Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF233 Psest_0234 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__psRCH2:GFF233 Length = 612 Score = 935 bits (2416), Expect = 0.0 Identities = 462/608 (75%), Positives = 518/608 (85%), Gaps = 2/608 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRS+T+THGRNMAGAR LWRATGMKD DF KPIIA+ NSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPDYRSKTSTHGRNMAGARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 AREIE GGVAKEFNTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCIS Sbjct: 61 AREIEKHGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA+LRLNIP VFVSGGPMEAGK + +H LDLVDAMV AAD+ SDE Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADESASDEK 178 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V ERSACPTCGSCSGMFTANSMNCL EALGL+LPGNGSTLATH DR++LF+ AG +V Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHSDREQLFLRAGRTVV 238 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 +L +RYY + D LPR IAS++AFENAMTLDIAMGGSTNT+LH+LAAA E E+DF + Sbjct: 239 ELCKRYYGEGDESVLPRNIASRRAFENAMTLDIAMGGSTNTILHLLAAAQEAEVDFDLRA 298 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 IDALSR+VP L KVAP HMEDVHRAGGI SILGEL +GGLL+ D PTVH+ TL + Sbjct: 299 IDALSRKVPQLCKVAPNIQKYHMEDVHRAGGIFSILGELARGGLLHTDVPTVHSRTLAEG 358 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 I +WDIT+T E V F++A P GIPTQ AFSQ RWD LD DRENG IRSVEH +S++G Sbjct: 359 IAQWDITQTQDEAVHTFFKAGPAGIPTQTAFSQSTRWDSLDDDRENGCIRSVEHAYSQEG 418 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A+DGC+VKTAGVDESI F G A+++ESQD++VK ILA+EVKAGD+V+IRY Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYESQDSAVKGILADEVKAGDIVIIRY 478 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 VR+GD + IDIPNR+I L+VS+ EL+ RR EQD KGW P + R R VTTALKAYA ATS Sbjct: 539 VRDGDKVLIDIPNRSIQLQVSDEELSHRRIEQDKKGWKPAQPRTRKVTTALKAYALLATS 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: 1203 Number of extensions: 30 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: 612 Length adjustment: 37 Effective length of query: 575 Effective length of database: 575 Effective search space: 330625 Effective search space used: 330625 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 GFF233 Psest_0234 (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.6632.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-255 834.4 1.3 2.3e-255 834.2 1.3 1.0 1 lcl|FitnessBrowser__psRCH2:GFF233 Psest_0234 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF233 Psest_0234 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 834.2 1.3 2.3e-255 2.3e-255 2 542 .. 18 606 .. 17 607 .. 0.98 Alignments for each domain: == domain 1 score: 834.2 bits; conditional E-value: 2.3e-255 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 aral++atG+kded++kPiia++ns+t++vPghvhlkdl++lv++eie+ Ggvakefntiav+DGiamgh+Gm+ys lcl|FitnessBrowser__psRCH2:GFF233 18 ARALWRATGMKDEDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKHGGVAKEFNTIAVDDGIAMGHDGMLYS 93 79************************************************************************** PP TIGR00110 78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavg 153 LpsreiiaDsve++v+ah++Da+v+is+CDki+PGmlmaalrlniP+++vsGGpmeagktkl + +d+++a++ lcl|FitnessBrowser__psRCH2:GFF233 94 LPSREIIADSVEYMVNAHCADAIVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKL--ASHGLDLVDAMV 167 *************************************************************8..557899****** PP TIGR00110 154 eyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkk 229 +a++ s+e++ e+ersacPt+gsCsG+ftansm+cl+ealGl+lPg++++lat++++++l+ ++g+++vel+k+ lcl|FitnessBrowser__psRCH2:GFF233 168 IAADESASDEKVAEYERSACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHSDREQLFLRAGRTVVELCKR 243 **************************************************************************** PP TIGR00110 230 nik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv 298 ++ Pr+i++++afena+tld+a+GGstnt+Lhlla+a+ea+v+++l +d lsrkvP+l+k++P+ +k+ lcl|FitnessBrowser__psRCH2:GFF233 244 YYGegdesvlPRNIASRRAFENAMTLDIAMGGSTNTILHLLAAAQEAEVDFDLRAIDALSRKVPQLCKVAPNIQKY 319 **99999******************************************************************999 PP TIGR00110 299 .iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................. 344 +ed+hraGG+ ++l+el + gllh+d+ tv +tlae +++ ++++ lcl|FitnessBrowser__psRCH2:GFF233 320 hMEDVHRAGGIFSILGELARGGLLHTDVPTVHSRTLAEGIAQWDITQtqdeavhtffkagpagiptqtafsqstrw 395 9********************************************999**************************** PP TIGR00110 345 ......vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 ++ +irs+++++++egglavL+Gn+a +G+vvk+agv+e+i +feG+ak++es++ a+++il+ +vk+G lcl|FitnessBrowser__psRCH2:GFF233 396 dsldddRENGCIRSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGTAKIYESQDSAVKGILADEVKAG 471 **77555555****************************************************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkiki 490 d+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv+dGDk+ i lcl|FitnessBrowser__psRCH2:GFF233 472 DIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDGDKVLI 547 **************************************************************************** PP TIGR00110 491 Dienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542 Di+nr ++l+vs+eel +rr +++kk++ r+v aL++ya l++sadkGav++ lcl|FitnessBrowser__psRCH2:GFF233 548 DIPNRSIQLQVSDEELSHRRIEQDKKGWkpaqprtRKVTTALKAYALLATSADKGAVRN 606 ***************************999***9999********************87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (612 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: 00:00:00.03 # Mc/sec: 10.88 // [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