Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >FitnessBrowser__Marino:GFF612 Length = 597 Score = 889 bits (2297), Expect = 0.0 Identities = 440/595 (73%), Positives = 499/595 (83%), Gaps = 2/595 (0%) Query: 15 MAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEF 74 MAGAR LWRATGMKD DFGKPIIAV NSFTQFVPGHVHLKDLGQLV REIE+AGGVAKEF Sbjct: 1 MAGARALWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEF 60 Query: 75 NTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMASL 134 NTIAVDDGIAMGHDGMLYSLPSRE+IADSVEYMVNAHCADA+VCISNCDKITPGMLMA++ Sbjct: 61 NTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAM 120 Query: 135 RLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDEDVQTIERSACPTCGS 194 RLNIPT+FVSGGPMEAGK + H LDLVDAMV AAD SDE V+ ER+ACPTCGS Sbjct: 121 RLNIPTIFVSGGPMEAGKTKL--SEHKLDLVDAMVIAADPNASDEQVEEYERNACPTCGS 178 Query: 195 CSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIVDLARRYYEQDDVKA 254 CSGMFTANSMNCLTEA+GL+LPGNGS LATH DR++LF++AG IV+ ARRYYE+DD Sbjct: 179 CSGMFTANSMNCLTEAIGLALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASV 238 Query: 255 LPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMADIDALSRRVPCLSKV 314 LP +IAS AFENAM +DIAMGGSTNT+LH+LAAA EG + FT+ +ID LSRRVP L KV Sbjct: 239 LPLSIASMAAFENAMVMDIAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKV 298 Query: 315 APAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDAIDRWDITRTNSETV 374 AP HMEDVHRAGGIM ILGEL++GGL+N D PTVH++T+ +A++ WDI R+ V Sbjct: 299 APNSPKYHMEDVHRAGGIMGILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEV 358 Query: 375 RKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDGGLAVLKGNLAIDGC 434 +FY+A P GIPTQ AFSQ RW LD DRE G IRSVE+ +S +GGLAVL GN+A+DGC Sbjct: 359 VEFYKAGPAGIPTQTAFSQSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGC 418 Query: 435 IVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRYEGPKGGPGMQEMLY 494 +VKTAGVDESI F G ARVFESQD++V IL++EVK G+VV+IRYEGP+GGPGMQEMLY Sbjct: 419 VVKTAGVDESIFVFEGKARVFESQDSAVAGILSDEVKPGEVVIIRYEGPRGGPGMQEMLY 478 Query: 495 PTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGLVREGDMIDIDIPNR 554 PTSYLKSKGLGK CAL+TDGRFSGGTSGLSIGHASPEAA GG IGL+ GD I IDIPNR Sbjct: 479 PTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRIDIPNR 538 Query: 555 TISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATSADRGAVRDL 609 +I++ + + EL RR +DAKGW P R R V+ ALKAYA ATSAD+GAVRDL Sbjct: 539 SINVELDQHELDRRREARDAKGWKPELPRDRKVSAALKAYALLATSADKGAVRDL 593 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: 26 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: 597 Length adjustment: 37 Effective length of query: 575 Effective length of database: 560 Effective search space: 322000 Effective search space used: 322000 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 GFF612 HP15_595 (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.21484.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-255 832.4 0.5 9.1e-255 832.2 0.5 1.0 1 lcl|FitnessBrowser__Marino:GFF612 HP15_595 dihydroxy-acid dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF612 HP15_595 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 832.2 0.5 9.1e-255 9.1e-255 2 542 .. 4 592 .. 3 593 .. 0.99 Alignments for each domain: == domain 1 score: 832.2 bits; conditional E-value: 9.1e-255 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmkys 77 aral++atG+kd d++kPiiav+ns+t++vPghvhlkdl++lv +eie+aGgvakefntiav+DGiamgh+Gm+ys lcl|FitnessBrowser__Marino:GFF612 4 ARALWRATGMKDGDFGKPIIAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTIAVDDGIAMGHDGMLYS 79 79************************************************************************** PP TIGR00110 78 LpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvfeavg 153 LpsreiiaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpmeagktklse +++d+++a++ lcl|FitnessBrowser__Marino:GFF612 80 LPSREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGKTKLSE--HKLDLVDAMV 153 *************************************************************977..589******* PP TIGR00110 154 eyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrivelvkk 229 +a+++ s+e++ee+er+acPt+gsCsG+ftansm+cltea+Gl+lPg+++llat+a++++l+ k+g++ive ++ lcl|FitnessBrowser__Marino:GFF612 154 IAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIGLALPGNGSLLATHADREQLFLKAGRQIVENARR 229 **************************************************************************** PP TIGR00110 230 nik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkkv 298 +++ P +i++ +afena+++d+a+GGstnt+Lhlla+a+e gv ++l+++d+lsr+vP+l+k++P++ k+ lcl|FitnessBrowser__Marino:GFF612 230 YYEeddasvlPLSIASMAAFENAMVMDIAMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKY 305 *************************************************************************998 PP TIGR00110 299 .iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............................. 344 +ed+hraGG++++l+el++ gl+++d tv kt+ e le+ +++r lcl|FitnessBrowser__Marino:GFF612 306 hMEDVHRAGGIMGILGELERGGLINTDLPTVHSKTMREALETWDIMRspptevvefykagpagiptqtafsqstrw 381 8*************************************************************************** PP TIGR00110 345 ......vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 ++ +irs++n++++egglavL+Gn+a +G+vvk+agv+e+i +feG+a+vfes++ a+++il+ +vk G lcl|FitnessBrowser__Marino:GFF612 382 ptldgdRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKARVFESQDSAVAGILSDEVKPG 457 **88655566****************************************************************** PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkiki 490 +vv+iryeGP+GgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+l+e+GD+i+i lcl|FitnessBrowser__Marino:GFF612 458 EVVIIRYEGPRGGPGMQEMLYPTSYLKSKGLGKDCALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLIENGDTIRI 533 **************************************************************************** PP TIGR00110 491 Dienrkldlevseeelaerrakakkkea.......revkgaLakyaklvssadkGavld 542 Di+nr +++e++++el++rr++ ++k++ r+v+ aL++ya l++sadkGav+d lcl|FitnessBrowser__Marino:GFF612 534 DIPNRSINVELDQHELDRRREARDAKGWkpelprdRKVSAALKAYALLATSADKGAVRD 592 ***************************999****99*********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (597 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: 12.43 // [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