Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_017549000.1 C792_RS0108265 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q5HG25 (295 letters) >NCBI__GCF_000330705.1:WP_017549000.1 Length = 297 Score = 324 bits (831), Expect = 1e-93 Identities = 160/292 (54%), Positives = 212/292 (72%), Gaps = 1/292 (0%) Query: 2 THLFEGVGVALTTPFTNNKVNIEALKTHVNFLLENNAQAIIVNGTTAESPTLTTDEKERI 61 T +FEG+GVA+TTPF N+ ++ A + H+ +L+EN+AQA+I+NGTT ESPTL +E + Sbjct: 3 TVIFEGIGVAMTTPFRNDVIDYGAFRNHIEYLIENDAQALIINGTTGESPTLRAEEIREL 62 Query: 62 LKTVIDLVDKRVPVIAGTGTNDTEKSIQASIQAKALGADAIMLITPYYNKTNQRGLVKHF 121 L+ ++ VD RVPVIAGTGTN T SI+ + A+ +GADAIMLITPYYNK+NQRGL++HF Sbjct: 63 LRVGVETVDGRVPVIAGTGTNSTSASIELTKYAEKIGADAIMLITPYYNKSNQRGLIRHF 122 Query: 122 EAIADAVKLPVVLYNVPSRTNMTIEPETVEILSQHPYIVALKDATNDFEYLEEVKKRIDT 181 AIAD +LP VLYNVP RT MTIEPETV LS H IVALKDA D EY EV + Sbjct: 123 TAIADNTELPAVLYNVPGRTGMTIEPETVRELSTHRNIVALKDAVGDLEYTREVLALTEN 182 Query: 182 NSFALYSGNDDNVVEYYQRGGQGVISVIANVIPKEFQALYDAQQSG-LDIQDQFKPIGTL 240 F LYSGNDDN+ ++ + GG+G+ISV+ N+IP E Q +Y+ Q+G QD+F + + Sbjct: 183 QDFVLYSGNDDNMHDFVKLGGKGLISVVGNIIPGELQDVYERIQNGDASAQDRFNRVMPM 242 Query: 241 LSALSVDINPIPIKALTSYLGFGNYELRLPLVSLEDTDTKVLRETYDTFKAG 292 +SA+ VD+NPIP+KA+T+ LG+GN ELRLPL+ LE+ + ET F+ G Sbjct: 243 ISAVQVDVNPIPVKAMTAELGYGNNELRLPLIPLENDALDEVIETLRQFREG 294 Lambda K H 0.315 0.133 0.365 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: 324 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: 295 Length of database: 297 Length adjustment: 26 Effective length of query: 269 Effective length of database: 271 Effective search space: 72899 Effective search space used: 72899 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 WP_017549000.1 C792_RS0108265 (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.3869199.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-94 300.6 0.0 4.5e-94 300.5 0.0 1.0 1 NCBI__GCF_000330705.1:WP_017549000.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549000.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 300.5 0.0 4.5e-94 4.5e-94 4 285 .. 11 290 .. 8 291 .. 0.96 Alignments for each domain: == domain 1 score: 300.5 bits; conditional E-value: 4.5e-94 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgs 76 +A+ TPf++d +d+ a+ + ie++ie++ +a+++ GtTGEs+tL eE ++++v ve+v++rvpviaGtg+ NCBI__GCF_000330705.1:WP_017549000.1 11 VAMTTPFRNDV-IDYGAFRNHIEYLIENDAQALIINGTTGESPTLRAEEIRELLRVGVETVDGRVPVIAGTGT 82 8*********9.************************************************************* PP TIGR00674 77 nateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLa 149 n+t+ +ieltk aek+g+d+++++tPyYnk +q+Gl++hf aia+++elP++lYnvP+Rtg+ +epetv++L+ NCBI__GCF_000330705.1:WP_017549000.1 83 NSTSASIELTKYAEKIGADAIMLITPYYNKSNQRGLIRHFTAIADNTELPAVLYNVPGRTGMTIEPETVRELS 155 ************************************************************************* PP TIGR00674 150 eeveivaiKeasgdlervseikaea.kedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaaleg 221 ++ +iva+K+a gdle e+ a + ++df+++sG+D ++++++lG+kG+iSV++n++p el+++++ +++g NCBI__GCF_000330705.1:WP_017549000.1 156 THRNIVALKDAVGDLEYTREVLALTeNQDFVLYSGNDDNMHDFVKLGGKGLISVVGNIIPGELQDVYERIQNG 228 *******************9988762679****************************************9999 PP TIGR00674 222 dteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 d + a+ ++ +++++a+ ++ NPipvK++ a lg ++ elRlPL +l++++ +++ e+l++ NCBI__GCF_000330705.1:WP_017549000.1 229 DAS-AQDRFNRVMPMISAVQVDVNPIPVKAMTAELGYGNN-ELRLPLIPLENDALDEVIETLRQ 290 975.5677889***************************99.************99999998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (297 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: 10.61 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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