Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate PfGW456L13_1889 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1889 Length = 608 Score = 196 bits (497), Expect = 3e-54 Identities = 162/518 (31%), Positives = 255/518 (49%), Gaps = 53/518 (10%) Query: 47 IGILNTWSDMTPCNGHLRELAEKVKAGVWE-------AGGFPLEVPVFSASENTFRPTAM 99 I I+++++DM + E +K + E AGG P + E ++ Sbjct: 68 IAIVSSYNDMLSAHQPYEVFPELIKKALREIGSVGQFAGGTPAMCDGVTQGEPGME-LSL 126 Query: 100 MYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYF 158 R + AL+ A+ DG +LL CDK P L+MGA LP I V GGPM++G Sbjct: 127 PSREVIALSTAVALSHNMFDGALLLGICDKIVPGLMMGALRFGHLPMIFVPGGPMVSGIS 186 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 ++ K++E G+ T+ E LE+E S GTC GTA+T + E +G+ Sbjct: 187 NKQKADVRQ---KYAE----GKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239 Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKD--DLKP-SEIMTKQAFENAIRTNAAIGG 275 L G + + R + + ++ ++ K D P EI+ +++ N+I A GG Sbjct: 240 HLPGASFVNPNTPLRDALTREAAHQVTRLTKQNGDFMPIGEIVDERSLVNSIVALHATGG 299 Query: 276 STNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKR 335 STN +H+ AIA GI L+ D VPT+ ++ P+GK + F AGG+ +++ Sbjct: 300 STNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIRE 359 Query: 336 LGEAGLLHKDALTV---------------SGETVWDE-VKDVVNWNEDVILPAEKALTSS 379 L EAGLLH++ TV +G+ VW E V D + +E ++ P +A ++ Sbjct: 360 LLEAGLLHENVNTVMGHGLSRYTQEPFLDNGQLVWREGVTD--SLDESILRPVARAFSAE 417 Query: 380 GGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDEN 435 GG+ V+ GNL V+K SA + + + A+VF+D D +KA + ++++ Sbjct: 418 GGLRVMEGNLG--RGVMKVSAVAVENQIVEAPAMVFQDQQDLADAFKAGL------LEKD 469 Query: 436 CIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSP 493 + VM+ GP+ GM E+ M VL+ + ++D RMSG A G + +H SP Sbjct: 470 FVAVMRFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSP 527 Query: 494 EAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531 EA VGG LA V+ GD+I +D L L + EE A R Sbjct: 528 EAYVGGALARVQEGDIIRVDGVKGTLELKVDAEEFAAR 565 Lambda K H 0.318 0.135 0.408 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: 769 Number of extensions: 42 Number of successful extensions: 6 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: 579 Length of database: 608 Length adjustment: 37 Effective length of query: 542 Effective length of database: 571 Effective search space: 309482 Effective search space used: 309482 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