Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011798485.1 PNAP_RS24065 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000015505.1:WP_011798485.1 Length = 356 Score = 357 bits (916), Expect = e-103 Identities = 183/351 (52%), Positives = 242/351 (68%), Gaps = 2/351 (0%) Query: 1 MNYQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGP 60 M+ Q D+ I + L P L + PA E A +A +R A IL+G DDRLLV++GP Sbjct: 1 MSTQISDIHIAQADPLPQPRLLQGELPAGEAEAAFIAASRAATRNILRGLDDRLLVIVGP 60 Query: 61 CSIHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQIN 120 CSIH+P +A EYA RL L L D L +VMRVYFEKPRT +GWKGLI DP +D I Sbjct: 61 CSIHEPESALEYAARLRRLAPRLDDSLLLVMRVYFEKPRTRMGWKGLIYDPELDGQGDIG 120 Query: 121 DGLRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLS 180 GLR AR++LL+ G+PAA E LD++TPQY A+L++WGAIGART +S +HR++AS LS Sbjct: 121 AGLRHARRILLECARLGVPAASEILDLVTPQYYAELLTWGAIGARTVQSPLHRQMASALS 180 Query: 181 CPVGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKE-P 239 PVGFKN T+G++ AIDAI+ A H F S++ G + ++ T+GN D H++LRG + P Sbjct: 181 APVGFKNATNGSVGAAIDAIHVAVQSHRFPSISLEGKAIVITTTGNPDGHLVLRGASDGP 240 Query: 240 NYSAKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGV 299 NY A V+ L++AGLPA+++ID SH NS+K F +Q V AD+ QQIA G +I G+ Sbjct: 241 NYDAASVSRAAASLSQAGLPARLVIDCSHGNSNKDFSRQPAVAADIAQQIASGSSSICGL 300 Query: 300 MVESHLVEGNQSLESG-EPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 M+ESHLVEG Q + G + L YG+S+TDACIGWE T A+L QLA +V+ RR Sbjct: 301 MIESHLVEGRQDIVDGRQGLRYGQSVTDACIGWEATVAVLEQLAASVRQRR 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: 362 Number of extensions: 16 Number of successful extensions: 3 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: 356 Length adjustment: 29 Effective length of query: 321 Effective length of database: 327 Effective search space: 104967 Effective search space used: 104967 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_011798485.1 PNAP_RS24065 (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.30609.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-142 459.7 0.0 2.7e-142 459.5 0.0 1.0 1 lcl|NCBI__GCF_000015505.1:WP_011798485.1 PNAP_RS24065 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015505.1:WP_011798485.1 PNAP_RS24065 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.5 0.0 2.7e-142 2.7e-142 2 342 .] 7 351 .. 6 351 .. 0.99 Alignments for each domain: == domain 1 score: 459.5 bits; conditional E-value: 2.7e-142 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 d++i++ d+l +P+ l+ + p+ e++a+ +a sr + +il+G ddrllv++GPcsih+pe+aleya r lcl|NCBI__GCF_000015505.1:WP_011798485.1 7 DIHIAQADPLPQPRLLQGELPAGEAEAAFIAASRAATRNILRGLDDRLLVIVGPCSIHEPESALEYAAR 75 6789999************************************************************** PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l++la +l+d+l +vmrvyfekPrt +GWkGli dP+l++ d+ +Glr ar++ll+ + lg+p+a+e+ lcl|NCBI__GCF_000015505.1:WP_011798485.1 76 LRRLAPRLDDSLLLVMRVYFEKPRTRMGWKGLIYDPELDGQGDIGAGLRHARRILLECARLGVPAASEI 144 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ld ++pqy+a+ll+wgaiGart +s +hr++as+ls pvgfkn+t+Gs+ aidai+ a ++h+f s++ lcl|NCBI__GCF_000015505.1:WP_011798485.1 145 LDLVTPQYYAELLTWGAIGARTVQSPLHRQMASALSAPVGFKNATNGSVGAAIDAIHVAVQSHRFPSIS 213 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 +G++ +++t+Gn+dgh++lrG + pnyda++v ++ ++l++agl ++l+id+shgnsnkd+ rq++v lcl|NCBI__GCF_000015505.1:WP_011798485.1 214 LEGKAIVITTTGNPDGHLVLRGASDgPNYDAASVSRAAASLSQAGLPARLVIDCSHGNSNKDFSRQPAV 282 ***********************999******************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavkerr 342 a+++++qia+G+ +i+G+mies+l+eG+q++ +++l yG+svtdacigwe t a+l++la++v++rr lcl|NCBI__GCF_000015505.1:WP_011798485.1 283 AADIAQQIASGSSSICGLMIESHLVEGRQDIvdgRQGLRYGQSVTDACIGWEATVAVLEQLAASVRQRR 351 ******************************9888899*****************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (356 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: 6.84 // [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