Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_037574832.1 BS73_RS21300 dihydroxy-acid dehydratase
Query= BRENDA::Q8NQZ9 (613 letters) >NCBI__GCF_000744815.1:WP_037574832.1 Length = 616 Score = 826 bits (2133), Expect = 0.0 Identities = 403/613 (65%), Positives = 493/613 (80%), Gaps = 3/613 (0%) Query: 1 MIPLRSKVTTVGRNAAGARALWRATGTKENEFG-KPIVAIVNSYTQFVPGHVHLKNVGDI 59 M LRS+ T GRN AGARAL RA+G + G KPI+A+ NS+T+FVPGH HL VG I Sbjct: 1 MPELRSRTVTHGRNMAGARALMRASGVAGADIGRKPIIAVANSFTEFVPGHTHLSPVGRI 60 Query: 60 VADAVRKAGGVPKEFNTIAVDDGIAMGHGGMLYSLPSREIIADSVEYMVNAHTADAMVCI 119 V++AV +AGG+P+EFNTIAVDDGIAMGHGGMLYSLPSR++IADSVEYMVNAH ADA+VCI Sbjct: 61 VSEAVSEAGGIPREFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADALVCI 120 Query: 120 SNCDKITPGMLNAAMRLNIPVVFVSGGPMEAGKAVVVDGVAHAPTDLITAISASASDAVD 179 SNCDKITPGML AAMRLNIP +FVSGGPME+G+A +VDG DLITAI+ SA+DAV Sbjct: 121 SNCDKITPGMLMAAMRLNIPTIFVSGGPMESGQATLVDGTVRK-LDLITAIAESANDAVS 179 Query: 180 DAGLAAVEASACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAARRALFEKAGE 239 D ++ +E +ACPTCGSCSGMFTANSMNCLTEA+GL+LPGNG+TLATH AR+AL+++AG Sbjct: 180 DEDISRIEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTTLATHTARKALYQEAGR 239 Query: 240 TVVELCRRYYGEEDESVLPRGIATKKAFENAMALDMAMGGSTNTILHILAAAQEGEVDFD 299 +++L RYYG++D +VLPR I ++ AFENAMALD+AMGGSTNTILH+LAAAQE E+DF Sbjct: 240 QILKLVDRYYGQDDSTVLPRSIGSRAAFENAMALDIAMGGSTNTILHLLAAAQEAELDFT 299 Query: 300 LADIDELSKNVPCLSKVAPNSDYHMEDVHRAGGIPALLGELNRGGLLNKDVHSVHSNDLE 359 + DID LS+ +PCL KVAPN Y++EDVHRAGGIP +LGEL R GLLN+DV +VHS+ L Sbjct: 300 MGDIDALSRRLPCLCKVAPNGSYYVEDVHRAGGIPGILGELYRAGLLNEDVTTVHSDSLA 359 Query: 360 GWLDDWDIRSGKTTEVATELFHAAPGGIRTTEAFSTENRWDELDTDAAKGCIRDVEHAYT 419 WL WD+R G + A ELFHAAPG R+ EAFS RWD LD DA +GCIRD+ HAY+ Sbjct: 360 DWLKRWDVRGGSPSPEAVELFHAAPGCKRSAEAFSQSERWDSLDLDAERGCIRDIGHAYS 419 Query: 420 ADGGLVVLRGNISPDGAVIKSAGIEEELWNFTGPARVVESQEEAVSVILTKTIQAGEVLV 479 +GGL VL GN++ +G V+K+AG++E +W FTGPA V ESQ+EAV IL K + G+V+V Sbjct: 420 TEGGLAVLHGNLAENGCVVKTAGVDESIWEFTGPAVVCESQDEAVERILNKEVGEGDVVV 479 Query: 480 VRYEGPSGGPGMQEMLHPTAFLKGSGLGKKCALITDGRFSGGSSGLSIGHVSPEAAHGGV 539 +RYEGP GGPGMQEML+PT+FLKG GLGK CALITDGRFSGG+SGLSIGH+SPEAA GG Sbjct: 480 IRYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIGHMSPEAAAGGT 539 Query: 540 IGLIENGDIVSIDVHNRKLEVQVSDEELQRRRDAMNASEKPWQPVNRNRVVTKALRAYAK 599 I L+ +GD ++I + R++ ++V + EL RR A+ A ++P NR R V+ ALRAYA Sbjct: 540 IALVRDGDRITISIPERRICLEVPEAELAERRAALEAG-TGYRPANRQRQVSAALRAYAA 598 Query: 600 MATSADKGAVRQV 612 MATSADKGAVR V Sbjct: 599 MATSADKGAVRDV 611 Lambda K H 0.315 0.132 0.385 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: 1145 Number of extensions: 40 Number of successful extensions: 4 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: 613 Length of database: 616 Length adjustment: 37 Effective length of query: 576 Effective length of database: 579 Effective search space: 333504 Effective search space used: 333504 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 (21.6 bits) S2: 53 (25.0 bits)
