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_041734913.1 BC1002_RS17315 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000092885.1:WP_041734913.1 Length = 577 Score = 780 bits (2015), Expect = 0.0 Identities = 387/576 (67%), Positives = 460/576 (79%), Gaps = 1/576 (0%) Query: 5 AEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLR 64 +E RKLRS EW+G ++ +R W+KNQG P FDGRPVIGI NTWS++TPCN H R Sbjct: 2 SEKKRKLRSAEWFGTADKNGFMYRSWMKNQGIPDHEFDGRPVIGICNTWSELTPCNAHFR 61 Query: 65 ELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLL 124 +LAE VK G++EAGGFP+E PVFS E+ RPTAM+ RNLAA+ VEEAIRG P+D VLL Sbjct: 62 KLAEHVKRGIYEAGGFPVEFPVFSNGESNLRPTAMLTRNLAAMDVEEAIRGNPIDAVVLL 121 Query: 125 VGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQA 184 GCDKTTP+LLMGAASCD+P+IVVTGGPMLNG G+ +GSGT +W+ E +KAGE+ Sbjct: 122 TGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKLDGKNIGSGTAVWQLHESLKAGEIDLH 181 Query: 185 EFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRI 244 +FL AEA MSRS+GTCNTMGTASTMA MAEALG +L NAAIP VDSRR V+A ++G RI Sbjct: 182 QFLSAEAGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGIRI 241 Query: 245 VQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGR 304 V+M +DLK S+I+T++AF NAIR NAAIGGSTNAVIHL AIAGR+GIDL LDDW GR Sbjct: 242 VEMALEDLKLSKILTREAFMNAIRVNAAIGGSTNAVIHLKAIAGRIGIDLELDDWVHIGR 301 Query: 305 DVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVVN 363 D PTIV+LMPSG++LMEEF+YAGGLP VL+RLGEA LL H DALTV+G+++WD VKD N Sbjct: 302 DTPTIVDLMPSGRFLMEEFYYAGGLPAVLRRLGEANLLPHPDALTVNGKSLWDNVKDAPN 361 Query: 364 WNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKA 423 N++VI P +K L + GGI VLRGNLAP+GAVLKPSAA+P LL H+GRAVVFE+ + YK+ Sbjct: 362 TNDEVIRPLDKPLVADGGIRVLRGNLAPRGAVLKPSAATPELLKHRGRAVVFENFEHYKS 421 Query: 424 KINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTA 483 +I D+ LD+D N ++VMKNCGPKGYPGMAEVGNMGLPPK+LK+G+ DMVRISDARMSGTA Sbjct: 422 RIVDETLDVDANSVLVMKNCGPKGYPGMAEVGNMGLPPKLLKQGVKDMVRISDARMSGTA 481 Query: 484 YGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPT 543 YGTVVLH +PEAA GGPLA V++GD IELD LHLD+SD EL RRLA+ P Sbjct: 482 YGTVVLHVTPEAAAGGPLAAVQDGDWIELDCDAGTLHLDVSDAELERRLAKHVPPEPPEG 541 Query: 544 SGYAFLHQQHVEGADTGADLDFLKGCRGNAVGKDSH 579 GY L+ HV AD G DLDFL GCRG+AV + SH Sbjct: 542 GGYRRLYIDHVLQADEGCDLDFLVGCRGSAVPRHSH 577 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: 1180 Number of extensions: 60 Number of successful extensions: 3 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: 577 Length adjustment: 36 Effective length of query: 543 Effective length of database: 541 Effective search space: 293763 Effective search space used: 293763 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