Align dihydroxy-acid dehydratase subunit (EC 4.2.1.9) (characterized)
to candidate WP_012674810.1 SULAZ_RS04380 dihydroxy-acid dehydratase
Query= metacyc::MONOMER-11919 (549 letters) >NCBI__GCF_000021545.1:WP_012674810.1 Length = 557 Score = 581 bits (1497), Expect = e-170 Identities = 293/555 (52%), Positives = 401/555 (72%), Gaps = 10/555 (1%) Query: 1 MKSDTIKRGIQRAPHRSLLARCGLTDDDFEKPFIGIANSYTDIVPGHIHLRELAEAVKEG 60 M+SD IK+GI+RAPHRSLL CGL D+DF KPFIG+ANSY DI+PGH+HL+E A+ VK+ Sbjct: 1 MRSDEIKKGIERAPHRSLLRACGLKDEDFGKPFIGVANSYIDIIPGHVHLQEFAKHVKQA 60 Query: 61 VNAAGGVAFEFNTMAICDGIAMNHDGMKYSLASREIVADTVESMAMAHALDGLVLLPTCD 120 + AGGV FEFN + + DGIAM H GM YSL SRE++AD+VE++ AH LDGLVL+P CD Sbjct: 61 IREAGGVPFEFNVIGVDDGIAMGHSGMFYSLPSRELIADSVETVVQAHKLDGLVLIPNCD 120 Query: 121 KIVPGMLMAAARLDIPAIVVTGGPMLPGEFK-GRKVDLINVYEGVGTVSAGEMSEDELEE 179 KIVPGM+MAAAR++IP I+V+GGPM G + G+ +DL V+E VG++ G + E+EL + Sbjct: 121 KIVPGMIMAAARVNIPTILVSGGPMAAGHTQTGKPIDLATVFEAVGSIKKGLIKEEELLD 180 Query: 180 LERCACPGPRSCAGLFTANTMACLTEALGMSLPGCATAHAVSSRKRQIARLSGKRIVEMV 239 +E ACP SC+G+FTAN+M CL E LG++LPG + AV R+ ++A+ +G++IV++V Sbjct: 181 IESHACPTCGSCSGMFTANSMNCLAEVLGIALPGNGSILAVDPRRIELAKQAGRQIVDLV 240 Query: 240 QENLKPTMIMSQEAFENAVMVDLALGGSTNTTLHIPAIAAEIDGLNINLDLFDELSRVIP 299 + N+K I++ + ENA +D+A+GGS+NT LH+ AIA E G+ ++ DE+SR P Sbjct: 241 KANIKFRDIVNYQTIENAFTLDIAMGGSSNTVLHLLAIAHEA-GIEFPMEKIDEISRRTP 299 Query: 300 HIASISPAGEHMMLDLDRAGGIPAVLKTLED----HINRECVTCTGRTVQENIENVKVGH 355 + ++PA ++ M DLD+AGGI A+LK L H++R V +T+ E I++ ++ Sbjct: 300 TLCKLAPASQYHMEDLDKAGGIYAILKELSKKNLLHLDRPTVLM--KTLGEAIKDAEIKD 357 Query: 356 RDVIRPLDSPVHSEGGLAILRGNLAPRGSVVKQGAVAEDMMVHEGPAKVFNSEDECMEAI 415 +VIRP+D+P GGLA+L GN+AP G VVK AV +MVH+G A VF+SE+E +E I Sbjct: 358 YNVIRPIDNPYSETGGLAVLFGNIAPNGCVVKAAAVDPKIMVHKGKAVVFDSEEEAIEGI 417 Query: 416 FGGRIDEGDVIVIRYEGPKGGPGMREMLNPTSAIAGMGL-ERVALITDGRFSGGTRGPCV 474 G++ EG+V+VIRYEGPKGGPGMREML PTS I GMGL ++V+LITDGRFSG TRG C+ Sbjct: 418 TNGKVKEGNVVVIRYEGPKGGPGMREMLAPTSTIMGMGLGDKVSLITDGRFSGATRGACI 477 Query: 475 GHVSPEAMEDGPLAAVNDGDIIRIDIPSRKLEVDLSPREIEERLQSAVKPRRSVKG-WLA 533 GHVSPEA GP+ + DGD I IDIP+RK+E+ + E E+R++ R+ + WL Sbjct: 478 GHVSPEAAAGGPIGIIQDGDEILIDIPNRKIELLIPQEEFEKRMKEFKPKRKEIPSPWLR 537 Query: 534 RYRKLAGSADTGAVL 548 RY K SAD GA+L Sbjct: 538 RYSKFVTSADKGAIL 552 Lambda K H 0.319 0.136 0.397 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: 973 Number of extensions: 45 Number of successful extensions: 6 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: 549 Length of database: 557 Length adjustment: 36 Effective length of query: 513 Effective length of database: 521 Effective search space: 267273 Effective search space used: 267273 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate WP_012674810.1 SULAZ_RS04380 (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.9263.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-261 853.5 2.5 3.7e-261 853.3 2.5 1.0 1 lcl|NCBI__GCF_000021545.1:WP_012674810.1 SULAZ_RS04380 dihydroxy-acid deh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021545.1:WP_012674810.1 SULAZ_RS04380 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 853.3 2.5 3.7e-261 3.7e-261 1 541 [. 