Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_046009164.1 OLEAN_RS10280 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000967895.1:WP_046009164.1 Length = 355 Score = 414 bits (1063), Expect = e-120 Identities = 205/355 (57%), Positives = 264/355 (74%), Gaps = 1/355 (0%) Query: 1 MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60 M + + +++I+ + L+TP+QLKA PLS A I R+ + DI+ +D R+ +V G Sbjct: 1 MTDNRVEDLNISSIETLITPDQLKALLPLSTDVVASIQKGRQEVRDILDRKDHRIFLVVG 60 Query: 61 PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120 PCSIHD + A +YA R K LA EV D+L +VMRVYFEKPRTTVGWKGLINDP+++ SF + Sbjct: 61 PCSIHDVDAAKDYAERLKGLAEEVKDTLCIVMRVYFEKPRTTVGWKGLINDPYLNDSFKI 120 Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180 E GL+I+R+LL++L GLPL+TEALDP SPQY+ DL SWSAIGARTTESQTHREMASGL Sbjct: 121 EDGLKISRQLLIDLAASGLPLSTEALDPISPQYIQDLISWSAIGARTTESQTHREMASGL 180 Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA- 239 S VGFKNGTDG+L A NA+++ A PHRF+GINQ+GQV++++T GN GH++LRGG Sbjct: 181 SSAVGFKNGTDGNLTVATNALKSVANPHRFLGINQSGQVSIVETAGNQYGHIVLRGGGGK 240 Query: 240 PNYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIG 299 PNY ++AQCE+ +E+AGL ++MVDCSH NS+KD QP V E+V QI +GN+SIIG Sbjct: 241 PNYDSVNIAQCEQTLEKAGLAQNIMVDCSHENSSKDAAIQPLVMENVTNQILEGNKSIIG 300 Query: 300 LMIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354 LMIESNI G Q + ++M YG SVTDACISW T+ +R +HQ L L R Sbjct: 301 LMIESNIEFGRQDICENLADMTYGQSVTDACISWTTTEESIRSMHQKLKDILPKR 355 Lambda K H 0.316 0.131 0.378 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: 400 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: 356 Length of database: 355 Length adjustment: 29 Effective length of query: 327 Effective length of database: 326 Effective search space: 106602 Effective search space used: 106602 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_046009164.1 OLEAN_RS10280 (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.1200.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-154 500.2 0.2 1.3e-154 500.0 0.2 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046009164.1 OLEAN_RS10280 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046009164.1 OLEAN_RS10280 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 500.0 0.2 1.3e-154 1.3e-154 1 339 [. 7 349 .. 7 352 .. 0.98 Alignments for each domain: == domain 1 score: 500.0 bits; conditional E-value: 1.3e-154 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 +dl+i +i+ l+tP++lka pl++++ ++++k r+e+ dil+ kd+r+++v+GPcsihd aa++ya+ lcl|NCBI__GCF_000967895.1:WP_046009164.1 7 EDLNISSIETLITPDQLKALLPLSTDVVASIQKGRQEVRDILDRKDHRIFLVVGPCSIHDVDAAKDYAE 75 6899***************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rlk lae++kd l ivmrvyfekPrttvGWkGlindP+ln+sf++++Gl+i+r+ll+dl+ glpl+te lcl|NCBI__GCF_000967895.1:WP_046009164.1 76 RLKGLAEEVKDTLCIVMRVYFEKPRTTVGWKGLINDPYLNDSFKIEDGLKISRQLLIDLAASGLPLSTE 144 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld+ispqy+ dl+sw+aiGarttesq+hre+asgls +vgfkngtdG+l va +a+++ a++h+fl++ lcl|NCBI__GCF_000967895.1:WP_046009164.1 145 ALDPISPQYIQDLISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGNLTVATNALKSVANPHRFLGI 213 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 +++Gqv+ivet+Gn++ghi+lrGG pnyd+ ++a+++++lekagl +++m+d+sh ns+kd q+ lcl|NCBI__GCF_000967895.1:WP_046009164.1 214 NQSGQVSIVETAGNQYGHIVLRGGGGkPNYDSVNIAQCEQTLEKAGLAQNIMVDCSHENSSKDAAIQPL 282 **********************98766****************************************** PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339 v+e+v++qi eG+k+iiG+miesn+e G+q++ ++++yG+svtdaci+w +te+ +r +++++k lcl|NCBI__GCF_000967895.1:WP_046009164.1 283 VMENVTNQILEGNKSIIGLMIESNIEFGRQDIcenLADMTYGQSVTDACISWTTTEESIRSMHQKLK 349 ********************************43234689***********************9887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (355 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: 00:00:00.01 # Mc/sec: 9.30 // [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