Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_011995749.1 XAUT_RS00355 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_000017645.1:WP_011995749.1 Length = 617 Score = 985 bits (2547), Expect = 0.0 Identities = 488/614 (79%), Positives = 547/614 (89%), Gaps = 5/614 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRSRT+THGRNMAGARGLWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSRTSTHGRNMAGARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADAMVCIS Sbjct: 61 AREIEKAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIP VFVSGGPMEAGKV++ +DL+DAM+AAADDK++D D Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVLLSTGEKKVDLIDAMIAAADDKVTDAD 180 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 VQ +ERSACPTCGSCSGMFTANSMNCLTEALGL+LPGNGSTLATH DR+RLFVEAGHLIV Sbjct: 181 VQVMERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLATHADRERLFVEAGHLIV 240 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 DLARRYYEQDD LPR++AS +AFENAMTLDI+MGGSTNTVLH+LAAA+EGE+ FTMAD Sbjct: 241 DLARRYYEQDDASVLPRSVASFKAFENAMTLDISMGGSTNTVLHLLAAANEGEVPFTMAD 300 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVP L KVAPA +++HMEDVHRAGGIM+ILGELD+GGL++ D PTVHA T+ DA Sbjct: 301 IDRLSRRVPVLCKVAPAVANIHMEDVHRAGGIMAILGELDRGGLIHTDLPTVHAATMADA 360 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 +DRWD+ RT SE+V F+RAAPGG+PTQVAFSQ RWD+LD DRE GVIR V H +SKDG Sbjct: 361 LDRWDVKRTKSESVATFFRAAPGGVPTQVAFSQSRRWDDLDLDRETGVIRDVAHAYSKDG 420 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILA-NEVKAGDVVVIR 479 GLAVL GN+A+DGCIVKTAGVD SILKF+G AR+FESQDA+V+AIL+ ++AGDVV+IR Sbjct: 421 GLAVLYGNIALDGCIVKTAGVDASILKFTGKARIFESQDAAVEAILSTGRIQAGDVVLIR 480 Query: 480 YEGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIG 539 YEGP+GGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGG+SGLSIGH SPEAA GG IG Sbjct: 481 YEGPRGGPGMQEMLYPTSYLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAIG 540 Query: 540 LVREGDMIDIDIPNRTISLRVSETELAARRAEQDAKG---WYPTEVRKRNVTTALKAYAA 596 LV EGD I+IDIPNR I + VS+ L+ RRA +AKG W P + RKR V+ AL+AYAA Sbjct: 541 LVEEGDTIEIDIPNRIIRVAVSDEVLSQRRAAMEAKGDAAWKPAD-RKRVVSQALQAYAA 599 Query: 597 FATSADRGAVRDLN 610 TSA RGAVRD++ Sbjct: 600 LTTSAARGAVRDVS 613 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: 1259 Number of extensions: 34 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: 612 Length of database: 617 Length adjustment: 37 Effective length of query: 575 Effective length of database: 580 Effective search space: 333500 Effective search space used: 333500 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_011995749.1 XAUT_RS00355 (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.29193.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-250 817.3 5.8 3.4e-250 817.1 5.8 1.0 1 lcl|NCBI__GCF_000017645.1:WP_011995749.1 XAUT_RS00355 dihydroxy-acid dehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_011995749.1 XAUT_RS00355 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 817.1 5.8 3.4e-250 3.4e-250 2 542 .. 18 611 .. 17 612 .. 0.98 Alignments for each domain: == domain 1 score: 817.1 bits; conditional E-value: 3.4e-250 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 ar l++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+DGiamg lcl|NCBI__GCF_000017645.1:WP_011995749.1 18 ARGLWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMG 86 689****************************************************************** PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPa++vsGGpmeagk+ l lcl|NCBI__GCF_000017645.1:WP_011995749.1 87 HDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKVLL 155 ********************************************************************* PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 s ++vd+++a++++a++k+++++++ +ersacPt+gsCsG+ftansm+cltealGl+lPg++++lat lcl|NCBI__GCF_000017645.1:WP_011995749.1 156 STGEKKVDLIDAMIAAADDKVTDADVQVMERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSTLAT 224 ********************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a++++l+ ++g+ iv+l +++++ Pr++++ +afena+tld+ +GGstntvLhlla+a+e + lcl|NCBI__GCF_000017645.1:WP_011995749.1 225 HADRERLFVEAGHLIVDLARRYYEqddasvlPRSVASFKAFENAMTLDISMGGSTNTVLHLLAAANEGE 293 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v +++ d+drlsr+vP+l+k++P+ ++ +ed+hraGG++a+l+eld+ gl+h+d tv t+a+ l+ lcl|NCBI__GCF_000017645.1:WP_011995749.1 294 VPFTMADIDRLSRRVPVLCKVAPAVANIhMEDVHRAGGIMAILGELDRGGLIHTDLPTVHAATMADALD 362 ************************99888**************************************** PP TIGR00110 339 kvkvlr...................................vdqd..virsldnpvkkegglavLkGnl 370 + +v+r + vir + ++++k+gglavL+Gn+ lcl|NCBI__GCF_000017645.1:WP_011995749.1 363 RWDVKRtksesvatffraapggvptqvafsqsrrwddldldR--EtgVIRDVAHAYSKDGGLAVLYGNI 429 *****9*****************************9988544..355********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeail.ggkvkeGdvvviryeGPkGgPGmremLaPts 438 a +G++vk+agv+ +ilkf+G+a++fes+++a+eail +g++++Gdvv+iryeGP+GgPGm+emL+Pts lcl|NCBI__GCF_000017645.1:WP_011995749.1 430 ALDGCIVKTAGVDASILKFTGKARIFESQDAAVEAILsTGRIQAGDVVLIRYEGPRGGPGMQEMLYPTS 498 ************************************9459***************************** PP TIGR00110 439 alvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeela 507 +l++ GLgk++aL+tDGrfsGg++GlsiGhvsPeaaegGai+lve+GD+i+iDi+nr + ++vs+e l lcl|NCBI__GCF_000017645.1:WP_011995749.1 499 YLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAIGLVEEGDTIEIDIPNRIIRVAVSDEVLS 567 ********************************************************************* PP TIGR00110 508 errakakkkea.........revkgaLakyaklvssadkGavld 542 +rra++++k++ r v+ aL++ya l +sa +Gav+d lcl|NCBI__GCF_000017645.1:WP_011995749.1 568 QRRAAMEAKGDaawkpadrkRVVSQALQAYAALTTSAARGAVRD 611 *********9999******999********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (617 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: 00:00:00.04 # Mc/sec: 8.08 // [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