Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_066923524.1 ACG33_RS14440 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_001579945.1:WP_066923524.1 Length = 367 Score = 396 bits (1018), Expect = e-115 Identities = 195/359 (54%), Positives = 261/359 (72%), Gaps = 6/359 (1%) Query: 81 VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140 V++DLG RSYPI IG L+D LL RH+ + +L+V+NTTVAPLYL + +L + Sbjct: 6 VDIDLGVRSYPILIGPDLIDDESLLARHVQARNLLIVSNTTVAPLYLQRLQHSLGERR-- 63 Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200 V SVILPDGEQ K +E++ + D IE RL+R +ALGGGVIGDM G+AAA Y RG Sbjct: 64 --VGSVILPDGEQHKTLESMALIIDALIEQRLNRDAAVLALGGGVIGDMAGFAAACYQRG 121 Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260 ++++Q+PTT++AQVDSSVGGKTG+NHP KNMIGAF+QP+CV+ DT L +L +RE +G Sbjct: 122 IDYVQVPTTLLAQVDSSVGGKTGVNHPQAKNMIGAFHQPRCVIADTRVLRSLAEREYRAG 181 Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320 +AE+IKYG+I DA +W EQ+ LLAR+ A YA++RSCE KA VV+ DE+E G+RA Sbjct: 182 IAEIIKYGMIHDAALLDWLEQSAEALLAREDEAIMYAVRRSCEIKAAVVAIDEREQGLRA 241 Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380 LNLGHTFGHA+ET GYG+WLHGEAVAAG V+A DMSRRLGW+ ++ +R+ ++L++ Sbjct: 242 ILNLGHTFGHAIETATGYGRWLHGEAVAAGMVIAADMSRRLGWLHEADCERLIRLLRRFG 301 Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRAF 439 LP P + + + +M +DKKV DG++RL+LL LG DY +ALD +LRA+ Sbjct: 302 LPVDAPH-IGAQRARDLMGLDKKVLDGRIRLVLLP-QLGQAQVVSDYTSEALDASLRAY 358 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: 416 Number of extensions: 12 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: 367 Length adjustment: 31 Effective length of query: 411 Effective length of database: 336 Effective search space: 138096 Effective search space used: 138096 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_066923524.1 ACG33_RS14440 (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.24987.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-120 388.2 0.0 2e-120 388.0 0.0 1.0 1 lcl|NCBI__GCF_001579945.1:WP_066923524.1 ACG33_RS14440 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001579945.1:WP_066923524.1 ACG33_RS14440 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.0 0.0 2e-120 2e-120 1 340 [. 15 352 .. 15 356 .. 0.95 Alignments for each domain: == domain 1 score: 388.0 bits; conditional E-value: 2e-120 TIGR01357 1 ykvkvgegllkklveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletv 68 y++ +g +l++ + ++ +a++l+++++ +v+ l+ ++l++ l + +v +++pdge++K+le++ lcl|NCBI__GCF_001579945.1:WP_066923524.1 15 YPILIGPDLIDDESLLARHvQARNLLIVSNTTVAPLYLQRLQHSLGE--RRVGSVILPDGEQHKTLESM 81 57889999999554444445679********************9977..99****************** PP TIGR01357 69 aklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplg 137 a ++d+l+e+ l+r+ +++a+GGGv+gD+aGF+Aa y+RGi++vqvPTtlla+vDssvGGKtg+n+p+ lcl|NCBI__GCF_001579945.1:WP_066923524.1 82 ALIIDALIEQRLNRDAAVLALGGGVIGDMAGFAAACYQRGIDYVQVPTTLLAQVDSSVGGKTGVNHPQA 150 ********************************************************************* PP TIGR01357 138 kNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeel 206 kN+iGaf+qP+ V+ d++vl++l+ere+r+G+aE+iK+g+i+da+l+++le+ +++ll + e ea+ + lcl|NCBI__GCF_001579945.1:WP_066923524.1 151 KNMIGAFHQPRCVIADTRVLRSLAEREYRAGIAEIIKYGMIHDAALLDWLEQSAEALLAR-EDEAIMYA 218 *******************************************************99975.6699**** PP TIGR01357 207 ikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllka 274 ++rs+e+Ka vV+ De+e+glRa+LN+GHt+gHaiE++++y+ + HGeaVa Gmv++a +s++lg l++ lcl|NCBI__GCF_001579945.1:WP_066923524.1 219 VRRSCEIKAAVVAIDEREQGLRAILNLGHTFGHAIETATGYGrWLHGEAVAAGMVIAADMSRRLGWLHE 287 ********************************************************************* PP TIGR01357 275 ellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevteeell 340 + erl++ll+++glp++ ++ + ++ + + + DKK +++i+lvll ++G+a++ s++t+e+l lcl|NCBI__GCF_001579945.1:WP_066923524.1 288 ADCERLIRLLRRFGLPVDAPH-IGAQRARDLMGLDKKVLDGRIRLVLLPQLGQAQVVSDYTSEALD 352 ********************7.**********************************9999888765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (367 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: 10.86 // [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