Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (characterized)
to candidate WP_011321383.1 AVA_RS23960 anthranilate synthase component I
Query= SwissProt::P20579 (493 letters) >NCBI__GCF_000204075.1:WP_011321383.1 Length = 504 Score = 402 bits (1033), Expect = e-116 Identities = 227/500 (45%), Positives = 321/500 (64%), Gaps = 21/500 (4%) Query: 2 NREEFLRLAAVGYNRIPLACETLADFDTPLSIYLKL-ADQPNSYLLESVQGGEKWGRYSM 60 N EF +LA G N +P+ E +AD DTP+S + K+ A +P S+LLESV+GGEK GRYS+ Sbjct: 5 NFSEFSQLALQG-NFVPVYQEWVADLDTPVSAWYKVCAGEPYSFLLESVEGGEKIGRYSL 63 Query: 61 IGLPSRTVMRVHGYHVSILH-DGVEVESHDVEDPLAFVESFKDRYKVADIPGLPRFNGGL 119 +G ++ G + + D +V DP + YK +P LP GGL Sbjct: 64 LGCDPLWILEARGETTTQTNRDASQVVF--TGDPFTALADCLAPYKPVKLPQLPPGIGGL 121 Query: 120 VGYFGYDCVRYVEKRLGVSPNPDPLGVPDILLMVSDAVVVFDNLAGKMHAIVLVDPAE-- 177 G++GY+ +R++E R+ V + D +PD L M D +++FD + K+ AI D + Sbjct: 122 FGFWGYELIRWIEPRVPVH-SQDERNIPDGLWMQVDHLLIFDQVKRKIWAIAYADLRDPN 180 Query: 178 ---EQAFEQGQARLQGLLETLRQPITPRRGLDLSGPQAAE-----PEFRSSYTREDYENA 229 + A++Q R+ ++ L P++P++ + P ++ E+ S++TR ++ + Sbjct: 181 VDLKAAYQQACDRVTQMVSKLSLPVSPQKTILEWTPPGSQNVGETQEYTSNFTRPEFCAS 240 Query: 230 VGRIKEYILAGDCMQVVPSQRMSIDFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSS 289 V + KEYI AGD QVV SQR+S + P LYR+LR NP+PYM +FNF D+ ++GSS Sbjct: 241 VQKAKEYIKAGDIFQVVISQRLSTQYTGDPFSLYRSLRQINPSPYMAYFNFQDWQIIGSS 300 Query: 290 PEVLVRVE-----DNLVTVRPIAGTRPRGATEEADRALEDDLLSDDKEIAEHLMLIDLGR 344 PEV+V+ E + + TVRPIAGTRPRG T + D L DLL D KEIAEH+ML+DLGR Sbjct: 301 PEVMVKAELDGDGEAVATVRPIAGTRPRGKTTKEDAELAADLLQDPKEIAEHVMLVDLGR 360 Query: 345 NDVGRVSSTGSVRLTEKMVIERYSNVMHIVSNVAGQLREGLTAMDALRAILPAGTLSGAP 404 ND+GRV ++G+V++ E MV+ERYS+VMHIVSNV G+L A D L+A PAGT+SGAP Sbjct: 361 NDLGRVCASGTVKVDELMVVERYSHVMHIVSNVVGKLAANKNAWDLLKACFPAGTVSGAP 420 Query: 405 KIRAMEIIDELEPVKRGVYGGAVGYFAWNGNMDTAIAIRTAVINDGELHVQAGGGIVADS 464 KIRAMEII+ELEP +RGVY G GY+ + G +++AIAIRT V+ D + VQAG G+VADS Sbjct: 421 KIRAMEIINELEPSRRGVYSGVYGYYDFEGQLNSAIAIRTMVVRDHTVTVQAGAGLVADS 480 Query: 465 VPALEWEETINKRRAMFRAV 484 P E+EET+NK R + A+ Sbjct: 481 DPEKEYEETLNKARGLLLAI 500 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: 622 Number of extensions: 33 Number of successful extensions: 6 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_011321383.1 AVA_RS23960 (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.847820.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-168 544.7 0.0 1.1e-167 544.6 0.0 1.0 1 NCBI__GCF_000204075.1:WP_011321383.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011321383.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 544.6 0.0 1.1e-167 1.1e-167 2 453 .. 