Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_028486352.1 B076_RS0105040 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_000483485.1:WP_028486352.1 Length = 291 Score = 362 bits (929), Expect = e-105 Identities = 181/291 (62%), Positives = 226/291 (77%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 M GSMVALVTP +D+ SL KLV+FH+ GT+AIVAVGTTGESATLD++EH +V+ Sbjct: 1 MFRGSMVALVTPMLEDESIDYKSLEKLVEFHIASGTDAIVAVGTTGESATLDMQEHCEVV 60 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120 + VVD+V RIPVIAGTGANST EA+ LT+ AK GADACLLVTPYYNKPTQEG+Y H++ Sbjct: 61 KFVVDKVNKRIPVIAGTGANSTTEAIELTQCAKKAGADACLLVTPYYNKPTQEGLYLHYK 120 Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180 IAE V IPQILYNVPGRT+CD+LPETV RL+K+ NIIGIKEATGD+ R ++ V + Sbjct: 121 KIAETVDIPQILYNVPGRTACDLLPETVIRLAKIKNIIGIKEATGDIGRIAQIKAGVSDE 180 Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240 F +Y+GDDATAV+ +L GG G ISVTANV P+ + ++ AA+ GD+ A+ ++ L LH Sbjct: 181 FDLYTGDDATAVDFILAGGHGGISVTANVTPKLLHEVYFAALEGDSEKAKRLDAPLTGLH 240 Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291 + LF+E+NPIPVKWAL EMGLI IRLP+T LS + H +R AM+Q GV+ Sbjct: 241 RDLFVEANPIPVKWALAEMGLIGHAIRLPMTQLSEKYHAVVRAAMQQAGVV 291 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: 273 Number of extensions: 8 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: 291 Length adjustment: 26 Effective length of query: 266 Effective length of database: 265 Effective search space: 70490 Effective search space used: 70490 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_028486352.1 B076_RS0105040 (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.12624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-118 379.3 0.1 4.8e-118 379.1 0.1 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028486352.1 B076_RS0105040 4-hydroxy-tetrahy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028486352.1 B076_RS0105040 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.1 0.1 4.8e-118 4.8e-118 2 285 .. 5 287 .. 4 288 .. 0.99 Alignments for each domain: == domain 1 score: 379.1 bits; conditional E-value: 4.8e-118 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 +++Al+TP+ ed+s+d+++lekl+e++i++g+daiv+vGtTGEsatL ++E+ +v++++v+ v++r+pv lcl|NCBI__GCF_000483485.1:WP_028486352.1 5 SMVALVTPMLEDESIDYKSLEKLVEFHIASGTDAIVAVGTTGESATLDMQEHCEVVKFVVDKVNKRIPV 73 799****************************************************************** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 iaGtg+n+t+eaielt+ a+k+g+d++l+vtPyYnkPtqeGly h+k+iae+v++P+ilYnvP+Rt+++ lcl|NCBI__GCF_000483485.1:WP_028486352.1 74 IAGTGANSTTEAIELTQCAKKAGADACLLVTPYYNKPTQEGLYLHYKKIAETVDIPQILYNVPGRTACD 142 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 l petv+rLa+ ++i++iKea+gd+ r+ +ika ++++f +++GdDa++ ++++ G++G iSV++nv+p lcl|NCBI__GCF_000483485.1:WP_028486352.1 143 LLPETVIRLAKIKNIIGIKEATGDIGRIAQIKAGVSDEFDLYTGDDATAVDFILAGGHGGISVTANVTP 211 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekke 277 k+l+e++ aalegd e+a+ +++ l+ l++ lf+e+NPipvK+ala +gli + ++RlP+t+lse+ + lcl|NCBI__GCF_000483485.1:WP_028486352.1 212 KLLHEVYFAALEGDSEKAKRLDAPLTGLHRDLFVEANPIPVKWALAEMGLIGH-AIRLPMTQLSEKYHA 279 *****************************************************.**************9 PP TIGR00674 278 klkevlke 285 +++++++ lcl|NCBI__GCF_000483485.1:WP_028486352.1 280 VVRAAMQQ 287 99999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (291 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: 00:00:00.00 # Mc/sec: 10.96 // [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