Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_092481607.1 BM299_RS01070 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_900115975.1:WP_092481607.1 Length = 345 Score = 275 bits (703), Expect = 1e-78 Identities = 154/331 (46%), Positives = 201/331 (60%), Gaps = 3/331 (0%) Query: 9 LQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREFS 68 L + + + E + M QIM G + A ++ LT L++K ETI EI G A VMR S Sbjct: 6 LNKVVAGENLTEAEAMQAMEQIMEGRATPAQIAGFLTALKLKGETIAEITGFARVMR--S 63 Query: 69 RRVEVTDRRHM-VDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADA 127 + V R + VD GTGGDG++TFNIST A V A G KVAKHGNRSVSS+ GSAD Sbjct: 64 KATPVCSRHPLLVDTCGTGGDGANTFNISTAAALVLAGAGVKVAKHGNRSVSSRCGSADV 123 Query: 128 LEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTN 187 LEALG ++L+P++ AA L + G+ F+YAP H AMK A RRE+G RT+FNILGPLTN Sbjct: 124 LEALGVNLDLEPDEAAACLERVGMAFLYAPALHGAMKFAAGPRRELGFRTVFNILGPLTN 183 Query: 188 PAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQV 247 PAG+ ++GV+ PDLV + A VL L AERA VV G G+DE+S LV E++DG + Sbjct: 184 PAGARAQVLGVYSPDLVRVLAEVLLRLEAERAYVVHGAGGLDEVSPAGPALVCEIKDGNI 243 Query: 248 HEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVAGV 307 EY + P +G A + +L ++ ++ +LD GP D V +NA L AGV Sbjct: 244 TEYTLDPGQYGFAHAGVEDLAGGTPEDNAHIVRSILDGERGPRRDAVLMNAALGLMAAGV 303 Query: 308 ADSIADGIVRARQVLADGSARACLDAYVAFT 338 A A G+ A + + G ARA L A V FT Sbjct: 304 AHDFAAGVELAARSIDQGLARARLQALVRFT 334 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: 316 Number of extensions: 17 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: 345 Length adjustment: 29 Effective length of query: 316 Effective length of database: 316 Effective search space: 99856 Effective search space used: 99856 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_092481607.1 BM299_RS01070 (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.2494.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-134 432.0 0.1 9.3e-134 431.8 0.1 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092481607.1 BM299_RS01070 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092481607.1 BM299_RS01070 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.8 0.1 9.3e-134 9.3e-134 1 329 [. 6 332 .. 6 333 .. 0.99 Alignments for each domain: == domain 1 score: 431.8 bits; conditional E-value: 9.3e-134 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 l+k++ +++L+e+ea+q+m++im+g+a++aqia +l+al+ kget+ ei+g+a+++r+ka+ v + + lcl|NCBI__GCF_900115975.1:WP_092481607.1 6 LNKVVAGENLTEAEAMQAMEQIMEGRATPAQIAGFLTALKLKGETIAEITGFARVMRSKATPVCSR-HP 73 57999**********************************************************995.99 PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 lvD++GTGGDg++t+NiSTa+alv+a+aGvkvaKhGnrsvss++GsaDvLealgvnl+l+p+++a++l lcl|NCBI__GCF_900115975.1:WP_092481607.1 74 LLVDTCGTGGDGANTFNISTAAALVLAGAGVKVAKHGNRSVSSRCGSADVLEALGVNLDLEPDEAAACL 142 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 e+vg++Fl+AP+ h a+k +a+ R+eLg+rtvfN+LGPL+nPa a++qvlGvys+dlv+vlaevl +l+ lcl|NCBI__GCF_900115975.1:WP_092481607.1 143 ERVGMAFLYAPALHGAMKFAAGPRRELGFRTVFNILGPLTNPAGARAQVLGVYSPDLVRVLAEVLLRLE 211 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 ++ra vvhg++glDE+s+ g++ v+e+kdg+i+eytl+p ++g+++a +e+l+gg++e+na++++++l lcl|NCBI__GCF_900115975.1:WP_092481607.1 212 AERAYVVHGAGGLDEVSPAGPALVCEIKDGNITEYTLDPGQYGFAHAGVEDLAGGTPEDNAHIVRSILD 280 ********************************************************************* PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 g+ +++rd+v++Naa l++ag+a+d+++gvela ++i++g a + l++lv+ lcl|NCBI__GCF_900115975.1:WP_092481607.1 281 GER-GPRRDAVLMNAALGLMAAGVAHDFAAGVELAARSIDQGLARARLQALVR 332 *98.999******************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (345 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.02 // [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