Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate 6936469 Sama_0657 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
Query= BRENDA::C3TIE2 (350 letters) >FitnessBrowser__SB2B:6936469 Length = 352 Score = 525 bits (1352), Expect = e-154 Identities = 259/349 (74%), Positives = 291/349 (83%) Query: 1 MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60 M YQNDD+RI E+KELLPP+A+LE+FPATENA+ TV +AR IH +L DDRLLVVIGP Sbjct: 1 MYYQNDDVRINEVKELLPPIAILERFPATENASATVFNARSNIHNLLAKKDDRLLVVIGP 60 Query: 61 CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120 CSIHDP AA EY RLLALRE+ D+LE+VMRVYFEKPRTTVGWKGLINDP+MDNSF++N Sbjct: 61 CSIHDPEAALEYGQRLLALREQYSDQLEVVMRVYFEKPRTTVGWKGLINDPYMDNSFKLN 120 Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180 DGLR ARKLLL++N G+P AGEFLDMITPQY+ADLM WGAIGARTTESQVHRELASGLS Sbjct: 121 DGLRTARKLLLELNHMGMPTAGEFLDMITPQYVADLMCWGAIGARTTESQVHRELASGLS 180 Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPN 240 CPVGFKNGTDGTIK+AIDAI AA APH FLSVTK+GHSAIV+T GN DCHIILRGG+EPN Sbjct: 181 CPVGFKNGTDGTIKIAIDAIGAAAAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGGREPN 240 Query: 241 YSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVM 300 YS +HVA+++ L AGLP VMIDFSHANSSKQF +QM V DV Q+A G K I GVM Sbjct: 241 YSREHVAKIQTELQSAGLPDNVMIDFSHANSSKQFTRQMVVADDVAGQLADGNKGIFGVM 300 Query: 301 VESHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 VESHL EG Q G PL YGKS+TDAC+GW+D+ LL L AV ARR Sbjct: 301 VESHLNEGRQEHIPGVPLEYGKSVTDACLGWDDSAKLLATLNQAVLARR 349 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: 455 Number of extensions: 7 Number of successful extensions: 1 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: 352 Length adjustment: 29 Effective length of query: 321 Effective length of database: 323 Effective search space: 103683 Effective search space used: 103683 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 6936469 Sama_0657 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
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.20108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-170 552.4 0.0 1.7e-170 552.2 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6936469 Sama_0657 phospho-2-dehydro-3-de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936469 Sama_0657 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 552.2 0.0 1.7e-170 1.7e-170 1 342 [] 6 349 .. 6 349 .. 0.99 Alignments for each domain: == domain 1 score: 552.2 bits; conditional E-value: 1.7e-170 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaek 77 dd+ri +++ell+P ++ ++fp+te+a ++v ++r++i+++la kddrllvviGPcsihdpeaaley +rl +l+e+ lcl|FitnessBrowser__SB2B:6936469 6 DDVRINEVKELLPPIAILERFPATENASATVFNARSNIHNLLAKKDDRLLVVIGPCSIHDPEAALEYGQRLLALREQ 82 799************************************************************************** PP TIGR00034 78 lkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllsw 154 ++d+le+vmrvyfekPrttvGWkGlindP++++sf++n+Glr arklll+l+++g+p+a+e+ld+i+pqy+adl++w lcl|FitnessBrowser__SB2B:6936469 83 YSDQLEVVMRVYFEKPRTTVGWKGLINDPYMDNSFKLNDGLRTARKLLLELNHMGMPTAGEFLDMITPQYVADLMCW 159 ***************************************************************************** PP TIGR00034 155 gaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGG 231 gaiGarttesqvhrelasgls+pvgfkngtdG++k+aidai aaaa+h+flsvtk G++aiv+tkGn+d+hiilrGG lcl|FitnessBrowser__SB2B:6936469 160 GAIGARTTESQVHRELASGLSCPVGFKNGTDGTIKIAIDAIGAAAAPHHFLSVTKFGHSAIVSTKGNPDCHIILRGG 236 ***************************************************************************** PP TIGR00034 232 kkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl. 307 ++pny+ e+va+++ el+ agl +++midfsh+ns+k++ rq+ va++v+ q+a+G+k i+Gvm+es+l+eG+q+ lcl|FitnessBrowser__SB2B:6936469 237 REPNYSREHVAKIQTELQSAGLPDNVMIDFSHANSSKQFTRQMVVADDVAGQLADGNKGIFGVMVESHLNEGRQEHi 313 **************************************************************************976 PP TIGR00034 308 .keelkyGksvtdacigwedteallrklaeavkerr 342 + +l+yGksvtdac+gw+d+ +ll+ l++av +rr lcl|FitnessBrowser__SB2B:6936469 314 pGVPLEYGKSVTDACLGWDDSAKLLATLNQAVLARR 349 899*****************************9885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (352 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: 8.69 // [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