Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_085639309.1 MGEO_RS14630 anthranilate synthase component I
Query= SwissProt::P20579 (493 letters) >NCBI__GCF_002115805.1:WP_085639309.1 Length = 504 Score = 422 bits (1086), Expect = e-122 Identities = 239/494 (48%), Positives = 319/494 (64%), Gaps = 21/494 (4%) Query: 4 EEFLRLAAVGYNRIPLACETLADFDTPLSIYLKLADQP-NSYLLESVQGGEKWGRYSMIG 62 + F R G N++ A AD DTP+S+ LKL ++++LESV GGE GRYS+IG Sbjct: 9 DSFARAYEAGQNQVVYA-RLAADLDTPVSLMLKLTGAAKDAFVLESVTGGEVRGRYSIIG 67 Query: 63 LPSRTVMRVHGYHVSILHDGVEVESHDVE----DPLAFVESFKDRYKVADIPGLPRFNGG 118 + + + HG S ++ + E DPL + + K+ LP+ G Sbjct: 68 MKPDVIWQCHGTR-SRINRAARYDPESFEELEGDPLTTLRALIAESKINLPDDLPQAAAG 126 Query: 119 LVGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPA-- 176 L GY GYD +R VE + NPDPLG+PD ++M V V D + G+ + +V PA Sbjct: 127 LFGYLGYDMIRLVEHLPNI--NPDPLGLPDAVMMRPSVVAVLDGVKGE---VTVVSPAWV 181 Query: 177 -----EEQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAEPEFRSSYTREDYENAVG 231 A+ Q R+ + L + + P++ ++ G A P S++T E Y+ AV Sbjct: 182 NDGLTARAAYAQAAERVMDAVRDLERAL-PQQAREM-GDAADIPAPVSNFTHEGYKQAVE 239 Query: 232 RIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPE 291 + KEYI AGD QVVP+QR + DF P LYR+LR NP+P+M++FNFG F V+G+SPE Sbjct: 240 KAKEYIRAGDIFQVVPAQRWTQDFPLPPFALYRSLRRTNPSPFMFYFNFGGFQVIGASPE 299 Query: 292 VLVRVEDNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGRNDVGRVS 351 +LVRV + VT+RPIAGTRPRGAT D ALE DLL+D KE AEHLML+DLGRNDVGRV+ Sbjct: 300 ILVRVFGSEVTIRPIAGTRPRGATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVA 359 Query: 352 STGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAPKIRAMEI 411 G+VR TEK +IERYS+VMHIVSNV G+L + A+ AL A LPAGT+SGAPK+RAMEI Sbjct: 360 KIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDHDALSALLAGLPAGTVSGAPKVRAMEI 419 Query: 412 IDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADSVPALEWE 471 IDELEP KRG+YGG VGYF+ G+MD IA+RTA++ D +L++QAGGG+V DS P E++ Sbjct: 420 IDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGGGVVYDSDPEAEYQ 479 Query: 472 ETINKRRAMFRAVA 485 ET++K A+ RA A Sbjct: 480 ETVHKSNAIRRAAA 493 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: 712 Number of extensions: 34 Number of successful extensions: 5 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: 504 Length adjustment: 34 Effective length of query: 459 Effective length of database: 470 Effective search space: 215730 Effective search space used: 215730 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 WP_085639309.1 MGEO_RS14630 (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.2791676.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-172 559.7 0.0 3.3e-172 559.5 0.0 1.0 1 NCBI__GCF_002115805.1:WP_085639309.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085639309.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 559.5 0.0 3.3e-172 3.3e-172 2 454 .. 30 492 .. 29 493 .. 0.92 Alignments for each domain: == domain 1 score: 559.5 bits; conditional E-value: 3.3e-172 TIGR00564 2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdg..kavlleaddeeak...ieede 68 d tp+s++lkl+ k f+lEsv+ +e +gRyS+ig++p+ +++++ ++ ++ d+e + e+d+ NCBI__GCF_002115805.1:WP_085639309.1 30 DLDTPVSLMLKLTGaAKDAFVLESVTGGEVRGRYSIIGMKPDVIWQCHGTrsRINRAARYDPE-SfeeLEGDP 101 778***********889******************************9984322222222322.234689*** PP TIGR00564 69 lkelrkllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkvi 141 l++lr+l+++ +++ ++ ++ ++g++Gylgyd++rlve+l++ ++d+l lpd++++ + v+v D v+ +v+ NCBI__GCF_002115805.1:WP_085639309.1 102 LTTLRALIAESKINLPDDLPQAAAGLFGYLGYDMIRLVEHLPNINPDPLGLPDAVMMRPSVVAVLDGVKGEVT 174 **********9777665556689************************************************** PP TIGR00564 142 lienarteaers...aeeeaaarleellaelqkelekavkaleekkes..ftsnvekeeyeekvakakeyika 209 +++ a +++ a+++aa+r+ + +++l+++l ++++++ ++++ sn+++e y+++v+kakeyi+a NCBI__GCF_002115805.1:WP_085639309.1 175 VVSPAWVNDGLTaraAYAQAAERVMDAVRDLERALPQQAREMGDAADIpaPVSNFTHEGYKQAVEKAKEYIRA 247 **9998888776566778888899999999999998876655555544567899******************* PP TIGR00564 210 GdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkR 282 Gdifqvv++qr ++++ ++pf+lYr+LR++NPSp+++y+++ +f+++g+SPE+lv+v g +v++rPiAGtr+R NCBI__GCF_002115805.1:WP_085639309.1 248 GDIFQVVPAQRWTQDFPLPPFALYRSLRRTNPSPFMFYFNFGGFQVIGASPEILVRVFGSEVTIRPIAGTRPR 320 ************************************************************************* PP TIGR00564 283 GatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdel 355 Gat++eD+ale++Llad Ke+AEHlmL+DL+RND+g+vak+g+v+ +e + ie+yshvmHivS+V+Gel d+ NCBI__GCF_002115805.1:WP_085639309.1 321 GATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVAKIGTVRPTEKFIIERYSHVMHIVSNVVGELSDDH 393 ************************************************************************* PP TIGR00564 356 tavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAga 428 +a+ al a lPaGT+sGAPKvrAme+idelE+ekRgiYgG+vgy+s+ gd+d++ia+Rt+++kd+++y+qAg+ NCBI__GCF_002115805.1:WP_085639309.1 394 DALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGIYGGGVGYFSAGGDMDMCIALRTALVKDKKLYIQAGG 466 ************************************************************************* PP TIGR00564 429 GiVaDSdpeaEyeEtlnKakallrai 454 G+V+DSdpeaEy+Et++K++a ra+ NCBI__GCF_002115805.1:WP_085639309.1 467 GVVYDSDPEAEYQETVHKSNAIRRAA 492 *********************99985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (504 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: 00:00:00.00 # Mc/sec: 33.20 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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