Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_013075710.1 BTUS_RS08545 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000092905.1:WP_013075710.1 Length = 354 Score = 282 bits (722), Expect = 8e-81 Identities = 155/335 (46%), Positives = 213/335 (63%), Gaps = 2/335 (0%) Query: 6 QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65 + L++ + ++ E M Q+M G+ + A V A LT LR+K E + EI+G A MR Sbjct: 2 RDVLEQLLRGEDLSEAEAQAAMEQVMSGKATHAQVGAFLTALRIKGERVEEISGFAKAMR 61 Query: 66 EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125 +F++ + V D ++D GTGGDG+ TFN+ST A VAAA GAKVAKHGNRSVSS+SGSA Sbjct: 62 KFAQPLPV-DGDKVIDTCGTGGDGARTFNVSTAAALVAAAAGAKVAKHGNRSVSSRSGSA 120 Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185 D L ALG + L PE+ A L + G+ F++AP +H AM+ R+E+G RT+FNILGPL Sbjct: 121 DVLAALGVEVNLSPEEAAQCLEEVGLCFLFAPSYHGAMRHAMAPRKELGFRTVFNILGPL 180 Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWG-RDGMDELSLGAGTLVGELRD 244 TNPAG+ +MG F DLV ARVL LGA A VV G D +DELS+ + V E++D Sbjct: 181 TNPAGARRQVMGTFAQDLVEKTARVLLRLGANHAWVVHGMEDHLDELSVSGPSFVAEVKD 240 Query: 245 GQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYV 304 G V + ++PED G+ S + DA E+ A++L VL G A DIV LNA A L+V Sbjct: 241 GAVRTFVLNPEDAGLTRSPLSEVAGGDARENAAIILDVLSGKRGGARDIVVLNAAAGLHV 300 Query: 305 AGVADSIADGIVRARQVLADGSARACLDAYVAFTQ 339 AG+A ++ G+ A+++L +G A+ LD V T+ Sbjct: 301 AGIAPTLEAGVTLAQRMLDEGRAKETLDRLVEVTK 335 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: 292 Number of extensions: 14 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: 354 Length adjustment: 29 Effective length of query: 316 Effective length of database: 325 Effective search space: 102700 Effective search space used: 102700 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_013075710.1 BTUS_RS08545 (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.19407.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-133 429.8 1.3 4.5e-133 429.6 1.3 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013075710.1 BTUS_RS08545 anthranilate phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013075710.1 BTUS_RS08545 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 429.6 1.3 4.5e-133 4.5e-133 1 329 [. 5 332 .. 5 333 .. 0.99 Alignments for each domain: == domain 1 score: 429.6 bits; conditional E-value: 4.5e-133 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 le+ll ++dLse+ea+++m+++msg+a++aq++A+l+alr+kge +eei+g+aka+r+ a+ ++++ + lcl|NCBI__GCF_000092905.1:WP_013075710.1 5 LEQLLRGEDLSEAEAQAAMEQVMSGKATHAQVGAFLTALRIKGERVEEISGFAKAMRKFAQPLPVD-GD 72 6899*************************************************************6.** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 +++D++GTGGDg++t+N+STa+alvaaaaG+kvaKhGnrsvss+sGsaDvL algv+++lspe++a++l lcl|NCBI__GCF_000092905.1:WP_013075710.1 73 KVIDTCGTGGDGARTFNVSTAAALVAAAAGAKVAKHGNRSVSSRSGSADVLAALGVEVNLSPEEAAQCL 141 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 eevg++FlfAP yh a++++++ RkeLg+rtvfN+LGPL+nPa a++qv+G++ +dlve+ a+vl +lg lcl|NCBI__GCF_000092905.1:WP_013075710.1 142 EEVGLCFLFAPSYHGAMRHAMAPRKELGFRTVFNILGPLTNPAGARRQVMGTFAQDLVEKTARVLLRLG 210 ********************************************************************* PP TIGR01245 208 vkralvvhg.edglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevl 275 +++a vvhg ed lDE+s+ g++ vae+kdg ++++ l+ped gl+r +l+e++gg+a+ena+++ +vl lcl|NCBI__GCF_000092905.1:WP_013075710.1 211 ANHAWVVHGmEDHLDELSVSGPSFVAEVKDGAVRTFVLNPEDAGLTRSPLSEVAGGDARENAAIILDVL 279 *********8899******************************************************** PP TIGR01245 276 egkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 +gk + +rdivvlNaaa l vag a +l++gv+la++++++g+a e+l++lv+ lcl|NCBI__GCF_000092905.1:WP_013075710.1 280 SGKR-GGARDIVVLNAAAGLHVAGIAPTLEAGVTLAQRMLDEGRAKETLDRLVE 332 ***9.556******************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (354 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: 00:00:00.01 # Mc/sec: 10.00 // [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