Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate WP_011841248.1 RSPH17029_RS09155 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000015985.1:WP_011841248.1 Length = 593 Score = 457 bits (1175), Expect = e-133 Identities = 254/552 (46%), Positives = 344/552 (62%), Gaps = 20/552 (3%) Query: 9 RKLRSQEWYGGTSRD---VIYHRGWLKNQGYPHDLFDG-RPVIGILNTWSDMTPCNGHLR 64 R+ RSQ W+ +Y + +NQG+ G RP+IGI + SD+ PCN Sbjct: 8 RRFRSQAWFDNPDNPGMTALYVERY-QNQGFTRRELQGDRPIIGIAQSGSDLAPCNKIHL 66 Query: 65 ELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLL 124 LAE+VKAG+ +AGG P+E PV E RPTA + RNLA L + E + G P+DG VL Sbjct: 67 FLAERVKAGIRDAGGVPMEFPVHPIQETGRRPTAALDRNLAYLGLVEVLHGYPIDGVVLT 126 Query: 125 VGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQA 184 GCDKTTP+ LM AA+ DLPSIV++G PML+G++ G+ GSGT +W+ ++ GE+ Sbjct: 127 TGCDKTTPAQLMAAATVDLPSIVLSGWPMLDGWWEGKLAGSGTIIWESRRLLAEGEIDYP 186 Query: 185 EFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRI 244 EF+E + + S G CNTMGTAST+ ++AEALGM+L G +AIP R MA TGRRI Sbjct: 187 EFMERACASAPSLGHCNTMGTASTLNALAEALGMSLPGCSAIPAPFRERMNMAYATGRRI 246 Query: 245 VQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGR 304 V+MV DLKPS+I+T+QAFENAIR N+AIGGSTNA HL AIA G++L+++DW G Sbjct: 247 VEMVLADLKPSDILTRQAFENAIRVNSAIGGSTNAPPHLQAIARHAGVELAVEDWQTVGF 306 Query: 305 DVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNW 364 D+P +VN+ P+G+YL E FF AGG+P V+ L AGLLH +ALTV+GE++ + + Sbjct: 307 DLPLLVNMQPAGEYLGESFFRAGGVPAVMGELLAAGLLHAEALTVTGESIGHNLAGERSR 366 Query: 365 NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAV 413 + VI E L G +VLRGNL A++K S S +H+ RAV Sbjct: 367 DRRVIRSVEDPLREKAGFLVLRGNLF-DSALMKTSVISAEFRHRFLAQPGREGIHEARAV 425 Query: 414 VFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVR 473 VFE +DY A+IND +L IDE I+ ++ G GYPG AEV NM P +L++G+ + Sbjct: 426 VFEGPEDYHARINDPDLGIDETTILFIRGVGCVGYPGSAEVVNMQPPDGLLREGVTHLPT 485 Query: 474 ISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLA 533 + D R SGT+ +L+ SPEAAVGG LA+++ GD + LD+ RL + + E R A Sbjct: 486 VGDGRQSGTSESPSILNASPEAAVGGGLALLRTGDRVRLDLNACRLDALVDEAEWEARRA 545 Query: 534 EWQP---NHDLP 542 W P +H P Sbjct: 546 AWTPPVLHHQTP 557 Lambda K H 0.318 0.135 0.408 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: 1015 Number of extensions: 65 Number of successful extensions: 2 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: 579 Length of database: 593 Length adjustment: 37 Effective length of query: 542 Effective length of database: 556 Effective search space: 301352 Effective search space used: 301352 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 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