Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_012567831.1 RC1_RS12835 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000016185.1:WP_012567831.1 Length = 394 Score = 290 bits (742), Expect = 6e-83 Identities = 169/370 (45%), Positives = 230/370 (62%), Gaps = 12/370 (3%) Query: 58 LATSATKVMDHSSSKASSQAPTV-VEVDLGTRSYPIYIGAGLLDQPD-LLQRHIHGKRVL 115 + T+ K D + ++ T V VDLG RSY I IG GL+ + L+ + G+ +L Sbjct: 1 MTTTDGKAADGRAEDGTATGGTATVRVDLGARSYDILIGPGLIARAGRLIADRLPGRPLL 60 Query: 116 VVTNTTVAPLYLDKTISALTDGNPNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRR 175 V+T+ TVA +L + L V E +++P GE K M L +V D + ++RR Sbjct: 61 VLTDATVAGHHLRPLLDGLAAAGAAVA-EPLVVPAGEATKEMGRLSEVMDGLLARGIERR 119 Query: 176 CTFVALGGGVIGDMCGYAAASYLRGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGA 235 VALGGGV+GD+ G+AAA LRG++F+Q+PTT++AQVDSSVGGKTG+N GKN+IGA Sbjct: 120 SVLVALGGGVVGDLGGFAAAIALRGIDFVQVPTTLLAQVDSSVGGKTGVNSRHGKNLIGA 179 Query: 236 FYQPQCVLIDTDTLNTLPDRELASGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFT 295 F+QP+ VL DT L+TLP REL +G AEV+KYG+I +FF+W E + P +L D A Sbjct: 180 FHQPRLVLADTAALDTLPRRELLAGYAEVVKYGMIDRPDFFDWLEAHGPAVLDGDAAARA 239 Query: 296 YAIKRSCENKADVVSQDEKESGVRATLNLGHTFGHAVETGVGYGQ-WLHGEAVAAGTVMA 354 +AI+ SCE KA +V+ DE ESG+R LNLGH+FGHA+E GYG LHGEAVA G VMA Sbjct: 240 HAIRVSCEAKAAIVAADETESGLRELLNLGHSFGHALEAEAGYGSALLHGEAVAIGMVMA 299 Query: 355 VDMSRRLGWIDDSLVQRVQKILQQAKLPTS--------PPETMTVEMFKSIMAVDKKVAD 406 D+S R+G + +R++ L A LP + P + + MA DKKV D Sbjct: 300 FDLSVRMGLCPAADARRLRDHLAAAGLPVTAAPLRAALPGGDWSPARLLAHMAKDKKVKD 359 Query: 407 GKLRLILLKG 416 G+L IL +G Sbjct: 360 GRLTFILARG 369 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: 401 Number of extensions: 10 Number of successful extensions: 4 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: 442 Length of database: 394 Length adjustment: 32 Effective length of query: 410 Effective length of database: 362 Effective search space: 148420 Effective search space used: 148420 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_012567831.1 RC1_RS12835 (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.22044.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-113 363.0 0.0 9.3e-113 362.8 0.0 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012567831.1 RC1_RS12835 3-dehydroquinate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012567831.1 RC1_RS12835 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.8 0.0 9.3e-113 9.3e-113 1 340 [. 34 385 .. 34 389 .. 0.96 Alignments for each domain: == domain 1 score: 362.8 bits; conditional E-value: 9.3e-113 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlv.lvvpdgeesKsle 66 y++ +g gl++++ + +a+ + l+v+td +v+ ++ + l++ l+++g++v + lvvp+ge +K++ lcl|NCBI__GCF_000016185.1:WP_012567831.1 34 YDILIGPGLIARAGRLIADrlPGRPLLVLTDATVAGHHLRPLLDGLAAAGAAVAEpLVVPAGEATKEMG 102 68999******9999999964449********************99999888765399*********** PP TIGR01357 67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135 ++++++d ll++++er+svlva+GGGvvgDl+GF+Aa+ lRGi++vqvPTtlla+vDssvGGKtg+n + lcl|NCBI__GCF_000016185.1:WP_012567831.1 103 RLSEVMDGLLARGIERRSVLVALGGGVVGDLGGFAAAIALRGIDFVQVPTTLLAQVDSSVGGKTGVNSR 171 ********************************************************************* PP TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204 +gkNliGaf+qP++Vl d++ l tlp+rel +G+aEv+K+g+i ++f++le + ++l+ + +a + lcl|NCBI__GCF_000016185.1:WP_012567831.1 172 HGKNLIGAFHQPRLVLADTAALDTLPRRELLAGYAEVVKYGMIDRPDFFDWLEAHGPAVLDG-DAAARA 239 *********************************************************99985.559999 PP TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271 ++i+ s+e Ka +V++De+esglR+lLN+GH++gHa+Ea+++y+ l HGeaVaiGmv+++ ls ++gl lcl|NCBI__GCF_000016185.1:WP_012567831.1 240 HAIRVSCEAKAAIVAADETESGLRELLNLGHSFGHALEAEAGYGsaLLHGEAVAIGMVMAFDLSVRMGL 308 *******************************************999*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk........klsveellkallkDKKnegskiklvlleeiGkaalas 332 ++a +++rl++ l ++glp++ + ++s ll+++ kDKK ++++++++l++ iG+a+ ++ lcl|NCBI__GCF_000016185.1:WP_012567831.1 309 CPAADARRLRDHLAAAGLPVTAAPlraalpggDWSPARLLAHMAKDKKVKDGRLTFILARGIGRAFRCR 377 **********************999******************************************99 PP TIGR01357 333 evteeell 340 +v + ++ lcl|NCBI__GCF_000016185.1:WP_012567831.1 378 DVAQADVA 385 88776655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (394 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: 12.84 // [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