Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 8501007 DvMF_1744 anthranilate phosphoribosyltransferase (RefSeq)
Query= SwissProt::Q8PD71 (345 letters) >FitnessBrowser__Miya:8501007 Length = 338 Score = 210 bits (535), Expect = 4e-59 Identities = 131/312 (41%), Positives = 177/312 (56%), Gaps = 9/312 (2%) Query: 29 QIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTD-RRHMVDIVGTGG 87 ++M GE++ A + L GLR+K ET E+ A V +R V VT +DIVGTGG Sbjct: 29 RLMDGEMTCAQAGSFLMGLRMKGETPQELTEA--VRAALARAVRVTGIDGPTIDIVGTGG 86 Query: 88 DGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQPEQVAASLA 147 DG +FN ST A G +V KHGNR+VSS G+ADA+E LG +EL PE V A +A Sbjct: 87 DGRSSFNCSTATALTLAGMGHRVVKHGNRAVSSSCGAADAVEGLGLPLELDPEDVRALVA 146 Query: 148 QTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGVFHPDLVGIQ 207 Q F++AP HPA + V P+RRE+GVRT+FN+LGPL NPA ++L+GV +L+ + Sbjct: 147 QRNFAFLFAPRFHPAFRNVMPIRRELGVRTLFNLLGPLLNPARPSHMLLGVARAELLPLM 206 Query: 208 ARVLQELGAERALVVWGRDGMDELS-LGAGTLVGELRDGQVH----EYEVHPEDFGIAMS 262 AR L G RA VV G G DEL+ +G ++ DGQ H E V P D+GIA Sbjct: 207 ARTLLLTGVRRAAVVHGAGGYDELTPMGPAHIMLLEGDGQGHGTLTEISVDPADYGIASC 266 Query: 263 ASRNLKVADAAESRAMLLQVLD-NVPGPALDIVALNAGAALYVAGVADSIADGIVRARQV 321 L V D + +L ++L P P D++ LN G AL++ ++ D + AR Sbjct: 267 TPEELAVPDRDTAVRVLRELLSGGGPAPMRDMLMLNVGMALHLLEPGLALPDAMAAARLA 326 Query: 322 LADGSARACLDA 333 LA G+ L A Sbjct: 327 LAAGAGGKVLHA 338 Lambda K H 0.320 0.134 0.377 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: 333 Number of extensions: 18 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: 345 Length of database: 338 Length adjustment: 29 Effective length of query: 316 Effective length of database: 309 Effective search space: 97644 Effective search space used: 97644 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: 49 (23.5 bits)
Align candidate 8501007 DvMF_1744 (anthranilate phosphoribosyltransferase (RefSeq))
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))
# 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/TIGR01245.hmm # target sequence database: /tmp/gapView.2571.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01245 [M=330] Accession: TIGR01245 Description: trpD: anthranilate phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-99 317.8 0.0 5e-99 317.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501007 DvMF_1744 anthranilate phosphori Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501007 DvMF_1744 anthranilate phosphoribosyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.7 0.0 5e-99 5e-99 1 324 [. 9 336 .. 9 338 .] 0.96 Alignments for each domain: == domain 1 score: 317.7 bits; conditional E-value: 5e-99 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGT 77 le+l+++ dL+ e ae+ ++ +m+ge++ aq +++l+ lr+kget++e++++++a +++a++v+ + +DivGT lcl|FitnessBrowser__Miya:8501007 9 LETLATGMDLAPELAEAGFSRLMDGEMTCAQAGSFLMGLRMKGETPQELTEAVRAALARAVRVTG-IDGPTIDIVGT 84 57899999*******************************************************99.699******** PP TIGR01245 78 GGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpa 154 GGDg +++N STa+al +a++G +v+KhGnr+vss++G+aD +e lg+ lel+pe v++ +++ +++FlfAP++hpa lcl|FitnessBrowser__Miya:8501007 85 GGDGRSSFNCSTATALTLAGMGHRVVKHGNRAVSSSCGAADAVEGLGLPLELDPEDVRALVAQRNFAFLFAPRFHPA 161 ***************************************************************************** PP TIGR01245 155 lkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkv 231 +++v+p+R+eLgvrt+fNlLGPLlnPar+++ +lGv++++l+ ++a++l gv+ra vvhg++g DE++++g++++ lcl|FitnessBrowser__Miya:8501007 162 FRNVMPIRRELGVRTLFNLLGPLLNPARPSHMLLGVARAELLPLMARTLLLTGVRRAAVVHGAGGYDELTPMGPAHI 238 ***************************************************************************** PP TIGR01245 232 aelk.....dgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakd 303 + l+ +g+ +e +++p+d+g++ ++ eel++ + + +++l+e+l+g++ + rd+++lN+++al + + + lcl|FitnessBrowser__Miya:8501007 239 MLLEgdgqgHGTLTEISVDPADYGIASCTPEELAVPDRDTAVRVLRELLSGGGPAPMRDMLMLNVGMALHLLEPGLA 315 ***93333335799**********************************************************99999 PP TIGR01245 304 lkegvelakeaiksgkalekl 324 l +++ +a+ a+ g+ ++l lcl|FitnessBrowser__Miya:8501007 316 LPDAMAAARLALAAGAGGKVL 336 999999999999999877766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (338 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.32 // [ok]
This GapMind analysis is from Apr 09 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