Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_012171167.1 AZC_RS13675 dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000010525.1:WP_012171167.1 Length = 576 Score = 330 bits (845), Expect = 1e-94 Identities = 206/546 (37%), Positives = 308/546 (56%), Gaps = 23/546 (4%) Query: 15 HRSLFYAMGYTPEDLK-KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS MGY E+ + KP+I I+N+ +++ H H + V+ VK G+ AGG P+E+P+ Sbjct: 24 HRSRMSQMGYAAEEYRGKPVIAIINTWSDLNQCHAHFKQRVEDVKRGILQAGGFPVELPA 83 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 I + + + + M Y R +A E + +H D VL+G CDK PG+L+GA Sbjct: 84 ISLSES-KVKPTTMLY----RNFLAMETEELIRSHPVDGAVLMGGCDKTTPGLLLGATSA 138 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 VPAIYV GPML G GK + AF+ G +SD D ++E + G C Sbjct: 139 GVPAIYVPAGPMLRGNWHGKVLGSGSDAFKYWDERRAGNISDKDWAEMEVGIARSYGVCM 198 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA +M +LA+ +G+ LPG +IPA ++ AG +I+E+V + + I T+ Sbjct: 199 TMGTAATMTALADVIGMTLPGASSIPAADANHIRMCAAAGRRIVEMVWEDLTPDKIQTEG 258 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAGTHH-M 312 AF+NAI + MA+G S+N +H++A+A A + LEDFD SR++P I + P+G + M Sbjct: 259 AFRNAINVAMAMGCSTNAVIHIIAMARRAGHAIGLEDFDAASRKVPVIANIRPSGERYLM 318 Query: 313 VDLDEAGGISAVLKEL---MDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYS 369 D AGG+ +L L +D +LI V+G+T ++++ + V ND VIRPL+NP Sbjct: 319 EDFYYAGGLLGLLTRLTPHLDLSLI-----NVSGQTWAQSLEGAEVYNDDVIRPLDNPIY 373 Query: 370 NEGGIAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDGEELAFDAIMNK---KIHPGD 426 EG +A+L+GNLAP G V+K SA P +L H G A VFD + A A +++ + P Sbjct: 374 AEGALALLKGNLAPSGCVMKPSAAAPHLLTHSGPALVFD-DYPALKANIDRDDLDVTPDT 432 Query: 427 VVVIRYEGPKGCPGMRE--MLSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEA 484 V+V+R GP G PGM E ML ++ G+ + I+D R SG + G CI H+SPE+ Sbjct: 433 VLVLRNAGPLGGPGMPEWGMLPIPKKLVKQGV-RDMVRISDARMSGTSYGACILHVSPES 491 Query: 485 SEGGPIALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYSKLV 544 GGP+AL+ GD+I +D+ NR I L VS EL +R+ PP + Y +S+ + Sbjct: 492 YIGGPLALVRTGDIITVDVPNRSIRLEVSDAELERRRVE-TPPPAPRYERGYGWMFSRHI 550 Query: 545 TSASTG 550 A G Sbjct: 551 GQADQG 556 Lambda K H 0.317 0.136 0.392 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: 784 Number of extensions: 40 Number of successful extensions: 5 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: 554 Length of database: 576 Length adjustment: 36 Effective length of query: 518 Effective length of database: 540 Effective search space: 279720 Effective search space used: 279720 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 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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