Align anthranilate synthase (subunit 1/2) (EC 4.1.3.27) (characterized)
to candidate WP_077277377.1 B1C78_RS01525 anthranilate synthase component I
Query= BRENDA::P20580 (492 letters) >NCBI__GCF_002000365.1:WP_077277377.1 Length = 489 Score = 616 bits (1588), Expect = 0.0 Identities = 316/488 (64%), Positives = 376/488 (77%), Gaps = 3/488 (0%) Query: 1 MNREEFLRLAADGYNRIPLSFETLADFDTPLSIYLKLADAPNSYLLESVQGGEKWGRYSI 60 M+ E+F L GYNRIPL E LAD DTPLS+YLKLA AP SYL ESVQGGEKWGRYS Sbjct: 1 MSPEQFDELIRQGYNRIPLVREVLADLDTPLSVYLKLAAAPYSYLFESVQGGEKWGRYSF 60 Query: 61 IGLPCRTVLRVYDHQVRISIDGVETERFDCADPLAFVEEFKARYQVPTVPGLPRFDGGLV 120 +GLP RTV++V +V + G E + ADPLA+VE+F+AR +VP + GLPRF GGLV Sbjct: 61 VGLPARTVVKVRGRRVTVEEGGAVVEDTEVADPLAWVEDFQARQRVPDIEGLPRFTGGLV 120 Query: 121 GYFGYDCVRYVEKRLATCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAIVLADPSEENA 180 GYFGYD +RY+E RLA PDPLG PDILLMVSD VVV+DNLAG+++ +V A P E Sbjct: 121 GYFGYDTIRYIEPRLAGTEKPDPLGVPDILLMVSDEVVVYDNLAGRLYLVVHARP--ETG 178 Query: 181 YERGQARLEELLERLRQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAG 240 QARLEEL RL P+ +A + E F + FT + ++ AV R KDYI+ G Sbjct: 179 LAAAQARLEELRGRLAAPVAAPAATG-DARKVHESDFVSGFTEDGFKAAVARCKDYIVEG 237 Query: 241 DCMQVVPSQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGL 300 D MQVV SQR+SI F A P++LYRALR NP+PYM+F + D VVGSSPE+LVR+ED + Sbjct: 238 DVMQVVLSQRLSIPFAAPPVNLYRALRSLNPSPYMFFLDLDDHQVVGSSPEILVRLEDDI 297 Query: 301 VTVRPIAGTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTE 360 VTVRPIAGTRPRG E D ALE +LL+D KE AEHLMLIDLGRND GRVS+ G+V++TE Sbjct: 298 VTVRPIAGTRPRGATEAEDHALEAELLADPKERAEHLMLIDLGRNDAGRVSETGSVQLTE 357 Query: 361 KMVIERYSNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKR 420 +MV+ERYS+VMHIVSNVTG+L+ G+SAMD LRA PAGT+SGAPKIRAMEIIDELEPVKR Sbjct: 358 QMVVERYSHVMHIVSNVTGRLKAGMSAMDVLRATFPAGTVSGAPKIRAMEIIDELEPVKR 417 Query: 421 GVYGGAVGYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAM 480 G+Y GAVGYL+W GNMDTAIAIRTAVIK+G+LH+QAG GIV DS+P EW ET+NK RA+ Sbjct: 418 GIYAGAVGYLSWAGNMDTAIAIRTAVIKDGQLHIQAGAGIVHDSIPDNEWAETMNKGRAI 477 Query: 481 FRAVALAE 488 FRAVA+ E Sbjct: 478 FRAVAMVE 485 Lambda K H 0.321 0.139 0.408 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: 733 Number of extensions: 29 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: 492 Length of database: 489 Length adjustment: 34 Effective length of query: 458 Effective length of database: 455 Effective search space: 208390 Effective search space used: 208390 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_077277377.1 B1C78_RS01525 (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.8373.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-178 580.5 0.0 1.6e-178 580.3 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077277377.1 B1C78_RS01525 anthranilate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077277377.1 B1C78_RS01525 anthranilate synthase component I # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 580.3 0.0 1.6e-178 1.6e-178 2 454 .. 