Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_011424717.1 RHE_RS07055 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q8UGL3 (294 letters) >NCBI__GCF_000092045.1:WP_011424717.1 Length = 294 Score = 493 bits (1269), Expect = e-144 Identities = 239/294 (81%), Positives = 269/294 (91%) Query: 1 MFKGSIPALITPFTDNGSVDEKAFAAHVEWQIAEGSNGLVPVGTTGESPTLSHDEHKRVV 60 MF GSIPAL+TPFTD G +DE +FAAHV+WQI EGS+GLVPVGTTGESPTLSH EHKRVV Sbjct: 1 MFNGSIPALVTPFTDAGLIDEASFAAHVDWQIKEGSSGLVPVGTTGESPTLSHAEHKRVV 60 Query: 61 ELCIEVAAKRVPVIAGAGSNNTDEAIELALHAQEAGADALLVVTPYYNKPTQKGLFAHFS 120 ELCIEVAAKRVPV+AGAGSNNT EA+ELA HAQ+ GADA+LVVTPYYNKPTQKGL AHFS Sbjct: 61 ELCIEVAAKRVPVMAGAGSNNTREAVELAQHAQKVGADAVLVVTPYYNKPTQKGLIAHFS 120 Query: 121 AVAEAVKLPIVIYNIPPRSVVDMSPETMGALVKAHKNIIGVKDATGKLDRVSEQRISCGK 180 A+AEAV LPI IYNIP RSV+DM+PETMGAL +AH NI+GVKDATGK++RVSEQRI+CGK Sbjct: 121 AIAEAVALPIYIYNIPGRSVIDMTPETMGALARAHSNIVGVKDATGKIERVSEQRITCGK 180 Query: 181 DFVQLSGEDGTALGFNAHGGVGCISVTANVAPRLCSEFQAAMLAGDYAKALEYQDRLMPL 240 DF QLSGED TALGFNAHGGVGCISVTANVAPRLC++FQAA LAG+YA+ALEYQDRLMPL Sbjct: 181 DFRQLSGEDATALGFNAHGGVGCISVTANVAPRLCADFQAATLAGEYARALEYQDRLMPL 240 Query: 241 HRAIFMEPGVCGTKYALSKTRGGNRRVRSPLMSTLEPATEAAIDAALKHAGLMN 294 H+AIF+EPG+CG KY LS+ +R VRSPL+STLEPATEAAIDAA++HAGL+N Sbjct: 241 HKAIFLEPGLCGAKYGLSRLGRMSRNVRSPLLSTLEPATEAAIDAAMRHAGLLN 294 Lambda K H 0.317 0.133 0.384 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: 387 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: 294 Length of database: 294 Length adjustment: 26 Effective length of query: 268 Effective length of database: 268 Effective search space: 71824 Effective search space used: 71824 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: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_011424717.1 RHE_RS07055 (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.3496.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-97 310.4 0.0 4.5e-97 310.3 0.0 1.0 1 lcl|NCBI__GCF_000092045.1:WP_011424717.1 RHE_RS07055 4-hydroxy-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092045.1:WP_011424717.1 RHE_RS07055 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 310.3 0.0 4.5e-97 4.5e-97 1 278 [. 4 282 .. 4 290 .. 0.96 Alignments for each domain: == domain 1 score: 310.3 bits; conditional E-value: 4.5e-97 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 g+++Al+TPf + g +d a+++ ++ qi++g++++v+vGtTGEs+tLs+ E+k+v+e+ +e++++rvp lcl|NCBI__GCF_000092045.1:WP_011424717.1 4 GSIPALVTPFTDAGLIDEASFAAHVDWQIKEGSSGLVPVGTTGESPTLSHAEHKRVVELCIEVAAKRVP 72 589****************************************************************** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 v+aG+gsn+t+ea+el+++a+k+g+d+vlvvtPyYnkPtq+Gl++hf aiae+v lPi +Yn+P+R+++ lcl|NCBI__GCF_000092045.1:WP_011424717.1 73 VMAGAGSNNTREAVELAQHAQKVGADAVLVVTPYYNKPTQKGLIAHFSAIAEAVALPIYIYNIPGRSVI 141 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnv 206 +++pet+ +La+ ++ iv++K+a+g++ervse + + ++df+ lsG+Da++l + a G+ G iSV++nv lcl|NCBI__GCF_000092045.1:WP_011424717.1 142 DMTPETMGALARAHSnIVGVKDATGKIERVSEQRITCGKDFRQLSGEDATALGFNAHGGVGCISVTANV 210 ***********98877***************************************************** PP TIGR00674 207 apkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtel.see 274 ap++++++ +a+l+g++++a+e + +l++l+ka+f+e+ + K+ l lg + ++R PL + + lcl|NCBI__GCF_000092045.1:WP_011424717.1 211 APRLCADFQAATLAGEYARALEYQDRLMPLHKAIFLEPGLCGAKYGLSRLGRMSR-NVRSPLLSTlEPA 278 ******************************************************9.*****86540444 PP TIGR00674 275 kkek 278 ++ lcl|NCBI__GCF_000092045.1:WP_011424717.1 279 TEAA 282 4444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (294 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: 7.77 // [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