Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_057508546.1 ABB28_RS10335 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >NCBI__GCF_001431535.1:WP_057508546.1 Length = 611 Score = 903 bits (2333), Expect = 0.0 Identities = 459/616 (74%), Positives = 507/616 (82%), Gaps = 6/616 (0%) Query: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+T GRNMAGAR LWRATGMKD DF KPIIA+ANSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPEYRSRTSTAGRNMAGARALWRATGMKDGDFHKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADAIVCIS Sbjct: 61 AREIEQAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120 Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 NCDKITPGMLMAA+RL+IPV+FVSGGPMEAGK + LDLVDAMV+AADDS SDE+ Sbjct: 121 NCDKITPGMLMAALRLDIPVIFVSGGPMEAGKTKLSE--HKLDLVDAMVIAADDSASDEK 178 Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 V E++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ LATHADRE LF+ AGRV+V Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTTLATHADREMLFRRAGRVIV 238 Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 +LC RWY ED ALP GIAT AAF NAM+LDIAMGGSTNT+LHLLAAA EGG+DF + Sbjct: 239 ELCHRWYGGEDPRALPSGIATAAAFGNAMTLDIAMGGSTNTILHLLAAAQEGGVDFDLTH 298 Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 ID LSR VP L KVAP H+EDVHRAGGV ILGEL+R GL+D S PTVH+P++ +A Sbjct: 299 IDALSRRVPQLCKVAPNTPQYHIEDVHRAGGVFGILGELDRAGLLDTSVPTVHSPSLADA 358 Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420 L RWD T+ HEFF A P G PTQVAFSQA RW LDLDR G IRS++H +S +G Sbjct: 359 LKRWDATLTDDAKVHEFFAAGPAGIPTQVAFSQATRWPSLDLDRAEGCIRSLQHAYSLEG 418 Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480 GLAVL GNLA +GC+VKTAGVDESI F G ARVFESQDAAV+GIL QVK G+VVVIRY Sbjct: 419 GLAVLRGNLAVDGCVVKTAGVDESIHVFEGNARVFESQDAAVAGILADQVKPGDVVVIRY 478 Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540 EGPKGGPGMQEMLYPT+YLKSKGLG CAL+TDGRFSGGTSGLSIGHVSPEA GG+I L Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKQCALLTDGRFSGGTSGLSIGHVSPEAASGGVIGL 538 Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLN-RKRDLTPALRAYAAM 599 V GD I IDIP RGITL V DA LA RR A ARG W PL R R +T AL+AYA + Sbjct: 539 VHDGDRIRIDIPARGITLLVDDATLAERRAAADARG---WKPLEARPRKVTSALKAYALL 595 Query: 600 TTNAARGAVRDVSQIE 615 T+A +GAVR+ + ++ Sbjct: 596 ATSADKGAVRNTALLD 611 Lambda K H 0.318 0.134 0.395 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: 1255 Number of extensions: 42 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: 617 Length of database: 611 Length adjustment: 37 Effective length of query: 580 Effective length of database: 574 Effective search space: 332920 Effective search space used: 332920 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)
Align candidate WP_057508546.1 ABB28_RS10335 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00110.hmm # target sequence database: /tmp/gapView.30137.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00110 [M=543] Accession: TIGR00110 Description: ilvD: dihydroxy-acid dehydratase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-247 808.7 0.3 1.4e-247 808.5 0.3 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508546.1 ABB28_RS10335 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508546.1 ABB28_RS10335 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 808.5 0.3 1.4e-247 1.4e-247 2 542 .. 18 606 .. 17 607 .. 0.98 Alignments for each domain: == domain 1 score: 808.5 bits; conditional E-value: 1.4e-247 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kd d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_001431535.1:WP_057508546.1 18 ARALWRATGMKDGDFHKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEQAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrl+iP+i+vsGGpmeagktkl lcl|NCBI__GCF_001431535.1:WP_057508546.1 87 HDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLDIPVIFVSGGPMEAGKTKL 155 ********************************************************************9 PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 se +++d+++a++ +a++ s+e++ e+ersacPt+gsCsG+ftansm+cltealGlslPg++t+lat lcl|NCBI__GCF_001431535.1:WP_057508546.1 156 SE--HKLDLVDAMVIAADDSASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTTLAT 222 77..589************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a+++ l++++g+ ivel+++ + P+ i+t +af na+tld+a+GGstnt+Lhlla+a+e g lcl|NCBI__GCF_001431535.1:WP_057508546.1 223 HADREMLFRRAGRVIVELCHRWYGgedpralPSGIATAAAFGNAMTLDIAMGGSTNTILHLLAAAQEGG 291 *********************9999999999************************************** PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++l ++d lsr+vP+l+k++P++ ++ ied+hraGGv ++l+eld++gll++ + tv +la+ l+ lcl|NCBI__GCF_001431535.1:WP_057508546.1 292 VDFDLTHIDALSRRVPQLCKVAPNTPQYhIEDVHRAGGVFGILGELDRAGLLDTSVPTVHSPSLADALK 360 *************************9988**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + + + + +irsl+++++ egglavL+Gnla lcl|NCBI__GCF_001431535.1:WP_057508546.1 361 RWDATLtddakvheffaagpagiptqvafsqatrwpsldldRAEGCIRSLQHAYSLEGGLAVLRGNLAV 429 ***99999*****************************88655555************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G+vvk+agv+e+i +feG+a+vfes+++a+++il+ +vk GdvvviryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_001431535.1:WP_057508546.1 430 DGCVVKTAGVDESIHVFEGNARVFESQDAAVAGILADQVKPGDVVVIRYEGPKGGPGMQEMLYPTSYLK 498 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGhvsPeaa+gG i+lv+dGD+i+iDi++r + l v+++ laerr lcl|NCBI__GCF_001431535.1:WP_057508546.1 499 SKGLGKQCALLTDGRFSGGTSGLSIGHVSPEAASGGVIGLVHDGDRIRIDIPARGITLLVDDATLAERR 567 ********************************************************************* PP TIGR00110 511 akakkkea.......revkgaLakyaklvssadkGavld 542 a+a+++++ r+v aL++ya l++sadkGav++ lcl|NCBI__GCF_001431535.1:WP_057508546.1 568 AAADARGWkplearpRKVTSALKAYALLATSADKGAVRN 606 *******999***9999********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (611 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 8.99 // [ok]
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