Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_028487311.1 B076_RS0110680 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8PD71 (345 letters) >NCBI__GCF_000483485.1:WP_028487311.1 Length = 340 Score = 311 bits (797), Expect = 2e-89 Identities = 162/332 (48%), Positives = 223/332 (67%) Query: 8 ALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGAATVMREF 67 AL++ + +++ ++M +MR++M GE SDA V AIL LR+K E++ EI A VMRE Sbjct: 6 ALEQLLNRQDLHENQMEAVMRKLMSGEASDAQVGAILAALRMKSESVPEITSAVKVMREL 65 Query: 68 SRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSSKSGSADA 127 + V V D+ H+VD GTGGDGS+TFNIST FV AA G VAKHGNRS SSKSGSAD Sbjct: 66 AAPVLVKDKSHLVDTCGTGGDGSNTFNISTACAFVVAAAGGHVAKHGNRSFSSKSGSADV 125 Query: 128 LEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFNILGPLTN 187 LEA G + L EQVA + + G+GFM+AP HH AMK V R+EMGVRT+FN+LGPLTN Sbjct: 126 LEAAGVNLGLSAEQVAQCVDEVGVGFMFAPAHHSAMKHVIGPRKEMGVRTLFNMLGPLTN 185 Query: 188 PAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVGELRDGQV 247 PAG+P ++GVF+ +L I A VLQ LG+E +VV DG+DE+S+ + T V EL++GQ+ Sbjct: 186 PAGAPYQVIGVFNKELGPIFAEVLQRLGSEHVMVVSAEDGLDEISIASETNVSELKNGQI 245 Query: 248 HEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGAALYVAGV 307 +++ P DF + ++L V A ES ++ V A DIV LNAGA++YV+G+ Sbjct: 246 SHWKIDPSDFDMDHPDLKDLAVDSAQESLNVIRSVFAGNASAATDIVCLNAGASIYVSGL 305 Query: 308 ADSIADGIVRARQVLADGSARACLDAYVAFTQ 339 + A+G+ AR+V+ +G A+ ++A TQ Sbjct: 306 TTTYAEGVALARKVIFEGLAQQKFSEFIAKTQ 337 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: 279 Number of extensions: 5 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: 340 Length adjustment: 29 Effective length of query: 316 Effective length of database: 311 Effective search space: 98276 Effective search space used: 98276 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_028487311.1 B076_RS0110680 (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.2644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-128 415.3 3.0 1.2e-128 415.1 3.0 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028487311.1 B076_RS0110680 anthranilate phos Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028487311.1 B076_RS0110680 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 415.1 3.0 1.2e-128 1.2e-128 1 329 [. 7 334 .. 7 335 .. 0.99 Alignments for each domain: == domain 1 score: 415.1 bits; conditional E-value: 1.2e-128 TIGR01245 1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeese 69 le+ll+++dL+e+++e++m+++msgeasdaq++Ail+alr+k+e++ ei+ ++k++re a v +++++ lcl|NCBI__GCF_000483485.1:WP_028487311.1 7 LEQLLNRQDLHENQMEAVMRKLMSGEASDAQVGAILAALRMKSESVPEITSAVKVMRELAAPVLVKDKS 75 689****************************************************************** PP TIGR01245 70 elvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsl 138 +lvD++GTGGDg++t+NiSTa a+v+aaaG +vaKhGnrs+ssksGsaDvLea gvnl ls+e+va+++ lcl|NCBI__GCF_000483485.1:WP_028487311.1 76 HLVDTCGTGGDGSNTFNISTACAFVVAAAGGHVAKHGNRSFSSKSGSADVLEAAGVNLGLSAEQVAQCV 144 ********************************************************************* PP TIGR01245 139 eevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlg 207 +evg+gF+fAP++h+a+k+v++ Rke+gvrt+fN+LGPL+nPa a++qv+Gv++k+l ++aevl++lg lcl|NCBI__GCF_000483485.1:WP_028487311.1 145 DEVGVGFMFAPAHHSAMKHVIGPRKEMGVRTLFNMLGPLTNPAGAPYQVIGVFNKELGPIFAEVLQRLG 213 ********************************************************************* PP TIGR01245 208 vkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevle 276 +++++vv++edglDEis+ et+v+elk+g+i++ +++p+df++++ +l++l+++sa+e+++++++v+ lcl|NCBI__GCF_000483485.1:WP_028487311.1 214 SEHVMVVSAEDGLDEISIASETNVSELKNGQISHWKIDPSDFDMDHPDLKDLAVDSAQESLNVIRSVFA 282 ********************************************************************* PP TIGR01245 277 gkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 g++ +a++div lNa+a +yv+g + +++egv la+++i +g a +k++e++a lcl|NCBI__GCF_000483485.1:WP_028487311.1 283 GNA-SAATDIVCLNAGASIYVSGLTTTYAEGVALARKVIFEGLAQQKFSEFIA 334 *99.777****************************************999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (340 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: 8.14 // [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