Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_027457672.1 K420_RS0108460 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000519045.1:WP_027457672.1 Length = 342 Score = 465 bits (1196), Expect = e-136 Identities = 237/338 (70%), Positives = 275/338 (81%) Query: 3 ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62 +TPQ ALQR IEHREIFHDEM+ LMRQIM GEVS M++AI+TGLRVKKETIGEIA AA+ Sbjct: 1 MTPQAALQRVIEHREIFHDEMISLMRQIMGGEVSPVMIAAIITGLRVKKETIGEIAAAAS 60 Query: 63 VMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKS 122 VMRE + V+V +H VDIVGTGGD +HTFNIS+ + FV AA G +VAKHG RSVSS S Sbjct: 61 VMRELATPVKVPYDKHFVDIVGTGGDAAHTFNISSTSAFVVAAAGGRVAKHGGRSVSSSS 120 Query: 123 GSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNIL 182 G+AD LEALGA I L PEQVAA +A+TG GFM+AP HH AMK VAPVRREMGVRTIFNIL Sbjct: 121 GAADVLEALGANIMLSPEQVAACIAETGFGFMFAPNHHSAMKHVAPVRREMGVRTIFNIL 180 Query: 183 GPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGEL 242 GPLTNPAG+PN LMGVFHPDLVGI RV+Q LGAER LVV G+D +DE+SLGA T+VGEL Sbjct: 181 GPLTNPAGAPNTLMGVFHPDLVGILVRVMQRLGAERVLVVHGKDCLDEISLGAATMVGEL 240 Query: 243 RDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAAL 302 +DG+V EYE+HPED+G+ M + R L+V A ESR MLL VL N PG A +IV LNAGAAL Sbjct: 241 KDGEVREYEIHPEDYGLQMQSLRQLRVGSAGESREMLLGVLANQPGAAREIVCLNAGAAL 300 Query: 303 YVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340 YVA VA+SI DGI +AR+ +A G+ARA LD +V TQ+ Sbjct: 301 YVANVAESIGDGIAKAREAIASGAARAKLDQFVQCTQR 338 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: 419 Number of extensions: 11 Number of successful extensions: 1 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: 342 Length adjustment: 29 Effective length of query: 316 Effective length of database: 313 Effective search space: 98908 Effective search space used: 98908 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_027457672.1 K420_RS0108460 (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.454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-129 415.7 1.5 8.5e-129 415.5 1.5 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027457672.1 K420_RS0108460 anthranilate phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027457672.1 K420_RS0108460 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.5 1.5 8.5e-129 8.5e-129 1 329 [. 7 334 .. 7 335 .. 0.99 Alignments for each domain: == domain 1 score: 415.5 bits; conditional E-value: 8.5e-129 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 l+++++++++ ++e+ +lm++im ge+s++ iaAi++ lrvk et+ eia++a ++re a+ v++ ++ lcl|NCBI__GCF_000519045.1:WP_027457672.1 7 LQRVIEHREIFHDEMISLMRQIMGGEVSPVMIAAIITGLRVKKETIGEIAAAASVMRELATPVKVPYDK 75 6899*************************************************************99** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 ++vDivGTGGD+++t+NiS +sa+v+aaaG +vaKhG rsvss+sG+aDvLealg+n+ lspe+va+++ lcl|NCBI__GCF_000519045.1:WP_027457672.1 76 HFVDIVGTGGDAAHTFNISSTSAFVVAAAGGRVAKHGGRSVSSSSGAADVLEALGANIMLSPEQVAACI 144 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 +e+g+gF+fAP++h+a+k+vapvR+e+gvrt+fN+LGPL+nPa a++ ++Gv+++dlv +l++v+++lg lcl|NCBI__GCF_000519045.1:WP_027457672.1 145 AETGFGFMFAPNHHSAMKHVAPVRREMGVRTIFNILGPLTNPAGAPNTLMGVFHPDLVGILVRVMQRLG 213 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 ++r+lvvhg+d lDEisl + t v elkdge++ey+++ped+gl++++l++l++gsa e+ e+l vl lcl|NCBI__GCF_000519045.1:WP_027457672.1 214 AERVLVVHGKDCLDEISLGAATMVGELKDGEVREYEIHPEDYGLQMQSLRQLRVGSAGESREMLLGVLA 282 ********************************************************************9 PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ +a+r+iv lNa+aalyva++a+++ +g+ a+eai sg+a +kl+++v+ lcl|NCBI__GCF_000519045.1:WP_027457672.1 283 NQP-GAAREIVCLNAGAALYVANVAESIGDGIAKAREAIASGAARAKLDQFVQ 334 998.999******************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (342 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: 00:00:00.00 # Mc/sec: 11.65 // [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