Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate WP_012853632.1 TCUR_RS16305 4-hydroxy-tetrahydrodipicolinate synthase
Query= SwissProt::P9WP25 (300 letters) >NCBI__GCF_000024385.1:WP_012853632.1 Length = 306 Score = 313 bits (801), Expect = 4e-90 Identities = 168/291 (57%), Positives = 202/291 (69%), Gaps = 2/291 (0%) Query: 10 ARLGTLLTAMVTPFSGDGSLDTATAARLANHLVD-QGCDGLVVSGTTGESPTTTDGEKIE 68 A G +LTAMVTP + DG +D AARLA +LVD Q DGLVVSGTTGE+PTT+D EK Sbjct: 9 APFGRMLTAMVTPMTPDGEVDYDGAARLAAYLVDEQRNDGLVVSGTTGEAPTTSDEEKDR 68 Query: 69 LLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAH 128 LLRAVLEAVGDRA V+AG GT DTAH++ LA+ GAHGLLVVTPYY+KPPQ GL AH Sbjct: 69 LLRAVLEAVGDRATVVAGVGTNDTAHTLELARRAERAGAHGLLVVTPYYNKPPQEGLLAH 128 Query: 129 FTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKDAKADLHSGAQIMADTG 188 FTAVADAT LP +LYDIPGR+ VPI DT+ LA HP IV VKDAK DL + +++MA T Sbjct: 129 FTAVADATGLPNMLYDIPGRTGVPIHTDTLLRLAEHPRIVAVKDAKGDLFAASRVMAATD 188 Query: 189 LAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLC 248 L +YSGDD LNLPWL++GA GF+SVI H+ L E++ A+ SGD A I+ + P+ Sbjct: 189 LVFYSGDDNLNLPWLSVGAAGFVSVIGHVVGADLHEMIEAYRSGDTGRALAIHRRLLPVV 248 Query: 249 NA-MSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASV 298 A M+R G +KA L L G+ G R P ATPE + L D+ V Sbjct: 249 TAIMTRTQGAIATKAALGLLGLPGGTLRPPLAPATPEFVARLREDLAQGGV 299 Lambda K H 0.318 0.133 0.382 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: 324 Number of extensions: 11 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: 300 Length of database: 306 Length adjustment: 27 Effective length of query: 273 Effective length of database: 279 Effective search space: 76167 Effective search space used: 76167 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_012853632.1 TCUR_RS16305 (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.27109.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-87 278.6 0.0 2.4e-87 278.4 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012853632.1 TCUR_RS16305 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012853632.1 TCUR_RS16305 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.4 0.0 2.4e-87 2.4e-87 2 281 .. 14 292 .. 13 296 .. 0.96 Alignments for each domain: == domain 1 score: 278.4 bits; conditional E-value: 2.4e-87 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqie.kgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 +ltA++TP+ dg+vd++ ++l ++++ ++ d++vv GtTGE++t s eEk ++++ ++e v +r lcl|NCBI__GCF_000024385.1:WP_012853632.1 14 MLTAMVTPMTPDGEVDYDGAARLAAYLVDeQRNDGLVVSGTTGEAPTTSDEEKDRLLRAVLEAVGDRAT 82 689**********************998516689*********************************** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 v+aG+g+n t+ ++el+++ae +g++g+lvvtPyYnkP qeGl++hf a+a+++ lP +lY++P+Rtgv lcl|NCBI__GCF_000024385.1:WP_012853632.1 83 VVAGVGTNDTAHTLELARRAERAGAHGLLVVTPYYNKPPQEGLLAHFTAVADATGLPNMLYDIPGRTGV 151 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 ++ +t++rLae+++iva+K+a gdl +s+++a + d++ +sGdD+l+l+ l++Ga+G++SV+++v+ lcl|NCBI__GCF_000024385.1:WP_012853632.1 152 PIHTDTLLRLAEHPRIVAVKDAKGDLFAASRVMAAT--DLVFYSGDDNLNLPWLSVGAAGFVSVIGHVV 218 *********************************977..6****************************** PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietN.PipvKtalallgliekdelRlPLtelseek 275 + +l+em++a+ gdt +a+ ih++ll++++a+ + t i K+al llgl+ + +lR+PL++++ e lcl|NCBI__GCF_000024385.1:WP_012853632.1 219 GADLHEMIEAYRSGDTGRALAIHRRLLPVVTAIMTRTQgAIATKAALGLLGLPGG-TLRPPLAPATPEF 286 ********************************999986379**************.********99997 PP TIGR00674 276 keklke 281 +l+e lcl|NCBI__GCF_000024385.1:WP_012853632.1 287 VARLRE 292 777765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (306 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.97 // [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