Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate 3608399 Dshi_1799 anthranilate phosphoribosyltransferase (RefSeq)
Query= SwissProt::P83827 (329 letters) >FitnessBrowser__Dino:3608399 Length = 339 Score = 243 bits (621), Expect = 4e-69 Identities = 146/309 (47%), Positives = 185/309 (59%), Gaps = 11/309 (3%) Query: 14 EEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMARAMREAARPLRVHRRPL 73 E E A+E+ L GE +P + GLL+AL RGE E AA A MR +R + Sbjct: 21 EAEAAFEI---LFEGEATPSQMGGLLMALRTRGETVAEYAAAAAVMRAKCNAVRAPEGAM 77 Query: 74 LDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSRAGSADLLEALGVDLEAPP 133 DIVGTGGDGKG +N+ST A V A GV VAKHGNR SS++G+AD L +G+++ P Sbjct: 78 -DIVGTGGDGKGTLNISTATAFVVAGAGVPVAKHGNRNLSSKSGAADALAQMGIEVMVGP 136 Query: 134 ERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNLLGPLTNPAGADAYVLGVF 193 V A+ E+G F+ A + HPA+RHV P RAELG RT+FN+LGPLTNPAG + G F Sbjct: 137 AVVERALSEIGIAFMMAPMHHPAIRHVMPTRAELGTRTMFNILGPLTNPAGVKRQLTGAF 196 Query: 194 SPEWLAPMAEALERLGAR-GLVVHG-EGADEL-VLGENRVVEVGKGA---YALTPEEVGL 247 S + + PMAE L LG+ +VHG +G DEL + G + V + GA + + PEE GL Sbjct: 197 SRDLIRPMAETLAALGSDVAWLVHGSDGTDELTITGVSWVAGLSDGAVTEFEVHPEEAGL 256 Query: 248 KRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGAGFYAAGKTPSLKEGVALA 307 P EA+ GG PEEN A R LL GE DAV L A A AG+ +L +GV LA Sbjct: 257 PVHPFEAILGGTPEENGAAFRALLAGEASA-YRDAVLLNAAAALKVAGRVTALPDGVMLA 315 Query: 308 REVLASGEA 316 E + SG A Sbjct: 316 AEAIDSGAA 324 Lambda K H 0.317 0.136 0.380 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: 329 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 329 Length of database: 339 Length adjustment: 28 Effective length of query: 301 Effective length of database: 311 Effective search space: 93611 Effective search space used: 93611 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate 3608399 Dshi_1799 (anthranilate phosphoribosyltransferase (RefSeq))
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.32264.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-113 365.2 2.6 2.1e-113 364.9 2.6 1.0 1 lcl|FitnessBrowser__Dino:3608399 Dshi_1799 anthranilate phosphori Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608399 Dshi_1799 anthranilate phosphoribosyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 364.9 2.6 2.1e-113 2.1e-113 7 329 .. 14 333 .. 10 334 .. 0.98 Alignments for each domain: == domain 1 score: 364.9 bits; conditional E-value: 2.1e-113 TIGR01245 7 nkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDivGTGGDglk 83 + L+++eae++++ +++gea+++q++ +l+alr++get+ e a++a ++r+k + v++ e ++DivGTGGDg lcl|FitnessBrowser__Dino:3608399 14 DRPLTRAEAEAAFEILFEGEATPSQMGGLLMALRTRGETVAEYAAAAAVMRAKCNAVRA--PEGAMDIVGTGGDGKG 88 679******************************************************88..79************** PP TIGR01245 84 tiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlfAPkyhpalkevap 160 t+NiSTa+a+v+a+aGv+vaKhGnr ssksG+aD L ++g+++ + p+ v+r+l+e gi+F++AP++hpa+++v+p lcl|FitnessBrowser__Dino:3608399 89 TLNISTATAFVVAGAGVPVAKHGNRNLSSKSGAADALAQMGIEVMVGPAVVERALSEIGIAFMMAPMHHPAIRHVMP 165 ***************************************************************************** PP TIGR01245 161 vRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedglDEisltgetkvaelkdg 237 +R eLg+rt+fN+LGPL+nPa +k+q+ G +s+dl++ +ae+l +lg++ a +vhg+dg+DE+++tg + va l+dg lcl|FitnessBrowser__Dino:3608399 166 TRAELGTRTMFNILGPLTNPAGVKRQLTGAFSRDLIRPMAETLAALGSDVAWLVHGSDGTDELTITGVSWVAGLSDG 242 ***************************************************************************** PP TIGR01245 238 eieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakea 314 ++e++++pe+ gl+ ++ e++ gg++een ++++++l g++ +a rd+v+lNaaaal+vag++ +l +gv la ea lcl|FitnessBrowser__Dino:3608399 243 AVTEFEVHPEEAGLPVHPFEAILGGTPEENGAAFRALLAGEA-SAYRDAVLLNAAAALKVAGRVTALPDGVMLAAEA 318 ***********************************9999999.899******************************* PP TIGR01245 315 iksgkalekleelva 329 i+sg+al+k++ l++ lcl|FitnessBrowser__Dino:3608399 319 IDSGAALAKVQGLAQ 333 ********9998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (339 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: 8.62 // [ok]
This GapMind analysis is from Apr 09 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