Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate WP_051335409.1 METAC_RS22525 anthranilate phosphoribosyltransferase
Query= SwissProt::P83827 (329 letters) >NCBI__GCF_000427445.1:WP_051335409.1 Length = 356 Score = 260 bits (664), Expect = 4e-74 Identities = 160/335 (47%), Positives = 198/335 (59%), Gaps = 14/335 (4%) Query: 1 MDAVK----KAILGEVLEEEEAYEVMRALMAGEVSPVRAAGLLVALSLRGERPHEIAAMA 56 MDA K K G L E EA + +GEV+P + G L+AL +RGE EI+ Sbjct: 1 MDAFKPLIAKVATGSSLTESEAEAAFHHIFSGEVTPAQLGGFLLALRVRGETVEEISGAV 60 Query: 57 RAMREAARPLRVHRRP-LLDIVGTGGDGKGLMNLSTLAALVAAAGGVAVAKHGNRAASSR 115 AMR A+ L V +DIVGTGGDG G N+STLA+L+ AA GV VAKHGNRAASSR Sbjct: 61 MAMR--AKMLAVEAPTGAIDIVGTGGDGHGTYNVSTLASLIVAACGVPVAKHGNRAASSR 118 Query: 116 AGSADLLEALGVDLEAPPERVGEAIEELGFGFLFARVFHPAMRHVAPVRAELGVRTVFNL 175 +G++D+L ALGV PPE V + E G GF+ A+ H AMRHVAP RAELG RT+FNL Sbjct: 119 SGASDVLSALGVRTGLPPEEVAACVAEAGIGFMMAQTHHAAMRHVAPARAELGARTIFNL 178 Query: 176 LGPLTNPAGADAYVLGVFSPEWLAPMAEALERLGA-RGLVVHG-EGADE-LVLGENRVVE 232 LGPL NPAG +LGVF+ WL P+A+ L RLG+ R ++HG +G DE G + V Sbjct: 179 LGPLANPAGVKRQLLGVFAARWLEPLAQVLRRLGSERVWLIHGTDGLDEATTTGPSFVTA 238 Query: 233 VGKGA---YALTPEEVGLKRAPLEALKGGGPEENAALARRLLKGEEKGPLADAVALAAGA 289 + GA + +TPE GL RA L L GG P NAA + +L G + P D L A A Sbjct: 239 LEGGAIRSFEITPEAAGLPRASLSDLIGGDPATNAAALKSVLDG-ARTPYRDIAVLNAAA 297 Query: 290 GFYAAGKTPSLKEGVALAREVLASGEAYLLLERYV 324 A K L+EG ALA E + G A L + V Sbjct: 298 ALVVAEKAVDLREGAALASEAIDRGAAADTLAKLV 332 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: 318 Number of extensions: 16 Number of successful extensions: 4 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: 329 Length of database: 356 Length adjustment: 29 Effective length of query: 300 Effective length of database: 327 Effective search space: 98100 Effective search space used: 98100 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 WP_051335409.1 METAC_RS22525 (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.24345.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-118 380.9 1.2 3.2e-118 380.7 1.2 1.0 1 lcl|NCBI__GCF_000427445.1:WP_051335409.1 METAC_RS22525 anthranilate phosp Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_051335409.1 METAC_RS22525 anthranilate phosphoribosyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.7 1.2 3.2e-118 3.2e-118 2 329 .. 9 333 .. 8 334 .. 0.99 Alignments for each domain: == domain 1 score: 380.7 bits; conditional E-value: 3.2e-118 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeesee 70 k++++ +L+e eae++++ i+sge+++aq++ +l alrv+get+eei+g++ a+r+k+ ve+ + lcl|NCBI__GCF_000427445.1:WP_051335409.1 9 AKVATGSSLTESEAEAAFHHIFSGEVTPAQLGGFLLALRVRGETVEEISGAVMAMRAKMLAVEA--PTG 75 689999********************************************************88..79* PP TIGR01245 71 lvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsle 139 ++DivGTGGDg t+N+ST ++l++aa+Gv+vaKhGnr++ss+sG++DvL+algv++ l pe+va++++ lcl|NCBI__GCF_000427445.1:WP_051335409.1 76 AIDIVGTGGDGHGTYNVSTLASLIVAACGVPVAKHGNRAASSRSGASDVLSALGVRTGLPPEEVAACVA 144 ********************************************************************* PP TIGR01245 140 evgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgv 208 e gigF++A ++h a+++vap R eLg rt+fNlLGPL+nPa +k+q+lGv+ + +e la+vl++lg+ lcl|NCBI__GCF_000427445.1:WP_051335409.1 145 EAGIGFMMAQTHHAAMRHVAPARAELGARTIFNLLGPLANPAGVKRQLLGVFAARWLEPLAQVLRRLGS 213 ********************************************************************* PP TIGR01245 209 kralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevleg 277 +r+ ++hg dglDE ++tg++ v+ l+ g i++++++pe gl+ra+l++l gg+++ na++lk+vl g lcl|NCBI__GCF_000427445.1:WP_051335409.1 214 ERVWLIHGTDGLDEATTTGPSFVTALEGGAIRSFEITPEAAGLPRASLSDLIGGDPATNAAALKSVLDG 282 ********************************************************************* PP TIGR01245 278 kekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329 ++ rdi vlNaaaal+va+ka dl+eg+ la+eai+ g+a+++l++lv+ lcl|NCBI__GCF_000427445.1:WP_051335409.1 283 AR-TPYRDIAVLNAAAALVVAEKAVDLREGAALASEAIDRGAAADTLAKLVK 333 98.899******************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (330 nodes) Target sequences: 1 (356 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.41 // [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