Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_078428493.1 BK574_RS09905 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_002019605.1:WP_078428493.1 Length = 341 Score = 240 bits (613), Expect = 3e-68 Identities = 130/320 (40%), Positives = 198/320 (61%), Gaps = 2/320 (0%) Query: 6 QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65 ++ LQ+ I+ ++ E M +IM G + + ++++LT LR + ET+ E+ G A M+ Sbjct: 3 KEILQKCIQGEQLTEKEATSAMDEIMSGAATHSQIASLLTVLRFRGETLDEMVGFAKSMK 62 Query: 66 EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125 + S + ++ ++D GTGGD + TFNIST V ++ G VAKHGNRSVSSKSGSA Sbjct: 63 QHSISIPHNEKG-VIDTCGTGGDHAKTFNISTATAIVLSSLGVTVAKHGNRSVSSKSGSA 121 Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185 D LE L I+ PE+ A L + + F++AP++H AMK VA R+E+G R+IFN+LGPL Sbjct: 122 DVLEQLNIQIQTSPEEAAVVLKEKKMSFLFAPLYHVAMKNVAIPRKELGFRSIFNLLGPL 181 Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245 TNPA + L+GVF I A+ L+ELG +RA++V G +G+DE+S+ T V EL++G Sbjct: 182 TNPANAEAQLIGVFDEKHGAIMAKTLRELGVKRAMLVTGAEGLDEISISTNTFVTELKEG 241 Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPG-PALDIVALNAGAALYV 304 ++ +Y + PED + +++V ES ++L V A +IVA NAGAALY+ Sbjct: 242 EISQYVLTPEDVSLPRGPLTDIQVNSPKESAEIILNVFQGGNNETARNIVAFNAGAALYI 301 Query: 305 AGVADSIADGIVRARQVLAD 324 A SI +G+ + +A+ Sbjct: 302 ANKVSSIEEGVKEVTKAIAN 321 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: 251 Number of extensions: 11 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: 345 Length of database: 341 Length adjustment: 29 Effective length of query: 316 Effective length of database: 312 Effective search space: 98592 Effective search space used: 98592 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_078428493.1 BK574_RS09905 (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.11675.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-128 412.3 5.6 8.9e-128 412.2 5.6 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078428493.1 BK574_RS09905 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078428493.1 BK574_RS09905 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 412.2 5.6 8.9e-128 8.9e-128 1 327 [. 6 331 .. 6 334 .. 0.99 Alignments for each domain: == domain 1 score: 412.2 bits; conditional E-value: 8.9e-128 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 l+k++++++L+e+ea+++m+eimsg a+++qia++l++lr +get +e++g+ak +++++ +++ +++ lcl|NCBI__GCF_002019605.1:WP_078428493.1 6 LQKCIQGEQLTEKEATSAMDEIMSGAATHSQIASLLTVLRFRGETLDEMVGFAKSMKQHSISIPH-NEK 73 689************************************************************99.6** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 ++D++GTGGD++kt+NiSTa+a+v++++Gv vaKhGnrsvssksGsaDvLe+l++++++spe++a l lcl|NCBI__GCF_002019605.1:WP_078428493.1 74 GVIDTCGTGGDHAKTFNISTATAIVLSSLGVTVAKHGNRSVSSKSGSADVLEQLNIQIQTSPEEAAVVL 142 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 +e+ ++FlfAP yh a+k+va RkeLg+r++fNlLGPL+nPa+a++q++Gv++++ ++a++l++lg lcl|NCBI__GCF_002019605.1:WP_078428493.1 143 KEKKMSFLFAPLYHVAMKNVAIPRKELGFRSIFNLLGPLTNPANAEAQLIGVFDEKHGAIMAKTLRELG 211 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 vkra++v g++glDEis+ ++t v+elk+gei++y l+ped l+r +l++++++s++e+ae++ +v++ lcl|NCBI__GCF_002019605.1:WP_078428493.1 212 VKRAMLVTGAEGLDEISISTNTFVTELKEGEISQYVLTPEDVSLPRGPLTDIQVNSPKESAEIILNVFQ 280 ********************************************************************* PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleel 327 g++++ +r+iv++Na+aaly+a+k+++++egv+ + +ai ++ ++e++ +l lcl|NCBI__GCF_002019605.1:WP_078428493.1 281 GGNNETARNIVAFNAGAALYIANKVSSIEEGVKEVTKAIANKTVYEQFINL 331 ********************************************9998666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (341 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: 6.75 // [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