Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate PP_1010 PP_1010 phosphogluconate dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__Putida:PP_1010 Length = 608 Score = 200 bits (508), Expect = 2e-55 Identities = 158/516 (30%), Positives = 248/516 (48%), Gaps = 48/516 (9%) Query: 44 IGICNTWSELTPCNAHFRKLAEHVKRGISE-------AGGFPVEFPVFSNGESNLRPSAM 96 + I + ++++ + + E +K+ + E AGG P + GE + A+ Sbjct: 68 VAIVSAYNDMLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEPGME-LAI 126 Query: 97 LTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASCD-VPAIVVSGGPMLNGKL 155 +R + +M A+ N DA ++L CDK P L+MGA +P I V GGPM++G Sbjct: 127 ASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGI- 185 Query: 156 EGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGMSRSAGTCNTMGTASTMACMAEALGV 215 S + + G+ L +E S GTC GTA+T + E +G+ Sbjct: 186 ------SNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGTANTNQLVMEVMGL 239 Query: 216 ALPHNAAIPAVDSRRYVLAHMSGIRIVEMALEG---LVLSKILTRAAFENAIRANAAIGG 272 LP + + R L + ++ M + L +I+ A N+I A A GG Sbjct: 240 HLPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGG 299 Query: 273 STNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDLMPSGRFPMEEFYYAGGLPAVLRR 332 STN +H+ AIA G+ L +D + PT+ + P+G+ + F AGG+ ++R Sbjct: 300 STNHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359 Query: 333 LGEGGLLPNPDALTV---------------NGKSLWDNVREAPNY--DEEVIRPLDRPLI 375 L + GLL + D TV NGK +W RE P + DE ++RP+ RP Sbjct: 360 LLDAGLL-HEDVNTVAGHGLRRYTQEPFLDNGKLVW---REGPQHSLDESILRPVSRPFS 415 Query: 376 ADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSV 435 A+GG+R++ GNL RG V+K SA +PE A VF+ D +A +++ V Sbjct: 416 AEGGLRVMEGNLG-RG-VMKVSAVAPEHQVVEAPARVFQ--DQQSLADAFKAGELERDFV 471 Query: 436 MVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGTAYGTV--VLHVAPEA 493 V++ GPR GM E+ + +L+ + ++D RMSG A G + +HV PEA Sbjct: 472 AVVRFQGPR-CNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSG-ASGKIPAAIHVCPEA 529 Query: 494 AAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRR 529 GGPLA VR+GD + +D GTL + ++ +EL R Sbjct: 530 YDGGPLARVRDGDIVRVDGVEGTLRIMVSAEELASR 565 Lambda K H 0.319 0.136 0.412 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: 827 Number of extensions: 46 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: 583 Length of database: 608 Length adjustment: 37 Effective length of query: 546 Effective length of database: 571 Effective search space: 311766 Effective search space used: 311766 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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