Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate CA265_RS02050 CA265_RS02050 4-hydroxy-tetrahydrodipicolinate synthase
Query= metacyc::BSU16770-MONOMER (290 letters) >FitnessBrowser__Pedo557:CA265_RS02050 Length = 295 Score = 226 bits (576), Expect = 5e-64 Identities = 116/288 (40%), Positives = 176/288 (61%) Query: 3 FGNVSTAMITPFDNKGNVDFQKLSTLIDYLLKNGTDSLVVAGTTGESPTLSTEEKIALFE 62 F A++TPF+ G+VD+ L LI++L+ G D LV GTTGE+ T++ +EK ++ Sbjct: 4 FQGTGVALVTPFNTDGSVDYNGLKNLINHLVDGGIDYLVSLGTTGETATMTKDEKKKVWA 63 Query: 63 YTVKEVNGRVPVIAGTGSNNTKDSIKLTKKAEEAGVDAVMLVTPYYNKPSQEGMYQHFKA 122 YT + N R+P++AG G NNT + K + AG A++ V+PYYNKP+QEG+YQH+K Sbjct: 64 YTAEINNNRLPLVAGIGGNNTLAVAEDIKSLDAAGYSAILSVSPYYNKPTQEGIYQHYKY 123 Query: 123 IAAETSLPVMLYNVPGRTVASLAPETTIRLAADIPNVVAIKEASGDLEAITKIIAETPED 182 +A + L ++LYNVPGRT ++++PETT RLA D N++A KEASG + +I+ + P D Sbjct: 124 LAEISPLDLILYNVPGRTGSNMSPETTCRLAHDFKNIIATKEASGSFDQFNQIMRDKPAD 183 Query: 183 FYVYSGDDALTLPILSVGGRGVVSVASHIAGTDMQQMIKNYTNGQTANAALIHQKLLPIM 242 F + SGDD +TLP++++G G++SV + M+K G A H L+ Sbjct: 184 FLLISGDDPVTLPMIALGAAGIISVIGNALPKQFSDMVKLCLAGDYKAALPAHLGLIEFT 243 Query: 243 KELFKAPNPAPVKTALQLRGLDVGSVRLPLVPLTEDERLSLSSTISEL 290 + F NPA +K AL+ G+ +VRLPLV + S+ + I +L Sbjct: 244 RLAFAEGNPAGIKAALKHLGVCGDTVRLPLVKASASLEKSIIAEIEKL 291 Lambda K H 0.313 0.131 0.356 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: 260 Number of extensions: 8 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: 290 Length of database: 295 Length adjustment: 26 Effective length of query: 264 Effective length of database: 269 Effective search space: 71016 Effective search space used: 71016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate CA265_RS02050 CA265_RS02050 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.16604.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-94 300.9 0.0 3.9e-94 300.7 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS02050 CA265_RS02050 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS02050 CA265_RS02050 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 300.7 0.0 3.9e-94 3.9e-94 4 281 .. 9 286 .. 6 291 .. 0.98 Alignments for each domain: == domain 1 score: 300.7 bits; conditional E-value: 3.9e-94 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpvi 71 +Al+TPf+ dgsvd++ l++li+++++ g+d +v++GtTGE+at++++Ekkkv +++e+++nr+p++ lcl|FitnessBrowser__Pedo557:CA265_RS02050 9 VALVTPFNTDGSVDYNGLKNLINHLVDGGIDYLVSLGTTGETATMTKDEKKKVWAYTAEINNNRLPLV 76 7******************************************************************* PP TIGR00674 72 aGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 aG+g+n+t + e +k ++ +g +++l+v+PyYnkPtqeG+y+h+k +ae + l +ilYnvP+Rtg + lcl|FitnessBrowser__Pedo557:CA265_RS02050 77 AGIGGNNTLAVAEDIKSLDAAGYSAILSVSPYYNKPTQEGIYQHYKYLAEISPLDLILYNVPGRTGSN 144 ******************************************************************** PP TIGR00674 140 lepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnv 206 ++pet+ rLa++ + i+a Keasg+ +++++i++ +++df + sGdD +tl+++alGa+G+iSV++n lcl|FitnessBrowser__Pedo557:CA265_RS02050 145 MSPETTCRLAHDFKnIIATKEASGSFDQFNQIMRDKPADFLLISGDDPVTLPMIALGAAGIISVIGNA 212 ***********9988***************************************************** PP TIGR00674 207 apkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelsee 274 +pk++++mvk l+gd++ a+ h l++ + f e NP ++K+al+ lg++ ++RlPL+++s + lcl|FitnessBrowser__Pedo557:CA265_RS02050 213 LPKQFSDMVKLCLAGDYKAALPAHLGLIEFTRLAFAEGNPAGIKAALKHLGVCGD-TVRLPLVKASAS 279 *****************************************************98.**********99 PP TIGR00674 275 kkeklke 281 ++++ + lcl|FitnessBrowser__Pedo557:CA265_RS02050 280 LEKSIIA 286 9887654 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (295 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: 6.48 // [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