Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_085637395.1 MGEO_RS11335 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_002115805.1:WP_085637395.1 Length = 338 Score = 258 bits (660), Expect = 1e-73 Identities = 145/309 (46%), Positives = 188/309 (60%), Gaps = 2/309 (0%) Query: 33 GEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFSRRVEVTDRRHMVDIVGTGGDGSHT 92 GE + A + +L LR + E + E A AA VMR V+ + +DIVGTGGDG T Sbjct: 32 GEATPAQMGGLLMALRARGEAVSEYAAAAAVMRAKCTAVKAPEGA--MDIVGTGGDGMGT 89 Query: 93 FNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADALEALGAVIELQPEQVAASLAQTGIG 152 NIST FV A G VAKHGNR++SSKSGSADAL +G + + PE V ++A+ GIG Sbjct: 90 LNISTATAFVVAGAGVPVAKHGNRNLSSKSGSADALTEMGINVMVSPEVVERAIAEVGIG 149 Query: 153 FMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTNPAGSPNILMGVFHPDLVGIQARVLQ 212 FM AP+HHPAMK V PVR+E+G +TIFNILGPLTNPAG L G F DL+ A L+ Sbjct: 150 FMMAPMHHPAMKHVMPVRQELGSKTIFNILGPLTNPAGVKRQLTGAFAIDLIFPMAETLK 209 Query: 213 ELGAERALVVWGRDGMDELSLGAGTLVGELRDGQVHEYEVHPEDFGIAMSASRNLKVADA 272 ELG+E+A +V G DG DE+S+ A T V L DG++ EVHPED G+ + R++ Sbjct: 210 ELGSEKAWLVHGGDGTDEISISAPTQVAVLEDGKIRGREVHPEDAGLPVHPFRDILGGTP 269 Query: 273 AESRAMLLQVLDNVPGPALDIVALNAGAALYVAGVADSIADGIVRARQVLADGSARACLD 332 AE+ +LD D V LNA AAL VA A + G+ A + + G+A+A ++ Sbjct: 270 AENAQAFRDLLDGAKNAYRDAVLLNAAAALVVADKAADLRVGVEMAAESIDSGAAKAKVE 329 Query: 333 AYVAFTQQA 341 A TQ A Sbjct: 330 ALARVTQAA 338 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: 363 Number of extensions: 19 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: 338 Length adjustment: 29 Effective length of query: 316 Effective length of database: 309 Effective search space: 97644 Effective search space used: 97644 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_085637395.1 MGEO_RS11335 (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.1796332.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-120 387.0 2.7 4.9e-120 386.7 2.7 1.0 1 NCBI__GCF_002115805.1:WP_085637395.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085637395.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 386.7 2.7 4.9e-120 4.9e-120 8 329 .. 15 333 .. 10 334 .. 0.98 Alignments for each domain: == domain 1 score: 386.7 bits; conditional E-value: 4.9e-120 TIGR01245 8 kdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGD 80 Ls+ +aeq+++ +++gea++aq++ +l+alr++ge ++e a++a ++r+k + v++ e ++DivGTGGD NCBI__GCF_002115805.1:WP_085637395.1 15 GPLSRSQAEQAFELLFDGEATPAQMGGLLMALRARGEAVSEYAAAAAVMRAKCTAVKA--PEGAMDIVGTGGD 85 579*****************************************************88..79*********** PP TIGR01245 81 glktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhp 153 g+ t+NiSTa+a+v+a+aGv+vaKhGnr ssksGsaD L ++g+n+ +spe v+r+++evgigF++AP++hp NCBI__GCF_002115805.1:WP_085637395.1 86 GMGTLNISTATAFVVAGAGVPVAKHGNRNLSSKSGSADALTEMGINVMVSPEVVERAIAEVGIGFMMAPMHHP 158 ************************************************************************* PP TIGR01245 154 alkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEislt 226 a+k+v+pvR+eLg +t+fN+LGPL+nPa +k+q+ G + dl+ +ae+lk+lg+++a +vhg dg+DEis+ NCBI__GCF_002115805.1:WP_085637395.1 159 AMKHVMPVRQELGSKTIFNILGPLTNPAGVKRQLTGAFAIDLIFPMAETLKELGSEKAWLVHGGDGTDEISIS 231 ************************************************************************* PP TIGR01245 227 getkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvag 299 ++t+va l+dg+i+ +++ped gl+ ++ +++ gg+++ena++++++l g + +a rd+v+lNaaaal+va+ NCBI__GCF_002115805.1:WP_085637395.1 232 APTQVAVLEDGKIRGREVHPEDAGLPVHPFRDILGGTPAENAQAFRDLLDGAK-NAYRDAVLLNAAAALVVAD 303 ***************************************************98.899**************** PP TIGR01245 300 kakdlkegvelakeaiksgkalekleelva 329 ka+dl+ gve+a e+i+sg+a +k+e+l++ NCBI__GCF_002115805.1:WP_085637395.1 304 KAADLRVGVEMAAESIDSGAAKAKVEALAR 333 ************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (338 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 14.17 // [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