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_086508318.1 BZY95_RS01905 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_002151265.1:WP_086508318.1 Length = 561 Score = 327 bits (838), Expect = 8e-94 Identities = 206/565 (36%), Positives = 314/565 (55%), Gaps = 21/565 (3%) Query: 8 PRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELA 67 PR+ S G + R L+ G+ + F +P +GI +TWS +TPCN H+ ELA Sbjct: 7 PRRRHSAPVVDGVGKSA--SRAMLRAVGFSDEDFT-KPQVGIASTWSMVTPCNSHIHELA 63 Query: 68 EKVKAGVWEAGGFPLEVPVFSASENTFRPT-----AMMYRNLAALAVEEAIRGQPMDGCV 122 E+ + G AGG + + S+ T +++ R + A ++E + DG V Sbjct: 64 ERARDGADAAGGKGVIFNTVTISDGIANGTEGMKYSLVSREVIADSIETVAGCEGFDGLV 123 Query: 123 LLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMT 182 + GCDK P LMG A + PS+ V GG + G + V + S G++ Sbjct: 124 AIGGCDKNMPGCLMGLARLNRPSVFVYGGTIQPGKNHTDIVSVFEAMGAHSR----GDLE 179 Query: 183 QAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGR 242 E + E + G+C M TA+TMAS EALGM+L G++A V ++ + G Sbjct: 180 LIELKQIEETAIPGPGSCGGMYTANTMASAIEALGMSLPGSSAQNAVSQAKRDDCEAAGA 239 Query: 243 RIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRC 302 ++++++ D+KPS+IMT+QAFENA+ A+GGSTNAV+HL+A+A VG+ LSL D+ Sbjct: 240 AVLELLERDIKPSDIMTRQAFENAVTVVIALGGSTNAVLHLIAMANTVGVPLSLVDFTEI 299 Query: 303 GRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVV 362 GR VP + +L PSG+Y+M E GG+ ++K L +AGLLH D LTV+G T+ + + +V Sbjct: 300 GRRVPVLADLRPSGRYMMSELVEIGGIQPLMKTLLDAGLLHGDCLTVTGRTLAENLANVA 359 Query: 363 NWNED--VILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDD 420 + +D +I + L + + +L GNLAP+GAV K + G A VF ++ Sbjct: 360 PYPDDQKIIAALDAPLKAESHLRILFGNLAPEGAVAKITGKEGTRF--SGTARVFGSEEE 417 Query: 421 YKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVR-ISDARM 479 +A+IND + + ++V++ GP+G PGM E+ + ++ +G+ D V I+D R Sbjct: 418 AQARINDGTVVAGD--VVVIRYEGPRGGPGMREM--LTPTSAIMGRGLGDSVALITDGRF 473 Query: 480 SGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNH 539 SG ++G VV H +PEA GGPLA+V++GDMI +D + +D+SDEEL RR A WQ Sbjct: 474 SGGSHGFVVGHVTPEAFDGGPLALVEDGDMITIDAEADTIDVDLSDEELMRRRAAWQQPA 533 Query: 540 DLPTSGYAFLHQQHVEGADTGADLD 564 T G + + V A TGA D Sbjct: 534 PRYTRGVLAKYARTVSSASTGAVTD 558 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: 845 Number of extensions: 47 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: 579 Length of database: 561 Length adjustment: 36 Effective length of query: 543 Effective length of database: 525 Effective search space: 285075 Effective search space used: 285075 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