Align Anthranilate phosphoribosyltransferase 2; EC 2.4.2.18 (characterized)
to candidate WP_085219434.1 B9N75_RS06205 anthranilate phosphoribosyltransferase
Query= SwissProt::Q8YXQ9 (362 letters) >NCBI__GCF_900177405.1:WP_085219434.1 Length = 356 Score = 248 bits (634), Expect = 1e-70 Identities = 146/355 (41%), Positives = 201/355 (56%), Gaps = 17/355 (4%) Query: 3 SSPTSTQESSTSWYLLLQQLIDGESLSRSQAAELMQGWLSEAVPPELSGAILTALNFKGV 62 ++P T + T+ L +L+ G+ L A+ L ++ A+ A+L AL +G Sbjct: 14 ATPPQTDPAETA----LTRLLSGDRLDERAASHLFTALVAGALSETAIAAMLVALRLQGE 69 Query: 63 SADELTGMAEVLQSQSKMGTGENYSQLPITNSPFSIIDTCGTGGDGSSTFNISTAVAFVA 122 +A L G A L++ + P + D+CGTGGDGS + N+STA A VA Sbjct: 70 TAPVLIGAARALRA----------ADAPFPRPDYLFADSCGTGGDGSGSINVSTAAALVA 119 Query: 123 AAYGVPVAKHGNRSASSLTGSADVLEALGVNLGASPEKVQAALQEVGITFLFAPGWHPAL 182 AA G+PVAKHGNRS +S GSADVLE LG L + AL + G FLFAP +HP L Sbjct: 120 AAAGLPVAKHGNRSFTSRCGSADVLETLGAKLDVDASVSRRALDQAGFCFLFAPLYHPGL 179 Query: 183 KAVATLRRTLRIRTVFNLLGPLVNPLRPTGQVVGLFTPKLLTTVAQALDNLGKQKAIVLH 242 + +RR L++RTV N+LGP VNP P Q++G+ LL VA+ L LG Q+A+V+H Sbjct: 180 RHAGPVRRALKVRTVMNILGPCVNPAEPRVQLLGVADRTLLVPVARTLAALGVQRALVVH 239 Query: 243 GRERLDEAGLGDLTDLAVLSDGELQLTTINPQEVGVTPAPIGALRGGDVQENAEILKAVL 302 G LDE L T+ A L DGE++ + ++VG+ P P+ A+ GG +ENA LKA+L Sbjct: 240 G-SGLDEVALHGETEAARLQDGEIETIFLYAEDVGIEPRPMDAIAGGGPEENAARLKALL 298 Query: 303 QGKGTQAQQDAVALNAALALQVAGAVPLLDHAQGVSVAKEILQTGTAWAKLAQLV 357 GKG+ A+ D VALNA L AG D GV +A ++L +G A LA V Sbjct: 299 DGKGSAAEADVVALNAGALLMTAGIA--ADFPAGVRLAADVLASGAAGRTLAAFV 351 Lambda K H 0.314 0.130 0.364 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: 270 Number of extensions: 9 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: 362 Length of database: 356 Length adjustment: 29 Effective length of query: 333 Effective length of database: 327 Effective search space: 108891 Effective search space used: 108891 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_085219434.1 B9N75_RS06205 (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.4178818.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-117 377.1 0.1 4.9e-117 376.9 0.1 1.0 1 NCBI__GCF_900177405.1:WP_085219434.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085219434.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.9 0.1 4.9e-117 4.9e-117 2 329 .. 27 352 .. 26 353 .. 0.99 Alignments for each domain: == domain 1 score: 376.9 bits; conditional E-value: 4.9e-117 TIGR01245 2 eklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkvekeeseelvDi 74 +ll++ L+e a +l++++++g +s++ iaA+lvalr +get+ + g+a+alr+ +++ +++ ++D+ NCBI__GCF_900177405.1:WP_085219434.1 27 TRLLSGDRLDERAASHLFTALVAGALSETAIAAMLVALRLQGETAPVLIGAARALRAADAPFPR-PDYLFADS 98 689999********************************************************99.7******* PP TIGR01245 75 vGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspekvarsleevgigFlf 147 +GTGGDg+ +iN+STa+alvaaaaG++vaKhGnrs++s++GsaDvLe lg++l++++ ++r+l++ g++Flf NCBI__GCF_900177405.1:WP_085219434.1 99 CGTGGDGSGSINVSTAAALVAAAAGLPVAKHGNRSFTSRCGSADVLETLGAKLDVDASVSRRALDQAGFCFLF 171 ************************************************************************* PP TIGR01245 148 APkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvevlaevlknlgvkralvvhgedgl 220 AP yhp+l+++ pvR+ L+vrtv+N+LGP +nPa++++q+lGv+++ l+ +a++l +lgv+ralvvhg +gl NCBI__GCF_900177405.1:WP_085219434.1 172 APLYHPGLRHAGPVRRALKVRTVMNILGPCVNPAEPRVQLLGVADRTLLVPVARTLAALGVQRALVVHG-SGL 243 *********************************************************************.*** PP TIGR01245 221 DEisltgetkvaelkdgeieeytlspedfglkraeleelkggsaeenaellkevlegkekkakrdivvlNaaa 293 DE++l+get+ a+l+dgeie+ l +ed g++++++++++gg +eena++lk++l gk++ a++d+v+lNa+a NCBI__GCF_900177405.1:WP_085219434.1 244 DEVALHGETEAARLQDGEIETIFLYAEDVGIEPRPMDAIAGGGPEENAARLKALLDGKGSAAEADVVALNAGA 316 ************************************************************************* PP TIGR01245 294 alyvagkakdlkegvelakeaiksgkalekleelva 329 +l++ag a+d+ +gv+la +++ sg+a +l+++v+ NCBI__GCF_900177405.1:WP_085219434.1 317 LLMTAGIAADFPAGVRLAADVLASGAAGRTLAAFVE 352 ******************************999886 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.61 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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