Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_012385788.1 BIND_RS14465 phosphogluconate dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >NCBI__GCF_000019845.1:WP_012385788.1 Length = 613 Score = 191 bits (484), Expect = 1e-52 Identities = 143/465 (30%), Positives = 228/465 (49%), Gaps = 36/465 (7%) Query: 74 AGGFPVEFPVFSNGESNLRPSAMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLM 133 AGG P + GE+ + S + +R++ ++ A+ DA V L CDK P L++ Sbjct: 111 AGGVPAMCDGITQGEAGMELS-LFSRDVIALSTAVALSHQTFDAAVYLGICDKIVPGLVI 169 Query: 134 GAASCD-VPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGMSR 192 GA S +PA+ + GPM +G + ++ + G++D L EA Sbjct: 170 GALSFGHLPAVFIPSGPMTSGVPNSEKA-------KVRQLFAEGKVDRAALLDIEAKSYH 222 Query: 193 SAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMALEG---L 249 GTC GTA+T + E +G+ LP ++ + R L + R + + G Sbjct: 223 GVGTCTFYGTANTNQMLMEIMGLHLPGSSFVTPNTPLRQALTRAAAERAMAITTFGNDYT 282 Query: 250 VLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTIVDL 309 + ++L AF N I A GGSTN +HL A+A G+ L+ +D+ + TP + + Sbjct: 283 PIGRMLDERAFINGIVGLNATGGSTNHTLHLVAMAAAAGLTLDWQDFADLAEVTPLLTRI 342 Query: 310 MPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVRE----------- 358 P+G + F+ AGG+ ++R L GLL + +A TV G+SL V+E Sbjct: 343 YPNGTADVNHFHAAGGMGFLIRELIGAGLL-HKNATTVFGQSLGSYVQEPWLDADGALAW 401 Query: 359 ----APNYDEEVIRPLDRPLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFE 414 A DE ++R +D+P GG+R+L G+L AV+K SA + E A +F Sbjct: 402 RDGAAKTGDETILRGVDKPFQPTGGLRVLNGDLG--RAVIKTSAVAAERHVIEAPARIFH 459 Query: 415 NLDHYKATINDEALDIDASSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVRISD 474 + + + +A +++ + V++ GP+ GM E+ + P +L+ + ++D Sbjct: 460 SQEALQTAF--KAGELEQDFIAVVRFQGPKAI-GMPELHKLMPPLGILQDRGFKVALVTD 516 Query: 475 ARMSGTAYGTV--VLHVAPEAAAGGPLAAVRNGDWIELDCEAGTL 517 R+SG A G V +HV PEAA GGP+A VR GD I LD AGTL Sbjct: 517 GRLSG-ASGKVPSAIHVTPEAAEGGPIAKVREGDLIRLDAVAGTL 560 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: 840 Number of extensions: 54 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: 613 Length adjustment: 37 Effective length of query: 546 Effective length of database: 576 Effective search space: 314496 Effective search space used: 314496 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 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