Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_077278004.1 B1C78_RS04760 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_002000365.1:WP_077278004.1 Length = 352 Score = 452 bits (1164), Expect = e-132 Identities = 224/349 (64%), Positives = 272/349 (77%) Query: 1 MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60 M YQ DDLRI EI+E+ PPV + E+ P T+ AA TV AR IH IL G DDRLLV+ GP Sbjct: 1 MRYQTDDLRILEIREVSPPVLVHEELPITDEAAATVHDARMDIHNILAGQDDRLLVIAGP 60 Query: 61 CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120 CSIHD AA EYA RL +R+EL D+L IVMRVYFEKPRTTVGWKGLINDP++D SFQIN Sbjct: 61 CSIHDVDAAMEYAGRLKHMRDELIDDLHIVMRVYFEKPRTTVGWKGLINDPNLDGSFQIN 120 Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180 GLR+AR LLLD+ G+PA E+LD+I+PQY+ADL++WGAIGARTTESQVHRELASGLS Sbjct: 121 KGLRLARGLLLDLAKMGMPAGTEYLDLISPQYVADLVAWGAIGARTTESQVHRELASGLS 180 Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240 CPVGFKN TDG+++VA+DAI +A PH FLSVTK GHSAI +T+GN DCHIILRGGKEPN Sbjct: 181 CPVGFKNSTDGSLQVAVDAIRSASRPHHFLSVTKAGHSAIFSTAGNTDCHIILRGGKEPN 240 Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300 + A + L AGLPA +M+D SHANS K +Q++V + +Q+AGG++ IIGVM Sbjct: 241 FDADSIEHAATRLKSAGLPASLMVDCSHANSRKDPARQVEVARVLGEQVAGGDRRIIGVM 300 Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 +ESHLV G Q + + L YG+SITDAC+ WEDT +L +LA AV++RR Sbjct: 301 LESHLVAGRQDVSRDKELTYGQSITDACMSWEDTRQVLTELAAAVRSRR 349 Lambda K H 0.317 0.134 0.397 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: 435 Number of extensions: 9 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: 350 Length of database: 352 Length adjustment: 29 Effective length of query: 321 Effective length of database: 323 Effective search space: 103683 Effective search space used: 103683 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_077278004.1 B1C78_RS04760 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))
# 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/TIGR00034.hmm # target sequence database: /tmp/gapView.14145.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00034 [M=342] Accession: TIGR00034 Description: aroFGH: 3-deoxy-7-phosphoheptulonate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-165 535.0 0.0 3.5e-165 534.8 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077278004.1 B1C78_RS04760 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077278004.1 B1C78_RS04760 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.8 0.0 3.5e-165 3.5e-165 1 342 [] 6 349 .. 6 349 .. 0.99 Alignments for each domain: == domain 1 score: 534.8 bits; conditional E-value: 3.5e-165 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri +i e+ +P ++++ p+t +aa++v+++r +i++ilaG+ddrllv+ GPcsihd aa+eya lcl|NCBI__GCF_002000365.1:WP_077278004.1 6 DDLRILEIREVSPPVLVHEELPITDEAAATVHDARMDIHNILAGQDDRLLVIAGPCSIHDVDAAMEYAG 74 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk+++++l ddl+ivmrvyfekPrttvGWkGlindP+l++sf++nkGlr+ar llldl+++g+p++te lcl|NCBI__GCF_002000365.1:WP_077278004.1 75 RLKHMRDELIDDLHIVMRVYFEKPRTTVGWKGLINDPNLDGSFQINKGLRLARGLLLDLAKMGMPAGTE 143 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld ispqy+adl++wgaiGarttesqvhrelasgls+pvgfkn+tdGsl+va+dair+a+++h+flsv lcl|NCBI__GCF_002000365.1:WP_077278004.1 144 YLDLISPQYVADLVAWGAIGARTTESQVHRELASGLSCPVGFKNSTDGSLQVAVDAIRSASRPHHFLSV 212 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tkaG++ai +t+Gn+d+hiilrGGk+pn+da++++++ +l+ agl ++lm+d+sh+ns+kd rq+ev lcl|NCBI__GCF_002000365.1:WP_077278004.1 213 TKAGHSAIFSTAGNTDCHIILRGGKEPNFDADSIEHAATRLKSAGLPASLMVDCSHANSRKDPARQVEV 281 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 a+ + eq+a G++ iiGvm+es+l+ G+q++ ++el+yG+s+tdac++wedt ++l +la+av++rr lcl|NCBI__GCF_002000365.1:WP_077278004.1 282 ARVLGEQVAGGDRRIIGVMLESHLVAGRQDVsrDKELTYGQSITDACMSWEDTRQVLTELAAAVRSRR 349 ******************************976789*****************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (352 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: 7.92 // [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