Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_011938633.1 GURA_RS08795 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000016745.1:WP_011938633.1 Length = 350 Score = 260 bits (665), Expect = 3e-74 Identities = 144/348 (41%), Positives = 206/348 (59%), Gaps = 13/348 (3%) Query: 6 QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65 ++A+ + +E ++ EM+ +M Q+M GE + A ++A +T LR+K ET+ EI GAA VMR Sbjct: 3 KKAIAKVVEREDLTESEMIQVMDQVMSGEATPAQIAAFITALRMKGETVAEITGAARVMR 62 Query: 66 EFSRRVEV-------------TDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAK 112 + R+ V D ++D GTGG ++TFN+ST FV +A G KVAK Sbjct: 63 DKVTRIRVGKNILDMDRDDINVDLETILDTCGTGGSCTNTFNVSTTVAFVVSACGVKVAK 122 Query: 113 HGNRSVSSKSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRRE 172 HGNRSVSS GSAD LE+LG +++ E + + + GIGF++AP H AMK R+E Sbjct: 123 HGNRSVSSACGSADVLESLGVNLDVTQETIERCINEIGIGFLFAPALHGAMKYAIGPRKE 182 Query: 173 MGVRTIFNILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELS 232 +G+RTIFNILGPLTNPAG+ ++GV+ DLV A VL+ LG +R VV G+DGMDE++ Sbjct: 183 IGIRTIFNILGPLTNPAGAGCQVLGVYREDLVEKLAHVLKNLGCKRGFVVHGQDGMDEMT 242 Query: 233 LGAGTLVGELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALD 292 L A T + E+ V PE+ G++ +L+ DAA + ++ +VL+ GP D Sbjct: 243 LTAETRIAEVTPAGVATRLFRPEELGLSRCGMDDLRGGDAAANAVIVRRVLEGEKGPKRD 302 Query: 293 IVALNAGAALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340 IV LNA L AG A G+ A + + G A A L+ V T + Sbjct: 303 IVLLNAAFGLVAAGRVVDPAAGLTMAAEAIDSGKALAQLEKLVKLTNE 350 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: 266 Number of extensions: 9 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: 350 Length adjustment: 29 Effective length of query: 316 Effective length of database: 321 Effective search space: 101436 Effective search space used: 101436 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_011938633.1 GURA_RS08795 (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.27345.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-127 410.4 4.6 1.3e-126 408.3 4.6 1.7 1 lcl|NCBI__GCF_000016745.1:WP_011938633.1 GURA_RS08795 anthranilate phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016745.1:WP_011938633.1 GURA_RS08795 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.3 4.6 1.3e-126 1.3e-126 2 329 .. 7 346 .. 6 347 .. 0.95 Alignments for each domain: == domain 1 score: 408.3 bits; conditional E-value: 1.3e-126 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekees.. 68 k+++++dL+e e+ q+m+++msgea++aqiaA+++alr+kget+ ei+g+a+++r+k +++++ ++ lcl|NCBI__GCF_000016745.1:WP_011938633.1 7 AKVVEREDLTESEMIQVMDQVMSGEATPAQIAAFITALRMKGETVAEITGAARVMRDKVTRIRVGKNil 75 689*******************************************************99987642111 PP TIGR01245 69 ...........eelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvn 126 e ++D++GTGG ++t+N+ST+ a+v++a+GvkvaKhGnrsvss++GsaDvLe lgvn lcl|NCBI__GCF_000016745.1:WP_011938633.1 76 dmdrddinvdlETILDTCGTGGSCTNTFNVSTTVAFVVSACGVKVAKHGNRSVSSACGSADVLESLGVN 144 112222222226789****************************************************** PP TIGR01245 127 lelspekvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdl 195 l+++ e ++r+++e gigFlfAP+ h a+k++++ Rke+g+rt+fN+LGPL+nPa a qvlGvy++dl lcl|NCBI__GCF_000016745.1:WP_011938633.1 145 LDVTQETIERCINEIGIGFLFAPALHGAMKYAIGPRKEIGIRTIFNILGPLTNPAGAGCQVLGVYREDL 213 ********************************************************************* PP TIGR01245 196 vevlaevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa 264 ve+la+vlknlg kr +vvhg+dg+DE++lt+et++ae++ + + ++pe++gl r+ +++l+gg+a lcl|NCBI__GCF_000016745.1:WP_011938633.1 214 VEKLAHVLKNLGCKRGFVVHGQDGMDEMTLTAETRIAEVTPAGVATRLFRPEELGLSRCGMDDLRGGDA 282 ********************************************************************* PP TIGR01245 265 eenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++na ++++vleg++ ++krdiv+lNaa+ l++ag++ d ++g+++a eai+sgkal++le+lv+ lcl|NCBI__GCF_000016745.1:WP_011938633.1 283 AANAVIVRRVLEGEK-GPKRDIVLLNAAFGLVAAGRVVDPAAGLTMAAEAIDSGKALAQLEKLVK 346 *************99.99********************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (350 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 3.36 // [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