Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate H281DRAFT_04741 H281DRAFT_04741 homogentisate 1,2-dioxygenase
Query= reanno::Cup4G11:RR42_RS31275 (449 letters) >FitnessBrowser__Burk376:H281DRAFT_04741 Length = 448 Score = 723 bits (1865), Expect = 0.0 Identities = 339/430 (78%), Positives = 377/430 (87%), Gaps = 1/430 (0%) Query: 21 PGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIR 80 PGYQSGF NEFATEALPGALP G+NSPQRA YGLYAEQ+SGTAFTAPR HNRR+W YRIR Sbjct: 19 PGYQSGFGNEFATEALPGALPEGRNSPQRAAYGLYAEQLSGTAFTAPRGHNRRTWLYRIR 78 Query: 81 AAAMHEPFTRVEQSRIVSHFDAVPPSP-NQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139 AA+H+PFT + R+V++F VPP+P NQ+RW MP EPTDFVDG +TMAGNG ++ Sbjct: 79 PAAVHKPFTPLPSERLVANFAEVPPTPPNQLRWDALPMPGEPTDFVDGWVTMAGNGAADS 138 Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199 MSGC IHLY ANRSMTDRFFY+ADGE+LIVPQ+GRL +ATE+G L+V P EI VIPRGVR Sbjct: 139 MSGCAIHLYAANRSMTDRFFYSADGELLIVPQEGRLDIATELGRLEVRPFEIAVIPRGVR 198 Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259 F V LPDG ARGYICEN+GAL RLPDLG IGSNGLANPRDFLTPHA YEDREGDFELVAK Sbjct: 199 FAVSLPDGTARGYICENFGALLRLPDLGPIGSNGLANPRDFLTPHAAYEDREGDFELVAK 258 Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319 GNLWRA IGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQS SDTP Sbjct: 259 MNGNLWRADIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSQSDTP 318 Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379 GVDS+DFVIF PRWLA ++TFRPPWFHRN+ASEFMGL+ GVYDAKA+GF PGGASLHNCM Sbjct: 319 GVDSLDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGVYDAKAEGFVPGGASLHNCM 378 Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439 SGHGPDA+TF KA+ +DTS+P ++GDTMAFMFET +I+PT +A E+AQLQ YY CWQG Sbjct: 379 SGHGPDADTFEKASHSDTSKPVKVGDTMAFMFETRTLIKPTRFALETAQLQAHYYECWQG 438 Query: 440 LKKHFNPNER 449 LKKHFNP +R Sbjct: 439 LKKHFNPEQR 448 Lambda K H 0.320 0.138 0.439 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: 852 Number of extensions: 33 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: 449 Length of database: 448 Length adjustment: 33 Effective length of query: 416 Effective length of database: 415 Effective search space: 172640 Effective search space used: 172640 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 (21.8 bits) S2: 51 (24.3 bits)
Align candidate H281DRAFT_04741 H281DRAFT_04741 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))
# 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.carbon/TIGR01015.hmm # target sequence database: /tmp/gapView.3002.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01015 [M=429] Accession: TIGR01015 Description: hmgA: homogentisate 1,2-dioxygenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-207 673.5 0.0 6.7e-207 673.3 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_04741 H281DRAFT_04741 homogentisate 1, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_04741 H281DRAFT_04741 homogentisate 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 673.3 0.0 6.7e-207 6.7e-207 3 429 .] 20 443 .. 18 443 .. 0.98 Alignments for each domain: == domain 1 score: 673.3 bits; conditional E-value: 6.7e-207 TIGR01015 3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaahea 68 y+sGfgnef++ea+pgalP+G+nsPq+a+yglyaeqlsG+aftaPr +n+r+wlyrirP+a h++ lcl|FitnessBrowser__Burk376:H281DRAFT_04741 20 GYQSGFGNEFATEALPGALPEGRNSPQRAAYGLYAEQLSGTAFTAPRGHNRRTWLYRIRPAAVHKP 85 6***************************************************************** PP TIGR01015 69 feelkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlya 133 f++l +e l+anf e+++ pnqlrw+ l++p+ e +dfv+g vt+ag+g a s +G a+hlya lcl|FitnessBrowser__Burk376:H281DRAFT_04741 86 FTPLP--SERLVANFAEVPPtPPNQLRWDALPMPG-EPTDFVDGWVTMAGNGAADSMSGCAIHLYA 148 ***99..6889999999988689***********7.99**************************** PP TIGR01015 134 vnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyile 198 +n sm+d+ fy+adG+llivpq+G l+i telGrl+v+P eiaviprGvrf+v++ + arGyi+e lcl|FitnessBrowser__Burk376:H281DRAFT_04741 149 ANRSMTDRFFYSADGELLIVPQEGRLDIATELGRLEVRPFEIAVIPRGVRFAVSLPdGTARGYICE 214 *******************************************************9889******* PP TIGR01015 199 vygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvaw 264 ++ga +lPdlGPiG+nglanprdf +P aa+ed+e+ +++++ k +g+l+ a ++hspldvvaw lcl|FitnessBrowser__Burk376:H281DRAFT_04741 215 NFGALLRLPDLGPIGSNGLANPRDFLTPHAAYEDREG--DFELVAKMNGNLWRADIGHSPLDVVAW 278 *************************************..9************************** PP TIGR01015 265 hGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyy 330 hGny+Pykydl++fn+i+s+sfdhpdPsif vl ++sd++G+ dfvifpPrwl ae+tfrPP++ lcl|FitnessBrowser__Burk376:H281DRAFT_04741 279 HGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSQSDTPGVDSLDFVIFPPRWLAAEDTFRPPWF 344 ****************************************************************** PP TIGR01015 331 hrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafm 395 hrnv sefmGl++G ydak+eGfvpgGaslhn+ms hGPd+++fekas+++ kP k++d t+afm lcl|FitnessBrowser__Burk376:H281DRAFT_04741 345 HRNVASEFMGLVHGVYDAKAEGFVPGGASLHNCMSGHGPDADTFEKASHSDTsKPVKVGD-TMAFM 409 ************************************************998549******.***** PP TIGR01015 396 fesslslavtklakelekldedyeevwqglkkkf 429 fe++ ++ t++a e+++l+++y+e+wqglkk+f lcl|FitnessBrowser__Burk376:H281DRAFT_04741 410 FETRTLIKPTRFALETAQLQAHYYECWQGLKKHF 443 *********************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (429 nodes) Target sequences: 1 (448 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: 11.69 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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