Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate HSERO_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >FitnessBrowser__HerbieS:HSERO_RS05205 Length = 585 Score = 382 bits (982), Expect = e-110 Identities = 225/546 (41%), Positives = 332/546 (60%), Gaps = 20/546 (3%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 +R+ + G+ D E + +P+IG+ N+W+E+ P + H K+AE V+ GI AGG P+EF Sbjct: 28 YRSWMKNQGIPDHEFQGKPVIGICNTWSELTPCNAHFRKIAEHVRRGIIEAGGFPVEFPV 87 Query: 74 IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132 + G +R ++ +R + + VE + + +DAVV++T CDK TP L+ AA Sbjct: 88 FS------NGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVLLTGCDKTTPALLMGAAS 141 Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSC 190 +VP I++ GGPM+ G + I ++ +++ +K G + E G+C Sbjct: 142 CDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITIHDFMAAEAGMSRSAGTC 201 Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250 + TA+TM ++E++G+ LP + +PAV+ARR A L+GMRIV MV EGLT KILTR Sbjct: 202 NTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMRIVDMVWEGLTLSKILTR 261 Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310 KA ENAI + A+GGSTN+V+HL+A+A +G+DL LE + I R P I + PSGR+ + Sbjct: 262 KAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIGRGTPTIVDLQPSGRYLM 321 Query: 311 VDLDRAGGIPAVLKELGEAGLI-HKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPF 369 + AGG+PAVL+ LGEA L+ HKDALTV G+T+W+NVKDA + + EV+RPL P Sbjct: 322 EEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAPIYNDEVVRPLAKPLIED 381 Query: 370 GGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIV 427 GG+ IL+G+LAP GAV+K SA EL K +G A VF+ + I +++ V+V Sbjct: 382 GGICILRGNLAPRGAVLKPSAATPELMKHRGRAVVFEDFNHYKERINDPDLDVDASCVLV 441 Query: 428 IRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAG 485 ++ GP+G PGM E+ + V+A G+ D V ++D R SG G I HV+PEAAAG Sbjct: 442 MKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMVR-ISDARMSGTAYGTVILHVAPEAAAG 500 Query: 486 GPIALVQDGDEIVIDIEKRRLDLLVDEKELEER---RARWKPKVKP-LRRGILRRYAKMA 541 GP+ +VQDGD I +D +L L + E+E++ R RA+ + KP + G Y Sbjct: 501 GPLGIVQDGDFIELDAYAGKLQLDISEEEMKRRLEARAKVLAERKPEMVGGYQSLYVDRV 560 Query: 542 LSADKG 547 L AD+G Sbjct: 561 LQADEG 566 Lambda K H 0.319 0.138 0.401 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: 843 Number of extensions: 45 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: 552 Length of database: 585 Length adjustment: 36 Effective length of query: 516 Effective length of database: 549 Effective search space: 283284 Effective search space used: 283284 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 Apr 09 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