Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_013459812.1 SULKU_RS04815 anthranilate phosphoribosyltransferase
Query= curated2:Q1IJR5 (347 letters) >NCBI__GCF_000183725.1:WP_013459812.1 Length = 326 Score = 240 bits (612), Expect = 4e-68 Identities = 128/317 (40%), Positives = 199/317 (62%), Gaps = 9/317 (2%) Query: 32 KTTDAQIGALLVGLQMKGETVDEIVGFAEAIRAAATPLIVRDS-ALDVSGTERDALLDTC 90 K +D Q+ L+ L + +T ++ A A ++ R + ALDV+ + L+D Sbjct: 15 KMSDEQMREFLLSLTLNADTPSSMI-------ATAAEVMKRHALALDVASELKSKLIDVV 67 Query: 91 GTGGDASGTFNISTATALVVAGAGVKVAKHGNRSVTSKCGSADVVEALGVNINLPAERMA 150 GTGGD SG+FN+S+ ++++A G VAKHGNRS+TSK GSADV+E LGV ++L + A Sbjct: 68 GTGGDKSGSFNVSSTVSILLAACGAHVAKHGNRSITSKSGSADVLEHLGVKLDLSLDNSA 127 Query: 151 ECLEKVGIAFLFAPAMHTAMKYVQPARRELKMRTVFNLLGPLTNPANASCQVVGVYTGQL 210 + LE+ G FLFA H AMK++ P RR + +T+FN+LGPLTNP S ++GV+ Sbjct: 128 KLLEETGFTFLFAQYHHPAMKFIMPIRRSIPEKTIFNILGPLTNPVGLSKILLGVFDEVF 187 Query: 211 VEKLAQALLQLGLKRALVVHGWDGLDEITISGPTKVAEVRDGKVTSYEISPEQFGLQRAP 270 V K+A+A +LG+ A+VV + +DEI+IS T +++ + +EI P+ FG+++AP Sbjct: 188 VPKMAEAARELGMTSAIVVSSREKMDEISISDITYAGRLKNNAIEYFEIDPQSFGIKKAP 247 Query: 271 LSALEGGDAQVNAAIIRAILDGERS-PKRDVVLLNAAAALVAAGQAETMGAAIPVAAYAI 329 A+ GGD + NAAI R +L + P+RD+VL+NAA AL+A G A + A+ +A + Sbjct: 248 FEAILGGDVEKNAAIFRDVLTNRATDPQRDMVLINAAYALIADGMARDVQEALEIARDGL 307 Query: 330 DSGQAKGRLRLLVEFTN 346 SG+A +L+ +V ++ Sbjct: 308 LSGKAAEKLKQIVSVSS 324 Lambda K H 0.318 0.133 0.369 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: 248 Number of extensions: 6 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: 347 Length of database: 326 Length adjustment: 28 Effective length of query: 319 Effective length of database: 298 Effective search space: 95062 Effective search space used: 95062 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_013459812.1 SULKU_RS04815 (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.13609.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-105 336.8 1.1 9.3e-105 336.5 1.1 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013459812.1 SULKU_RS04815 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013459812.1 SULKU_RS04815 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 336.5 1.1 9.3e-105 9.3e-105 19 329 .. 8 321 .. 3 322 .. 0.97 Alignments for each domain: == domain 1 score: 336.5 bits; conditional E-value: 9.3e-105 TIGR01245 19 mkeimsgeasdaqiaAilvalrvkgeteee.iaglakalrekakkveke..eseelvDivGTGGDglkt 84 +++++++++sd+q+ +l l+ + t+++ ia +a++++++a +++ +++l+D+vGTGGD++ + lcl|NCBI__GCF_000183725.1:WP_013459812.1 8 FEALFEHKMSDEQMREFLLSLTLNADTPSSmIATAAEVMKRHALALDVAseLKSKLIDVVGTGGDKSGS 76 789999*********************9983577899*****987766533789*************** PP TIGR01245 85 iNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhp 153 +N+S + ++++aa+G++vaKhGnrs++sksGsaDvLe+lgv+l+ls +++a+ lee+g++FlfA +hp lcl|NCBI__GCF_000183725.1:WP_013459812.1 77 FNVSSTVSILLAACGAHVAKHGNRSITSKSGSADVLEHLGVKLDLSLDNSAKLLEETGFTFLFAQYHHP 145 ********************************************************************* PP TIGR01245 154 alkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDE 222 a+k ++p+R+++ +t+fN+LGPL+nP+ + +lGv+++ +v ++ae++++lg+ a+vv++++ +DE lcl|NCBI__GCF_000183725.1:WP_013459812.1 146 AMKFIMPIRRSIPEKTIFNILGPLTNPVGLSKILLGVFDEVFVPKMAEAARELGMTSAIVVSSREKMDE 214 ********************************************************************* PP TIGR01245 223 isltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNa 291 is+ + t+ +lk++ ie ++++p++fg+k+a+ e++ gg+ e+na+++++vl++++++++rd+v++Na lcl|NCBI__GCF_000183725.1:WP_013459812.1 215 ISISDITYAGRLKNNAIEYFEIDPQSFGIKKAPFEAILGGDVEKNAAIFRDVLTNRATDPQRDMVLINA 283 ********************************************************************* PP TIGR01245 292 aaalyvagkakdlkegvelakeaiksgkalekleelva 329 a al++ g+a+d++e++e a++ + sgka+ekl+++v+ lcl|NCBI__GCF_000183725.1:WP_013459812.1 284 AYALIADGMARDVQEALEIARDGLLSGKAAEKLKQIVS 321 ***********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (326 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.66 // [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