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_012385795.1 BIND_RS14500 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000019845.1:WP_012385795.1 Length = 599 Score = 473 bits (1216), Expect = e-137 Identities = 260/550 (47%), Positives = 352/550 (64%), Gaps = 18/550 (3%) Query: 1 MKKKAEWPRKLRSQEWYGGTSRD---VIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMT 57 MKKK P +LRS+ W+ + +Y +L +L G+P+IGI T SD++ Sbjct: 3 MKKK---PEELRSRAWFDNPANPDMTALYLERYLNYGLTAKELQSGKPIIGIAQTGSDLS 59 Query: 58 PCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQP 117 PCN ELA++V+ G+ EAGG +E PV E RPTA + RNLA L + E + G P Sbjct: 60 PCNRPHLELAKRVREGIREAGGIAIEFPVHPIQETGKRPTAALDRNLAYLGLVEILYGYP 119 Query: 118 MDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVK 177 +DG VL GCDKTTP+ LM AA+ DLP+IV+TGGPMLNG+F GER GSGT +WK E++ Sbjct: 120 LDGVVLTTGCDKTTPACLMAAATVDLPAIVLTGGPMLNGWFNGERTGSGTIIWKARELLA 179 Query: 178 AGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMA 237 GE+ +F+E AS + S+G CNTMGTA+TM S+AEALGM+L G AAIP R +A Sbjct: 180 KGEIDYQKFIELVASSAPSAGYCNTMGTATTMNSLAEALGMSLPGCAAIPAPYRERGQIA 239 Query: 238 QLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLD 297 TG+RIV MV +DLKPS+I+T+QA EN I N+AIGGSTNA IH+ AIA VG+ L +D Sbjct: 240 YETGKRIVDMVFEDLKPSDIITRQALENVIIVNSAIGGSTNAPIHINAIARHVGVPLEVD 299 Query: 298 DWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDE 357 DW+R G VP IVNL P+G YL E+F AGG+P V+ L GL+H++ALTV+G T+ D Sbjct: 300 DWERVGGQVPLIVNLQPAGTYLGEDFHRAGGVPAVVHELMRHGLIHENALTVNGRTMGDN 359 Query: 358 VKDVVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH--------- 408 + + DVI E AL + G V+RGNL A++K S Sbjct: 360 CHERAALDADVIRTFETALVPAAGFKVVRGNLF-DSAIMKTCVISDEFRTRYLSNPQDPD 418 Query: 409 --KGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKK 466 +GRAVVF+ +DY +I+D +L+IDE+C++ ++ G G+PG AEV NM P +L++ Sbjct: 419 AFEGRAVVFDGPEDYHQRIDDPSLNIDEHCLLFIRGTGAIGFPGSAEVVNMRAPSYLLQR 478 Query: 467 GILDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526 I + I D R SGT+ +L+ SPEAA GG LA+++ GD + +D+ R + ISDE Sbjct: 479 NITSLPCIGDGRQSGTSGSPSILNASPEAAAGGGLALLRTGDRVRIDLLKGRADILISDE 538 Query: 527 ELARRLAEWQ 536 ELA+R A++Q Sbjct: 539 ELAQRRADFQ 548 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: 988 Number of extensions: 63 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: 599 Length adjustment: 37 Effective length of query: 542 Effective length of database: 562 Effective search space: 304604 Effective search space used: 304604 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