Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_010526299.1 GQW_RS0101505 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >NCBI__GCF_000220155.1:WP_010526299.1 Length = 608 Score = 798 bits (2061), Expect = 0.0 Identities = 406/606 (66%), Positives = 481/606 (79%), Gaps = 6/606 (0%) Query: 5 RSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLVAREI 64 RS TTT GR MAGAR LWRA GMK+ GKP+IA+ NSFTQFVPGHVHL +GQ + I Sbjct: 6 RSDTTTQGRRMAGARSLWRANGMKESQMGKPLIAIVNSFTQFVPGHVHLHHIGQEIKEII 65 Query: 65 EAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCISNCDK 124 E G A EFNTIAVDDGIAMGH GMLYSLPSRDLIADSVEYMVNAH ADA++CISNCDK Sbjct: 66 EKQGCFAAEFNTIAVDDGIAMGHDGMLYSLPSRDLIADSVEYMVNAHRADAMICISNCDK 125 Query: 125 ITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEEVEAI 184 ITPGMLMAAMRLNIP +FVSGGPMEAG K ALDL+DAMV+AADDS SDEEV A+ Sbjct: 126 ITPGMLMAAMRLNIPTIFVSGGPMEAGNSNGK----ALDLIDAMVMAADDSVSDEEVLAV 181 Query: 185 EKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVVDLCQ 244 E+ ACPTCGSCSGMFTANSMNCL EA+GL+LPGNG+++ATH +R+ LF+EA +V+L Sbjct: 182 EQNACPTCGSCSGMFTANSMNCLNEAIGLALPGNGTIVATHVNRKRLFEEAANKIVELAW 241 Query: 245 RWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRL 304 R+Y D + LPR IATR AF NAM+LDIAMGGSTNTVLHLLA AHE G+DF+M DID+L Sbjct: 242 RYYRDGDDSVLPRSIATRQAFMNAMTLDIAMGGSTNTVLHLLAIAHEAGVDFTMEDIDQL 301 Query: 305 SRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEALARW 364 SR P L+KVAP S H+EDV+RAGG++ IL EL R LID S + PT+ EAL Sbjct: 302 SRKTPVLAKVAP-NSHYHIEDVNRAGGILGILAELARHNLIDTSVGRIDYPTLAEALKEH 360 Query: 365 DIGRTN-SQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDGGLA 423 D+ + + IA E +K+AP G SQ A ++E DLDR+NG IR VEH +SKDGGLA Sbjct: 361 DLRSASVTDIAKEKYKSAPAGFRNLKLGSQNAVYDEFDLDRQNGCIRDVEHAYSKDGGLA 420 Query: 424 VLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRYEGP 483 VLFGN+A +GCIVKTAGVDESIL F GTARV+ESQD+A GIL G+VKAG+VVVI+YEGP Sbjct: 421 VLFGNIAKDGCIVKTAGVDESILHFEGTARVYESQDSACEGILSGEVKAGDVVVIKYEGP 480 Query: 484 KGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIALVET 543 KGGPGMQEMLYPT+Y+KS+ LG CAL+TDGRFSGGTSGLSIGH+SPEA GG IALV+T Sbjct: 481 KGGPGMQEMLYPTSYIKSRHLGKECALITDGRFSGGTSGLSIGHISPEAAAGGEIALVKT 540 Query: 544 GDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMTTNA 603 GD I+IDIP R I +++S+ L RR+ +L +G +A+ PL+R R ++ AL+AYA+M ++A Sbjct: 541 GDKIIIDIPQRSINVDISEEELEKRRQQELNKGTEAFKPLSRNRYVSKALQAYASMVSSA 600 Query: 604 ARGAVR 609 +GAVR Sbjct: 601 DKGAVR 606 Lambda K H 0.318 0.134 0.395 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: 1104 Number of extensions: 39 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: 617 Length of database: 608 Length adjustment: 37 Effective length of query: 580 Effective length of database: 571 Effective search space: 331180 Effective search space used: 331180 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_010526299.1 GQW_RS0101505 (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.3884990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-244 796.0 5.7 9.9e-244 795.8 5.7 1.0 1 NCBI__GCF_000220155.1:WP_010526299.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010526299.