Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_011372781.1 SUDEN_RS06030 anthranilate phosphoribosyltransferase
Query= curated2:A7HXZ5 (341 letters) >NCBI__GCF_000012965.1:WP_011372781.1 Length = 328 Score = 241 bits (616), Expect = 1e-68 Identities = 130/322 (40%), Positives = 204/322 (63%), Gaps = 6/322 (1%) Query: 21 EARAAFEIVMSGEATQAQIGAFLMGLRVRGETVAE-ITAGATVMRERALRVTAP----AN 75 EA+ F + E + ++ FL+ +++ ET E I A A VMR A+++ + Sbjct: 5 EAKKVFNALFMHEMSDDEMLRFLLSIKLDEETQTEVIAAAAEVMRSFAIKLPISDELCSE 64 Query: 76 AIDIVGTGGDGVGTWNISTATALVVAAAGVPVAKHGNRKASSLSGTADALQALGVNLDID 135 ID+VGTGGD +G++NIS+ A++ A+ G VAKHG+R +S SG+AD + LGV LD+ Sbjct: 65 VIDVVGTGGDKIGSFNISSTVAILCASCGSMVAKHGSRSVTSKSGSADMFEELGVRLDLS 124 Query: 136 PATIAASIEKAGIGFMFAQAHHAAMKHVAPVRADLGIKTIFNMLGPLSNPALVKRQLLGV 195 A +E++G FMFAQAHH AMK + P+R + KTIFN+LGPL+NPA K+ LLGV Sbjct: 125 LKDSAKLLEESGFTFMFAQAHHPAMKFIMPIRKKIPQKTIFNILGPLTNPAESKKSLLGV 184 Query: 196 FAAEWVKPFAEALRNLGSDSAWVVHGSDGMDELTTTGPSAVAELKGGSIRVFEVTPEDAG 255 F +V AEALR G+ S VV +GMDE++ + + ++LKGG++ F + P++ G Sbjct: 185 FHKSFVSKIAEALRINGATSTMVVSSIEGMDEISISDITYASQLKGGAVHEFIIDPQEYG 244 Query: 256 LPRASIEDLKGGDPEQNAAAIRRLLDGEA-GAYRDIVLLNTAAALIVSGKAATLKEGAGL 314 + + ++ + GGD ++N+ + + +G A A RDIV++NTA+AL+V G A +++G + Sbjct: 245 IKKVPLKAIIGGDAKENSLILHNIFNGRATDAQRDIVMINTASALMVDGLARDIQDGLEM 304 Query: 315 AAKAIDSGAAKQTLAKLVAATN 336 A AI +G AK+ L +++ +N Sbjct: 305 AQSAIKTGKAKEKLKQIIEISN 326 Lambda K H 0.316 0.130 0.361 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: 203 Number of extensions: 10 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: 341 Length of database: 328 Length adjustment: 28 Effective length of query: 313 Effective length of database: 300 Effective search space: 93900 Effective search space used: 93900 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_011372781.1 SUDEN_RS06030 (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.4420.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-106 340.0 3.1 9.3e-106 339.8 3.1 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011372781.1 SUDEN_RS06030 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011372781.1 SUDEN_RS06030 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.8 3.1 9.3e-106 9.3e-106 10 329 .. 1 323 [. 1 324 [. 0.97 Alignments for each domain: == domain 1 score: 339.8 bits; conditional E-value: 9.3e-106 TIGR01245 10 LseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteee.iaglakalrekakkveke..eseelvDiv 75 +s eea++++++++ +e+sd ++ +l ++ et+ e ia++a+++r+ a k++ + ++e++D+v lcl|NCBI__GCF_000012965.1:WP_011372781.1 1 MSYEEAKKVFNALFMHEMSDDEMLRFLLSIKLDEETQTEvIAAAAEVMRSFAIKLPISdeLCSEVIDVV 69 6789*******************************99883567899*******9886644789****** PP TIGR01245 76 GTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgig 144 GTGGD++ ++NiS + a++ a++G vaKhG+rsv+sksGsaD+ e+lgv+l+ls + +a+ lee g++ lcl|NCBI__GCF_000012965.1:WP_011372781.1 70 GTGGDKIGSFNISSTVAILCASCGSMVAKHGSRSVTSKSGSADMFEELGVRLDLSLKDSAKLLEESGFT 138 ********************************************************************* PP TIGR01245 145 FlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralv 213 F+fA ++hpa+k ++p+Rk++ +t+fN+LGPL+nPa+ k ++lGv++k++v+++ae+l+ g+ +v lcl|NCBI__GCF_000012965.1:WP_011372781.1 139 FMFAQAHHPAMKFIMPIRKKIPQKTIFNILGPLTNPAESKKSLLGVFHKSFVSKIAEALRINGATSTMV 207 ********************************************************************* PP TIGR01245 214 vhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekka 282 v++ +g+DEis+ + t+ ++lk g ++e+ ++p+++g+k+ +l+++ gg+a+en+ +l+++++g++++a lcl|NCBI__GCF_000012965.1:WP_011372781.1 208 VSSIEGMDEISISDITYASQLKGGAVHEFIIDPQEYGIKKVPLKAIIGGDAKENSLILHNIFNGRATDA 276 ********************************************************************* PP TIGR01245 283 krdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 +rdiv++N+a al+v g a+d+++g+e+a+ aik+gka ekl+++++ lcl|NCBI__GCF_000012965.1:WP_011372781.1 277 QRDIVMINTASALMVDGLARDIQDGLEMAQSAIKTGKAKEKLKQIIE 323 ********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (328 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: 11.56 // [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