Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_066922243.1 ACG33_RS14510 dihydroxy-acid dehydratase
Query= SwissProt::Q1MIB2 (612 letters) >NCBI__GCF_001579945.1:WP_066922243.1 Length = 611 Score = 917 bits (2370), Expect = 0.0 Identities = 456/610 (74%), Positives = 510/610 (83%), Gaps = 2/610 (0%) Query: 1 MPVYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 MP YRS+T+T GRNMAGAR LWRATGMKD DFGKPIIAVVNSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPQYRSKTSTAGRNMAGARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120 REIE AG VAKEFNTIAVDDGIAMGHDGMLYSLPSR++IADSVEYMVNAHCADAMVCIS Sbjct: 61 CREIEKAGAVAKEFNTIAVDDGIAMGHDGMLYSLPSRDIIADSVEYMVNAHCADAMVCIS 120 Query: 121 NCDKITPGMLMASLRLNIPTVFVSGGPMEAGKVVMHGKTHALDLVDAMVAAADDKISDED 180 NCDKITPGMLMA++RLNIP VFVSGGPMEAGK + + LDL+DAMV AAD +SDE+ Sbjct: 121 NCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKTKLAERK--LDLIDAMVMAADSGVSDEE 178 Query: 181 VQTIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHLDRKRLFVEAGHLIV 240 V +ERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNG+ LATH DR+ LFV AG LIV Sbjct: 179 VVEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTILATHADRRELFVRAGRLIV 238 Query: 241 DLARRYYEQDDVKALPRTIASKQAFENAMTLDIAMGGSTNTVLHILAAAHEGEIDFTMAD 300 D+ RRYYEQD+ LPR+IAS AFENAM+LDIAMGGSTNT+LH+LA A EGE+ FTM D Sbjct: 239 DITRRYYEQDEASLLPRSIASFAAFENAMSLDIAMGGSTNTILHLLAMAQEGEVSFTMKD 298 Query: 301 IDALSRRVPCLSKVAPAKSDVHMEDVHRAGGIMSILGELDKGGLLNRDCPTVHAETLGDA 360 ID LSRRVP L KVAP + H+EDVHRAGGIM+IL EL++ G L+ TVH++T+ +A Sbjct: 299 IDRLSRRVPQLCKVAPNTQEYHVEDVHRAGGIMAILAELERAGKLHTQVRTVHSKTMEEA 358 Query: 361 IDRWDITRTNSETVRKFYRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420 + RWDI +T E V+ FY+A P GIPTQ AFSQ RW LD DRE G IRS H FS +G Sbjct: 359 LCRWDILQTGDEAVKTFYKAGPAGIPTQEAFSQSTRWPSLDVDRERGCIRSASHAFSSEG 418 Query: 421 GLAVLKGNLAIDGCIVKTAGVDESILKFSGPARVFESQDASVKAILANEVKAGDVVVIRY 480 GLAVL GN+A DGC+VKTAGVD+++L F GPA V ESQD +V IL +VKAGDVV++RY Sbjct: 419 GLAVLYGNIARDGCVVKTAGVDDALLIFEGPAHVTESQDQAVGHILEGKVKAGDVVIVRY 478 Query: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHASPEAANGGTIGL 540 EGPKGGPGMQEMLYPTSY+KSKGLGKACAL+TDGRFSGGTSGLSIGH SPEAA GG IGL Sbjct: 479 EGPKGGPGMQEMLYPTSYIKSKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGL 538 Query: 541 VREGDMIDIDIPNRTISLRVSETELAARRAEQDAKGWYPTEVRKRNVTTALKAYAAFATS 600 VR GD I IDIPNRTI + VS+ ELA RRA QDA+GW P R R V+TAL+AYA ATS Sbjct: 539 VRNGDRIRIDIPNRTIDVLVSDEELAQRRAAQDARGWKPAAPRPRKVSTALQAYAKMATS 598 Query: 601 ADRGAVRDLN 610 ADRGAVRD++ Sbjct: 599 ADRGAVRDIS 608 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: 1178 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: 611 Length adjustment: 37 Effective length of query: 575 Effective length of database: 574 Effective search space: 330050 Effective search space used: 330050 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_066922243.1 ACG33_RS14510 (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.23367.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-257 839.9 2.7 4.7e-257 839.7 2.7 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066922243.1 ACG33_RS14510 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066922243.1 ACG33_RS14510 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 839.7 2.7 4.7e-257 4.7e-257 2 542 .. 