Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_106719069.1 CU100_RS23480 3-dehydroquinate synthase
Query= SwissProt::U3KRF2 (445 letters) >NCBI__GCF_003010935.1:WP_106719069.1 Length = 374 Score = 271 bits (694), Expect = 2e-77 Identities = 157/347 (45%), Positives = 211/347 (60%), Gaps = 10/347 (2%) Query: 80 APTIVDVDLGDRSYPIYIGSGLLDQPDL-LQRHVHGKRVLVVTNSTVAPIYLDKVVGALT 138 A T V V LGDRSY I IG+GL+D+ + RV +V++ TVA ++LD++ +L+ Sbjct: 6 AITTVPVKLGDRSYDILIGAGLIDRAGAAIASRAGSVRVAIVSDETVAALHLDRLTRSLS 65 Query: 139 NGNPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAA 198 + +++ GEK K TL V + + +RL+R +A GGGVIGD+ G+AA Sbjct: 66 GAG--IDSTPILVTAGEKSKGFATLEAVTNAILAARLERGDVVIAFGGGVIGDLAGFAAG 123 Query: 199 SFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLPDR 258 RG+ FIQ+PT+++AQVDSSVGGKTGIN GKNL+G FYQPQ VL DTD L+TL R Sbjct: 124 IARRGMRFIQMPTSLLAQVDSSVGGKTGINTAHGKNLVGVFYQPQLVLADTDVLDTLTPR 183 Query: 259 ELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDEKE 318 E +G AEV KYGLI ++FF W EKN + P AI SC++KA+VV+ DEKE Sbjct: 184 EFRAGYAEVAKYGLIDRSDFFAWLEKNWRGIFDGGPER-TEAIAVSCQSKADVVARDEKE 242 Query: 319 SGLRATLNLGHTFGHAIETGFGY--GQWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRAH 376 +G RA LNLGHTFGHA+ET Y + +HGE V+ G+V+A S ++ + R Sbjct: 243 TGDRALLNLGHTFGHALETATNYDSARLVHGEGVSIGIVLAHQFSTKMNLASQDDAGRVE 302 Query: 377 NILQQAKLPTA----PPETMTVEMFKSVMAVDKKVADGLLRLILLKG 419 +Q LP + P E + E +A DKKVA G L IL +G Sbjct: 303 AHFRQVGLPVSIGDIPGELPSAEKLMDYIAQDKKVARGALTFILTRG 349 Lambda K H 0.318 0.133 0.385 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: 375 Number of extensions: 14 Number of successful extensions: 5 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: 445 Length of database: 374 Length adjustment: 31 Effective length of query: 414 Effective length of database: 343 Effective search space: 142002 Effective search space used: 142002 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: 50 (23.9 bits)
Align candidate WP_106719069.1 CU100_RS23480 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))
# 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/TIGR01357.hmm # target sequence database: /tmp/gapView.72195.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01357 [M=344] Accession: TIGR01357 Description: aroB: 3-dehydroquinate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-106 341.7 0.0 2.9e-106 341.5 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106719069.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106719069.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 341.5 0.0 2.9e-106 2.9e-106 1 341 [. 19 366 .. 19 369 .. 0.96 Alignments for each domain: == domain 1 score: 341.5 bits; conditional E-value: 2.9e-106 TIGR01357 1 ykvkvgegllkklveelaeka..sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvakl 71 y++ +g gl++++ +++a++a ++ +++de+v++l+ ++l + l+ +g+ + ++v +ge+sK ++t++++ NCBI__GCF_003010935.1:WP_106719069.1 19 YDILIGAGLIDRAGAAIASRAgsVRVAIVSDETVAALHLDRLTRSLSGAGIDSTPILVTAGEKSKGFATLEAV 91 6899*******999999995545899*********************************************** PP TIGR01357 72 ldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGaf 144 ++++l++ ler +v++a+GGGv+gDlaGF+A + RG+r++q+PT+lla+vDssvGGKtgin+++gkNl+G f NCBI__GCF_003010935.1:WP_106719069.1 92 TNAILAARLERGDVVIAFGGGVIGDLAGFAAGIARRGMRFIQMPTSLLAQVDSSVGGKTGINTAHGKNLVGVF 164 ************************************************************************* PP TIGR01357 145 yqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaev 217 yqP++Vl d++vl tl+ re+r+G+aEv K+gli +++f++lekn++ + + +e+i+ s++ Ka+v NCBI__GCF_003010935.1:WP_106719069.1 165 YQPQLVLADTDVLDTLTPREFRAGYAEVAKYGLIDRSDFFAWLEKNWRGIFD--GGPERTEAIAVSCQSKADV 235 ***********************************************98775..67999************** PP TIGR01357 218 VeeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgllkaellerlvallkkl 287 V++Deke+g RalLN+GHt+gHa+E++++y+ l HGe V+iG+v++ ++s k+ l++++++ r++a ++++ NCBI__GCF_003010935.1:WP_106719069.1 236 VARDEKETGDRALLNLGHTFGHALETATNYDsarLVHGEGVSIGIVLAHQFSTKMNLASQDDAGRVEAHFRQV 308 ******************************99999************************************** PP TIGR01357 288 glptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevteeelle 341 glp+++ + s+e+l++++ +DKK ++ ++++l + iG+a++a++v+ +++l+ NCBI__GCF_003010935.1:WP_106719069.1 309 GLPVSIGDipgeLPSAEKLMDYIAQDKKVARGALTFILTRGIGQAFIAKDVPPSAVLS 366 ******9999977899********************************9998887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (374 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 18.86 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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