Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011802045.1 PNAP_RS13320 dihydroxy-acid dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000015505.1:WP_011802045.1 Length = 579 Score = 367 bits (942), Expect = e-106 Identities = 216/543 (39%), Positives = 325/543 (59%), Gaps = 17/543 (3%) Query: 15 HRALWRASGLIDEELR-RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGT 73 +R+ + G+ D E + +P+IG+ N+W+E+ P + H K+AE V+ G+ AGG P+EF Sbjct: 25 YRSWMKNQGIPDHEFQGKPIIGICNTWSELTPCNAHFRKIAEHVRRGVFEAGGFPVEFPV 84 Query: 74 IAVCDGIAMGHEGMR-YSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAAR 132 + G +R ++ +R + + VE + + +DAVV++ CDK TP L+ AA Sbjct: 85 FS------NGESNLRPTAMFTRNLASIDVEESIRGNPIDAVVLLAGCDKTTPALLMGAAS 138 Query: 133 LEVPVILINGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTE--ELRKLEESALPGPGSC 190 ++P I+++GGPM+ G + + I ++ +++ +K G E E G+C Sbjct: 139 CDIPAIVVSGGPMLNGKHQGKDIGSGTVVWQLHEAVKAGHISMHEFMSAEAGMSRSAGTC 198 Query: 191 AGLFTANTMNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTR 250 + TA+TM ++EA+G LP + +PAV+ARR A ++GMRIV+M E L KILTR Sbjct: 199 NTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHMSGMRIVEMALEDLRLSKILTR 258 Query: 251 KALENAIAVDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFV 310 +A ENAI V+ A+GGSTN+V+HL+A+A LGI L LE + I R P I + PSGR + Sbjct: 259 EAFENAIRVNAAIGGSTNAVIHLKAIAGRLGIPLELEDWTSIGRGTPTIVDLMPSGRFLM 318 Query: 311 VDLDRAGGIPAVLKELGEAGLI-HKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPF 369 DL AGG+PAVL+ +GEA L+ H ALTV GK++WENV++A + + EVIRPL P Sbjct: 319 EDLYYAGGLPAVLRRMGEADLLRHPGALTVNGKSLWENVREAPIYNDEVIRPLAKPLIED 378 Query: 370 GGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGG--EIEPGTVIV 427 G + IL+G+LAP GAV+K SA L + +G A VF+ + I E++ +V++ Sbjct: 379 GAICILRGNLAPRGAVLKPSAASPHLMQHRGQAVVFEDFDHYKSRINDPDLEVDANSVLL 438 Query: 428 IRYEGPRGGPGMREM--LTATAAVMALGLGDKVALVTDGRFSGATRGPAIGHVSPEAAAG 485 ++ GP+G PGM E+ + ++A G+ D V ++D R SG G + HV+PEAAAG Sbjct: 439 MKNCGPKGYPGMAEVGNMGLPPKLLAQGVTDMVR-ISDARMSGTAYGTVVLHVAPEAAAG 497 Query: 486 GPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKPLRRGILRR-YAKMALSA 544 GP+A+V+DGD I +D RL L +DE E+ R + + P R G R Y L A Sbjct: 498 GPLAIVRDGDWIELDCAGGRLHLEIDEAEMAARFENLQARKPPERTGGYRELYIDHVLQA 557 Query: 545 DKG 547 D+G Sbjct: 558 DQG 560 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: 854 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: 552 Length of database: 579 Length adjustment: 36 Effective length of query: 516 Effective length of database: 543 Effective search space: 280188 Effective search space used: 280188 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 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