Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)
Query= reanno::BFirm:BPHYT_RS19730 (577 letters) >FitnessBrowser__ANA3:7024978 Length = 608 Score = 208 bits (530), Expect = 4e-58 Identities = 164/516 (31%), Positives = 263/516 (50%), Gaps = 44/516 (8%) Query: 47 IGICNTWSELTPCNAHFRELAEYVKKGVHE-------AGGLPLEFPVMSLGETNLRPTAM 99 IGI ++++ + + E +KK E AGG+P ++ G+ + ++ Sbjct: 68 IGIITAFNDMLSAHQPYETYPELLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGME-LSL 126 Query: 100 LFRNLASMDVEESIRGNPMDGVILLVGCDKTTPALLMGAASC-NLPALAVSGGPMLNGRF 158 L R + +M + N DG +LL CDK P LL+GA S +LP L V GPM +G Sbjct: 127 LSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIP 186 Query: 159 RGKNIGSGTGVWQMSEEVRAGTMTQEEFTEAESCMNRSRGHCMTMGTASTMASMVESLGM 218 + ++ ++ G + + + EAE+ S G C GTA++ M+E +G+ Sbjct: 187 NKEKA-------RIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGL 239 Query: 219 GLPHNAAIPAVDARRQVLAHLAGR---RIVDMVREDLTMDKILTRQAFENAIRTNAAIGG 275 LP ++ + D R+ L +A + R+ ++ + + +++ ++ N I A GG Sbjct: 240 QLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSVVNGIVALLATGG 299 Query: 276 STNAVVHLIALAKRIGVELSLEDW-ELGSNVPCLVNLQPSGEYLMEDFYYAGGLPAVLKQ 334 STN +H++A A+ G+ ++ +D+ EL VP L + P+G + F+ AGG+ ++K+ Sbjct: 300 STNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKE 359 Query: 335 LGEQGLLHKEALTVNG----------KTLWDNVR----NAANYDEKVITTFAEPFKPKAG 380 L + GLLH++ TV G K L +R + D +V+T+ A PF+ G Sbjct: 360 LLDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGG 419 Query: 381 IAVLKGNLAPNGAVIKPSAATASLLKHRGRAVVFENIEELHAKIDDESLDIDEHCIMVLK 440 + +LKGNL AVIK SA AVV ++ +L A +LD D C++V+K Sbjct: 420 LKLLKGNLGR--AVIKVSAVQEKHRVVEAPAVVIDDQNKLDALFKSGALDRD--CVVVVK 475 Query: 441 GAGPKGYPGFAEVGNM-PLPKKVLQKGITDMVRISDGRMSGTAYGAV--VLHVSPEAAAG 497 G GPK G E+ + PL + KG + ++DGRMSG A G V +H++PEA G Sbjct: 476 GQGPKAN-GMPELHKLTPLLGSLQDKGFK-VALMTDGRMSG-ASGKVPAAIHLTPEAIDG 532 Query: 498 GPLAFVQTGDMIELDVEERRLHLDVTDEELARRRAA 533 G +A VQ GD+I +D L L V+D ELA R AA Sbjct: 533 GLIAKVQDGDLIRVDALTGELSLLVSDAELAARTAA 568 Lambda K H 0.318 0.135 0.401 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: 772 Number of extensions: 39 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 577 Length of database: 608 Length adjustment: 37 Effective length of query: 540 Effective length of database: 571 Effective search space: 308340 Effective search space used: 308340 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