Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_006746919.1 THITH_RS15385 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000227685.2:WP_006746919.1 Length = 343 Score = 299 bits (765), Expect = 8e-86 Identities = 164/339 (48%), Positives = 216/339 (63%), Gaps = 3/339 (0%) Query: 3 ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62 +T Q+A+ IE + + M +MR +M G+ + A + A+L LR+K ET EI AA Sbjct: 1 MTIQEAIAALIERKNLDAGAMTSVMRTVMTGQATPAQIGALLVALRMKGETPDEIVAAAR 60 Query: 63 VMREFSRRVEV-TDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSK 121 VMRE + RV V TD +VD GTGGD S TFN+ST + VAAA GA+VAKHGNRSVSS+ Sbjct: 61 VMRELATRVPVPTDG--LVDTCGTGGDASGTFNVSTASALVAAAAGARVAKHGNRSVSSR 118 Query: 122 SGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNI 181 SGSAD LEALG + + P+ VA + + G+GF++AP HH AM+ RRE+GVRT+FN+ Sbjct: 119 SGSADVLEALGVRLGIAPDGVATCIERIGVGFLFAPAHHGAMRHAIGPRRELGVRTMFNV 178 Query: 182 LGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGE 241 LGPLTNPAG+PN ++GVF + A LQ LG+ LVV DG+DE+S+ A T V E Sbjct: 179 LGPLTNPAGAPNQVLGVFSEQWLRPLAEALQMLGSRHVLVVHAEDGLDEISIAAPTRVAE 238 Query: 242 LRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAA 301 LRD + EY + P D G+ + +++V S AM+ VL PG A DIV +NAGAA Sbjct: 239 LRDATIREYTLAPGDLGLQSAPLDSIRVDGVEASAAMIRSVLAGDPGAARDIVLMNAGAA 298 Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340 LYV G A+S G+ RA Q + G+A L V TQ+ Sbjct: 299 LYVGGYAESHLQGVARAAQAIDSGAAADRLRQLVELTQE 337 Lambda K H 0.320 0.134 0.377 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: 347 Number of extensions: 18 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: 345 Length of database: 343 Length adjustment: 29 Effective length of query: 316 Effective length of database: 314 Effective search space: 99224 Effective search space used: 99224 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: 49 (23.5 bits)
Align candidate WP_006746919.1 THITH_RS15385 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))
# 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/TIGR01245.hmm # target sequence database: /tmp/gapView.2367268.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01245 [M=330] Accession: TIGR01245 Description: trpD: anthranilate phosphoribosyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-131 423.5 0.5 3.7e-131 423.3 0.5 1.0 1 NCBI__GCF_000227685.2:WP_006746919.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000227685.2:WP_006746919.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 423.3 0.5 3.7e-131 3.7e-131 2 329 .. 8 333 .. 7 334 .. 0.99 Alignments for each domain: == domain 1 score: 423.3 bits; conditional E-value: 3.7e-131 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 l+++k+L+++ ++++m+++m+g+a++aqi+A+lvalr+kget++ei+++a+++re a++v++ +++ lvD+ NCBI__GCF_000227685.2:WP_006746919.1 8 AALIERKNLDAGAMTSVMRTVMTGQATPAQIGALLVALRMKGETPDEIVAAARVMRELATRVPV-PTDGLVDT 79 5799************************************************************.7******* PP TIGR01245 75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147 +GTGGD++ t+N+STasalvaaaaG++vaKhGnrsvss+sGsaDvLealgv+l + p+ va ++e+ g+gFlf NCBI__GCF_000227685.2:WP_006746919.1 80 CGTGGDASGTFNVSTASALVAAAAGARVAKHGNRSVSSRSGSADVLEALGVRLGIAPDGVATCIERIGVGFLF 152 ************************************************************************* PP TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220 AP++h a++++++ R+eLgvrt+fN+LGPL+nPa a++qvlGv+s++ ++ lae+l+ lg++++lvvh+edgl NCBI__GCF_000227685.2:WP_006746919.1 153 APAHHGAMRHAIGPRRELGVRTMFNVLGPLTNPAGAPNQVLGVFSEQWLRPLAEALQMLGSRHVLVVHAEDGL 225 ************************************************************************* PP TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293 DEis+ ++t+vael+d +i+eytl p d+gl+ a+l++++++ e++a+++++vl g +a+rdiv++Na+a NCBI__GCF_000227685.2:WP_006746919.1 226 DEISIAAPTRVAELRDATIREYTLAPGDLGLQSAPLDSIRVDGVEASAAMIRSVLAGDP-GAARDIVLMNAGA 297 *********************************************************99.999********** PP TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelva 329 alyv g+a+++ +gv +a +ai+sg+a++ l++lv+ NCBI__GCF_000227685.2:WP_006746919.1 298 ALYVGGYAESHLQGVARAAQAIDSGAAADRLRQLVE 333 ********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (343 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: 00:00:00.00 # Mc/sec: 16.83 // [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