Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)
Query= reanno::pseudo6_N2E2:Pf6N2E2_609 (578 letters) >FitnessBrowser__Korea:Ga0059261_0354 Length = 608 Score = 186 bits (473), Expect = 2e-51 Identities = 156/532 (29%), Positives = 247/532 (46%), Gaps = 43/532 (8%) Query: 44 IGICNTWSELTPCNAHFRQIAEHVKRGVIEAG-------GFPVEFPVFSNGESNLRPTAM 96 IGI ++++ +A + + E +K +EAG G P + G + + ++ Sbjct: 71 IGIVTAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQGYAGME-LSL 129 Query: 97 LTRNLASMDVEEAIRGNPIDGVVLLTGCDKTTPALLMGAASCD-VPAIVVTGGPMLNGKH 155 +R+ +M A+ N +G LL CDK P LLMGA +P +++ GG M G Sbjct: 130 FSRDTIAMSTAVALSHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIPGGAMPTGIA 189 Query: 156 KGQDIGSGTVVWQLSEQVKAGTITIDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGT 215 + ++ E G + ++ L +E GTC GTA++ M EA+G Sbjct: 190 NKEKA-------RVRELYAEGKASREELLDSEIAAYHGKGTCTFYGTANSNQMMVEAMGL 242 Query: 216 SLPHNAAIPAVDARRYVLAHMSGMRAVEM---VREDLKLSKILTKEAFENAIRVNAAIGG 272 +P A I R L + R E+ + + +I+ + A NA V A GG Sbjct: 243 HMPGAAFIHPGTKLRQALTRAAVQRLPEIGWDSNDYRPIGEIVDERAIVNAAVVLLATGG 302 Query: 273 STNAVIHLKAIAGRIGVQLDLDDWTRIGRGMPTIVDLQPSGRFLMEEFYYAGGLPAVLRR 332 STN +IHL AIA GV +D DD+ R+ R +P + + P+G + F AGG V+R Sbjct: 303 STNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGFEDAGGPTFVIRE 362 Query: 333 LGEANLIPHPNALTVSGKSIGENTK------DAPIY-------GQDEVIRTLDNPIRADG 379 L + ++ H + LTV+G S+ + + D ++ G D ++RT+D P +G Sbjct: 363 LIKGGVL-HGDTLTVAGDSLADYVRRPVLEDDTLVWKDHGAKSGDDSILRTIDAPFSEEG 421 Query: 380 GICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVDASSILVM 439 G +L GNL A +K SA + VF E + ELD D ++V+ Sbjct: 422 GFRILSGNLG--RACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDV--VVVV 477 Query: 440 KNCGPKGYPGMAEVGNMGLPAKLLAQGVTDMVRISDARMSGTAYGTV--VLHVAPEAAAG 497 + GP+ GM E+ + P +L + ++D RMSG A G V +H++PEA G Sbjct: 478 RFQGPRA-NGMPELHKLTPPLGVLQNKGFRVALVTDGRMSG-ASGKVPAAIHLSPEAIGG 535 Query: 498 GPLAAVKEGDWIELDCTSGRLHLDIPDAELAARLADIVPPQQLLVGGYRQLY 549 GP+ +++GD + L G L + AE AR PP L G R+L+ Sbjct: 536 GPIGKLRDGDVVRLCAEEGILQALVEPAEWEARELAAAPPPDLGTG--RELF 585 Lambda K H 0.319 0.136 0.409 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: 874 Number of extensions: 50 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: 578 Length of database: 608 Length adjustment: 37 Effective length of query: 541 Effective length of database: 571 Effective search space: 308911 Effective search space used: 308911 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 (21.8 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