Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_034995980.1 DL88_RS11215 dihydroxy-acid dehydratase
Query= curated2:A0Q0E8 (554 letters) >NCBI__GCF_000745425.1:WP_034995980.1 Length = 576 Score = 337 bits (865), Expect = 6e-97 Identities = 203/542 (37%), Positives = 314/542 (57%), Gaps = 15/542 (2%) Query: 15 HRSLFYAMGYTPEDLK-KPLIGIVNSHNEIIPGHFHLNEIVQAVKLGVASAGGTPIEIPS 73 HRS MGYT E+ + KP+I I+N+ +++ H H V VK G+ AGG P+E+P+ Sbjct: 24 HRSRMAQMGYTGEEYRGKPVIAIINTWSDLNQCHAHFKTRVDDVKRGILQAGGFPVELPA 83 Query: 74 IGICDGISMNHSGMKYPLASRELIADSIEAMTIAHKFDALVLVGNCDKIVPGMLMGAARL 133 + + + + + M Y R +A E + +H D VL+G CDK PG+++GA Sbjct: 84 LSLSES-KVKPTTMLY----RNFLAMETEELIRSHPVDGAVLMGGCDKTTPGLILGATSA 138 Query: 134 NVPAIYVSGGPMLPGKLKGKKIDLVHGAFEAVGSYAEGILSDDDLNKIEQHSCPTCGSCA 193 VPAIYV GPML G GK + AF+ G +S D N++E + G C Sbjct: 139 GVPAIYVPAGPMLRGNWHGKVLGSGSDAFKYWDERRAGNISTQDWNEMEVGIARSYGHCM 198 Query: 194 GLFTANSMNSLAEALGVALPGNGTIPAPYGRRKQLAKYAGVKIMELVKKKIKLRDILTKE 253 + TA++M +LA+ LG+ LPG +IPA ++ AG +I+++V + + I T+ Sbjct: 199 TMGTASTMTALADVLGLTLPGTSSIPAADANHIRMCSAAGRRIVDMVWEDLTPNTIQTEA 258 Query: 254 AFKNAIALDMAIGGSSNTTLHLMAIAHEAKVYLTLEDFDEISRRIPHITKLSPAG-THHM 312 A++N I + MA+G S+N +H++A+A A +TL+DFD +SR++P + + P+G T+ M Sbjct: 259 AYRNVIVVAMAMGCSTNAVIHIIAMARRAGYAITLDDFDAMSRKVPVLANVRPSGDTYLM 318 Query: 313 VDLDEAGGISAVLKELMDANLIFKDQLTVTGKTLEENIKNSLVLNDSVIRPLNNPYSNEG 372 D AGG+ ++ L A + Q+ V+GK+ E++K++ V N+ VIRPL+ P EG Sbjct: 319 EDFYYAGGLIGLMTRL--APFLDLTQINVSGKSWVESLKDAKVYNEDVIRPLDKPIYEEG 376 Query: 373 GIAILRGNLAPDGAVVKQSAVEPEMLYHKGVARVFDG-EELAFDAIMNK-KIHPGDVVVI 430 +A+LRGNLAP+G V+K SA P +L+H G A VFD EL + + + P V+V+ Sbjct: 377 ALAVLRGNLAPNGCVMKPSAAAPHLLHHTGPALVFDNYAELKANIDRDDLDVTPDHVLVL 436 Query: 431 RYEGPKGCPGMRE--MLSPTAAIIGLGLEKSTALITDGRFSGGTRGPCIGHISPEASEGG 488 R GP G PGM E ML ++ G+ + I+D R SG + G CI H+SPE+ GG Sbjct: 437 RNAGPLGGPGMPEWGMLPIPKKLVKQGV-RDMVRISDARMSGTSYGACILHVSPESYIGG 495 Query: 489 PIALIEEGDLIEIDISNRRISLLVSPEELSKRKENWIQPPCKAPDGTYLKRYSKLVTSAS 548 P++LIE GD+I +D+ R I+L VS EEL++R+ + + P K + Y +S+ + A Sbjct: 496 PLSLIETGDMISVDVPARSINLEVSEEELARRR-SALPIPRKRYERGYGWMFSQHIRQAD 554 Query: 549 TG 550 G Sbjct: 555 EG 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: 729 Number of extensions: 41 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: 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