Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 6939274 Sama_3367 3-dehydroquinate synthase (RefSeq)
Query= BRENDA::P07639 (362 letters) >FitnessBrowser__SB2B:6939274 Length = 359 Score = 438 bits (1127), Expect = e-128 Identities = 221/348 (63%), Positives = 263/348 (75%) Query: 1 MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60 M++I V L RSYPI I LF + F P+ SG++V++V+NET+APLYLDK+ L Sbjct: 1 MKQIQVDLANRSYPIHIGPNLFEDQELFAPVVSGKKVLVVSNETIAPLYLDKISATLSAR 60 Query: 61 GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120 V SVILPDGEQYK+L L+ +F ALL+ RD LVALGGGV+GD+TGFAAA YQR Sbjct: 61 AAQVASVILPDGEQYKTLDYLNEIFDALLEGNFARDCVLVALGGGVIGDMTGFAAACYQR 120 Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180 GV FIQ+PTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQP VV+D++CLKTLP RE A+ Sbjct: 121 GVDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPKLVVIDINCLKTLPAREFAA 180 Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240 G+AEVIKYGII D F WLE+N+ AL LD A+ + I RCCE+KAEVV+ DE E G+R Sbjct: 181 GMAEVIKYGIIRDSELFTWLEQNVSALKALDQDAIIHVIARCCEIKAEVVSEDETEQGVR 240 Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMV+AA+TS LG + RI L++ Sbjct: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVLAAQTSVTLGLIDKSILCRIAALIQAF 300 Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVS 348 LPV P M +++ HM RDKKVL G++RL+LPL IG +EV S S Sbjct: 301 DLPVQAPESMDFNSFIKHMRRDKKVLGGQLRLVLPLGIGAAEVSSQAS 348 Lambda K H 0.320 0.136 0.392 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: 334 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: 362 Length of database: 359 Length adjustment: 29 Effective length of query: 333 Effective length of database: 330 Effective search space: 109890 Effective search space used: 109890 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate 6939274 Sama_3367 (3-dehydroquinate synthase (RefSeq))
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.26868.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-126 406.8 0.0 4.4e-126 406.7 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6939274 Sama_3367 3-dehydroquinate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6939274 Sama_3367 3-dehydroquinate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.7 0.0 4.4e-126 4.4e-126 1 341 [. 13 354 .. 13 357 .. 0.96 Alignments for each domain: == domain 1 score: 406.7 bits; conditional E-value: 4.4e-126 TIGR01357 1 ykvkvgegllk..klveelaekasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKsletvaklldql 75 y++++g +l++ +l++ + + +k++v+++e+++ l+ +k++++l++++++v +++pdge++K+l+ ++++ d+l lcl|FitnessBrowser__SB2B:6939274 13 YPIHIGPNLFEdqELFAPVV-SGKKVLVVSNETIAPLYLDKISATLSARAAQVASVILPDGEQYKTLDYLNEIFDAL 88 68999999999534444444.479***************************************************** PP TIGR01357 76 leeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlplgkNliGafyqPkaVli 152 le ++ r+ vlva+GGGv+gD++GF+Aa y+RG++++q+PTtll++vDssvGGKt++n+plgkN+iGafyqPk+V+i lcl|FitnessBrowser__SB2B:6939274 89 LEGNFARDCVLVALGGGVIGDMTGFAAACYQRGVDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPKLVVI 165 ***************************************************************************** PP TIGR01357 153 dlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealeelikrsievKaevVeeDekesglRa 229 d+++l+tlp re+++GmaEviK+g+i d+elf++le+n ++l+ l +++a+ ++i+r++e+KaevV+eDe+e+g+Ra lcl|FitnessBrowser__SB2B:6939274 166 DINCLKTLPAREFAAGMAEVIKYGIIRDSELFTWLEQNVSALKAL-DQDAIIHVIARCCEIKAEVVSEDETEQGVRA 241 ****************************************88875.66***************************** PP TIGR01357 230 lLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllkaellerlvallkklglptklkkklsveellka 305 lLN+GHt+gHaiEa+++y+ + HGeaVa Gmv++a++s lgl+++++l r++al++++ lp++ ++++++++++k+ lcl|FitnessBrowser__SB2B:6939274 242 LLNLGHTFGHAIEAEMGYGnWLHGEAVAAGMVLAAQTSVTLGLIDKSILCRIAALIQAFDLPVQAPESMDFNSFIKH 318 ***************************************************************************** PP TIGR01357 306 llkDKKnegskiklvlleeiGkaalasevteeelle 341 + +DKK g++++lvl+ iG a+++s+ ++ el e lcl|FitnessBrowser__SB2B:6939274 319 MRRDKKVLGGQLRLVLPLGIGAAEVSSQASDAELAE 354 **************************9887777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (359 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: 00:00:00.01 # Mc/sec: 11.94 // [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