Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_086510254.1 BZY95_RS12485 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_002151265.1:WP_086510254.1 Length = 358 Score = 435 bits (1119), Expect = e-127 Identities = 213/355 (60%), Positives = 270/355 (76%), Gaps = 1/355 (0%) Query: 1 MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60 M ++N+++ + VL+TPE LK PL E + + R++I +I+ G DPRLLVV G Sbjct: 1 MSDQQVSNLNVLSQDVLITPEALKNEIPLGDVAERTVIEGRRTIQNILDGSDPRLLVVVG 60 Query: 61 PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120 PCSIHD + AL+YARR + LA EV DSL++VMRVYFEKPRTTVGWKGLINDPH++GSF++ Sbjct: 61 PCSIHDVDAALDYARRLRRLADEVKDSLFIVMRVYFEKPRTTVGWKGLINDPHLNGSFEI 120 Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180 E GL IARKLL+EL +GLPLATEALDP SPQYL D SWSAIGARTTESQTHREM+SGL Sbjct: 121 EEGLHIARKLLVELSELGLPLATEALDPISPQYLQDCISWSAIGARTTESQTHREMSSGL 180 Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA- 239 S PVGFKNGTDGSL AINA+++ + PH F+GINQ+GQVA+++T+GN HV+LRGG Sbjct: 181 SSPVGFKNGTDGSLDVAINALQSVSHPHNFLGINQSGQVAIIRTRGNAYAHVVLRGGNGK 240 Query: 240 PNYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIG 299 PNY VA E+E+++AG++P++M+DCSH NSNKD QP V ++V QI +GNRSI+G Sbjct: 241 PNYDSVSVALAEQELKKAGIKPNIMIDCSHANSNKDPALQPLVLDNVTNQILEGNRSIMG 300 Query: 300 LMIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354 LM+ESNI G+Q S+M+YGVSVTDACI W T+ + + L+ LT R Sbjct: 301 LMVESNIGWGSQKILDDHSQMQYGVSVTDACIDWATTEETMTRMASKLSPVLTER 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: 442 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: 358 Length adjustment: 29 Effective length of query: 327 Effective length of database: 329 Effective search space: 107583 Effective search space used: 107583 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_086510254.1 BZY95_RS12485 (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.10214.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-155 501.4 0.0 6.2e-155 501.1 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510254.1 BZY95_RS12485 3-deoxy-7-phosphoh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510254.1 BZY95_RS12485 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 501.1 0.0 6.2e-155 6.2e-155 2 338 .. 8 348 .. 7 352 .. 0.98 Alignments for each domain: == domain 1 score: 501.1 bits; conditional E-value: 6.2e-155 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 +l++ + d l+tPe+lk+++pl a+ +v++ r++i++il+G+d+rllvv+GPcsihd aal+ya+r lcl|NCBI__GCF_002151265.1:WP_086510254.1 8 NLNVLSQDVLITPEALKNEIPLGDVAERTVIEGRRTIQNILDGSDPRLLVVVGPCSIHDVDAALDYARR 76 577888899************************************************************ PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l++la+++kd+l ivmrvyfekPrttvGWkGlindP+ln+sf++++Gl+iarkll++l elglplate+ lcl|NCBI__GCF_002151265.1:WP_086510254.1 77 LRRLADEVKDSLFIVMRVYFEKPRTTVGWKGLINDPHLNGSFEIEEGLHIARKLLVELSELGLPLATEA 145 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ld+ispqyl d++sw+aiGarttesq+hre++sgls pvgfkngtdGsl vai+a+++ +++h fl+++ lcl|NCBI__GCF_002151265.1:WP_086510254.1 146 LDPISPQYLQDCISWSAIGARTTESQTHREMSSGLSSPVGFKNGTDGSLDVAINALQSVSHPHNFLGIN 214 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 ++Gqvai++t+Gn ++h++lrGG+ pnyd+ +va +++el+kag k+++mid+sh+nsnkd q+ v lcl|NCBI__GCF_002151265.1:WP_086510254.1 215 QSGQVAIIRTRGNAYAHVVLRGGNGkPNYDSVSVALAEQELKKAGIKPNIMIDCSHANSNKDPALQPLV 283 ***********************988******************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeav 338 ++v++qi eG+++i+G+m+esn+ G+q++ +++++yG+svtdaci+w +te+ + ++a+++ lcl|NCBI__GCF_002151265.1:WP_086510254.1 284 LDNVTNQILEGNRSIMGLMVESNIGWGSQKIlddHSQMQYGVSVTDACIDWATTEETMTRMASKL 348 ******************************9876789*********************9999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (358 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: 10.76 // [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