Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate WP_011306166.1 MBAR_RS06160 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::Q57695 (289 letters) >NCBI__GCF_000195895.1:WP_011306166.1 Length = 291 Score = 276 bits (706), Expect = 4e-79 Identities = 145/293 (49%), Positives = 205/293 (69%), Gaps = 7/293 (2%) Query: 1 MFKGVYPAIITPF-KNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVI 59 MF+G PA+ITPF K+ +D +GL+ NI F+ E GV+GIV GTTGES TLS EH++VI Sbjct: 1 MFEGAMPALITPFTKDDRIDREGLQRNIEFVEEGGVAGIVPCGTTGESATLSALEHEEVI 60 Query: 60 EKVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFG 119 + V+ +V VIAG GSN T EA++ + A D G D VL I+PYYNKP GL HF Sbjct: 61 DIAVEC--SKVPVIAGTGSNNTGEALQFTKHAADAGVDGVLLISPYYNKPNPAGLLTHFK 118 Query: 120 KVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIH---D 176 K+AE++++P+V+YN+PSRT ++ + + LA+ NI +KEA+ N+ +VS+++ D Sbjct: 119 KIAEAVDVPMVMYNIPSRTGQDMPLEVIVELAK-VENIVGIKEASGNIGKVSQILENTID 177 Query: 177 AKITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFP 236 V+SG D LTLPI+++GG+GVISV ANIVP MVN AL GD+E AR+IH+++ P Sbjct: 178 EDFVVISGEDNLTLPILSVGGQGVISVAANIVPDRMSRMVNAALAGDYETARKIHFEIAP 237 Query: 237 LMKAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDLGLI 289 L++A+F+ETNPIPVK A + G +G LRLPL +SE + + + + L+ LG+I Sbjct: 238 LIRALFLETNPIPVKKAAELAGLASGNLRLPLAPLSETNTQKVADELRKLGVI 290 Lambda K H 0.315 0.135 0.374 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: 278 Number of extensions: 10 Number of successful extensions: 4 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: 289 Length of database: 291 Length adjustment: 26 Effective length of query: 263 Effective length of database: 265 Effective search space: 69695 Effective search space used: 69695 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: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate WP_011306166.1 MBAR_RS06160 (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.2604.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-109 351.3 0.1 1.7e-109 351.1 0.1 1.0 1 lcl|NCBI__GCF_000195895.1:WP_011306166.1 MBAR_RS06160 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011306166.1 MBAR_RS06160 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.1 0.1 1.7e-109 1.7e-109 2 285 .. 5 286 .. 4 287 .. 0.98 Alignments for each domain: == domain 1 score: 351.1 bits; conditional E-value: 1.7e-109 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 ++AliTPf +d +d + l+++ie+ +e gv +iv++GtTGEsatLs E+++vi +ave +k vpv lcl|NCBI__GCF_000195895.1:WP_011306166.1 5 AMPALITPFTKDDRIDREGLQRNIEFVEEGGVAGIVPCGTTGESATLSALEHEEVIDIAVECSK--VPV 71 579**********************************************************998..9** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 iaGtgsn+t ea+++tk+a+++gvdgvl+++PyYnkP+ Gl+ hfk+iae+v++P+++Yn+PsRtg++ lcl|NCBI__GCF_000195895.1:WP_011306166.1 72 IAGTGSNNTGEALQFTKHAADAGVDGVLLISPYYNKPNPAGLLTHFKKIAEAVDVPMVMYNIPSRTGQD 140 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseika.eakedfkvlsGdDaltleilalGakGviSVasnva 207 + e++ +La+ ++iv+iKeasg++ +vs+i + + +edf+v sG+D+ltl+il++G++GviSVa+n++ lcl|NCBI__GCF_000195895.1:WP_011306166.1 141 MPLEVIVELAKVENIVGIKEASGNIGKVSQILEnTIDEDFVVISGEDNLTLPILSVGGQGVISVAANIV 209 ******************************97615689******************************* PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p++++ mv+aal+gd+e ar+ih ++ +l++alf+etNPipvK+a++l+gl+ + +lRlPL++lse ++ lcl|NCBI__GCF_000195895.1:WP_011306166.1 210 PDRMSRMVNAALAGDYETARKIHFEIAPLIRALFLETNPIPVKKAAELAGLASG-NLRLPLAPLSETNT 277 ******************************************************.************** PP TIGR00674 277 eklkevlke 285 +k+++ l++ lcl|NCBI__GCF_000195895.1:WP_011306166.1 278 QKVADELRK 286 ***998876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.31 // [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