Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate GFF2865 PS417_14640 dihydrodipicolinate synthase
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__WCS417:GFF2865 Length = 287 Score = 153 bits (387), Expect = 4e-42 Identities = 94/285 (32%), Positives = 146/285 (51%), Gaps = 8/285 (2%) Query: 2 FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61 F+G++ ++TPF + +DF GL ++ L+E V+GI+ TTGE+ LS +E V++ Sbjct: 4 FQGIWVPVVTPFHDGAIDFTGLHRLVSHLLEKHVAGIMVCTTTGEAAALSRQEQLAVLDA 63 Query: 62 VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSI---TPYYNKPTQEGLRKHF 118 V+ V V+ AG N IEL F ++ V + P Y +P+Q GL F Sbjct: 64 VLQWVPAHRVVMGLAGYN----QIELLQFQREILQRPVAGLLVPAPSYIRPSQAGLEAFF 119 Query: 119 GKVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK 178 VA++ ++PI+LY++P RT E T+ L + I A+K+ NL L+ Sbjct: 120 RTVADASSVPIILYDIPYRTGATFEQATL-LNIVAHERIVAIKDCGGNLGNTLALLASGD 178 Query: 179 ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLM 238 + VL G D + LG G I+ A++ ++FV + + +AR ++L PL+ Sbjct: 179 VEVLCGEDVQIFNALCLGATGAIAASAHLQTEQFVALCQLVRDNQLAEARATFFELLPLI 238 Query: 239 KAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVL 283 AMF+E NP PVK AL + G ELR P+ S L+ VL Sbjct: 239 NAMFMEPNPAPVKAALALQGLIGSELRAPMQAASTAVVARLQQVL 283 Lambda K H 0.315 0.135 0.374 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: 192 Number of extensions: 8 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: 289 Length of database: 287 Length adjustment: 26 Effective length of query: 263 Effective length of database: 261 Effective search space: 68643 Effective search space used: 68643 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: 42 (22.0 bits) S2: 47 (22.7 bits)
Align candidate GFF2865 PS417_14640 (dihydrodipicolinate 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.12753.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-71 224.2 0.0 9e-71 224.0 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF2865 PS417_14640 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF2865 PS417_14640 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 224.0 0.0 9e-71 9e-71 4 284 .. 9 284 .. 6 286 .. 0.97 Alignments for each domain: == domain 1 score: 224.0 bits; conditional E-value: 9e-71 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsna 78 + ++TPf++ +df+ l++l+++++ek+v +i+v+ tTGE+a+Ls +E+ +v+ +++ v +v+ G ++ + lcl|FitnessBrowser__WCS417:GFF2865 9 VPVVTPFHDGA-IDFTGLHRLVSHLLEKHVAGIMVCTTTGEAAALSRQEQLAVLDAVLQWVPA-HRVVMGLAGYN 81 668****8877.*************************************************98.99********* PP TIGR00674 79 teeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve 153 e +++ +e+ + +v+g+lv +P+Y +P+q Gl ++f ++a+++++PiilY++P Rtg+ +e+ t+++++++++ lcl|FitnessBrowser__WCS417:GFF2865 82 QIELLQFQREILQRPVAGLLVPAPSYIRPSQAGLEAFFRTVADASSVPIILYDIPYRTGATFEQATLLNIVAHER 156 *************************************************************************** PP TIGR00674 154 ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeare 228 ivaiK+++g+l + + a + d++vl+G+D+ + l+lGa+G i +++ ++++ +++ + +++ +ear lcl|FitnessBrowser__WCS417:GFF2865 157 IVAIKDCGGNLGNTLALLA--SGDVEVLCGEDVQIFNALCLGATGAIAASAHLQTEQFVALCQLVRDNQLAEARA 229 ************9999988..569*************************************************** PP TIGR00674 229 ihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284 +ll+l++a+f+e+NP pvK+alal+gli + elR P+ ++s+ +l++vl+ lcl|FitnessBrowser__WCS417:GFF2865 230 TFFELLPLINAMFMEPNPAPVKAALALQGLIGS-ELRAPMQAASTAVVARLQQVLN 284 ********************************9.***********99999999985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (287 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: 10.87 // [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