Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate Dsui_0219 Dsui_0219 anthranilate synthase component I
Query= SwissProt::P20579 (493 letters) >FitnessBrowser__PS:Dsui_0219 Length = 491 Score = 571 bits (1471), Expect = e-167 Identities = 296/488 (60%), Positives = 364/488 (74%), Gaps = 5/488 (1%) Query: 1 MNREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQPNSYLLESVQGGEKWGRYSM 60 M EF LAA GYNRIP+ ET AD DTPLSIYLKLA+ P +YLLESVQGGE++GRYS+ Sbjct: 1 MTETEFNALAAQGYNRIPVTLETFADLDTPLSIYLKLANGPYTYLLESVQGGERFGRYSI 60 Query: 61 IGLPSRTVMRVHGYHVSILHDGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGLV 120 IGL S T + V+G+ V +L E + +PL F+ES++ R++VA GLPRF GGLV Sbjct: 61 IGLASPTRIAVYGHQVMVLTGQRIAERENDTNPLEFIESYQKRFRVAPYAGLPRFCGGLV 120 Query: 121 GYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAEEQA 180 G FGYD VRYVE RL S D LG PDILL++S+ + V DNL+GK+ +V +P A Sbjct: 121 GCFGYDTVRYVETRLTKSAKHDELGTPDILLLLSEEIAVVDNLSGKLTLVVYAEPGFPGA 180 Query: 181 FEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVGRIKEYILAG 240 F++ +ARL+ LL LR P + P ++P S + ++ AV + KEYI G Sbjct: 181 FQKARARLKELLAQLRTPAP----IPEEKPATSQPAV-SIFGEAPFKQAVAKAKEYITEG 235 Query: 241 DCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDNL 300 D MQVV SQRM+ F A+P+ LYRALR NP+PYMY+F+F DFHVVG+SPE+L R+E + Sbjct: 236 DIMQVVLSQRMTKPFSASPLSLYRALRTLNPSPYMYYFDFEDFHVVGASPEILTRLEGDT 295 Query: 301 VTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVSSTGSVRLTE 360 VTVRPIAGTR RGAT E D AL +DLL+D KEIAEH+ L+DLGRNDVGRV+ TGSV+LTE Sbjct: 296 VTVRPIAGTRKRGATPEEDAALAEDLLADQKEIAEHVQLLDLGRNDVGRVAQTGSVKLTE 355 Query: 361 KMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420 +M IERYS+VMHIVSNV G+L+ GL+A+D L+A PAGTLSGAPK+RAMEIIDELEPVKR Sbjct: 356 RMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAPKVRAMEIIDELEPVKR 415 Query: 421 GVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWEETINKRRAM 480 G+YGGA+GY +NG+MD AIAIRTAVI DG+LHVQAG GIVADS P EW+ET NK RA+ Sbjct: 416 GIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADSDPTSEWQETQNKARAV 475 Query: 481 FRAVALAE 488 RA +AE Sbjct: 476 LRAAEMAE 483 Lambda K H 0.320 0.138 0.403 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: 703 Number of extensions: 24 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: 493 Length of database: 491 Length adjustment: 34 Effective length of query: 459 Effective length of database: 457 Effective search space: 209763 Effective search space used: 209763 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: 52 (24.6 bits)
Align candidate Dsui_0219 Dsui_0219 (anthranilate synthase component I)
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))
# 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/TIGR00564.hmm # target sequence database: /tmp/gapView.15817.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00564 [M=455] Accession: TIGR00564 Description: trpE_most: anthranilate synthase component I 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-176 573.9 0.0 1.6e-176 573.7 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_0219 Dsui_0219 anthranilate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_0219 Dsui_0219 anthranilate synthase component I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 573.7 0.0 1.6e-176 1.6e-176 2 454 .. 26 479 .. 25 480 .. 0.94 Alignments for each domain: == domain 1 score: 573.7 bits; conditional E-value: 1.6e-176 TIGR00564 2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeak.ieedelkelrklle 77 d tp+s+ylkla+ ++++llEsv+ +e+ gRyS+igl + ++i++ +++++ l+ + +++ +++++l+ +++ + lcl|FitnessBrowser__PS:Dsui_0219 26 DLDTPLSIYLKLANGPYTYLLESVQGGERFGRYSIIGLASPTRIAVYGHQVMVLTGQRIAEReNDTNPLEFIESYQK 102 778**********99*************************************999888777768999********** PP TIGR00564 78 ka.eesedeldeplsggavGylgydtvrlveklke.ea.edelelpdlllllvetvivfDhvekkvilienarteae 151 ++ +l+ ++gg+vG +gydtvr+ve+ + +a +del +pd+llll e+++v D+ + k++l+ +a+ lcl|FitnessBrowser__PS:Dsui_0219 103 RFrVAPYAGLPR-FCGGLVGCFGYDTVRYVETRLTkSAkHDELGTPDILLLLSEEIAVVDNLSGKLTLVVYAEPGFP 178 *94444555655.******************865534459*******************************977665 PP TIGR00564 152 rsaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdifqvvlSqrleakveak 228 a+++a+arl+ella+l++++ + ++ ++++ s + ++ ++++vakakeyi++Gdi+qvvlSqr++++++a+ lcl|FitnessBrowser__PS:Dsui_0219 179 G-AFQKARARLKELLAQLRTPAPIPEE-KPATSQPAVSIFGEAPFKQAVAKAKEYITEGDIMQVVLSQRMTKPFSAS 253 5.9******************974333.33334446688899*********************************** PP TIGR00564 229 pfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDealeeeLladeKerAE 305 p++lYr+LRt NPSpy+yy+d+edf++vg+SPE+l +++g++v++rPiAGtrkRGat+eeD+al+e+Llad+Ke AE lcl|FitnessBrowser__PS:Dsui_0219 254 PLSLYRALRTLNPSPYMYYFDFEDFHVVGASPEILTRLEGDTVTVRPIAGTRKRGATPEEDAALAEDLLADQKEIAE 330 ***************************************************************************** PP TIGR00564 306 HlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmeli 382 H+ L+DL+RND+g+va++gsv+ +e ++ie+yshvmHivS+VeG+l+ +l+a+D+l+aa+PaGTlsGAPKvrAme+i lcl|FitnessBrowser__PS:Dsui_0219 331 HVQLLDLGRNDVGRVAQTGSVKLTERMSIERYSHVMHIVSNVEGKLQAGLSALDVLKAAFPAGTLSGAPKVRAMEII 407 ***************************************************************************** PP TIGR00564 383 delEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454 delE++kRgiYgGa+gyl+f+gd+d aiaiRt+v+kdg+++vqAgaGiVaDSdp++E++Et nKa+a+lra+ lcl|FitnessBrowser__PS:Dsui_0219 408 DELEPVKRGIYGGAIGYLGFNGDMDLAIAIRTAVIKDGQLHVQAGAGIVADSDPTSEWQETQNKARAVLRAA 479 *********************************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (491 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: 00:00:00.02 # Mc/sec: 10.24 // [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