14 552 .. 14 554 .. 1.00 Alignments for each domain: == domain 1 score: 853.3 bits; conditional E-value: 3.7e-261 TIGR00110 1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 ++r+ll+a+Glkded++kP+i+v+nsy++i+Pghvhl+++ak vk++i++aGgv++efn+i+v+DGiam lcl|NCBI__GCF_000021545.1:WP_012674810.1 14 PHRSLLRACGLKDEDFGKPFIGVANSYIDIIPGHVHLQEFAKHVKQAIREAGGVPFEFNVIGVDDGIAM 82 69******************************************************************* PP TIGR00110 70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138 gh+Gm ysLpsre+iaDsvetvv+ah+lD+lv+i++CDkivPGm+maa+r+niP+i+vsGGpm+ag+t+ lcl|NCBI__GCF_000021545.1:WP_012674810.1 83 GHSGMFYSLPSRELIADSVETVVQAHKLDGLVLIPNCDKIVPGMIMAAARVNIPTILVSGGPMAAGHTQ 151 ********************************************************************* PP TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207 +++ idl vfeavg++++g ++eeel +ie +acPt+gsCsG+ftansm+cl+e+lG++lPg++++la lcl|NCBI__GCF_000021545.1:WP_012674810.1 152 TGKPIDLATVFEAVGSIKKGLIKEEELLDIESHACPTCGSCSGMFTANSMNCLAEVLGIALPGNGSILA 220 ********************************************************************* PP TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276 ++ ++ elak++g++iv+lvk nik rdi++ +++ena+tld+a+GGs+ntvLhllaia+eag+++ ++ lcl|NCBI__GCF_000021545.1:WP_012674810.1 221 VDPRRIELAKQAGRQIVDLVKANIKFRDIVNYQTIENAFTLDIAMGGSSNTVLHLLAIAHEAGIEFPME 289 ********************************************************************* PP TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345 ++d++sr++P+l+kl+P++++ +edl++aGG+ a+lkel+k++llh d tv+ ktl+e +++++++ lcl|NCBI__GCF_000021545.1:WP_012674810.1 290 KIDEISRRTPTLCKLAPASQYHMEDLDKAGGIYAILKELSKKNLLHLDRPTVLMKTLGEAIKDAEIK-- 356 *******************************************************************.. PP TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414 d++vir++dnp++++gglavL+Gn+a++G+vvk+a+v+ +i++++G+a vf+seeea+e+i +gkvkeG lcl|NCBI__GCF_000021545.1:WP_012674810.1 357 DYNVIRPIDNPYSETGGLAVLFGNIAPNGCVVKAAAVDPKIMVHKGKAVVFDSEEEAIEGITNGKVKEG 425 ********************************************************************* PP TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483 +vvviryeGPkGgPGmremLaPts+++g+GLg+kv+LitDGrfsG+trG +iGhvsPeaa+gG+i++++ lcl|NCBI__GCF_000021545.1:WP_012674810.1 426 NVVVIRYEGPKGGPGMREMLAPTSTIMGMGLGDKVSLITDGRFSGATRGACIGHVSPEAAAGGPIGIIQ 494 ********************************************************************* PP TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGavl 541 dGD+i iDi+nrk++l + +ee+++r ++ k+k+++ + +L++y+k+v+sadkGa+l lcl|NCBI__GCF_000021545.1:WP_012674810.1 495 DGDEILIDIPNRKIELLIPQEEFEKRMKEFKPKRKEIPSPWLRRYSKFVTSADKGAIL 552 **********************************99********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (557 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: 00:00:00.02 # Mc/sec: 12.00 // [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