Align Anthranilate synthase component 1; AS; ASI; EC 4.1.3.27 (uncharacterized)
to candidate WP_010529287.1 ON01_RS01750 anthranilate synthase component I
Query= curated2:Q02001 (456 letters) >NCBI__GCF_000224785.1:WP_010529287.1 Length = 467 Score = 367 bits (943), Expect = e-106 Identities = 192/454 (42%), Positives = 290/454 (63%), Gaps = 5/454 (1%) Query: 3 KIKEISADTMTPISVYLRLKGKNKVILESIPRENDQSRFSIIALNPVKHIKFTDGILSVN 62 K +++ADT+TPI +Y L G+ K +LES + ++ ++S I +P + K ++ ++ Sbjct: 10 KYIKLNADTLTPIGIYENLYGRKKFLLESSIQHKEKGKYSFIGADPYQEFKGSNNATTIL 69 Query: 63 DEI--ISDENPMEFLEKLVCQPESTDENLDLPFTSGAIGYAGFDTYGIFEGIQPELKDSI 120 + I S+ L + D L PF GA+GY G+D +E I EL+D I Sbjct: 70 NHIRETSENRSEPVLTAFQKEFPKMDAELPFPFFGGAVGYIGYDAIRSYENIGDELRDDI 129 Query: 121 GTPDMYFMLYESALIFDHKREKLIFIEDNTYSQRSEKELQNALSANIESLSLLTEAENEL 180 PD++ MLY++ +++DH + + + N Q+ E L + L+ ++L A+ + Sbjct: 130 EMPDVHLMLYQNMIVYDHSNQSVFLVVTNL-DQQPEHVLDDRLAFLKKALIPFPTAD--V 186 Query: 181 TELSKLNFVSNMSQELFEEKVAKAKELIRNGDMFQVVLSQRLTADFTDNPFNYYRKLRVE 240 + ++ F M ++ F V AK+ I+NGD++QVVLSQR+ A +PF +YRKLR Sbjct: 187 STGKEVVFEPEMDKQHFMHNVEIAKDHIKNGDIYQVVLSQRMKAAMQGDPFTFYRKLRKV 246 Query: 241 NPSSYMYFMEFDNFHVIGSSPERLVAVHGNQVSTNPIAGTRKRGQTEFEDQALIEDLESD 300 NPS YM+++ FD++ V+G+SPE L+ G + TNPIAGTR RG T D AL +L +D Sbjct: 247 NPSPYMFYINFDDYVVLGASPESLIETSGRDIMTNPIAGTRPRGSTTDGDGALRNELLTD 306 Query: 301 PKEVAEHKMLVDLGRNDIGKISKYGSIEVPVFMKVEKYRYVMHITSEVTGELRPEFTAMD 360 KE++EH+MLVDL RND+G++ + S+ VP +MKVE Y++VMH+ SEV G+L FT++D Sbjct: 307 EKEISEHRMLVDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSID 366 Query: 361 ALRATLPAGTLSGAPKHRAYQRIYEFETQKRGIYGGAIGYLTKNGNCDFAIAIRTMVLKD 420 AL A LPAGT+SGAPK RA Q I + E KRG Y G +GY++ N N + A+AIR++++K+ Sbjct: 367 ALIACLPAGTVSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKE 426 Query: 421 KKAHVQAGAGIVYDSVPEHEYQETLNKAQGLLKV 454 A++QAGAGIVYDS PE EY ETL+KA+ L++V Sbjct: 427 NFAYLQAGAGIVYDSDPETEYNETLHKARSLMEV 460 Lambda K H 0.316 0.134 0.374 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: 584 Number of extensions: 26 Number of successful extensions: 3 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: 456 Length of database: 467 Length adjustment: 33 Effective length of query: 423 Effective length of database: 434 Effective search space: 183582 Effective search space used: 183582 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_010529287.1 ON01_RS01750 (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.2905282.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-178 578.4 0.0 6.8e-178 578.2 0.0 1.0 1 NCBI__GCF_000224785.1:WP_010529287.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010529287.