Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_086511634.1 BZY95_RS19950 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_002151265.1:WP_086511634.1 Length = 340 Score = 320 bits (820), Expect = 3e-92 Identities = 164/318 (51%), Positives = 218/318 (68%), Gaps = 1/318 (0%) Query: 6 QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65 + A+ + + D+ +M+QIM GE SDA + L GL +K ET EI AA VMR Sbjct: 4 RDAIAAVMRRENLSFDQTHAVMQQIMTGEASDAQIGGFLVGLAMKGETAEEIGAAAQVMR 63 Query: 66 EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125 E +RV + ++VDIVGTGGDG++ FN+ST + FVAAA GA+VAKHGNRSVSS SGSA Sbjct: 64 ELMKRVHLQRSENVVDIVGTGGDGANLFNVSTASSFVAAASGAQVAKHGNRSVSSSSGSA 123 Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185 D + G ++L+PEQVA + G+GFM+AP HHPAM+ RREMGVRT+FNILGPL Sbjct: 124 DLFDMAGIHLDLRPEQVARCIEHVGVGFMFAPNHHPAMRFAIGPRREMGVRTLFNILGPL 183 Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245 TNPAG+PN ++GV+ +LV + A VL++LG+ +VV DG+DE+SL A T V EL+DG Sbjct: 184 TNPAGAPNQVLGVYSAELVPLMAEVLRQLGSRHVMVVHAEDGLDEISLAAPTQVAELKDG 243 Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVA 305 ++ Y + PEDFGI A LKV A +S ++ + L GPA DIV+LNAGAALY A Sbjct: 244 EIRRYTIAPEDFGIERQALSPLKVVSAEDSLRLVREALVG-EGPAADIVSLNAGAALYCA 302 Query: 306 GVADSIADGIVRARQVLA 323 GVAD++ +G++ A+ A Sbjct: 303 GVADTLKEGVMMAQDAQA 320 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: 355 Number of extensions: 11 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: 340 Length adjustment: 29 Effective length of query: 316 Effective length of database: 311 Effective search space: 98276 Effective search space used: 98276 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_086511634.1 BZY95_RS19950 (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.11347.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-130 420.2 1.8 3.7e-130 420.0 1.8 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086511634.1 BZY95_RS19950 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086511634.1 BZY95_RS19950 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.0 1.8 3.7e-130 3.7e-130 2 329 .. 8 333 .. 7 334 .. 0.99 Alignments for each domain: == domain 1 score: 420.0 bits; conditional E-value: 3.7e-130 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 ++ +++Ls ++ +++m++im+geasdaqi+ +lv l++kget+eei ++a+++re +k+v+ + se+ lcl|NCBI__GCF_002151265.1:WP_086511634.1 8 AAVMRRENLSFDQTHAVMQQIMTGEASDAQIGGFLVGLAMKGETAEEIGAAAQVMRELMKRVHLQRSEN 76 57899**************************************************************** PP TIGR01245 71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsle 139 +vDivGTGGDg++ +N+STas++vaaa G++vaKhGnrsvss+sGsaD+ ++ g++l+l+pe+var++e lcl|NCBI__GCF_002151265.1:WP_086511634.1 77 VVDIVGTGGDGANLFNVSTASSFVAAASGAQVAKHGNRSVSSSSGSADLFDMAGIHLDLRPEQVARCIE 145 ********************************************************************* PP TIGR01245 140 evgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgv 208 +vg+gF+fAP++hpa++ +++ R+e+gvrt+fN+LGPL+nPa a++qvlGvys++lv ++aevl++lg+ lcl|NCBI__GCF_002151265.1:WP_086511634.1 146 HVGVGFMFAPNHHPAMRFAIGPRREMGVRTLFNILGPLTNPAGAPNQVLGVYSAELVPLMAEVLRQLGS 214 ********************************************************************* PP TIGR01245 209 kralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevleg 277 ++++vvh+edglDEisl ++t+vaelkdgei++yt+ pedfg++r+ l+ lk+ sae++++l++e+l g lcl|NCBI__GCF_002151265.1:WP_086511634.1 215 RHVMVVHAEDGLDEISLAAPTQVAELKDGEIRRYTIAPEDFGIERQALSPLKVVSAEDSLRLVREALVG 283 ********************************************************************* PP TIGR01245 278 kekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ +++div lNa+aaly ag+a++lkegv +a++a s+ +lek++el++ lcl|NCBI__GCF_002151265.1:WP_086511634.1 284 EG--PAADIVSLNAGAALYCAGVADTLKEGVMMAQDAQASKLPLEKMKELAD 333 99..888****************************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (340 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.72 // [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