Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_029131996.1 A3GO_RS0102120 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000428045.1:WP_029131996.1 Length = 616 Score = 943 bits (2438), Expect = 0.0 Identities = 475/613 (77%), Positives = 526/613 (85%), Gaps = 4/613 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRTTTHGRNMAGAR LWRATGM D DF KPIIAVVNSFTQFVPGHVHLKD+GQLV Sbjct: 1 MPQYRSRTTTHGRNMAGARALWRATGMTDGDFDKPIIAVVNSFTQFVPGHVHLKDMGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEKAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP VFVSGGPME+GK +HGK LDLVDAMV A DD SDED Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMESGKTRLHGKDLKLDLVDAMVMAVDDSESDED 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V IERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATH DR+ LF+EAG L+V Sbjct: 181 VAAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHEDRRELFLEAGRLVV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 D++RRYYEQD+V LPR+IA+ AFENAM LDIAMGGSTNTVLH+LAAAHE E+DFTMAD Sbjct: 241 DISRRYYEQDEVGVLPRSIANFAAFENAMCLDIAMGGSTNTVLHLLAAAHEAEVDFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR+VP LSKVAP+ HMEDVHRAGG++SILGEL+KGGL++ D +VH+ TLG A Sbjct: 301 IDRLSRKVPHLSKVAPSTQQYHMEDVHRAGGVISILGELEKGGLIHADAGSVHSGTLGQA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 I++WDI R+ ET Y A P GIP+Q AFSQ RW +LD DR+ G IR +EH +S+DG Sbjct: 361 IEKWDIGRSRDETACSRYLAGPAGIPSQTAFSQSTRWPDLDLDRQGGCIRDIEHAYSQDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GNLA GCIVKTA VDESILKFSGPAR+FESQ+A+V AIL ++++AGDVV+IRY Sbjct: 421 GLAVLYGNLAEAGCIVKTASVDESILKFSGPARIFESQEAAVDAILHDQIQAGDVVLIRY 480 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGH SPEAA GGTIGL Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHCSPEAAEGGTIGL 540 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAAF 597 V+EGD I+IDIP RTI+L VS+ LA RRA +AKG W P R+R V+ AL+AYAA Sbjct: 541 VQEGDRIEIDIPGRTINLVVSDEVLADRRALMEAKGEQAWQPVN-RERVVSQALRAYAAL 599 Query: 598 ATSADRGAVRDLN 610 TSA RGAVRDL+ Sbjct: 600 TTSAARGAVRDLS 612 Lambda K H 0.318 0.134 0.391 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: 1288 Number of extensions: 42 Number of successful extensions: 2 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: 612 Length of database: 616 Length adjustment: 37 Effective length of query: 575 Effective length of database: 579 Effective search space: 332925 Effective search space used: 332925 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_029131996.1 A3GO_RS0102120 (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.32376.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-252 823.2 1.9 5.6e-252 823.0 1.9 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029131996.1 A3GO_RS0102120 dihydroxy-acid de Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029131996.1 A3GO_RS0102120 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 823.0 1.9 5.6e-252 5.6e-252 2 542 .. 18 610 .. 17 611 .. 0.98 Alignments for each domain: == domain 1 score: 823.0 bits; conditional E-value: 5.6e-252 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG++d d++kPiiavvns+t++vPghvhlkd+++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000428045.1:WP_029131996.1 18 ARALWRATGMTDGDFDKPIIAVVNSFTQFVPGHVHLKDMGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniPa++vsGGpme+gkt+l lcl|NCBI__GCF_000428045.1:WP_029131996.1 87 HGGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRLNIPAVFVSGGPMESGKTRL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 k ++d+++a++++ ++ s+e++ +iersacPt+gsCsG+ftansm+cltealGlslPg+++llat lcl|NCBI__GCF_000428045.1:WP_029131996.1 156 HGKDLKLDLVDAMVMAVDDSESDEDVAAIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLAT 224 8888899************************************************************** PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +++++el+ ++g+ +v++ +++++ Pr+i++ +afena+ ld+a+GGstntvLhlla+a+ea+ lcl|NCBI__GCF_000428045.1:WP_029131996.1 225 HEDRRELFLEAGRLVVDISRRYYEqdevgvlPRSIANFAAFENAMCLDIAMGGSTNTVLHLLAAAHEAE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v++++ d+drlsrkvP+l+k++Ps++++ +ed+hraGGv+++l+el+k gl+h da +v tl++ +e lcl|NCBI__GCF_000428045.1:WP_029131996.1 294 VDFTMADIDRLSRKVPHLSKVAPSTQQYhMEDVHRAGGVISILGELEKGGLIHADAGSVHSGTLGQAIE 362 **************************999**************************************** PP TIGR00110 339 kvkvlr.................................vdqd..virsldnpvkkegglavLkGnlae 372 k ++ r +d++ +ir ++++++++gglavL+Gnlae lcl|NCBI__GCF_000428045.1:WP_029131996.1 363 KWDIGRsrdetacsrylagpagipsqtafsqstrwpdldLDRQggCIRDIEHAYSQDGGLAVLYGNLAE 431 ****999****************************9987444366************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 G++vk+a+v+e+ilkf Gpa++fes+e+a++ail+ ++++Gdvv+iryeGPkGgPGm+emL+Pts+l+ lcl|NCBI__GCF_000428045.1:WP_029131996.1 432 AGCIVKTASVDESILKFSGPARIFESQEAAVDAILHDQIQAGDVVLIRYEGPKGGPGMQEMLYPTSYLK 500 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aLitDGrfsGgt+GlsiGh sPeaaegG+i+lv++GD+i+iDi+ r+++l vs+e la+rr lcl|NCBI__GCF_000428045.1:WP_029131996.1 501 SKGLGKACALITDGRFSGGTSGLSIGHCSPEAAEGGTIGLVQEGDRIEIDIPGRTINLVVSDEVLADRR 569 ********************************************************************* PP TIGR00110 511 akakkkea.........revkgaLakyaklvssadkGavld 542 a +++k++ r v+ aL++ya l +sa +Gav+d lcl|NCBI__GCF_000428045.1:WP_029131996.1 570 ALMEAKGEqawqpvnreRVVSQALRAYAALTTSAARGAVRD 610 **999998899****999*********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (616 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 9.87 // [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