Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_090221190.1 CV091_RS19330 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_002796795.1:WP_090221190.1 Length = 356 Score = 410 bits (1053), Expect = e-119 Identities = 207/349 (59%), Positives = 255/349 (73%), Gaps = 1/349 (0%) Query: 1 MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60 M ++ +LRI ++EL P L+ + PA+ A TV H+R AI IL+G DDRL+VV+GP Sbjct: 1 MPHKTANLRITAMQELASPETLIAELPASSVALETVVHSRTAIQNILQGQDDRLIVVVGP 60 Query: 61 CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120 CSIHDP AA +YA RLL L++EL D+LEIVMRVYFEKPRT GWKGLINDP +D SFQIN Sbjct: 61 CSIHDPSAALDYARRLLPLKQELGDQLEIVMRVYFEKPRTIGGWKGLINDPGLDESFQIN 120 Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180 DGL++AR L +IN GLP EFLD PQY++DL++W AIGARTTESQ+HRE+ASGLS Sbjct: 121 DGLKLARSLCEEINALGLPVGTEFLDASVPQYISDLVAWAAIGARTTESQIHREMASGLS 180 Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240 CPVGFKNGT G +++AIDA+ +A PH F++++K G +AI T+GN DCHIILRGG N Sbjct: 181 CPVGFKNGTRGNVQIAIDAVRSAARPHHFMALSKTGRAAIAGTAGNPDCHIILRGGGGTN 240 Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300 + A V K G+ QVMID SHANS K +KQ +V ADV Q+A G+ I GVM Sbjct: 241 FDADSVDAACRIAEKDGIRGQVMIDASHANSGKDPEKQPEVLADVGGQMAAGDTRITGVM 300 Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 +ESHLV GNQ L +PL YG+SITD CIGW+DT A L +LA AV RR Sbjct: 301 IESHLVAGNQKL-GEDPLTYGQSITDGCIGWQDTVAELHKLAEAVSRRR 348 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: 404 Number of extensions: 7 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: 350 Length of database: 356 Length adjustment: 29 Effective length of query: 321 Effective length of database: 327 Effective search space: 104967 Effective search space used: 104967 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_090221190.1 CV091_RS19330 (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.2505605.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-155 502.8 0.0 2.2e-155 502.6 0.0 1.0 1 NCBI__GCF_002796795.1:WP_090221190.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090221190.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.6 0.0 2.2e-155 2.2e-155 2 342 .] 7 348 .. 6 348 .. 0.99 Alignments for each domain: == domain 1 score: 502.6 bits; conditional E-value: 2.2e-155 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkkl 74 +lri++++el++Pe+l+a+ p+++ a e+v +sr++i++il+G+ddrl+vv+GPcsihdp+aal+ya+rl +l NCBI__GCF_002796795.1:WP_090221190.1 7 NLRITAMQELASPETLIAELPASSVALETVVHSRTAIQNILQGQDDRLIVVVGPCSIHDPSAALDYARRLLPL 79 689********************************************************************** PP TIGR00034 75 aeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqy 147 +++l d+leivmrvyfekPrt+ GWkGlindP l+esf++n+Gl++ar l +++ lglp++te+ld+ pqy NCBI__GCF_002796795.1:WP_090221190.1 80 KQELGDQLEIVMRVYFEKPRTIGGWKGLINDPGLDESFQINDGLKLARSLCEEINALGLPVGTEFLDASVPQY 152 ************************************************************************* PP TIGR00034 148 ladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkG 220 ++dl++w+aiGarttesq+hre+asgls+pvgfkngt G++++aida+r+aa++h+f++ +k+G++ai t+G NCBI__GCF_002796795.1:WP_090221190.1 153 ISDLVAWAAIGARTTESQIHREMASGLSCPVGFKNGTRGNVQIAIDAVRSAARPHHFMALSKTGRAAIAGTAG 225 ************************************************************************* PP TIGR00034 221 nedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiG 293 n+d+hiilrGG +n+da++v+++++ ek g + ++mid+sh+ns kd ++q+ev ++v q+a G++ i+G NCBI__GCF_002796795.1:WP_090221190.1 226 NPDCHIILRGGGGTNFDADSVDAACRIAEKDGIRGQVMIDASHANSGKDPEKQPEVLADVGGQMAAGDTRITG 298 ************************************************************************* PP TIGR00034 294 vmiesnleeGnqsl.keelkyGksvtdacigwedteallrklaeavkerr 342 vmies+l+ Gnq+l +++l+yG+s+td cigw+dt a l+klaeav++rr NCBI__GCF_002796795.1:WP_090221190.1 299 VMIESHLVAGNQKLgEDPLTYGQSITDGCIGWQDTVAELHKLAEAVSRRR 348 **************8889****************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.42 // [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