Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_028990669.1 G579_RS0114020 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000423825.1:WP_028990669.1 Length = 558 Score = 532 bits (1370), Expect = e-155 Identities = 280/560 (50%), Positives = 376/560 (67%), Gaps = 16/560 (2%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SDTIK+G +R PHR+LL CGLTD D +KPFIG+ NSY DI+PGH+HL+E VKE Sbjct: 1 MRSDTIKKGFERTPHRALLKACGLTDADMDKPFIGVCNSYIDIIPGHVHLQEFGRIVKEE 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV FEFNT+ + DGI M HDGM+YSL SREI+AD++E++ AH LD L+ +P CD Sbjct: 61 IRKAGGVPFEFNTIGVDDGIVMGHDGMRYSLPSREIIADSLETVVRAHHLDALICIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179 KIVPGMLM A R D+P + V+GGPM G G VDL+ +E VG G++++ L+E Sbjct: 121 KIVPGMLMGAIRCDVPTVFVSGGPMEAGHLSDGTPVDLVTAFEAVGQYKLGKITDLRLKE 180 Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239 +E ACP SC+G+FTAN+M CL EALG++LP T A S R+R + R + +RIV + Sbjct: 181 IEDKACPTCGSCSGMFTANSMNCLMEALGVALPENGTILATSPRRRDLVRQAAQRIVALA 240 Query: 240 QENLKPTM--IMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRV 297 + PTM ++ EA +NA ++D+A+GGSTNT LH AIA E G++ L+ ++LS Sbjct: 241 KAG-GPTMRQLVDFEAIDNAFVLDMAMGGSTNTVLHTLAIAREA-GIDYPLERLNQLSEQ 298 Query: 298 IPHIASISPAGEHMML-DLDRAGGIPAVLKTLE----DHINRECVTCTGRTVQENIENVK 352 + ++A +SPA + + D+ RAGGI A++ + + ++ + +T +G T++ +E + Sbjct: 299 VAYLAKVSPALSTVHIEDIGRAGGISAIMHEVHRRNPEVLHLDKMTVSGETLRAIVERAE 358 Query: 353 VGHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECM 412 V +IR ++P+ + GGL +L GNLAP GS++K GAVA +M GPAK+++S + Sbjct: 359 VKDEQIIRRAENPISATGGLRVLFGNLAPEGSIIKAGAVAPNMRKFAGPAKIYDSMESAS 418 Query: 413 EAIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRG 471 E I G ++ GDV+VIRYEGPKGGPGM E L PT+ I GMGL E VALITDGRFSG TRG Sbjct: 419 EGILDGEVNAGDVVVIRYEGPKGGPGMPEQLAPTANIMGMGLGESVALITDGRFSGATRG 478 Query: 472 PCVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREI---EERLQSAVKPRRSV 528 C+GHVSPEA E GP+ + DGDII IDI L V LS E+ E Q KP S Sbjct: 479 ACIGHVSPEAAEGGPIGLLRDGDIIEIDIDGGSLNVRLSDAELAARRETWQPVEKPLSS- 537 Query: 529 KGWLARYRKLAGSADTGAVL 548 WL RYRKL +A GAVL Sbjct: 538 -SWLRRYRKLVTNASKGAVL 556 Lambda K H 0.319 0.136 0.397 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: 971 Number of extensions: 51 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: 549 Length of database: 558 Length adjustment: 36 Effective length of query: 513 Effective length of database: 522 Effective search space: 267786 Effective search space used: 267786 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)
Align candidate WP_028990669.1 G579_RS0114020 (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.12135.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-242 791.3 1.8 2.5e-242 791.1 1.8 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028990669.1 G579_RS0114020 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028990669.1 G579_RS0114020 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 791.1 1.8 2.5e-242 2.5e-242 1 542 [. 14 557 .. 14 558 .] 0.98 Alignments for each domain: == domain 1 score: 791.1 bits; conditional E-value: 2.5e-242 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++rallka+Gl+d+d++kP+i+v+nsy++i+Pghvhl++++++vkeei++aGgv++efnti+v+DGi m lcl|NCBI__GCF_000423825.1:WP_028990669.1 14 PHRALLKACGLTDADMDKPFIGVCNSYIDIIPGHVHLQEFGRIVKEEIRKAGGVPFEFNTIGVDDGIVM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm+ysLpsreiiaDs+etvv+ah+lDal++i++CDkivPGmlm+a+r ++P+++vsGGpmeag+++ lcl|NCBI__GCF_000423825.1:WP_028990669.1 83 GHDGMRYSLPSREIIADSLETVVRAHHLDALICIPNCDKIVPGMLMGAIRCDVPTVFVSGGPMEAGHLS 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + +dlv +feavg+y+ gk+++ +l+eie+ acPt+gsCsG+ftansm+cl+ealG++lP+++t+la lcl|NCBI__GCF_000423825.1:WP_028990669.1 152 DGTPVDLVTAFEAVGQYKLGKITDLRLKEIEDKACPTCGSCSGMFTANSMNCLMEALGVALPENGTILA 220 ********************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkkni.kPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsl 275 ts ++++l++++++riv l k + r+++ ea++na++ld+a+GGstntvLh+laia+eag+++ l lcl|NCBI__GCF_000423825.1:WP_028990669.1 221 TSPRRRDLVRQAAQRIVALAKAGGpTMRQLVDFEAIDNAFVLDMAMGGSTNTVLHTLAIAREAGIDYPL 289 *******************9986516799**************************************** PP TIGR00110 276 ddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk..egllhkdaltvtGktlaetlekvk 341 +++++ls++v lak++P+ ++v ied+ raGG+sa+++e+++ ++lh d +tv+G+tl ++e+++ lcl|NCBI__GCF_000423825.1:WP_028990669.1 290 ERLNQLSEQVAYLAKVSPALSTVhIEDIGRAGGISAIMHEVHRrnPEVLHLDKMTVSGETLRAIVERAE 358 *******************99888*****************9843479********************* PP TIGR00110 342 vlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggk 410 v+ d+++ir +np++++ggl+vL+Gnla+eG+++k+++v+ ++ kf Gpak+++s e a e+il+g+ lcl|NCBI__GCF_000423825.1:WP_028990669.1 359 VK--DEQIIRRAENPISATGGLRVLFGNLAPEGSIIKAGAVAPNMRKFAGPAKIYDSMESASEGILDGE 425 **..***************************************************************** PP TIGR00110 411 vkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGai 479 v++GdvvviryeGPkGgPGm+e LaPt+ ++g+GLg++vaLitDGrfsG+trG +iGhvsPeaaegG+i lcl|NCBI__GCF_000423825.1:WP_028990669.1 426 VNAGDVVVIRYEGPKGGPGMPEQLAPTANIMGMGLGESVALITDGRFSGATRGACIGHVSPEAAEGGPI 494 ********************************************************************* PP TIGR00110 480 alvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 +l++dGD+i+iDi+ l++++s++ela+rr+++++ e+ + +L++y+klv++a+kGavl+ lcl|NCBI__GCF_000423825.1:WP_028990669.1 495 GLLRDGDIIEIDIDGGSLNVRLSDAELAARRETWQPVEKPLSSSWLRRYRKLVTNASKGAVLE 557 **************************************999********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (558 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: 00:00:00.02 # Mc/sec: 11.46 // [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