Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013075572.1 BTUS_RS07835 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000092905.1:WP_013075572.1 Length = 305 Score = 265 bits (677), Expect = 1e-75 Identities = 136/292 (46%), Positives = 184/292 (63%), Gaps = 1/292 (0%) Query: 3 QGSIVALITPF-KEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEF 61 +GSIV L+TPF +EG D + LI+F +++G+ I GTTGE +L+ EE E VIE Sbjct: 9 KGSIVPLVTPFDEEGRFDEKTFQRLIDFQIESGSHGISCTGTTGEPSSLSLEEREYVIET 68 Query: 62 AVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121 A++ GR+ V+ GTG N E + LT HA+ +GAD ALV+VPYYN+P+Q GLY +F+ + Sbjct: 69 AIRHVGGRVPVVPGTGTNNYEETLRLTRHAQRLGADAALVIVPYYNRPSQEGLYRYFRAL 128 Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181 A EVDIPIIIYNIP RT + T+ +L E +NI+ KES N +++S ++ G F Sbjct: 129 ADEVDIPIIIYNIPGRTATNMEPSTVARLRRESKNIIGIKESNKNFEQVSWVLHLNGRDF 188 Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241 V SG ++L PM+ LG G +S N++PREV L G + AR++HY L +L Sbjct: 189 LVYSGIETLCYPMLCLGGAGHVSATANLLPREVARLYDLTAAGRWEEARDLHYQLLELND 248 Query: 242 VLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLK 293 VLF+ETNP P+K A + GM R PL E SPEN K+R VL KY L K Sbjct: 249 VLFVETNPGPLKYAMGLAGMIHPRLRPPLCEPSPENREKIRTVLAKYGLLAK 300 Lambda K H 0.318 0.136 0.390 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: 217 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: 294 Length of database: 305 Length adjustment: 27 Effective length of query: 267 Effective length of database: 278 Effective search space: 74226 Effective search space used: 74226 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_013075572.1 BTUS_RS07835 (2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase)
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.6460.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-97 311.0 0.0 3.2e-97 310.8 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013075572.1 BTUS_RS07835 2,4-dihydroxyhept-2 Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013075572.1 BTUS_RS07835 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 310.8 0.0 3.2e-97 3.2e-97 2 285 .. 11 294 .. 10 295 .. 0.99 Alignments for each domain: == domain 1 score: 310.8 bits; conditional E-value: 3.2e-97 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 +++ l+TPf+e+g d +++++li++qie+g+ +i GtTGE +LsleE++ vie+a+ v +rvpv lcl|NCBI__GCF_000092905.1:WP_013075572.1 11 SIVPLVTPFDEEGRFDEKTFQRLIDFQIESGSHGISCTGTTGEPSSLSLEEREYVIETAIRHVGGRVPV 79 7899***************************************************************** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 + Gtg+n+ ee+++lt++a+ lg+d++lv++PyYn+P+qeGly++f a+a+ev++Pii+Yn+P+Rt+++ lcl|NCBI__GCF_000092905.1:WP_013075572.1 80 VPGTGTNNYEETLRLTRHAQRLGADAALVIVPYYNRPSQEGLYRYFRALADEVDIPIIIYNIPGRTATN 148 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 +ep tv+rL +e + i++iKe++++ e+vs + + + df v+sG ++l ++l+lG++G +S ++n++ lcl|NCBI__GCF_000092905.1:WP_013075572.1 149 MEPSTVARLRRESKnIIGIKESNKNFEQVSWVLHLNGRDFLVYSGIETLCYPMLCLGGAGHVSATANLL 217 **********99988****************************************************** PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p+e++ ++ +++g+ eear +h++ll+l ++lf+etNP p+K+a+ l+g+i+ +lR+PL+e s e++ lcl|NCBI__GCF_000092905.1:WP_013075572.1 218 PREVARLYDLTAAGRWEEARDLHYQLLELNDVLFVETNPGPLKYAMGLAGMIHP-RLRPPLCEPSPENR 285 ****************************************************98.************** PP TIGR00674 277 eklkevlke 285 ek++ vl++ lcl|NCBI__GCF_000092905.1:WP_013075572.1 286 EKIRTVLAK 294 ******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (305 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: 00:00:00.00 # Mc/sec: 9.69 // [ok]
This GapMind analysis is from Apr 10 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