Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate Pf1N1B4_2548 Anthranilate phosphoribosyltransferase (EC 2.4.2.18)
Query= SwissProt::Q8PD71 (345 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 Length = 349 Score = 294 bits (753), Expect = 2e-84 Identities = 160/335 (47%), Positives = 211/335 (62%), Gaps = 4/335 (1%) Query: 8 ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67 AL R + H ++ DEM D+MR+IM G+ +DA + A + +R+K E+I EI GA T MRE Sbjct: 6 ALSRIVGHLDLTTDEMRDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVTAMREL 65 Query: 68 SRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADA 127 + +VE+ +VD+VGTGGDG++ FN+ST + FV AA G VAKHGNR+VS KSGSAD Sbjct: 66 ADKVELNTLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGSADL 125 Query: 128 LEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTN 187 LEA G + L P QVA + GIGFM+A HH AMK A RRE+G+RT+FN+LGPLTN Sbjct: 126 LEAAGIYLNLTPVQVARCIDNVGIGFMFAQTHHSAMKHAAGPRRELGLRTLFNMLGPLTN 185 Query: 188 PAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQV 247 PAG + ++GVF L A VLQ LG++ LVV +DG+DE SL A T V EL++ Q+ Sbjct: 186 PAGVKHQVVGVFSQALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKNDQI 245 Query: 248 HEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVP----GPALDIVALNAGAALY 303 E+ V PED G+ + L V A S ++ L A +++ LNAGAALY Sbjct: 246 TEFWVEPEDLGMKSQSLHGLAVESPAASLELIRDALGKRKTENGQKAAEMIVLNAGAALY 305 Query: 304 VAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338 A VA S+ +G+ A L G AR L+ AFT Sbjct: 306 AADVASSLKEGVALAHDALHTGLAREKLEELGAFT 340 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: 302 Number of extensions: 12 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: 345 Length of database: 349 Length adjustment: 29 Effective length of query: 316 Effective length of database: 320 Effective search space: 101120 Effective search space used: 101120 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 Pf1N1B4_2548 (Anthranilate phosphoribosyltransferase (EC 2.4.2.18))
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.7338.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-126 407.5 3.4 2.6e-126 407.3 3.4 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 Anthranilate phosphoribosyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 Anthranilate phosphoribosyltransferase (EC 2.4.2.18) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 407.3 3.4 2.6e-126 2.6e-126 2 328 .. 8 337 .. 7 339 .. 0.97 Alignments for each domain: == domain 1 score: 407.3 bits; conditional E-value: 2.6e-126 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvek 65 ++++ + dL+++e++++m+eim+g+++daqi+A+++a+r+k+e+++ei+g+++a+re a+kve lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 8 SRIVGHLDLTTDEMRDVMREIMTGQCTDAQIGAFMMAMRMKSESIDEIVGAVTAMRELADKVEL 71 67788889******************************************************** PP TIGR01245 66 eeseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlel 129 ++ + +vD+vGTGGDg++ +N+STas++v+aaaG vaKhGnr+vs+ksGsaD+Lea g+ l+l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 72 NTLDGVVDVVGTGGDGANIFNVSTASSFVVAAAGCTVAKHGNRAVSGKSGSADLLEAAGIYLNL 135 **************************************************************** PP TIGR01245 130 spekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvysk 193 +p +var++++vgigF+fA ++h+a+k++a+ R+eLg+rt+fN+LGPL+nPa +k+qv+Gv+s+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 136 TPVQVARCIDNVGIGFMFAQTHHSAMKHAAGPRRELGLRTLFNMLGPLTNPAGVKHQVVGVFSQ 199 **************************************************************** PP TIGR01245 194 dlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraele 257 l++ laevl++lg+k++lvvh++dglDE+sl ++t vaelk+++i+e+ ++ped+g+k ++l+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 200 ALCRPLAEVLQRLGSKHVLVVHSKDGLDEFSLAAPTFVAELKNDQITEFWVEPEDLGMKSQSLH 263 **************************************************************** PP TIGR01245 258 elkggsaeenaellkevlegke...kkakrdivvlNaaaalyvagkakdlkegvelakeaiksg 318 l+++s+++++el++++l ++ +++++++vlNa+aaly+a++a++lkegv la++a+++g lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 264 GLAVESPAASLELIRDALGKRKtenGQKAAEMIVLNAGAALYAADVASSLKEGVALAHDALHTG 327 ******************7776333567789********************************* PP TIGR01245 319 kalekleelv 328 a ekleel lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2548 328 LAREKLEELG 337 *******986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (349 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: 8.44 // [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