Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinate synthase
Query= SwissProt::Q9X1K9 (294 letters) >FitnessBrowser__BFirm:BPHYT_RS29250 Length = 307 Score = 164 bits (414), Expect = 3e-45 Identities = 96/296 (32%), Positives = 156/296 (52%), Gaps = 15/296 (5%) Query: 1 MFRGVGTAIVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVS 60 +F G+ ++TPF +G +D + LVR G+ L+ LGTTGE ++ E++ +++ Sbjct: 3 IFSGIWVPLITPFADGAVDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDAVLA 62 Query: 61 RTLEIV--------DGK-IPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQ 111 L+ DG+ +PV+ G N T + Q L GVL+ PYY +P+Q Sbjct: 63 TILDEAQSAAHLARDGQALPVVAGVSGNHTASMRVRIGQLNALPLAGVLMAAPYYIRPSQ 122 Query: 112 EGLYQHYKYISERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQID 171 G+ H+ +++ ++ +V+Y++P RTGV + +T +A + I+ +D Sbjct: 123 AGIVAHFMALADASEKPVVLYDIPYRTGVRLELDTLLALATHPR----IQAVKDCAGSLD 178 Query: 172 RTVSLTKQARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEK 231 T++L + AR V +G D F LC GG G I+ ++V P++ VE+ +G L Sbjct: 179 TTLALIRDAR--LQVLAGEDINIFNTLCLGGSGAIAASAHVRPERFVEMYRALAAGRLAD 236 Query: 232 SREVHRKLRPLMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNV 287 R + L PL++ALFVE NP PVKA L G I +ELR+P+ AS +E L + Sbjct: 237 GRRIFHALAPLIEALFVEPNPAPVKALLAAQGLIRDELRMPMTRASGALIERLEGL 292 Lambda K H 0.316 0.135 0.378 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: 183 Number of extensions: 5 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: 307 Length adjustment: 27 Effective length of query: 267 Effective length of database: 280 Effective search space: 74760 Effective search space used: 74760 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 (21.5 bits) S2: 48 (23.1 bits)
Align candidate BPHYT_RS29250 BPHYT_RS29250 (dihydrodipicolinate 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.1153.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-73 233.5 0.0 1.3e-73 233.3 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS29250 BPHYT_RS29250 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 233.3 0.0 1.3e-73 1.3e-73 4 279 .. 9 289 .. 6 295 .. 0.96 Alignments for each domain: == domain 1 score: 233.3 bits; conditional E-value: 1.3e-73 TIGR00674 4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn....... 66 + liTPf + vd aal l+++ +g+ ++v++GtTGE a+L E+ +v+ + ++ ++ lcl|FitnessBrowser__BFirm:BPHYT_RS29250 9 VPLITPFADGA-VDHAALRALVRRYTGAGIAGLVALGTTGEPAALDAAEQDAVLATILDEAQSaahlard 77 679****8877.***********************************************99999999999 PP TIGR00674 67 ..rvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPs 134 +pv+aG+++n t+ + +++ l+ +gvl+ +PyY +P+q G+++hf a+a+++e+P++lY++P lcl|FitnessBrowser__BFirm:BPHYT_RS29250 78 gqALPVVAGVSGNHTASMRVRIGQLNALPLAGVLMAAPYYIRPSQAGIVAHFMALADASEKPVVLYDIPY 147 999*************999999************************************************ PP TIGR00674 135 RtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVas 204 Rtgv le +t+++La++++i a+K+++g+l+ +++ a ++vl+G+D + l+lG++G i + lcl|FitnessBrowser__BFirm:BPHYT_RS29250 148 RTGVRLELDTLLALATHPRIQAVKDCAGSLDTTLALIRDA--RLQVLAGEDINIFNTLCLGGSGAIAASA 215 *********************************9999966..5*************************** PP TIGR00674 205 nvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelsee 274 +v p+++ em++a ++g+ ++ r i + l +l++alf+e+NP pvK++la++gli elR+P+t +s lcl|FitnessBrowser__BFirm:BPHYT_RS29250 216 HVRPERFVEMYRALAAGRLADGRRIFHALAPLIEALFVEPNPAPVKALLAAQGLIRD-ELRMPMTRASGA 284 ********************************************************9.*******99977 PP TIGR00674 275 kkekl 279 e+l lcl|FitnessBrowser__BFirm:BPHYT_RS29250 285 LIERL 289 66665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (307 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: 00:00:00.01 # Mc/sec: 7.99 // [ok]
This GapMind analysis is from Apr 09 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