Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_012674011.1 SULAZ_RS00880 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000021545.1:WP_012674011.1 Length = 336 Score = 290 bits (743), Expect = 3e-83 Identities = 156/328 (47%), Positives = 220/328 (67%), Gaps = 1/328 (0%) Query: 6 QQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMR 65 ++ +++ E + + +E++ L ++IM +++DA + A+L GL++K ET+ EI+ AATVMR Sbjct: 3 KELIKKITEKKNLSKEEVLFLFQEIMDRKLTDAQLGAVLIGLKMKGETVNEISAAATVMR 62 Query: 66 EFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSA 125 + + +V V D+ +VD GTGGD TFN+ST + FV AA GAKVAKHGNRSVSSK GSA Sbjct: 63 DKAIKVNVKDKSKLVDTCGTGGDNIGTFNVSTISAFVVAASGAKVAKHGNRSVSSKCGSA 122 Query: 126 DALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPL 185 D +E+LG I++ PE+V + + G+GF++AP+ HPAMK V RRE+GVRTIFNILGPL Sbjct: 123 DLMESLGVKIDMPPEKVERCIDEVGLGFLFAPIFHPAMKNVVRQRREIGVRTIFNILGPL 182 Query: 186 TNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDG 245 +NPA +P LMGV+ DLV A+VL LG +RA VV G +G+DE+SL A TLV ++ Sbjct: 183 SNPADAPYQLMGVYDKDLVEPIAKVLVNLGIKRAFVVHGLEGLDEVSLTAETLVAQVDGE 242 Query: 246 QVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVP-GPALDIVALNAGAALYV 304 + Y V PEDFG+ + +LK D E++ + L +L P D VALN+G AL V Sbjct: 243 DIKVYTVKPEDFGLKRVSIEDLKGGDIIENKEIALNILTGKDYSPKTDFVALNSGFALKV 302 Query: 305 AGVADSIADGIVRARQVLADGSARACLD 332 AGV SI +GI A++ + A L+ Sbjct: 303 AGVVSSIKEGIELAKESIYSKKAYEVLE 330 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: 274 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: 336 Length adjustment: 28 Effective length of query: 317 Effective length of database: 308 Effective search space: 97636 Effective search space used: 97636 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_012674011.1 SULAZ_RS00880 (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.862644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-139 449.0 1.0 6.2e-139 448.8 1.0 1.0 1 NCBI__GCF_000021545.1:WP_012674011.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021545.1:WP_012674011.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.8 1.0 6.2e-139 6.2e-139 1 328 [. 6 333 .. 6 335 .. 0.99 Alignments for each domain: == domain 1 score: 448.8 bits; conditional E-value: 6.2e-139 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvD 73 ++k++++k+Ls+ee+ l++eim+ +++daq++A+l+ l++kget++ei+++a+++r+ka kv+++++++lvD NCBI__GCF_000021545.1:WP_012674011.1 6 IKKITEKKNLSKEEVLFLFQEIMDRKLTDAQLGAVLIGLKMKGETVNEISAAATVMRDKAIKVNVKDKSKLVD 78 689********************************************************************** PP TIGR01245 74 ivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFl 146 ++GTGGD++ t+N+ST+sa+v+aa G+kvaKhGnrsvssk+GsaD++e lgv++++ pekv+r+++evg+gFl NCBI__GCF_000021545.1:WP_012674011.1 79 TCGTGGDNIGTFNVSTISAFVVAASGAKVAKHGNRSVSSKCGSADLMESLGVKIDMPPEKVERCIDEVGLGFL 151 ************************************************************************* PP TIGR01245 147 fAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedg 219 fAP +hpa+k+v+ R+e+gvrt+fN+LGPL+nPa a++q++Gvy+kdlve +a+vl nlg+kra+vvhg +g NCBI__GCF_000021545.1:WP_012674011.1 152 FAPIFHPAMKNVVRQRREIGVRTIFNILGPLSNPADAPYQLMGVYDKDLVEPIAKVLVNLGIKRAFVVHGLEG 224 ************************************************************************* PP TIGR01245 220 lDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaa 292 lDE+slt+et va+++ ++i+ yt++pedfglkr ++e+lkgg+ en e+ ++l+gk ++k+d+v+lN + NCBI__GCF_000021545.1:WP_012674011.1 225 LDEVSLTAETLVAQVDGEDIKVYTVKPEDFGLKRVSIEDLKGGDIIENKEIALNILTGKDYSPKTDFVALNSG 297 ************************************************************************* PP TIGR01245 293 aalyvagkakdlkegvelakeaiksgkalekleelv 328 +al+vag+++++keg+elake+i s+ka+e+le+l NCBI__GCF_000021545.1:WP_012674011.1 298 FALKVAGVVSSIKEGIELAKESIYSKKAYEVLEKLR 333 *********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (336 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: 17.73 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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