Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_011883152.1 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000016205.1:WP_011883152.1 Length = 343 Score = 495 bits (1274), Expect = e-145 Identities = 252/340 (74%), Positives = 285/340 (83%) Query: 1 MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60 M ITPQ+ALQRTIEHREIFHDEM+ LMR IMRG++S M +AI+TGLRVKKETIGEIA A Sbjct: 1 MTITPQEALQRTIEHREIFHDEMLHLMRLIMRGDMSPVMAAAIITGLRVKKETIGEIAAA 60 Query: 61 ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120 ATVMREF+ VEV D + VDIVGTGGDG+HTFNIST +MFV AA GAKVAKHGNR VSS Sbjct: 61 ATVMREFAHHVEVPDNSNFVDIVGTGGDGAHTFNISTASMFVTAAAGAKVAKHGNRGVSS 120 Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180 KSGSAD LEALG I+LQP+QVAAS+A+TG+GFM+AP HHPAMK +A VRRE+GVRTIFN Sbjct: 121 KSGSADVLEALGVNIDLQPDQVAASIAETGMGFMFAPNHHPAMKNIAAVRRELGVRTIFN 180 Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240 ILGPLTNPAG+PN LMGVFH DLVGIQ RV+Q LGA+ LVV+G+DGMDE+SLGA TLVG Sbjct: 181 ILGPLTNPAGAPNQLMGVFHADLVGIQVRVMQRLGAQHVLVVYGKDGMDEVSLGAATLVG 240 Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300 ELRDGQVHEYE+HPEDFG+ M ++R LKV +A ESR MLL LDN PG A +IV LNAG Sbjct: 241 ELRDGQVHEYEIHPEDFGLQMVSNRTLKVENADESRVMLLGALDNQPGVAREIVTLNAGT 300 Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340 ALY A VA SIADGI AR+ +A G ARA +D V FTQQ Sbjct: 301 ALYAANVAASIADGIQLAREAIASGKARAKVDELVRFTQQ 340 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: 10 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: 343 Length adjustment: 29 Effective length of query: 316 Effective length of database: 314 Effective search space: 99224 Effective search space used: 99224 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_011883152.1 (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.10518.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-128 413.7 5.8 3.5e-128 413.5 5.8 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011883152.1 anthranilate phosphoribosyltrans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011883152.1 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.5 5.8 3.5e-128 3.5e-128 1 329 [. 9 336 .. 9 337 .. 0.99 Alignments for each domain: == domain 1 score: 413.5 bits; conditional E-value: 3.5e-128 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 l++ ++++++ ++e+ +lm+ im+g++s++ aAi++ lrvk et+ eia++a+++re a++ve+ +++ lcl|NCBI__GCF_000016205.1:WP_011883152.1 9 LQRTIEHREIFHDEMLHLMRLIMRGDMSPVMAAAIITGLRVKKETIGEIAAAATVMREFAHHVEVPDNS 77 578999*************************************************************** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 ++vDivGTGGDg++t+NiSTas++v aaaG+kvaKhGnr vssksGsaDvLealgvn++l+p++va+s+ lcl|NCBI__GCF_000016205.1:WP_011883152.1 78 NFVDIVGTGGDGAHTFNISTASMFVTAAAGAKVAKHGNRGVSSKSGSADVLEALGVNIDLQPDQVAASI 146 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 +e+g+gF+fAP++hpa+k++a+vR+eLgvrt+fN+LGPL+nPa a++q++Gv+++dlv + ++v+++lg lcl|NCBI__GCF_000016205.1:WP_011883152.1 147 AETGMGFMFAPNHHPAMKNIAAVRRELGVRTIFNILGPLTNPAGAPNQLMGVFHADLVGIQVRVMQRLG 215 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 ++++lvv g+dg+DE+sl + t v el+dg+++ey+++pedfgl++ + + lk+++a+e+ +l +l lcl|NCBI__GCF_000016205.1:WP_011883152.1 216 AQHVLVVYGKDGMDEVSLGAATLVGELRDGQVHEYEIHPEDFGLQMVSNRTLKVENADESRVMLLGALD 284 ********************************************************************* PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ + +r+iv lNa++aly+a++a+++++g++la+eai sgka +k++elv+ lcl|NCBI__GCF_000016205.1:WP_011883152.1 285 NQP-GVAREIVTLNAGTALYAANVAASIADGIQLAREAIASGKARAKVDELVR 336 999.788******************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (343 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.08 // [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