Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate BPHYT_RS25650 BPHYT_RS25650 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >FitnessBrowser__BFirm:BPHYT_RS25650 Length = 588 Score = 298 bits (762), Expect = 5e-85 Identities = 193/542 (35%), Positives = 299/542 (55%), Gaps = 27/542 (4%) Query: 24 YRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAGGFPVEFPV 83 +R++++ G+ D +P + I +T+ E TPC+ +++++V+ GI+ GG P+ Sbjct: 21 HRAFLRATGLDDESMQ-KPFVAIVDTFGENTPCSMSLNQVSDNVRLGIAAGGGVPIRGSA 79 Query: 84 FSNGE------SNLRPSAMLTRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPALLMGAAS 137 S + S +R S +++R + + VE +R + DA++ +AGCDKT P +LMG Sbjct: 80 ISVSDGTSMNHSGMRMS-LVSREVVADSVELFVRAHNYDALIGVAGCDKTLPGILMGMVR 138 Query: 138 CDVPAIVVSGGPMLNGKLEGKNIG-SGTAVWQLHEAL---------KAGEIDVHHFLSAE 187 +VP + + GG ML G G+ G +GT + + L + G++ + E Sbjct: 139 VNVPGVFLFGGAMLPGVAPGQLPGGAGTGLQRQSTILTTIEAVGTTQRGDMSRAQLDAIE 198 Query: 188 AGMSRSAGTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMALE 247 + +AG+C TA+TMA +AE LG+A +A +PAV S R +A +G ++ + + Sbjct: 199 KQCTPTAGSCPGQFTANTMAMVAETLGLAPLGSAMVPAVYSERIAIARRAGETVMRILTQ 258 Query: 248 GLVLSK-ILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRIGRDTPTI 306 G L + ++T + ENA A AA GGSTNA +H+ AIA G+ L+D R+ P I Sbjct: 259 GGPLPRDLVTMESLENACAAVAATGGSTNAALHIPAIANEAGIRFALDDVQRVFAKIPLI 318 Query: 307 VDLMPSGRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSLWDNVREAPNYDEEV 366 DL P GR+ ++ ++AGG+PAVL L GG L + D G +L + + D V Sbjct: 319 GDLQPGGRYLAQDLHHAGGVPAVLNALLAGGFL-HGDVPAFGGGTLAEALSAFSGPDGIV 377 Query: 367 IRPLDRPLIADGGIRILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDE 426 +RP D PL +GG+ ILRGNLAP GA LK A + L G VFE + A + Sbjct: 378 VRPCDEPLGENGGLVILRGNLAPDGACLK--IAGLKSLSFTGAVRVFECEEDCMAVV--A 433 Query: 427 ALDIDASSVMVLKNCGPRGYPGMAEVGNMGLPPKLLRQGVKDMVR-ISDARMSGTAYGTV 485 A D V+V++N GP+G PGM E+ +G+ + QG+ + V ++D R SG G Sbjct: 434 ARDYREGDVLVIRNEGPKGGPGMREM--LGVTAAIYGQGMGEKVALLTDGRFSGATRGMC 491 Query: 486 VLHVAPEAAAGGPLAAVRNGDWIELDCEAGTLHLDITDDELHRRLSDVDPTAAPGVAGQL 545 + +V PEAAAGGP+ +RN D + +D AG L +D++DDEL RR +D A+ +AG L Sbjct: 492 IGYVGPEAAAGGPIGLLRNDDRVHIDARAGILRVDLSDDELARRRADAPARASRRLAGVL 551 Query: 546 GK 547 K Sbjct: 552 EK 553 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: 942 Number of extensions: 54 Number of successful extensions: 7 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: 588 Length adjustment: 37 Effective length of query: 546 Effective length of database: 551 Effective search space: 300846 Effective search space used: 300846 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