Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_057508811.1 ABB28_RS11735 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_001431535.1:WP_057508811.1 Length = 297 Score = 228 bits (580), Expect = 2e-64 Identities = 123/279 (44%), Positives = 166/279 (59%), Gaps = 2/279 (0%) Query: 2 IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61 ++G + AL TPF A G LD D +L+ L+ G +V G+TGE+ATL E+ Q++ Sbjct: 3 LSGLITALATPFRADGSLDTDGWQRLLHLQLEGGVRGVVVAGSTGEAATLSDAEYDQLLA 62 Query: 62 RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121 V+++ GR+PV+AGTG + T + + T A + GA L+VTP Y +PTQ G+ H+R Sbjct: 63 SAVERIAGRVPVLAGTGLSGTAKTIEQTRRAAAAGATHALVVTPPYVRPTQAGLIAHYRA 122 Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181 +A+ +P +LYNVPGRT CDMLPETV L+ PNI+GIKEA GD R K ++ G DF Sbjct: 123 VADHGGLPVVLYNVPGRTGCDMLPETVAELAAHPNIVGIKEAVGDNGRVKALLALRGDDF 182 Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHK 241 + SGDD TA + G G ISV +N P A +C A D A + + RL P H Sbjct: 183 AILSGDDGTAARSIQAGMDGLISVGSNALPGAYRRMCELAAAHDHDATESWDARLQPFHD 242 Query: 242 ALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEP 280 +E NPIPVK L +G I +RLPL LS H+P Sbjct: 243 FCGVEPNPIPVKALLRRIG-IGHDLRLPLLPLS-AAHQP 279 Lambda K H 0.319 0.134 0.393 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: 250 Number of extensions: 11 Number of successful extensions: 1 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: 292 Length of database: 297 Length adjustment: 26 Effective length of query: 266 Effective length of database: 271 Effective search space: 72086 Effective search space used: 72086 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_057508811.1 ABB28_RS11735 (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.25966.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-84 268.0 0.0 4.2e-84 267.7 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508811.1 ABB28_RS11735 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508811.1 ABB28_RS11735 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.7 0.0 4.2e-84 4.2e-84 2 278 .. 6 280 .. 5 286 .. 0.98 Alignments for each domain: == domain 1 score: 267.7 bits; conditional E-value: 4.2e-84 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 ++tAl TPf++dgs+d + ++l++ q+e gv ++vv+G+TGE+atLs E+ +++ ave ++rvpv lcl|NCBI__GCF_001431535.1:WP_057508811.1 6 LITALATPFRADGSLDTDGWQRLLHLQLEGGVRGVVVAGSTGEAATLSDAEYDQLLASAVERIAGRVPV 74 79******************************************************************* PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 +aGtg t+++ie t++a+ +g+ +lvvtP Y++Ptq Gl++h+ a+a++ lP++lYnvP+Rtg++ lcl|NCBI__GCF_001431535.1:WP_057508811.1 75 LAGTGLSGTAKTIEQTRRAAAAGATHALVVTPPYVRPTQAGLIAHYRAVADHGGLPVVLYNVPGRTGCD 143 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 + petv++La++++iv+iKea gd rv+ + a ++df++lsGdD ++ ++ G G+iSV sn +p lcl|NCBI__GCF_001431535.1:WP_057508811.1 144 MLPETVAELAAHPNIVGIKEAVGDNGRVKALLALRGDDFAILSGDDGTAARSIQAGMDGLISVGSNALP 212 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekke 277 + m++ a++ d + + +++l + ++ +e+NPipvK++l g+ + lRlPL +ls ++ lcl|NCBI__GCF_001431535.1:WP_057508811.1 213 GAYRRMCELAAAHDHDATESWDARLQPFHDFCGVEPNPIPVKALLRRIGIGHD--LRLPLLPLSAAHQP 279 *************************************************9877..********998876 PP TIGR00674 278 k 278 lcl|NCBI__GCF_001431535.1:WP_057508811.1 280 A 280 5 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.42 // [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