Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_012115801.1 XAUT_RS19385 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q6G468 (294 letters) >NCBI__GCF_000017645.1:WP_012115801.1 Length = 299 Score = 368 bits (944), Expect = e-106 Identities = 180/290 (62%), Positives = 226/290 (77%), Gaps = 2/290 (0%) Query: 3 KGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIEL 62 +G+ TAL+TPF D GA+DEKAF FV+WQI +G +G+ PVGTTGESPTL+HEEH R++E Sbjct: 11 RGSFTALVTPFRD-GALDEKAFRAFVDWQIAEGTHGLVPVGTTGESPTLSHEEHNRVVEW 69 Query: 63 CVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSSI 122 V+Q A RVPV+AGAGSN+T+EAV LA+HA+K GADA+LVVTPYYN+P Q GLY HF +I Sbjct: 70 TVQQSAGRVPVMAGAGSNNTAEAVALAQHAQKVGADALLVVTPYYNKPTQEGLYQHFKAI 129 Query: 123 AKAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGKDF 182 A A+ +PI IYNIPSRSVIDM+VETM L + KNI GVKDAT + R S QR+ G DF Sbjct: 130 ANAVELPIFIYNIPSRSVIDMSVETMARLF-EIKNIAGVKDATANLARVSLQRQVLGPDF 188 Query: 183 VQLSGDDCTALGFNAHGGVGCISVSSNVAPKLCAQLHAACLCSDYKTALKLNDLLMPLNR 242 +QLSG+D TALGFNAHGG GCISV+SNVAP+LC+ ACL DYK AL + D+LMPL+ Sbjct: 189 IQLSGEDATALGFNAHGGQGCISVASNVAPRLCSDFQTACLSGDYKAALAIQDILMPLHT 248 Query: 243 AVFIEPSPAGIKYAAAKLGLCGTIVRSPIVPLSDTTKKIIDEALYHAGLL 292 A+F+E +PA KYA + LG R P+VP+S+TT+ ++ A+ HAGL+ Sbjct: 249 ALFVETNPAPTKYALSLLGKMSEEARLPMVPVSETTRAVVKSAMVHAGLI 298 Lambda K H 0.318 0.134 0.394 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: 281 Number of extensions: 10 Number of successful extensions: 3 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: 299 Length adjustment: 26 Effective length of query: 268 Effective length of database: 273 Effective search space: 73164 Effective search space used: 73164 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_012115801.1 XAUT_RS19385 (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.18279.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-106 340.6 0.0 3e-106 340.4 0.0 1.0 1 lcl|NCBI__GCF_000017645.1:WP_012115801.1 XAUT_RS19385 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017645.1:WP_012115801.1 XAUT_RS19385 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 340.4 0.0 3e-106 3e-106 2 283 .. 13 292 .. 12 295 .. 0.98 Alignments for each domain: == domain 1 score: 340.4 bits; conditional E-value: 3e-106 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 + tAl+TPf++ +d +a+ ++ qi++g+ ++v+vGtTGEs+tLs+eE+++v+e +v+ +++rvpv lcl|NCBI__GCF_000017645.1:WP_012115801.1 13 SFTALVTPFRDGA-LDEKAFRAFVDWQIAEGTHGLVPVGTTGESPTLSHEEHNRVVEWTVQQSAGRVPV 80 789******9877.******************************************************* PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 +aG+gsn+t+ea+ l+++a+k+g+d++lvvtPyYnkPtqeGly+hfkaia++velPi +Yn+PsR++++ lcl|NCBI__GCF_000017645.1:WP_012115801.1 81 MAGAGSNNTAEAVALAQHAQKVGADALLVVTPYYNKPTQEGLYQHFKAIANAVELPIFIYNIPSRSVID 149 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 +++et++rL+e ++i ++K+a+ +l+rvs ++ + df lsG+Da++l + a G++G iSVasnvap lcl|NCBI__GCF_000017645.1:WP_012115801.1 150 MSVETMARLFEIKNIAGVKDATANLARVSLQRQVLGPDFIQLSGEDATALGFNAHGGQGCISVASNVAP 218 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekke 277 ++++++ +a l gd++ a+ i+ l++l++alf+etNP p K+al llg + + e RlP+++ se ++ lcl|NCBI__GCF_000017645.1:WP_012115801.1 219 RLCSDFQTACLSGDYKAALAIQDILMPLHTALFVETNPAPTKYALSLLGKMSE-EARLPMVPVSETTRA 286 ***************************************************99.**************9 PP TIGR00674 278 klkevl 283 +k+++ lcl|NCBI__GCF_000017645.1:WP_012115801.1 287 VVKSAM 292 999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (299 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: 9.39 // [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