Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_026090203.1 C792_RS0103170 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8YXQ9 (362 letters) >NCBI__GCF_000330705.1:WP_026090203.1 Length = 339 Score = 249 bits (636), Expect = 8e-71 Identities = 139/334 (41%), Positives = 196/334 (58%), Gaps = 12/334 (3%) Query: 26 ESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGVSADELTGMAEVLQSQSKMGTGEN 85 E+L + AE M+ L++ V A L AL KG + +E+ + EVL+ + Sbjct: 12 ENLEFEEMAEAMEIILNDTVSDSEVAAFLMALKAKGETVEEIAALVEVLRENA------- 64 Query: 86 YSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVAAAYGVPVAKHGNRSASSLTGSAD 145 LPI + +++D CGTGGDGS +FNIST AFV A V VAKHGNRS +S TGS+D Sbjct: 65 ---LPIRRTMTNVMDNCGTGGDGSHSFNISTTSAFVLAGANVTVAKHGNRSVTSRTGSSD 121 Query: 146 VLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPALKAVATLRRTLRIRTVFNLLGPLV 205 VL LGV L PE LQE I FLFAP HP L+ + +R+ LR+ T+FNL+GPL+ Sbjct: 122 VLSELGVALDFGPEDTDLMLQENNIAFLFAPHVHPKLRQIMKVRQDLRVPTIFNLIGPLI 181 Query: 206 NPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLHGRERLDEAGLGDLTDLAVLSDGE 265 NP+ Q +G++ L +A + LG+++AIV++G +DEA L +A+L G Sbjct: 182 NPVELDHQFLGIYDRSQLVMMATVMKRLGRKRAIVINGAGHMDEASLAGENHMALLEKGA 241 Query: 266 LQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVLQGKGTQAQQDAVALNAALALQVA 325 + P+ VG+ P+ + GGD ENAEILK VL+G AQ+D V LNA L + A Sbjct: 242 IYEMKFTPESVGLPTYPLEEIAGGDSCENAEILKNVLEGTAAPAQRDTVLLNAGLGMYAA 301 Query: 326 GAVPLLDHAQGVSVAKEILQTGTAWAKLAQLVYF 359 GA ++ G+ +A+E ++TG A AKL +V + Sbjct: 302 GAADSIE--AGIELARESIETGNALAKLRNMVKY 333 Lambda K H 0.314 0.130 0.364 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: 250 Number of extensions: 11 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: 362 Length of database: 339 Length adjustment: 29 Effective length of query: 333 Effective length of database: 310 Effective search space: 103230 Effective search space used: 103230 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_026090203.1 C792_RS0103170 (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.76371.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-118 379.7 2.3 7.4e-118 379.6 2.3 1.0 1 NCBI__GCF_000330705.1:WP_026090203.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_026090203.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.6 2.3 7.4e-118 7.4e-118 3 329 .. 7 332 .. 5 333 .. 0.99 Alignments for each domain: == domain 1 score: 379.6 bits; conditional E-value: 7.4e-118 TIGR01245 3 klldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDiv 75 kl +++L+ ee++++m+ i+++ +sd+++aA+l+al++kget+eeia+l+++lre+a +++ + ++++D++ NCBI__GCF_000330705.1:WP_026090203.1 7 KLSARENLEFEEMAEAMEIILNDTVSDSEVAAFLMALKAKGETVEEIAALVEVLRENALPIRR-TMTNVMDNC 78 78899********************************************************99.59******* PP TIGR01245 76 GTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfA 148 GTGGDg++++NiST+sa+v+a+a v vaKhGnrsv+s+ Gs+DvL++lgv+l+ pe +l+e++i+FlfA NCBI__GCF_000330705.1:WP_026090203.1 79 GTGGDGSHSFNISTTSAFVLAGANVTVAKHGNRSVTSRTGSSDVLSELGVALDFGPEDTDLMLQENNIAFLFA 151 ************************************************************************* PP TIGR01245 149 PkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglD 221 P+ hp+l+++++vR++L v+t+fNl+GPL+nP++ ++q lG+y+++ + ++a v+k+lg kra+v++g++ +D NCBI__GCF_000330705.1:WP_026090203.1 152 PHVHPKLRQIMKVRQDLRVPTIFNLIGPLINPVELDHQFLGIYDRSQLVMMATVMKRLGRKRAIVINGAGHMD 224 ************************************************************************* PP TIGR01245 222 EisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaa 294 E sl ge+++a l++g i e++++pe+ gl++++lee++gg+ enae+lk+vleg + a+rd v+lNa+ NCBI__GCF_000330705.1:WP_026090203.1 225 EASLAGENHMALLEKGAIYEMKFTPESVGLPTYPLEEIAGGDSCENAEILKNVLEGTAAPAQRDTVLLNAGLG 297 ************************************************************************* PP TIGR01245 295 lyvagkakdlkegvelakeaiksgkalekleelva 329 +y+ag+a+++++g+ela+e+i++g+al+kl+++v+ NCBI__GCF_000330705.1:WP_026090203.1 298 MYAAGAADSIEAGIELARESIETGNALAKLRNMVK 332 *******************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (339 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: 25.86 // [ok]
This GapMind analysis is from Jul 26 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