Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_013461274.1 SULKU_RS12160 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000183725.1:WP_013461274.1 Length = 562 Score = 499 bits (1284), Expect = e-145 Identities = 264/560 (47%), Positives = 372/560 (66%), Gaps = 12/560 (2%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SDTIKRG + PHRSLL GL D+DF KPFIG+ANS+ DI+PGH L+E VKE Sbjct: 1 MRSDTIKRGFDKTPHRSLLRATGLKDEDFNKPFIGVANSHIDIIPGHFFLQEYGRIVKEA 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV FEFNT+ + DGIAM HDGM YSL SRE++AD++E++ AH LDGL+ +P CD Sbjct: 61 IREAGGVPFEFNTIGVDDGIAMGHDGMLYSLPSRELIADSIETVMNAHKLDGLICIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179 KIVPGMLM A R+++P I V+GGPM G K G +DL +E VG + G+MS++EL E Sbjct: 121 KIVPGMLMGALRVNVPTIFVSGGPMKAGHKKDGTPIDLATAFEAVGKHADGKMSDEELYE 180 Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239 +E ACP SC+G+FTAN+M L EA+G++LPG T A++ + ++ + + +RIVEMV Sbjct: 181 IECEACPSGGSCSGMFTANSMNTLCEAMGVALPGNGTVLAMTPERIEMVKTAARRIVEMV 240 Query: 240 QENLKPTM----IMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELS 295 ++ I++ +A NA +VD+A+GGS+NT LH+ +IA E G++ ++ +++S Sbjct: 241 KDENSQQWNMQNILNDKAIHNAFVVDMAMGGSSNTVLHMLSIAKEA-GVDFDITQINKIS 299 Query: 296 RVIPHIASISPAGEHM-MLDLDRAGGIPAVLKTLEDH---INRECVTCTGRTVQENIENV 351 + HIA ISP+ + M D++RAGG+ AV+K + + + +T TG T+ E I++ Sbjct: 300 ENVAHIAKISPSLSTVHMDDINRAGGVNAVMKEVSRRGGILYTDAMTVTGETLGERIKDA 359 Query: 352 KVGHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDEC 411 + ++I ++ GGL+IL GNLA G+VVK + +M +G A FNS+ E Sbjct: 360 VIKDPNIIHTNENAYSPVGGLSILFGNLAEEGAVVKTAGITPNMRKFKGSAVCFNSQQEA 419 Query: 412 MEAIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTR 470 + I G ++ GDV+VIRYEGPKGGPGM+EML PTS I GMGL E VALITDGRFSG TR Sbjct: 420 IAGIVGHKVKAGDVVVIRYEGPKGGPGMQEMLAPTSLIMGMGLGESVALITDGRFSGATR 479 Query: 471 GPCVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKG 530 G +GHVSPEA E G +A + DGD I +D+ + L++++S +E+R ++ + Sbjct: 480 GASIGHVSPEAAEGGLIALIEDGDEIELDVDTHLLQLNVSYEVLEQRRLHWKPIKKEIPS 539 Query: 531 -WLARYRKLAGSADTGAVLR 549 WL RY L +A GA L+ Sbjct: 540 KWLKRYSLLVSNASNGAALK 559 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: 917 Number of extensions: 55 Number of successful extensions: 8 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: 562 Length adjustment: 36 Effective length of query: 513 Effective length of database: 526 Effective search space: 269838 Effective search space used: 269838 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_013461274.1 SULKU_RS12160 (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.3813.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-237 773.0 9.0 9.2e-237 772.8 9.0 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013461274.1 SULKU_RS12160 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013461274.1 SULKU_RS12160 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 772.8 9.0 9.2e-237 9.2e-237 1 542 [. 14 559 .. 14 560 .. 0.98 Alignments for each domain: == domain 1 score: 772.8 bits; conditional E-value: 9.2e-237 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ll+atGlkded++kP+i+v+ns+++i+Pgh l++ +++vke+i++aGgv++efnti+v+DGiam lcl|NCBI__GCF_000183725.1:WP_013461274.1 14 PHRSLLRATGLKDEDFNKPFIGVANSHIDIIPGHFFLQEYGRIVKEAIREAGGVPFEFNTIGVDDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm+ysLpsre+iaDs+etv++ah+lD+l++i++CDkivPGmlm+alr+n+P+i+vsGGpm+ag+ k lcl|NCBI__GCF_000183725.1:WP_013461274.1 83 GHDGMLYSLPSRELIADSIETVMNAHKLDGLICIPNCDKIVPGMLMGALRVNVPTIFVSGGPMKAGHKK 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + idl +feavg+ a+gk+s+eel+eie acP+ gsCsG+ftansm++l ea+G++lPg++t+la lcl|NCBI__GCF_000183725.1:WP_013461274.1 152 DGTPIDLATAFEAVGKHADGKMSDEELYEIECEACPSGGSCSGMFTANSMNTLCEAMGVALPGNGTVLA 220 ********************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknik....PrdiltkeafenaitldlalGGstntvLhllaiakeagvk 272 ++ e+ e++k++++rive+vk + ++il+ +a+ na+++d+a+GGs+ntvLh+l+iakeagv+ lcl|NCBI__GCF_000183725.1:WP_013461274.1 221 MTPERIEMVKTAARRIVEMVKDENSqqwnMQNILNDKAIHNAFVVDMAMGGSSNTVLHMLSIAKEAGVD 289 ********************97655455599************************************** PP TIGR00110 273 lslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlek 339 +++ +++++s++v ++ak++Ps ++v + d++raGGv+av+ke+++ g+l +da+tvtG+tl+e++++ lcl|NCBI__GCF_000183725.1:WP_013461274.1 290 FDITQINKISENVAHIAKISPSLSTVhMDDINRAGGVNAVMKEVSRrGGILYTDAMTVTGETLGERIKD 358 **********************99888*****************9845799****************** PP TIGR00110 340 vkvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailg 408 + ++ d ++i++ +n+++ ggl +L+GnlaeeGavvk+ag+ ++ kf+G+a f+s++ea+++i+g lcl|NCBI__GCF_000183725.1:WP_013461274.1 359 AVIK--DPNIIHTNENAYSPVGGLSILFGNLAEEGAVVKTAGITPNMRKFKGSAVCFNSQQEAIAGIVG 425 *999..*************************************************************** PP TIGR00110 409 gkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegG 477 kvk+GdvvviryeGPkGgPGm+emLaPts ++g+GLg++vaLitDGrfsG+trG siGhvsPeaaegG lcl|NCBI__GCF_000183725.1:WP_013461274.1 426 HKVKAGDVVVIRYEGPKGGPGMQEMLAPTSLIMGMGLGESVALITDGRFSGATRGASIGHVSPEAAEGG 494 ********************************************************************* PP TIGR00110 478 aialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ial+edGD+i++D++ + l+l+vs e l++rr ++k+ +++ + +L++y+ lvs+a++Ga+l+ lcl|NCBI__GCF_000183725.1:WP_013461274.1 495 LIALIEDGDEIELDVDTHLLQLNVSYEVLEQRRLHWKPIKKEIPSKWLKRYSLLVSNASNGAALK 559 ****************************************99********************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (562 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.90 // [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