26 481 .. 25 482 .. 0.93 Alignments for each domain: == domain 1 score: 580.3 bits; conditional E-value: 1.6e-178 TIGR00564 2 dtltpisvylklakrkesfllEsvekeeelgRySliglnpvleikakdgkavlleaddeeakieedelk 70 d tp+svylkla ++s+l+Esv+ +e++gRyS++gl ++++k+++ ++++++ a +e+ e+ lcl|NCBI__GCF_002000365.1:WP_077277377.1 26 DLDTPLSVYLKLAAAPYSYLFESVQGGEKWGRYSFVGLPARTVVKVRGR---RVTVEEGGAVVEDTEVA 91 778*******************************************987...55555666666777777 PP TIGR00564 71 elrklleka..eesedeld..eplsggavGylgydtvrlveklke..eaedelelpdlllllvetvivf 133 + +++e + +++ ++++ + ++gg+vGy+gydt+r++e+ + e++d+l +pd+ll++ ++v+v+ lcl|NCBI__GCF_002000365.1:WP_077277377.1 92 DPLAWVEDFqaRQRVPDIEglPRFTGGLVGYFGYDTIRYIEPRLAgtEKPDPLGVPDILLMVSDEVVVY 160 78888887755566777778888******************98775466******************** PP TIGR00564 134 Dhvekkvilienarteaersaeeeaaarleellaelqkeleka...vkaleekkesftsnvekeeyeek 199 D+ + +++l+ +ar e++ ++a+arleel +l +++ +a + ++ +f s ++++ ++++ lcl|NCBI__GCF_002000365.1:WP_077277377.1 161 DNLAGRLYLVVHARPETGL---AAAQARLEELRGRLAAPVAAPaatGDARKVHESDFVSGFTEDGFKAA 226 *************888655...799************9998773223344455566************* PP TIGR00564 200 vakakeyikaGdifqvvlSqrleakveakpfelYrkLRtvNPSpylyyldledfelvgsSPEllvkvkg 268 va+ k+yi +Gd++qvvlSqrl+ ++ a+p++lYr+LR+ NPSpy+++ldl+d ++vgsSPE+lv++++ lcl|NCBI__GCF_002000365.1:WP_077277377.1 227 VARCKDYIVEGDVMQVVLSQRLSIPFAAPPVNLYRALRSLNPSPYMFFLDLDDHQVVGSSPEILVRLED 295 ********************************************************************9 PP TIGR00564 269 krvetrPiAGtrkRGatkeeDealeeeLladeKerAEHlmLvDLaRNDigkvaklgsvevkellkieky 337 + v++rPiAGtr+RGat++eD+ale+eLlad+KerAEHlmL+DL+RND g+v+++gsv+ +e + +e+y lcl|NCBI__GCF_002000365.1:WP_077277377.1 296 DIVTVRPIAGTRPRGATEAEDHALEAELLADPKERAEHLMLIDLGRNDAGRVSETGSVQLTEQMVVERY 364 99******************************************************************* PP TIGR00564 338 shvmHivSeVeGelkdeltavDalraalPaGTlsGAPKvrAmelidelEkekRgiYgGavgylsfdgdv 406 shvmHivS+V+G+lk +++a+D+lra++PaGT+sGAPK+rAme+idelE++kRgiY+Gavgyls +g++ lcl|NCBI__GCF_002000365.1:WP_077277377.1 365 SHVMHIVSNVTGRLKAGMSAMDVLRATFPAGTVSGAPKIRAMEIIDELEPVKRGIYAGAVGYLSWAGNM 433 ********************************************************************* PP TIGR00564 407 dtaiaiRtmvlkdgvayvqAgaGiVaDSdpeaEyeEtlnKakallrai 454 dtaiaiRt+v+kdg++++qAgaGiV DS p++E+ Et+nK +a ra+ lcl|NCBI__GCF_002000365.1:WP_077277377.1 434 DTAIAIRTAVIKDGQLHIQAGAGIVHDSIPDNEWAETMNKGRAIFRAV 481 *******************************************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (455 nodes) Target sequences: 1 (489 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.66 // [ok]
This GapMind analysis is from Apr 10 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