Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_011371701.1 SUDEN_RS00345 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000012965.1:WP_011371701.1 Length = 561 Score = 489 bits (1258), Expect = e-142 Identities = 264/561 (47%), Positives = 371/561 (66%), Gaps = 15/561 (2%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SDTIK+G +APHRSLL GL D+DF+KPFIGIANSY DI+PGH L E E VK Sbjct: 1 MRSDTIKKGFDKAPHRSLLRATGLRDEDFDKPFIGIANSYIDIIPGHFFLHEYGEIVKAA 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV F FNT+ + DGIAM HDGM YSL SREI+AD++E++ AH LD L+ +P CD Sbjct: 61 IREAGGVPFVFNTIGVDDGIAMGHDGMLYSLPSREIIADSIETVMNAHKLDALICIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179 KIVPGM+M A R+++P + V+GGPM G K G +DL +E VG + G+++++EL + Sbjct: 121 KIVPGMIMGALRVNVPTVFVSGGPMAAGHKKDGTPIDLATAFEAVGEHAEGKITDEELYD 180 Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239 +E ACP SC+G+FTAN+M L EA+G++LPG T A++ R+ ++ + + KRIVEM Sbjct: 181 IECNACPSGGSCSGMFTANSMNTLCEAMGIALPGNGTVLAMTPRRIEMVKAAAKRIVEMA 240 Query: 240 QE-----NLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDEL 294 + NLK +++++A NA +VD+A+GGS+NT LH+ AIA E G++ ++ +E+ Sbjct: 241 KADDSKYNLK--NVLNEKAVHNAFVVDMAMGGSSNTVLHMLAIAREA-GVDFPIEKINEI 297 Query: 295 SRVIPHIASISPAGEHM-MLDLDRAGGIPAVLKTLEDH---INRECVTCTGRTVQENIEN 350 + + HIA ISP+ + M D+D+AGG+ AV+K + + E T TG T+ E I + Sbjct: 298 ADNVAHIAKISPSLTTVHMDDIDKAGGVNAVMKEISRRGGLLYLENPTVTGETLGERIAD 357 Query: 351 VKVGHRDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDE 410 K+ + ++I ++ GGL+IL GNLA G+VVK + +M +G A FNS+ E Sbjct: 358 AKILNEEIIHRNENAYSQVGGLSILFGNLATEGAVVKTAGIELNMRQFKGTAICFNSQPE 417 Query: 411 CMEAIFGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGT 469 + I ++ G+V+VIRYEGPKGGPGM+EML PT+ I GMGL + VALITDGRFSG T Sbjct: 418 AITGIMKHKVKPGNVVVIRYEGPKGGPGMQEMLAPTALIQGMGLGDSVALITDGRFSGAT 477 Query: 470 RGPCVGHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVK 529 +G +GHVSPEA E G +A + DGD I +D L +++S I R + + VK Sbjct: 478 KGASIGHVSPEAAEGGLIAFIEDGDEIELDTDKHLLRLNVSDDVIAARKANYKPYKNEVK 537 Query: 530 G-WLARYRKLAGSADTGAVLR 549 WL RY+ L +A GAVL+ Sbjct: 538 SKWLKRYQLLVSNASNGAVLK 558 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: 906 Number of extensions: 47 Number of successful extensions: 9 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: 561 Length adjustment: 36 Effective length of query: 513 Effective length of database: 525 Effective search space: 269325 Effective search space used: 269325 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_011371701.1 SUDEN_RS00345 (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.23473.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-230 752.6 9.7 1.4e-230 752.4 9.7 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011371701.1 SUDEN_RS00345 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011371701.1 SUDEN_RS00345 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 752.4 9.7 1.4e-230 1.4e-230 1 542 [. 14 558 .. 14 559 .. 0.98 Alignments for each domain: == domain 1 score: 752.4 bits; conditional E-value: 1.4e-230 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ll+atGl+ded++kP+i+++nsy++i+Pgh l++ +++vk++i++aGgv++ fnti+v+DGiam lcl|NCBI__GCF_000012965.1:WP_011371701.1 14 PHRSLLRATGLRDEDFDKPFIGIANSYIDIIPGHFFLHEYGEIVKAAIREAGGVPFVFNTIGVDDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm+ysLpsreiiaDs+etv++ah+lDal++i++CDkivPGm+m+alr+n+P+++vsGGpm+ag+ k lcl|NCBI__GCF_000012965.1:WP_011371701.1 83 GHDGMLYSLPSREIIADSIETVMNAHKLDALICIPNCDKIVPGMIMGALRVNVPTVFVSGGPMAAGHKK 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 + idl +feavge a+gk+++eel++ie +acP+ gsCsG+ftansm++l ea+G++lPg++t+la lcl|NCBI__GCF_000012965.1:WP_011371701.1 152 DGTPIDLATAFEAVGEHAEGKITDEELYDIECNACPSGGSCSGMFTANSMNTLCEAMGIALPGNGTVLA 220 ********************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkk...nikPrdiltkeafenaitldlalGGstntvLhllaiakeagvkl 273 ++ ++ e++k ++krive+ k +++ +++l+++a+ na+++d+a+GGs+ntvLh+laia+eagv++ lcl|NCBI__GCF_000012965.1:WP_011371701.1 221 MTPRRIEMVKAAAKRIVEMAKAddsKYNLKNVLNEKAVHNAFVVDMAMGGSSNTVLHMLAIAREAGVDF 289 *******************99622257799*************************************** PP TIGR00110 274 slddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldk.egllhkdaltvtGktlaetlekv 340 ++++++++++v ++ak++Ps +v + d+++aGGv+av+ke+++ gll + tvtG+tl+e+++++ lcl|NCBI__GCF_000012965.1:WP_011371701.1 290 PIEKINEIADNVAHIAKISPSLTTVhMDDIDKAGGVNAVMKEISRrGGLLYLENPTVTGETLGERIADA 358 *********************88888*****************984578999***************** PP TIGR00110 341 kvlrvdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailgg 409 k+l ++++i+ +n++++ ggl +L+Gnla+eGavvk+ag+e ++ +f+G+a f+s+ ea+ +i++ lcl|NCBI__GCF_000012965.1:WP_011371701.1 359 KIL--NEEIIHRNENAYSQVGGLSILFGNLATEGAVVKTAGIELNMRQFKGTAICFNSQPEAITGIMKH 425 **9..9*************************************************************** PP TIGR00110 410 kvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGa 478 kvk G+vvviryeGPkGgPGm+emLaPt+ ++g+GLg++vaLitDGrfsG+t+G siGhvsPeaaegG lcl|NCBI__GCF_000012965.1:WP_011371701.1 426 KVKPGNVVVIRYEGPKGGPGMQEMLAPTALIQGMGLGDSVALITDGRFSGATKGASIGHVSPEAAEGGL 494 ********************************************************************* PP TIGR00110 479 ialvedGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavld 542 ia++edGD+i++D +++ l l+vs++ +a+r+a+ k+ +++ ++ +L++y+ lvs+a++Gavl+ lcl|NCBI__GCF_000012965.1:WP_011371701.1 495 IAFIEDGDEIELDTDKHLLRLNVSDDVIAARKANYKPYKNEVKSKWLKRYQLLVSNASNGAVLK 558 ***************************************999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (561 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.48 // [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