18 606 .. 17 607 .. 0.99 Alignments for each domain: == domain 1 score: 839.7 bits; conditional E-value: 4.7e-257 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamg 70 aral++atG+kd d++kPiiavvns+t++vPghvhlkdl++lv +eie+aG+vakefntiav+DGiamg lcl|NCBI__GCF_001579945.1:WP_066922243.1 18 ARALWRATGMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVCREIEKAGAVAKEFNTIAVDDGIAMG 86 79******************************************************************* PP TIGR00110 71 heGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktkl 139 h+Gm+ysLpsr+iiaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniPa++vsGGpmeagktkl lcl|NCBI__GCF_001579945.1:WP_066922243.1 87 HDGMLYSLPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGKTKL 155 ********************************************************************9 PP TIGR00110 140 sekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllat 208 +e ++d+++a++++a++ +s+ee+ e+ersacPt+gsCsG+ftansm+cltealGlslPg++t+lat lcl|NCBI__GCF_001579945.1:WP_066922243.1 156 AE--RKLDLIDAMVMAADSGVSDEEVVEVERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGTILAT 222 65..5899************************************************************* PP TIGR00110 209 saekkelakksgkrivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeag 270 +a+++el+ ++g+ iv++++++++ Pr+i++ +afena++ld+a+GGstnt+Lhlla+a+e + lcl|NCBI__GCF_001579945.1:WP_066922243.1 223 HADRRELFVRAGRLIVDITRRYYEqdeasllPRSIASFAAFENAMSLDIAMGGSTNTILHLLAMAQEGE 291 ********************************************************************* PP TIGR00110 271 vklslddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetle 338 v+++++d+drlsr+vP+l+k++P+++++ +ed+hraGG++a+l el+++g+lh+++ tv kt++e l lcl|NCBI__GCF_001579945.1:WP_066922243.1 292 VSFTMKDIDRLSRRVPQLCKVAPNTQEYhVEDVHRAGGIMAILAELERAGKLHTQVRTVHSKTMEEALC 360 **************************999**************************************** PP TIGR00110 339 kvkvlr...................................vdqdvirsldnpvkkegglavLkGnlae 372 + ++l+ ++ +irs ++++++egglavL+Gn+a lcl|NCBI__GCF_001579945.1:WP_066922243.1 361 RWDILQtgdeavktfykagpagiptqeafsqstrwpsldvdRERGCIRSASHAFSSEGGLAVLYGNIAR 429 ****999******************************99555555************************ PP TIGR00110 373 eGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalv 441 +G+vvk+agv++ +l feGpa+v es+++a+ il+gkvk+Gdvv++ryeGPkGgPGm+emL+Pts+++ lcl|NCBI__GCF_001579945.1:WP_066922243.1 430 DGCVVKTAGVDDALLIFEGPAHVTESQDQAVGHILEGKVKAGDVVIVRYEGPKGGPGMQEMLYPTSYIK 498 ********************************************************************* PP TIGR00110 442 glGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerr 510 + GLgk++aL+tDGrfsGgt+GlsiGh sPeaa+gGai+lv++GD+i+iDi+nr++d+ vs+eela+rr lcl|NCBI__GCF_001579945.1:WP_066922243.1 499 SKGLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGLVRNGDRIRIDIPNRTIDVLVSDEELAQRR 567 ********************************************************************* PP TIGR00110 511 akakkkea.......revkgaLakyaklvssadkGavld 542 a+++++++ r+v+ aL++yak+++sad+Gav+d lcl|NCBI__GCF_001579945.1:WP_066922243.1 568 AAQDARGWkpaaprpRKVSTALQAYAKMATSADRGAVRD 606 *******999***99**********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (611 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: 00:00:00.03 # Mc/sec: 9.82 // [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