Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_057509110.1 ABB28_RS13455 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_001431535.1:WP_057509110.1 Length = 343 Score = 527 bits (1357), Expect = e-154 Identities = 268/338 (79%), Positives = 295/338 (87%) Query: 1 MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60 M +PQ+ALQRTIEHREIF +EMVDLMRQIMRG+VS M +AILTGLRVKKET+ EIA A Sbjct: 1 MRFSPQEALQRTIEHREIFFEEMVDLMRQIMRGDVSPMMTAAILTGLRVKKETVDEIAAA 60 Query: 61 ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120 ATVMREF+ V V D RHMVDIVGTGGDGSHTFNISTC+MFVAAA GA+VAKHGNRSVSS Sbjct: 61 ATVMREFALPVPVADTRHMVDIVGTGGDGSHTFNISTCSMFVAAAAGARVAKHGNRSVSS 120 Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180 KSGSADA+EALGAVIELQP QVA ++ QTG+GFM+AP+HHPAMKVVAPVRREMGVRTIFN Sbjct: 121 KSGSADAVEALGAVIELQPAQVAQAIEQTGVGFMFAPIHHPAMKVVAPVRREMGVRTIFN 180 Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240 ILGPLTNPA +P++LMGVFHPDLVGIQARVL+EL RA+VVWGRD MDE+SLGAGTLVG Sbjct: 181 ILGPLTNPASAPSVLMGVFHPDLVGIQARVLRELDTRRAMVVWGRDNMDEISLGAGTLVG 240 Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300 ELRDG+V EYE+HPEDFGIAMSASRNL+V +S AML VLDN PGPALDIVALNAGA Sbjct: 241 ELRDGKVREYEIHPEDFGIAMSASRNLRVDGPEQSIAMLRAVLDNEPGPALDIVALNAGA 300 Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFT 338 ALYVA VA I DG+ RAR +ADGSARA L YV T Sbjct: 301 ALYVADVASDIGDGLARARAAIADGSARARLQQYVDIT 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: 480 Number of extensions: 14 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_057509110.1 ABB28_RS13455 (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.17159.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-129 416.4 0.6 5.3e-129 416.2 0.6 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509110.1 ABB28_RS13455 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509110.1 ABB28_RS13455 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.2 0.6 5.3e-129 5.3e-129 1 329 [. 9 336 .. 9 337 .. 0.99 Alignments for each domain: == domain 1 score: 416.2 bits; conditional E-value: 5.3e-129 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 l++ ++++++ ee+ +lm++im+g++s++ aAil+ lrvk et++eia++a+++re a v++ +++ lcl|NCBI__GCF_001431535.1:WP_057509110.1 9 LQRTIEHREIFFEEMVDLMRQIMRGDVSPMMTAAILTGLRVKKETVDEIAAAATVMREFALPVPVADTR 77 5788999************************************************************** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 ++vDivGTGGDg++t+NiST s++vaaaaG++vaKhGnrsvssksGsaD +ealg+ +el+p++va+++ lcl|NCBI__GCF_001431535.1:WP_057509110.1 78 HMVDIVGTGGDGSHTFNISTCSMFVAAAAGARVAKHGNRSVSSKSGSADAVEALGAVIELQPAQVAQAI 146 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 e++g+gF+fAP +hpa+k vapvR+e+gvrt+fN+LGPL+nPa+a+ ++Gv+++dlv + a+vl++l lcl|NCBI__GCF_001431535.1:WP_057509110.1 147 EQTGVGFMFAPIHHPAMKVVAPVRREMGVRTIFNILGPLTNPASAPSVLMGVFHPDLVGIQARVLRELD 215 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 ++ra+vv g+d++DEisl + t v el+dg+++ey+++pedfg+++ ++l+++ +e++ ++l++vl lcl|NCBI__GCF_001431535.1:WP_057509110.1 216 TRRAMVVWGRDNMDEISLGAGTLVGELRDGKVREYEIHPEDFGIAMSASRNLRVDGPEQSIAMLRAVLD 284 *****************************************************************9999 PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ +++ div+lNa+aalyva++a+d+ +g+ +a++ai +g+a + l+++v+ lcl|NCBI__GCF_001431535.1:WP_057509110.1 285 NEP-GPALDIVALNAGAALYVADVASDIGDGLARARAAIADGSARARLQQYVD 336 998.999*******************************************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.60 // [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