Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__psRCH2:GFF835 Length = 608 Score = 193 bits (491), Expect = 1e-53 Identities = 165/528 (31%), Positives = 256/528 (48%), Gaps = 46/528 (8%) Query: 44 IGICNTWSELTPCNAHFRKLAEHVKRGISE-------AGGFPVEFPVFSNGESNLRPSAM 96 + I ++++ + + E +++ + + AGG P + GE + A+ Sbjct: 68 VAIVTAYNDMLSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEPGME-LAI 126 Query: 97 LTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAASCD-VPAIVVSGGPMLNGKL 155 +R + +M A+ N DA +LL CDK P LL+GA +PA+ V GPM +G L Sbjct: 127 ASREVIAMSTAVALSHNLFDAALLLGICDKIVPGLLIGALRFGHLPAVFVPAGPMPSG-L 185 Query: 156 EGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGMSRSAGTCNTMGTASTMACMAEALGV 215 K+ AV Q + KA ++ L+AE S GTC GTA+T + E +G+ Sbjct: 186 ANKD---KAAVRQRYAEGKASRDEL---LAAEMQAYHSPGTCTFYGTANTNQMLMEVMGL 239 Query: 216 ALPHNAAIPAVDSRRYVLAHMSGIRIVEMALEG---LVLSKILTRAAFENAIRANAAIGG 272 LP ++ + R L + ++ + +G L +++ NAI A A GG Sbjct: 240 HLPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGG 299 Query: 273 STNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDLMPSGRFPMEEFYYAGGLPAVLRR 332 STN +H+ AIA G+ L +D + PT+ + P+G + F+ AGG+ ++R Sbjct: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVRE 359 Query: 333 LGEGGLLPNPDALTVNGKSLWDNVRE--------------APNYDEEVIRPLDRPLIADG 378 L GLL + D TV G+ L +E A + DE ++RP+ RP A+G Sbjct: 360 LLAAGLL-HEDVHTVMGRGLSRYTQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEG 418 Query: 379 GIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVMVL 438 G+R++ GNL RG V+K SA +PE A VF D + +A +++ V V+ Sbjct: 419 GLRVMSGNLG-RG-VMKVSAVAPEHRVVEAPARVF--ADQLELVEAFKAGELERDVVAVV 474 Query: 439 KNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVRISDARMSGTAYGTV--VLHVAPEAAAG 496 + GPR GM E+ + LL+ + ++D RMSG A G V +HV PEA G Sbjct: 475 RFQGPRA-NGMPELHKLTPYLGLLQDRGFKVALVTDGRMSG-ASGKVPAAIHVCPEAIDG 532 Query: 497 GPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAGQ 544 GPLA VR+GD + +D +AG L + + EL R P AAP + Q Sbjct: 533 GPLARVRDGDLLRVDGQAGVLEVLVDAAELAGR----SPVAAPAASVQ 576 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: 910 Number of extensions: 58 Number of successful extensions: 5 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