Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate GFF989 PS417_05015 homogentisate 1,2-dioxygenase
Query= reanno::pseudo3_N2E3:AO353_15550 (434 letters) >FitnessBrowser__WCS417:GFF989 Length = 427 Score = 816 bits (2108), Expect = 0.0 Identities = 386/425 (90%), Positives = 405/425 (95%) Query: 10 LVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEARRTWMYRIQ 69 L Y SGFGNEF+SEALPGALP+GQNSPQKAPYGLYTELFSGTAFTM RSEARRTW+YRIQ Sbjct: 3 LEYLSGFGNEFASEALPGALPIGQNSPQKAPYGLYTELFSGTAFTMVRSEARRTWLYRIQ 62 Query: 70 PSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAANSGSEKPAG 129 PSANHPAF+KLERQLAGGPLG VTPNRLRWNPL++P EPTDFIDGLV M ANSG+EKP+G Sbjct: 63 PSANHPAFIKLERQLAGGPLGAVTPNRLRWNPLDMPSEPTDFIDGLVGMVANSGAEKPSG 122 Query: 130 ISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVLPRGLKFRIE 189 ISIY YRANRSMERVFFNADGE L+VPE GRLRIATELGVLE+EPLEI VLPRGLKFR+E Sbjct: 123 ISIYTYRANRSMERVFFNADGELLIVPELGRLRIATELGVLEVEPLEIVVLPRGLKFRVE 182 Query: 190 LLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPTTLVQKFLGE 249 LLD QARGY+AENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YED+K+PTTLVQKFLGE Sbjct: 183 LLDTQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYEDVKKPTTLVQKFLGE 242 Query: 250 LWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLAN 309 LW CELDHSPLNVVAWHGNNVPYKYDLRRFNT+GTVSFDHPDPSIFTVLTSPTS HGLAN Sbjct: 243 LWACELDHSPLNVVAWHGNNVPYKYDLRRFNTLGTVSFDHPDPSIFTVLTSPTSTHGLAN 302 Query: 310 LDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGASLHSCMSAHG 369 LDFVIFPPRWMVAENTFRPPWFHRNLMNE+MGLIQG YDAKAEGFLPGGASLHSCMSAHG Sbjct: 303 LDFVIFPPRWMVAENTFRPPWFHRNLMNEYMGLIQGAYDAKAEGFLPGGASLHSCMSAHG 362 Query: 370 PDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDACWASLPVTF 429 PDGETCTKAIN +LAP KIDNTMAFMFETSQVLRP++FALDCPQLQN YDACWASLP TF Sbjct: 363 PDGETCTKAINVDLAPHKIDNTMAFMFETSQVLRPTQFALDCPQLQNTYDACWASLPATF 422 Query: 430 NPNRR 434 NPNRR Sbjct: 423 NPNRR 427 Lambda K H 0.320 0.137 0.433 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: 857 Number of extensions: 21 Number of successful extensions: 1 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: 434 Length of database: 427 Length adjustment: 32 Effective length of query: 402 Effective length of database: 395 Effective search space: 158790 Effective search space used: 158790 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 GFF989 PS417_05015 (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.28000.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-196 636.8 0.0 9e-196 636.6 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF989 PS417_05015 homogentisate 1,2-di Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF989 PS417_05015 homogentisate 1,2-dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 636.6 0.0 9e-196 9e-196 2 428 .. 3 421 .. 2 422 .. 0.97 Alignments for each domain: == domain 1 score: 636.6 bits; conditional E-value: 9e-196 TIGR01015 2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkesee 77 l+ylsGfgnef+sea+pgalP GqnsPqkapygly+e +sG+aft+ r+e +r+wlyri+Psa+h af +l+ + lcl|FitnessBrowser__WCS417:GFF989 3 LEYLSGFGNEFASEALPGALPIGQNSPQKAPYGLYTELFSGTAFTMVRSEARRTWLYRIQPSANHPAFIKLE--RQ 76 79*****************************************************************99998..44 PP TIGR01015 78 kltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdlliv 153 + a++pn+lrw+pl++ps e +df++glv + +++ a++ +G+++++y +n sm ++vf+nadG+lliv lcl|FitnessBrowser__WCS417:GFF989 77 LAGGPL--GAVTPNRLRWNPLDMPS-EPTDFIDGLVGMVANSGAEKPSGISIYTYRANRSM-ERVFFNADGELLIV 148 555554..47789***********8.99*********************************.89************ PP TIGR01015 154 pqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlGPiGanglanprdfeaPva 228 p+ G l+i telG+l+veP ei+v+prG++frve+ +arGy+ e++ga +lPdlGPiG+nglanprdf +Pva lcl|FitnessBrowser__WCS417:GFF989 149 PELGRLRIATELGVLEVEPLEIVVLPRGLKFRVELLdTQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVA 224 **********************************99788************************************* PP TIGR01015 229 afedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdke 304 +ed + ++++++kf g+l+a++ dhspl+vvawhGn vPykydl++fn++++vsfdhpdPsiftvlt+p++++ lcl|FitnessBrowser__WCS417:GFF989 225 RYEDVKK--PTTLVQKFLGELWACELDHSPLNVVAWHGNNVPYKYDLRRFNTLGTVSFDHPDPSIFTVLTSPTSTH 298 ***9888..89***************************************************************** PP TIGR01015 305 GtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasna 380 G+a+ dfvifpPrw+vae+tfrPP++hrn+m e+mGli+G+ydak+eGf pgGaslh++msahGPd e+ ka n+ lcl|FitnessBrowser__WCS417:GFF989 299 GLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEYMGLIQGAYDAKAEGFLPGGASLHSCMSAHGPDGETCTKAINV 374 **************************************************************************** PP TIGR01015 381 elkPekiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428 +l+P+kid+ t+afmfe+s +l+ t++a + +l++ y+++w +l lcl|FitnessBrowser__WCS417:GFF989 375 DLAPHKIDN-TMAFMFETSQVLRPTQFALDCPQLQNTYDACWASLPAT 421 *********.*********************************99866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (429 nodes) Target sequences: 1 (427 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.93 // [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