28 499 .. 27 501 .. 0.93 Alignments for each domain: == domain 1 score: 544.6 bits; conditional E-value: 1.1e-167 TIGR00564 2 dtltpisvylklak.rkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 d tp+s+ k+ +++sfllEsve +e++gRySl+g++p ++a+++++++ + d ++ ++d+ ++l NCBI__GCF_000204075.1:WP_011321383.1 28 DLDTPVSAWYKVCAgEPYSFLLESVEGGEKIGRYSLLGCDPLWILEARGETTTQTNRDASQVVFTGDPFTALA 100 778*****99999889*********************************99999999999999********** PP TIGR00564 74 klleka.eesedeldeplsggavGylgydtvrlveklkeea.edelelpdlllllvetvivfDhvekkvilie 144 ++l+ + + ++l++ gg++G+ gy+++r +e+ + + +de+++pd l + v+++++fD+v++k+ i+ NCBI__GCF_000204075.1:WP_011321383.1 101 DCLAPYkPVKLPQLPP-GIGGLFGFWGYELIRWIEPRVPVHsQDERNIPDGLWMQVDHLLIFDQVKRKIWAIA 172 ****986667777765.78******************99887******************************9 PP TIGR00564 145 narteaers....aeeeaaarleellaelqkeleka...vkaleekkes......ftsnvekeeyeekvakak 204 +a ++ + a+++a +r+++++++l+ +++++ + +++ +++ +tsn+++ e+ ++v+kak NCBI__GCF_000204075.1:WP_011321383.1 173 YADLRDPNVdlkaAYQQACDRVTQMVSKLSLPVSPQktiLEWTPPGSQNvgetqeYTSNFTRPEFCASVQKAK 245 9866554335888999****************999855533333333336666679999999*********** PP TIGR00564 205 eyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvk....gkr.ve 272 eyikaGdifqvv+Sqrl+++ + +pf+lYr+LR++NPSpy++y++++d +++gsSPE++vk + g+ + NCBI__GCF_000204075.1:WP_011321383.1 246 EYIKAGDIFQVVISQRLSTQYTGDPFSLYRSLRQINPSPYMAYFNFQDWQIIGSSPEVMVKAEldgdGEAvAT 318 *************************************************************999886666678 PP TIGR00564 273 trPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivS 345 +rPiAGtr+RG+t++eD+ l+++Ll+d+Ke AEH+mLvDL+RND+g+v+ g+v+v+el+ +e+yshvmHivS NCBI__GCF_000204075.1:WP_011321383.1 319 VRPIAGTRPRGKTTKEDAELAADLLQDPKEIAEHVMLVDLGRNDLGRVCASGTVKVDELMVVERYSHVMHIVS 391 9************************************************************************ PP TIGR00564 346 eVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlk 418 +V+G+l+ +++a+D l+a++PaGT+sGAPK+rAme+i+elE+++Rg+Y+G+ gy++f+g++++aiaiRtmv++ NCBI__GCF_000204075.1:WP_011321383.1 392 NVVGKLAANKNAWDLLKACFPAGTVSGAPKIRAMEIINELEPSRRGVYSGVYGYYDFEGQLNSAIAIRTMVVR 464 ************************************************************************* PP TIGR00564 419 dgvayvqAgaGiVaDSdpeaEyeEtlnKakallra 453 d+++ vqAgaG+VaDSdpe+EyeEtlnKa++ll a NCBI__GCF_000204075.1:WP_011321383.1 465 DHTVTVQAGAGLVADSDPEKEYEETLNKARGLLLA 499 ******************************99866 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: 31.55 // [ok]
This GapMind analysis is from Jul 25 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