Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 Length = 613 Score = 940 bits (2430), Expect = 0.0 Identities = 464/608 (76%), Positives = 522/608 (85%), Gaps = 2/608 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRS+T+THGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE AGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS Sbjct: 61 AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMASLRLNIP +FVSGGPMEAGK + +H LDLVDAMV AAD SDE Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEK 178 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V ERSACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DR++LF++AG IV Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 +L +RYY ++D LPR IA+ +AFENAMTLDIAMGGSTNT+LH+LAAA E EIDF + D Sbjct: 239 ELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSR VP L KVAP HMEDVHRAGGI SILG L +GGLL+ D PTVH++++ + Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEG 358 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 I +WDIT+T E V F++A P GIPTQ AFSQ RW+ LD DRENG IRSVEH +SK+G Sbjct: 359 IAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEG 418 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A+DGC+VKTAGVDESI F G A++FESQD++V+ ILA+EVKAGD+V+IRY Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRY 478 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGKACAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 V++GD + IDIPNR+I+L +S+ E+AARRAEQD KGW P EVR R VTTALKAYA ATS Sbjct: 539 VQDGDKVLIDIPNRSINLLISDEEMAARRAEQDKKGWKPVEVRPRKVTTALKAYALLATS 598 Query: 601 ADRGAVRD 608 AD+GAVR+ Sbjct: 599 ADKGAVRN 606 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: 1215 Number of extensions: 33 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: 613 Length adjustment: 37 Effective length of query: 575 Effective length of database: 576 Effective search space: 331200 Effective search space used: 331200 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 Pf1N1B4_2303 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
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.4273.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-255 834.0 1.8 3e-255 833.8 1.8 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4.2.1.9) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 833.8 1.8 3e-255 3e-255 2 542 .. 18 606 .. 17 607 .. 0.98 Alignments for each domain: == domain 1 score: 833.8 bits; conditional E-value: 3e-255 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsD 65 aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvakefntiav+D lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDD 81 79************************************************************** PP TIGR00110 66 GiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsG 129 Giamgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlma+lrlniP+i+vsG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 82 GIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMASLRLNIPVIFVSG 145 **************************************************************** PP TIGR00110 130 GpmeagktklsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmaclte 193 Gpmeagktkl + +d+++a++ +a++ s+e++ e+ersacPt+gsCsG+ftansm+cl e lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 146 GPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEKVAEYERSACPTCGSCSGMFTANSMNCLVE 207 *********8..557899********************************************** PP TIGR00110 194 alGlslPgsstllatsaekkelakksgkrivelvkknik.......Prdiltkeafenaitldl 250 alGl+lPg++++lat++++++l+ ++g++ivel+k+++ Pr+i++ +afena+tld+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 208 ALGLALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGendesvlPRNIANFKAFENAMTLDI 271 **************************************99999********************* PP TIGR00110 251 alGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlk 313 a+GGstnt+Lhlla+a+ea+++++l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 272 AMGGSTNTILHLLAAAQEAEIDFDLRDIDRLSRHVPQLCKVAPNIQKYhMEDVHRAGGIFSILG 335 *********************************************9999*************** PP TIGR00110 314 eldkegllhkdaltvtGktlaetlekvkvlr................................. 344 +l + gllh+d tv k++ae ++k ++++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 336 SLARGGLLHTDLPTVHSKSMAEGIAKWDITQttdeavhhffkagpagiptqtafsqstrwetld 399 *****************************999******************************77 PP TIGR00110 345 ..vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeai 406 ++ +irs++++++kegglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +i lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 400 ddRENGCIRSVEHAYSKEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGI 463 555555********************************************************** PP TIGR00110 407 lggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvs 470 l+ +vk+Gd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh s lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 464 LADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHAS 527 **************************************************************** PP TIGR00110 471 PeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLak 527 Peaa+gGai+lv+dGDk+ iDi+nr ++l +s+ee+a+rra+++kk++ r+v aL++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 528 PEAAAGGAIGLVQDGDKVLIDIPNRSINLLISDEEMAARRAEQDKKGWkpvevrpRKVTTALKA 591 ************************************************9*****999******* PP TIGR00110 528 yaklvssadkGavld 542 ya l++sadkGav++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303 592 YALLATSADKGAVRN 606 *************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (613 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: 11.26 // [ok]
This GapMind analysis is from Apr 09 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