Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate Pf1N1B4_1025 Homogentisate 1,2-dioxygenase (EC 1.13.11.5)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4962 (434 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 Length = 434 Score = 865 bits (2236), Expect = 0.0 Identities = 415/434 (95%), Positives = 423/434 (97%) Query: 1 MNPDSTTPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60 MN DST PALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTM RSEA Sbjct: 1 MNLDSTAPALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMTRSEA 60 Query: 61 RRTWMYRIQPSANHPAFFKLDRQLTGGPLGEVTPNRLRWNPLDIPAEPTDFIDGLVSMAA 120 RRTWMYRIQPSANHPAF KLDRQL GGPLGEVTPNRLRWNPLD+P EPTDFIDGLVSMAA Sbjct: 61 RRTWMYRIQPSANHPAFVKLDRQLAGGPLGEVTPNRLRWNPLDMPTEPTDFIDGLVSMAA 120 Query: 121 NSGAEKPAGISIYNYRANRSMERAFFNADGEMLLVPELGRLRIATELGVLELEPLEIAVL 180 NSGAEKP+GISIYNYRANRSMER FFNADGE+LLVP+LGRLRIATELGVLELEPLEIAVL Sbjct: 121 NSGAEKPSGISIYNYRANRSMERVFFNADGELLLVPQLGRLRIATELGVLELEPLEIAVL 180 Query: 181 PRGLKFRIELLDPQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAAYENLQQPT 240 PRGLKFR+ELLDPQARGY+AENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YENL+QPT Sbjct: 181 PRGLKFRVELLDPQARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLKQPT 240 Query: 241 TLVQKFLGQLWACELNHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300 TLVQKFLGQLW CEL+HSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS Sbjct: 241 TLVQKFLGQLWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300 Query: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGAS 360 Query: 361 LHSCMSAHGPDGETCTKAINAELKPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNTYDA 420 LHSCMSAHGPDGETCTKAINAEL PAKIDNTMAFMFETSQVLRPSRFALDCPQLQN YDA Sbjct: 361 LHSCMSAHGPDGETCTKAINAELAPAKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 420 Query: 421 CWATLPATFDPTRR 434 CWATLPATFDPTRR Sbjct: 421 CWATLPATFDPTRR 434 Lambda K H 0.320 0.137 0.426 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: 912 Number of extensions: 25 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: 434 Length adjustment: 32 Effective length of query: 402 Effective length of database: 402 Effective search space: 161604 Effective search space used: 161604 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 Pf1N1B4_1025 (Homogentisate 1,2-dioxygenase (EC 1.13.11.5))
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.1612.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-195 636.0 0.0 1.5e-195 635.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 Homogentisate 1,2-dioxygenase (E Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 Homogentisate 1,2-dioxygenase (EC 1.13.11.5) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 635.8 0.0 1.5e-195 1.5e-195 2 428 .. 10 428 .. 9 429 .. 0.97 Alignments for each domain: == domain 1 score: 635.8 bits; conditional E-value: 1.5e-195 TIGR01015 2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaa 65 l+y+sGfgnef+sea+pgalPvGqnsPqkapygly+e +sG+aft+ r+e +r+w+yri+Psa+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 10 LAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMTRSEARRTWMYRIQPSAN 73 78************************************************************** PP TIGR01015 66 heafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlav 129 h af++l+ + + +++pn+lrw+pl++p+ e +df++glv++a+++ a++ +G+++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 74 HPAFVKLD--RQLAGGPLG--EVTPNRLRWNPLDMPT-EPTDFIDGLVSMAANSGAEKPSGISI 132 *****999..455555555..5679***********7.99************************ PP TIGR01015 130 hlyavnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee.a 192 + y +n sm ++vf+nadG+ll+vpq G l+i telG+l++eP eiav+prG++frve+ ++ a lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 133 YNYRANRSM-ERVFFNADGELLLVPQLGRLRIATELGVLELEPLEIAVLPRGLKFRVELLDPqA 195 *********.89***********************************************96559 PP TIGR01015 193 rGyilevygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdh 256 rGyi e++ga +lPdlGPiG+nglanprdf +Pva +e+ + ++++++kf g+l+ ++ dh lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 196 RGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLKQ--PTTLVQKFLGQLWGCELDH 257 ***************************************9988..88***************** PP TIGR01015 257 spldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlv 320 spl+vvawhGn vPykydl++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifpPrw+v lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 258 SPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFPPRWMV 321 **************************************************************** PP TIGR01015 321 aektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkP 384 aektfrPP++hrn+m efmGli+G+ydak+eGfvpgGaslh++msahGPd e+ ka nael+P lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 322 AEKTFRPPWFHRNLMNEFMGLIQGEYDAKAEGFVPGGASLHSCMSAHGPDGETCTKAINAELAP 385 **************************************************************** PP TIGR01015 385 ekiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428 kid+ t+afmfe+s +l+ +++a + +l+++y+++w +l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1025 386 AKIDN-TMAFMFETSQVLRPSRFALDCPQLQNNYDACWATLPAT 428 *****.*********************************99866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (429 nodes) Target sequences: 1 (434 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.31 // [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