Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate GFF1857 HP15_1814 phospho-2-dehydro-3-heoxyheptonate aldolase
Query= BRENDA::P00888 (356 letters) >FitnessBrowser__Marino:GFF1857 Length = 358 Score = 416 bits (1070), Expect = e-121 Identities = 205/355 (57%), Positives = 263/355 (74%), Gaps = 1/355 (0%) Query: 1 MQKDALNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCG 60 M + L N+++ ++ L+TPE LK PLS + ++ R++I DI+ G+D RL VV G Sbjct: 1 MSGNKLENLNVASQEALITPEALKKEMPLSDKAAETVSKGRQAIYDIMDGKDHRLFVVVG 60 Query: 61 PCSIHDPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDV 120 PCSIHD E A +YA R K LA EVSD+L +VMRVYFEKPRTTVGWKGLINDPH++ +FD+ Sbjct: 61 PCSIHDVEAARDYAARLKKLADEVSDTLLIVMRVYFEKPRTTVGWKGLINDPHLNDTFDI 120 Query: 121 EAGLQIARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGL 180 E GL I R+LLL++ +GLP ATEALDP SPQYL D +WSAIGARTTESQTHREM+SGL Sbjct: 121 EQGLHIGRRLLLDINELGLPAATEALDPISPQYLQDTIAWSAIGARTTESQTHREMSSGL 180 Query: 181 SMPVGFKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA- 239 SM +GFKNGTDGSL A+NAM++ + PH F+GI+Q GQVA+++T+GN GHV+LRGG Sbjct: 181 SMAIGFKNGTDGSLDVAVNAMKSVSHPHSFLGIDQQGQVAIIRTKGNNYGHVVLRGGGGK 240 Query: 240 PNYSPADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIG 299 PNY VA CE+ +++AGLR S+M+DCSH NS+KD QP V + V QI +GN SI Sbjct: 241 PNYDSVSVALCEQALDKAGLRKSMMIDCSHANSSKDPAIQPLVMQDVTHQILEGNTSIQS 300 Query: 300 LMIESNIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354 LM+ESNI+ GNQS + +++KYGVSVTDACI W T+ +R++ L L R Sbjct: 301 LMVESNINWGNQSIPENLADLKYGVSVTDACIDWPTTEKAIRDMRDKLKDVLPKR 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: 422 Number of extensions: 10 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 GFF1857 HP15_1814 (phospho-2-dehydro-3-heoxyheptonate aldolase)
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.15046.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-156 505.6 0.1 3.1e-156 505.3 0.1 1.0 1 lcl|FitnessBrowser__Marino:GFF1857 HP15_1814 phospho-2-dehydro-3-he Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1857 HP15_1814 phospho-2-dehydro-3-heoxyheptonate aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.3 0.1 3.1e-156 3.1e-156 2 339 .. 8 349 .. 7 352 .. 0.97 Alignments for each domain: == domain 1 score: 505.3 bits; conditional E-value: 3.1e-156 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklae 76 +l++++ + l+tPe+lk+++pl+ kaae+v k r++i di++Gkd+rl+vv+GPcsihd eaa +ya rlkkla+ lcl|FitnessBrowser__Marino:GFF1857 8 NLNVASQEALITPEALKKEMPLSDKAAETVSKGRQAIYDIMDGKDHRLFVVVGPCSIHDVEAARDYAARLKKLAD 82 78889999******************************************************************* PP TIGR00034 77 klkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladl 151 +++d l ivmrvyfekPrttvGWkGlindP+ln++fd+++Gl+i r+llld++elglp+ate+ld+ispqyl d+ lcl|FitnessBrowser__Marino:GFF1857 83 EVSDTLLIVMRVYFEKPRTTVGWKGLINDPHLNDTFDIEQGLHIGRRLLLDINELGLPAATEALDPISPQYLQDT 157 *************************************************************************** PP TIGR00034 152 lswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghi 226 ++w+aiGarttesq+hre++sgls+++gfkngtdGsl va++a+++ +++h fl+++++Gqvai++tkGn++gh+ lcl|FitnessBrowser__Marino:GFF1857 158 IAWSAIGARTTESQTHREMSSGLSMAIGFKNGTDGSLDVAVNAMKSVSHPHSFLGIDQQGQVAIIRTKGNNYGHV 232 *************************************************************************** PP TIGR00034 227 ilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnl 300 +lrGG pnyd+ +va +++ l+kagl++++mid+sh+ns+kd q+ v+++v++qi eG+++i +m+esn+ lcl|FitnessBrowser__Marino:GFF1857 233 VLRGGGGkPNYDSVSVALCEQALDKAGLRKSMMIDCSHANSSKDPAIQPLVMQDVTHQILEGNTSIQSLMVESNI 307 ***98766******************************************************************* PP TIGR00034 301 eeGnqsl...keelkyGksvtdacigwedteallrklaeavk 339 + Gnqs+ ++lkyG+svtdaci+w +te+ +r++ +++k lcl|FitnessBrowser__Marino:GFF1857 308 NWGNQSIpenLADLKYGVSVTDACIDWPTTEKAIRDMRDKLK 349 *******53234689*********************999876 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.54 // [ok]
This GapMind analysis is from Apr 09 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