Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_044414020.1 NA59_RS13545 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000934765.1:WP_044414020.1 Length = 354 Score = 429 bits (1104), Expect = e-125 Identities = 211/348 (60%), Positives = 261/348 (75%), Gaps = 1/348 (0%) Query: 3 YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62 YQ DDLRI I E+LPP L EK P TE AA TV R+ IH+IL G DDRLLVVIGPCS Sbjct: 4 YQTDDLRINHITEVLPPCELHEKQPITEQAAKTVFETRRQIHEILNGKDDRLLVVIGPCS 63 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHD A +EYA RL ++ +++L IVMRVYFEKPRTTVGWKGLINDP ++ +F IN G Sbjct: 64 IHDTEAGREYAQRLKQQIDQHQEDLLIVMRVYFEKPRTTVGWKGLINDPDLNETFHINKG 123 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 L +AR LLD+N G+PAA EFLD+I+PQY++DL+SWGAIGARTTESQ HREL+SGLSCP Sbjct: 124 LELARGFLLDVNHMGVPAATEFLDLISPQYISDLVSWGAIGARTTESQGHRELSSGLSCP 183 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGK-EPNY 241 VGFKNGTDG+ ++A+DAI AA PH F+S+TK GHSAI +T+GN DCH+ILRGG PNY Sbjct: 184 VGFKNGTDGSFRIAVDAIRAANKPHIFMSLTKSGHSAIFSTTGNEDCHVILRGGNGGPNY 243 Query: 242 SAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMV 301 A+ V + L A + ++M+D SHANSSK +QM V + +Q+A G +I+G MV Sbjct: 244 EAEFVEQAVNELRAAKVQTRLMVDCSHANSSKDHNRQMQVAQSISEQLASGSNSIMGAMV 303 Query: 302 ESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 ESHLV G Q + +G+PL YG+SITDACI W+++ LL LA V+ RR Sbjct: 304 ESHLVAGRQDVVAGQPLTYGQSITDACIDWDNSLTLLETLAEGVRQRR 351 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: 433 Number of extensions: 8 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: 354 Length adjustment: 29 Effective length of query: 321 Effective length of database: 325 Effective search space: 104325 Effective search space used: 104325 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_044414020.1 NA59_RS13545 (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.26219.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.7e-167 540.1 0.0 9.9e-167 539.9 0.0 1.0 1 lcl|NCBI__GCF_000934765.1:WP_044414020.1 NA59_RS13545 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000934765.1:WP_044414020.1 NA59_RS13545 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 539.9 0.0 9.9e-167 9.9e-167 1 342 [] 7 351 .. 7 351 .. 0.99 Alignments for each domain: == domain 1 score: 539.9 bits; conditional E-value: 9.9e-167 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 ddlri +i e+l+P el++k p+te+aa++v ++r++i++il+GkddrllvviGPcsihd ea eya+ lcl|NCBI__GCF_000934765.1:WP_044414020.1 7 DDLRINHITEVLPPCELHEKQPITEQAAKTVFETRRQIHEILNGKDDRLLVVIGPCSIHDTEAGREYAQ 75 799****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk+ ++ ++dl ivmrvyfekPrttvGWkGlindPdlne+f++nkGl++ar +lld++++g+p+ate lcl|NCBI__GCF_000934765.1:WP_044414020.1 76 RLKQQIDQHQEDLLIVMRVYFEKPRTTVGWKGLINDPDLNETFHINKGLELARGFLLDVNHMGVPAATE 144 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld ispqy++dl+swgaiGarttesq hrel+sgls+pvgfkngtdGs ++a+dairaa+++h+f+s lcl|NCBI__GCF_000934765.1:WP_044414020.1 145 FLDLISPQYISDLVSWGAIGARTTESQGHRELSSGLSCPVGFKNGTDGSFRIAVDAIRAANKPHIFMSL 213 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 tk+G++ai +t+Gned+h+ilrGG+ pny+ae v+++ +el++a+ + +lm+d+sh+ns+kd++rq++ lcl|NCBI__GCF_000934765.1:WP_044414020.1 214 TKSGHSAIFSTTGNEDCHVILRGGNGgPNYEAEFVEQAVNELRAAKVQTRLMVDCSHANSSKDHNRQMQ 282 *************************99****************************************** PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 va+s++eq+a+G+++i+G m+es+l+ G+q++ +++l+yG+s+tdaci+w+++ +ll+ lae v++rr lcl|NCBI__GCF_000934765.1:WP_044414020.1 283 VAQSISEQLASGSNSIMGAMVESHLVAGRQDVvaGQPLTYGQSITDACIDWDNSLTLLETLAEGVRQRR 351 *******************************98899******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (354 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: 8.40 // [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