Align candidate WP_037574832.1 BS73_RS21300 (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.148245.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-241 788.4 1.4 2e-241 788.2 1.4 1.0 1 NCBI__GCF_000744815.1:WP_037574832.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037574832.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 788.2 1.4 2e-241 2e-241 2 542 .. 18 610 .. 17 611 .. 0.98 Alignments for each domain: == domain 1 score: 788.2 bits; conditional E-value: 2e-241 TIGR00110 2 arallkatGlkdedle.kPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheG 73 aral++a G+ +d++ kPiiav+ns+te+vPgh hl+ ++++v+e++++aGg++ efntiav+DGiamgh+G NCBI__GCF_000744815.1:WP_037574832.1 18 ARALMRASGVAGADIGrKPIIAVANSFTEFVPGHTHLSPVGRIVSEAVSEAGGIPREFNTIAVDDGIAMGHGG 90 79************9748******************************************************* PP TIGR00110 74 mkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl.sekidl 145 m+ysLpsr++iaDsve++v+ah++Dalv+is+CDki+PGmlmaa+rlniP+i+vsGGpme+g+ +l + + NCBI__GCF_000744815.1:WP_037574832.1 91 MLYSLPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPTIFVSGGPMESGQATLvDGTVRK 163 ***************************************************************9983557999 PP TIGR00110 146 vdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakk 218 +d++ a+ e a++ +s+e++++ie++acPt+gsCsG+ftansm+cltea+Gl+lPg++t+lat++ +k+l ++ NCBI__GCF_000744815.1:WP_037574832.1 164 LDLITAIAESANDAVSDEDISRIEENACPTCGSCSGMFTANSMNCLTEAIGLALPGNGTTLATHTARKALYQE 236 ************************************************************************* PP TIGR00110 219 sgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrk 284 +g++i +lv +++ Pr+i +++afena++ld+a+GGstnt+Lhlla+a+ea++++++ d+d lsr+ NCBI__GCF_000744815.1:WP_037574832.1 237 AGRQILKLVDRYYGqddstvlPRSIGSRAAFENAMALDIAMGGSTNTILHLLAAAQEAELDFTMGDIDALSRR 309 ************999999******************************************************* PP TIGR00110 285 vPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............. 344 +P+l+k++P+g++++ed+hraGG++++l+el+++gll++d++tv ++la+ l++ +v+ NCBI__GCF_000744815.1:WP_037574832.1 310 LPCLCKVAPNGSYYVEDVHRAGGIPGILGELYRAGLLNEDVTTVHSDSLADWLKRWDVRGgspspeavelfha 382 **********************************************************9999*********** PP TIGR00110 345 .......................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpak 394 +++ +ir + ++++ egglavL+Gnlae+G+vvk+agv+e+i++f+Gpa NCBI__GCF_000744815.1:WP_037574832.1 383 apgckrsaeafsqserwdsldldAERGCIRDIGHAYSTEGGLAVLHGNLAENGCVVKTAGVDESIWEFTGPAV 455 *******************99777777********************************************** PP TIGR00110 395 vfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiG 467 v es++ea+e il+++v eGdvvviryeGPkGgPGm+emL+Pts+l+g GLgk++aLitDGrfsGgt+GlsiG NCBI__GCF_000744815.1:WP_037574832.1 456 VCESQDEAVERILNKEVGEGDVVVIRYEGPKGGPGMQEMLYPTSFLKGRGLGKACALITDGRFSGGTSGLSIG 528 ************************************************************************* PP TIGR00110 468 hvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.......revkgaLakyaklvs 533 h+sPeaa+gG+ialv+dGD+i+i i++r++ lev e+elaerra+ ++ + r+v+ aL++ya +++ NCBI__GCF_000744815.1:WP_037574832.1 529 HMSPEAAAGGTIALVRDGDRITISIPERRICLEVPEAELAERRAALEAGTGyrpanrqRQVSAALRAYAAMAT 601 ********************************************998765567788889************** PP TIGR00110 534 sadkGavld 542 sadkGav+d NCBI__GCF_000744815.1:WP_037574832.1 602 SADKGAVRD 610 *******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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 17.36 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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