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 795.8 5.7 9.9e-244 9.9e-244 2 541 .. 19 606 .. 18 608 .] 0.98 Alignments for each domain: == domain 1 score: 795.8 bits; conditional E-value: 9.9e-244 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 ar+l++a G+k+ +++kP+ia+vns+t++vPghvhl+++++ +ke ie+ G a efntiav+DGiamgh+Gm NCBI__GCF_000220155.1:WP_010526299.1 19 ARSLWRANGMKESQMGKPLIAIVNSFTQFVPGHVHLHHIGQEIKEIIEKQGCFAAEFNTIAVDDGIAMGHDGM 91 69*********************************************************************** PP TIGR00110 75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147 +ysLpsr++iaDsve++v+ah++Da+++is+CDki+PGmlmaa+rlniP+i+vsGGpmeag+ + ++ +d NCBI__GCF_000220155.1:WP_010526299.1 92 LYSLPSRDLIADSVEYMVNAHRADAMICISNCDKITPGMLMAAMRLNIPTIFVSGGPMEAGNSN-GK---ALD 160 **************************************************************99.55...567 PP TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220 +++a++++a++ +s+ee+ ++e++acPt+gsCsG+ftansm+cl ea+Gl+lPg++t+ at+ ++k+l+++++ NCBI__GCF_000220155.1:WP_010526299.1 161 LIDAMVMAADDSVSDEEVLAVEQNACPTCGSCSGMFTANSMNCLNEAIGLALPGNGTIVATHVNRKRLFEEAA 233 7899********************************************************************* PP TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286 ++ivel ++++ Pr+i+t++af na+tld+a+GGstntvLhllaia+eagv+++++d+d+lsrk+P NCBI__GCF_000220155.1:WP_010526299.1 234 NKIVELAWRYYRdgddsvlPRSIATRQAFMNAMTLDIAMGGSTNTVLHLLAIAHEAGVDFTMEDIDQLSRKTP 306 ***********9************************************************************* PP TIGR00110 287 llaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr............... 344 +lak++P++++ ied++raGG+ ++l el +++l+++ + + tlae l++++++ NCBI__GCF_000220155.1:WP_010526299.1 307 VLAKVAPNSHYHIEDVNRAGGILGILAELARHNLIDTSVGRIDYPTLAEALKEHDLRSasvtdiakekyksap 379 ********************************************************999************** PP TIGR00110 345 .....................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396 ++ +ir ++++++k+gglavL+Gn+a++G++vk+agv+e+il+feG+a+v+ NCBI__GCF_000220155.1:WP_010526299.1 380 agfrnlklgsqnavydefdldRQNGCIRDVEHAYSKDGGLAVLFGNIAKDGCIVKTAGVDESILHFEGTARVY 452 ****************999766666************************************************ PP TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhv 469 es++ a e+il+g+vk+Gdvvvi+yeGPkGgPGm+emL+Pts++++ Lgk++aLitDGrfsGgt+GlsiGh+ NCBI__GCF_000220155.1:WP_010526299.1 453 ESQDSACEGILSGEVKAGDVVVIKYEGPKGGPGMQEMLYPTSYIKSRHLGKECALITDGRFSGGTSGLSIGHI 525 ************************************************************************* PP TIGR00110 470 sPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyaklvs 533 sPeaa+gG ialv+ GDki+iDi++r +++++seeel++rr++ +k++ r+v+ aL++ya++vs NCBI__GCF_000220155.1:WP_010526299.1 526 SPEAAAGGEIALVKTGDKIIIDIPQRSINVDISEEELEKRRQQELNKGTeafkplsrnRYVSKALQAYASMVS 598 *******************************************99999999********************** PP TIGR00110 534 sadkGavl 541 sadkGav+ NCBI__GCF_000220155.1:WP_010526299.1 599 SADKGAVR 606 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (608 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: 29.17 // [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