Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_004322778.1 C665_RS16195 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000310185.1:WP_004322778.1 Length = 347 Score = 466 bits (1199), Expect = e-136 Identities = 239/339 (70%), Positives = 275/339 (81%), Gaps = 1/339 (0%) Query: 3 ITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAAT 62 IT QQALQRTIEHREIF DEM+ LMRQIM GE+S M +AILTGLRVKKETIGEI AAT Sbjct: 4 ITAQQALQRTIEHREIFFDEMLSLMRQIMAGEISPVMTAAILTGLRVKKETIGEITAAAT 63 Query: 63 VMREFSRRVEVTDRR-HMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSK 121 VMRE S +V V H +D+VGTGGDG++TFNIST +FVAAA GA+VAKHG R VSSK Sbjct: 64 VMREMSTKVVVEPPHDHFLDVVGTGGDGANTFNISTTTIFVAAAAGARVAKHGGRGVSSK 123 Query: 122 SGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNI 181 SG+AD +EALG ++L P+QVA + TGIGFMYAP HH AMK VAPVRREMGVRTIFNI Sbjct: 124 SGAADVIEALGVNLDLTPQQVAECIEATGIGFMYAPAHHSAMKNVAPVRREMGVRTIFNI 183 Query: 182 LGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGE 241 LGPLTNPAG+PN LMGVFHPDLVGIQARV+Q LGA LVV G DGMDE+SLG TLVGE Sbjct: 184 LGPLTNPAGAPNTLMGVFHPDLVGIQARVMQRLGANHVLVVHGLDGMDEVSLGGATLVGE 243 Query: 242 LRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAA 301 L+D +V EYE+HPEDFG+AM+ SR L+V DAAESR +LL VLDN PGPA +IVA NAG A Sbjct: 244 LKDNKVVEYEIHPEDFGLAMAGSRQLRVEDAAESREVLLGVLDNRPGPAREIVAFNAGVA 303 Query: 302 LYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340 LY A + D+I GI+RAR+++ G+ARA LD +V FT+Q Sbjct: 304 LYTANLVDTIGAGILRAREIIESGAARAKLDEFVRFTRQ 342 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: 418 Number of extensions: 12 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: 347 Length adjustment: 29 Effective length of query: 316 Effective length of database: 318 Effective search space: 100488 Effective search space used: 100488 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_004322778.1 C665_RS16195 (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.20487.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-127 408.8 1.6 1e-126 408.6 1.6 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004322778.1 C665_RS16195 anthranilate phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004322778.1 C665_RS16195 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.6 1.6 1e-126 1e-126 1 329 [. 10 338 .. 10 339 .. 0.99 Alignments for each domain: == domain 1 score: 408.6 bits; conditional E-value: 1e-126 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke.es 68 l++ ++++++ +e+ +lm++im+ge+s++ aAil+ lrvk et+ ei+++a+++re ++kv +e ++ lcl|NCBI__GCF_000310185.1:WP_004322778.1 10 LQRTIEHREIFFDEMLSLMRQIMAGEISPVMTAAILTGLRVKKETIGEITAAATVMREMSTKVVVEpPH 78 5788999********************************************************999788 PP TIGR01245 69 eelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvars 137 ++++D+vGTGGDg++t+NiST++ +vaaaaG++vaKhG r vssksG+aDv+ealgvnl+l+p++va++ lcl|NCBI__GCF_000310185.1:WP_004322778.1 79 DHFLDVVGTGGDGANTFNISTTTIFVAAAAGARVAKHGGRGVSSKSGAADVIEALGVNLDLTPQQVAEC 147 89******************************************************************* PP TIGR01245 138 leevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknl 206 +e +gigF++AP++h+a+k+vapvR+e+gvrt+fN+LGPL+nPa a++ ++Gv+++dlv + a+v+++l lcl|NCBI__GCF_000310185.1:WP_004322778.1 148 IEATGIGFMYAPAHHSAMKNVAPVRREMGVRTIFNILGPLTNPAGAPNTLMGVFHPDLVGIQARVMQRL 216 ********************************************************************* PP TIGR01245 207 gvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevl 275 g++++lvvhg dg+DE+sl g t v elkd+++ ey+++pedfgl++a ++l++++a+e+ e+l vl lcl|NCBI__GCF_000310185.1:WP_004322778.1 217 GANHVLVVHGLDGMDEVSLGGATLVGELKDNKVVEYEIHPEDFGLAMAGSRQLRVEDAAESREVLLGVL 285 ********************************************************************* PP TIGR01245 276 egkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ +++r+iv++Na++aly+a+ ++++ +g+ +a+e i+sg+a +kl+e+v+ lcl|NCBI__GCF_000310185.1:WP_004322778.1 286 DNRP-GPAREIVAFNAGVALYTANLVDTIGAGILRAREIIESGAARAKLDEFVR 338 ***9.899*******************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (347 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: 7.53 // [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