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 578.2 0.0 6.8e-178 6.8e-178 1 453 [. 16 460 .. 16 462 .. 0.92 Alignments for each domain: == domain 1 score: 578.2 bits; conditional E-value: 6.8e-178 TIGR00564 1 adtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelkelr 73 adtltpi +y++l +++fllEs+ +++e+g+yS+ig++p++e+k +++ +++l++ e+++ + +l NCBI__GCF_000224785.1:WP_010529287.1 16 ADTLTPIGIYENLYG-RKKFLLESSIQHKEKGKYSFIGADPYQEFKGSNNATTILNHIRETSE--NRSEPVLT 85 69************8.9*******************************996666665555444..33334455 PP TIGR00564 74 kllekaeesedeldeplsggavGylgydtvrlveklkeeaedelelpdlllllvetvivfDhvekkviliena 146 ++ +++ + + el+ p+ ggavGy+gyd +r++e++ +e +d++e+pd++l+l++++iv+Dh +++v+l+ ++ NCBI__GCF_000224785.1:WP_010529287.1 86 AFQKEFPKMDAELPFPFFGGAVGYIGYDAIRSYENIGDELRDDIEMPDVHLMLYQNMIVYDHSNQSVFLVVTN 158 666666778999************************************************************9 PP TIGR00564 147 rteaersaeeeaaarleellaelqkelekavkaleekkesftsnvekeeyeekvakakeyikaGdifqvvlSq 219 +++ + + +++rl l + l ++++ + k++ f+++++k++++++v+ ak++ik+Gdi+qvvlSq NCBI__GCF_000224785.1:WP_010529287.1 159 LDQQPE---HVLDDRLAFLKKALIPFP--TADVSTGKEVVFEPEMDKQHFMHNVEIAKDHIKNGDIYQVVLSQ 226 766555...344444444433333222..36677888999********************************* PP TIGR00564 220 rleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkgkrvetrPiAGtrkRGatkeeDeal 292 r++a ++ +pf +YrkLR+vNPSpy++y++++d+ ++g+SPE+l++++g+++ t+PiAGtr+RG+t++ D al NCBI__GCF_000224785.1:WP_010529287.1 227 RMKAAMQGDPFTFYRKLRKVNPSPYMFYINFDDYVVLGASPESLIETSGRDIMTNPIAGTRPRGSTTDGDGAL 299 ************************************************************************* PP TIGR00564 293 eeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkiekyshvmHivSeVeGelkdeltavDalraal 365 ++eLl+deKe EH mLvDL+RND+g+v+++ sv+v+ ++k+e+y+hvmH+vSeV+G+l++++t++Dal+a+l NCBI__GCF_000224785.1:WP_010529287.1 300 RNELLTDEKEISEHRMLVDLSRNDLGRVCEIDSVSVPTYMKVENYQHVMHMVSEVHGKLAEGFTSIDALIACL 372 ************************************************************************* PP TIGR00564 366 PaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdvdtaiaiRtmvlkdgvayvqAgaGiVaDSdpea 438 PaGT+sGAPK+rAm++i++lEk+kRg Y+G+vgy+sf+ ++++a+aiR++++k++ ay+qAgaGiV+DSdpe+ NCBI__GCF_000224785.1:WP_010529287.1 373 PAGTVSGAPKIRAMQIINDLEKVKRGAYAGGVGYISFNDNLNIALAIRSLIVKENFAYLQAGAGIVYDSDPET 445 ************************************************************************* PP TIGR00564 439 EyeEtlnKakallra 453 Ey+Etl+Ka++l+++ NCBI__GCF_000224785.1:WP_010529287.1 446 EYNETLHKARSLMEV 460 ************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (467 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 17.85 // [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