Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 5209914 Shew_2362 dihydrodipicolinate synthase (RefSeq)
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__PV4:5209914 Length = 304 Score = 150 bits (380), Expect = 3e-41 Identities = 90/287 (31%), Positives = 159/287 (55%), Gaps = 4/287 (1%) Query: 2 FKGVYPAIITPFKNK-EVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIE 60 ++GV+PAI T F + ++++ + LI +G+ G++A+GT GE+ +LS EE ++ I+ Sbjct: 5 WQGVFPAISTQFNDDGSINYESNARMLEDLIRDGIDGVIALGTIGENASLSPEEKREFIK 64 Query: 61 KVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGK 120 V+ VNGR+ V++G N ++A + + E +G D ++ + + T + H+ Sbjct: 65 HTVETVNGRILVLSGCTENTAQQAAKYAQDVEALGVDGLMLLPAMVYRGTDREVIAHYQH 124 Query: 121 VAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSEL--IHDAK 178 VA S LPI++YN P V++ + +LAEE NI A+KE+ + +++EL + Sbjct: 125 VARSTKLPIMIYNNPVGYGVDINLEMTAVLAEE-PNIVAIKESTTDTRRLTELQSRFGDR 183 Query: 179 ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLM 238 +L G D++ L I LG G IS + N+ P+E V + A G E+AREI+ PL+ Sbjct: 184 FNILCGVDDIALESILLGATGWISGLTNVFPRESVTLFKLARAGRIEEAREIYRWFMPLL 243 Query: 239 KAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKD 285 + I T +K A ++GR + +RLP + + + +E V+ + Sbjct: 244 RLDTIPTLVQCIKFAEQIVGRGSENVRLPRMTLIGDERAYVEKVMAE 290 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: 215 Number of extensions: 9 Number of successful extensions: 2 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: 304 Length adjustment: 26 Effective length of query: 263 Effective length of database: 278 Effective search space: 73114 Effective search space used: 73114 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: 48 (23.1 bits)
Align candidate 5209914 Shew_2362 (dihydrodipicolinate synthase (RefSeq))
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.17652.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-66 209.6 0.0 2.5e-66 209.4 0.0 1.0 1 lcl|FitnessBrowser__PV4:5209914 Shew_2362 dihydrodipicolinate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209914 Shew_2362 dihydrodipicolinate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 209.4 0.0 2.5e-66 2.5e-66 2 285 .. 8 290 .. 7 291 .. 0.98 Alignments for each domain: == domain 1 score: 209.4 bits; conditional E-value: 2.5e-66 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsnat 79 v +A+ T f++dgs+ +++ ++++e +i+ g+d+++++Gt GE a+Ls eEk + i+ +ve+v++r+ v++G++ n+ lcl|FitnessBrowser__PV4:5209914 8 VFPAISTQFNDDGSINYESNARMLEDLIRDGIDGVIALGTIGENASLSPEEKREFIKHTVETVNGRILVLSGCTENTA 85 789*************************************************************************** PP TIGR00674 80 eeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeveivai 157 ++a + ++ +e lgvdg+++ + + t + +++h++ +a +++lPi++Yn+P gv+++ e+++ Laee++ivai lcl|FitnessBrowser__PV4:5209914 86 QQAAKYAQDVEALGVDGLMLLPAMVYRGTDREVIAHYQHVARSTKLPIMIYNNPVGYGVDINLEMTAVLAEEPNIVAI 163 ****************************************************************************** PP TIGR00674 158 KeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihqkllk 235 Ke+++d +r++e++++ ++ f++l+G D ++le ++lGa+G+iS ++nv p+e + k a +g++eearei + +++ lcl|FitnessBrowser__PV4:5209914 164 KESTTDTRRLTELQSRFGDRFNILCGVDDIALESILLGATGWISGLTNVFPRESVTLFKLARAGRIEEAREIYRWFMP 241 ****************************************************************************** PP TIGR00674 236 lfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 l++ i t +K a ++ g + ++RlP ++l +++ +++v++e lcl|FitnessBrowser__PV4:5209914 242 LLRLDTIPTLVQCIKFAEQIVGRGSE-NVRLPRMTLIGDERAYVEKVMAE 290 **99999999999**********999.*********99999999999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (304 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: 7.37 // [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