 273 Query: 298 GGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAFL 356 GGSTN LH+ A AQ G+ + LS VP L V PN + I AGG+ + Sbjct: 274 GGSTNTILHLLAAAQEGGVDFDLTHIDALSRRVPQLCKVAPNTPQYHIEDVHRAGGVFGI 333 Query: 357 IRELLEAGLLHEDVNTVAGRGLS---RYTQEPFLDNGKL--VWRDGPI------------ 399 + EL AGLL V TV L+ + D+ K+ + GP Sbjct: 334 LGELDRAGLLDTSVPTVHSPSLADALKRWDATLTDDAKVHEFFAAGPAGIPTQVAFSQAT 393 Query: 400 --ESLD----ENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPAVVF 451 SLD E +R + A+S EGGL V+ GNL V+K + V + E A VF Sbjct: 394 RWPSLDLDRAEGCIRSLQHAYSLEGGLAVLRGNLAVDGCVVKTAGVDESIHVFEGNARVF 453 Query: 452 QDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVTDG 510 + Q A +++ V V+R++GP+ GM E+ T +L + G + AL+TDG Sbjct: 454 ESQDAAVAGILADQVKPGDVVVIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKQCALLTDG 512 Query: 511 RMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREPAKG 570 R SG + + HVSPEA GG + V DGD IR+D + L VD A R A Sbjct: 513 RFSGGTSGLSIG-HVSPEAASGGVIGLVHDGDRIRIDIPARGITLLVDDATLAERRAAAD 571 Query: 571 LLG--------NNVGSGRELFGFMRMAFSSAEQGASAFTSALE 605 G V S + + + +SA++GA T+ L+ Sbjct: 572 ARGWKPLEARPRKVTSALKAYALLA---TSADKGAVRNTALLD 611 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: 927 Number of extensions: 56 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: 611 Length adjustment: 37 Effective length of query: 571 Effective length of database: 574 Effective search space: 327754 Effective search space used: 327754 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