Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Pf1N1B4_5813 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= SwissProt::Q9X1K9 (294 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 Length = 291 Score = 161 bits (408), Expect = 1e-44 Identities = 100/289 (34%), Positives = 157/289 (54%), Gaps = 11/289 (3%) Query: 2 FRGVGTAIVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSR 61 F+G+ IVTPF +G +D RLV + LE GV+ ++V GTTGE+ + + E+ ++ Sbjct: 4 FQGIWVPIVTPFHDGAIDFAGLRRLVSHLLEKGVDGIVVCGTTGEAAALGKHEQLAVLDA 63 Query: 62 TLEIVDGKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQEGLYQHYKYI 121 LE+V + V++G N+ + L+ + K G+LV PYY +P+Q GL +K + Sbjct: 64 VLELVPPE-RVVMGLAGNNLAELLQFQSEILKRPLAGLLVPPPYYIRPSQAGLEAFFKTV 122 Query: 122 SERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEA--NPDIDQIDRTVSLTKQ 179 ++ + + +++Y++P RTG+ T RI A + +V IK+ NP T++L Sbjct: 123 ADASSVPVILYDIPYRTGIAFEQATLLRIVAH-ERIVAIKDCGGNPAT-----TLALLSS 176 Query: 180 ARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKL 239 + D V G D + F LC G G I+ ++V P+ V L + L R +L Sbjct: 177 GKVD--VLCGEDHQIFGALCLGATGAIAASAHVHPELFVALYQQIRDNQLAVGRATFFQL 234 Query: 240 RPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVL 288 PL+ +LF+E NP PVK AL L G I +ELR P+ +SE T L+ VL Sbjct: 235 LPLIHSLFIEPNPAPVKTALALEGLIRDELRSPMQRSSETTAVRLKEVL 283 Lambda K H 0.316 0.135 0.378 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: 194 Number of extensions: 5 Number of successful extensions: 3 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: 294 Length of database: 291 Length adjustment: 26 Effective length of query: 268 Effective length of database: 265 Effective search space: 71020 Effective search space used: 71020 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 (21.5 bits) S2: 48 (23.1 bits)
Align candidate Pf1N1B4_5813 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
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.14592.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-76 240.6 0.0 9e-76 240.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 240.4 0.0 9e-76 9e-76 4 284 .. 9 284 .. 6 286 .. 0.96 Alignments for each domain: == domain 1 score: 240.4 bits; conditional E-value: 9e-76 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknr 67 + ++TPf++ +dfa l +l+++++ekgvd+ivv+GtTGE+a+L + E+ +v+ ++elv lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 9 VPIVTPFHDGA-IDFAGLRRLVSHLLEKGVDGIVVCGTTGEAAALGKHEQLAVLDAVLELVPP- 70 679****8877.*************************************************97. PP TIGR00674 68 vpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYn 131 +v+ G ++n+++e +++ +e+ k + +g+lv PyY +P+q Gl ++fk++a+++++P+ilY+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 71 ERVVMGLAGNNLAELLQFQSEILKRPLAGLLVPPPYYIRPSQAGLEAFFKTVADASSVPVILYD 134 89************************************************************** PP TIGR00674 132 vPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalG 195 +P Rtg+ +e+ t++r++++++ivaiK+++g+ + + + + ++ vl+G+D+ l+lG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 135 IPYRTGIAFEQATLLRIVAHERIVAIKDCGGNPATTLALLS--SGKVDVLCGEDHQIFGALCLG 196 *******************************8776666665..668****************** PP TIGR00674 196 akGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgli 259 a+G i ++v p+++ +++++ +++ + r +ll+l++ lfie+NP pvKtalal+gli lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 197 ATGAIAASAHVHPELFVALYQQIRDNQLAVGRATFFQLLPLIHSLFIEPNPAPVKTALALEGLI 260 **************************************************************** PP TIGR00674 260 ekdelRlPLtelseekkeklkevlk 284 elR P+ se + +lkevl+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5813 261 RD-ELRSPMQRSSETTAVRLKEVLA 284 *9.******************9996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (291 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: 11.14 // [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