Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate RR42_RS17475 RR42_RS17475 dihydrodipicolinate synthase
Query= SwissProt::Q9X1K9 (294 letters) >FitnessBrowser__Cup4G11:RR42_RS17475 Length = 303 Score = 171 bits (432), Expect = 2e-47 Identities = 103/281 (36%), Positives = 147/281 (52%), Gaps = 10/281 (3%) Query: 9 IVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSRTLEIVDG 68 +VTP + GE DL +RL + + +GV+ L++LGTTGE + DER + LE VDG Sbjct: 16 LVTPMQGGEPDLACAQRLAAHYVASGVDGLVILGTTGEGGLLTRDERLMFTAAVLEAVDG 75 Query: 69 KIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQEGLYQHYKYISERTDLG 128 +PV+ G G T + V+Q ++ G LV PYY +P EG+ H + +++ T Sbjct: 76 ALPVLAGVGGVDTRVVCEQVRQLDRFDLAGYLVPPPYYLRPGDEGIAWHVERVADATWRP 135 Query: 129 IVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQIDRTVSLTKQARSD-FMVW 187 +++YNVP RTG N+ P R+AA VV +KE + L A +D V+ Sbjct: 136 LMLYNVPKRTGCNMSPALVQRLAAH-PRVVAVKECD--------AAGLRALAGNDRLAVF 186 Query: 188 SGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKLRPLMKALF 247 G D L AGG GV+ +++ P V L G + +R + L PL+ LF Sbjct: 187 CGEDAAMLDHLLAGGGGVVPACAHIRPDLFVRLLQLVAQGRVAAARALFASLAPLISLLF 246 Query: 248 VETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVL 288 E NP PVK+AL L G +E+R PLVPAS E L V+ Sbjct: 247 SEPNPAPVKSALALCGLASSEVRRPLVPASRALRERLDQVI 287 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: 236 Number of extensions: 2 Number of successful extensions: 2 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: 303 Length adjustment: 27 Effective length of query: 267 Effective length of database: 276 Effective search space: 73692 Effective search space used: 73692 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 RR42_RS17475 RR42_RS17475 (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.1263.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-68 217.2 0.0 1.3e-68 216.9 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS17475 RR42_RS17475 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS17475 RR42_RS17475 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.9 0.0 1.3e-68 1.3e-68 6 285 .. 16 289 .. 12 290 .. 0.96 Alignments for each domain: == domain 1 score: 216.9 bits; conditional E-value: 1.3e-68 TIGR00674 6 liTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 l+TP++ + d+a+ ++l + +++gvd++v++GtTGE+ L+ +E+ ++e v++ +pv+aG+ lcl|FitnessBrowser__Cup4G11:RR42_RS17475 16 LVTPMQGGE-PDLACAQRLAAHYVASGVDGLVILGTTGEGGLLTRDERLMFTAAVLEAVDGALPVLAGV 83 89***9887.9********************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepe 143 g+ t+ + e +++++ + +g lv PyY +P eG+ h +++a+++ P++lYnvP Rtg++++p lcl|FitnessBrowser__Cup4G11:RR42_RS17475 84 GGVDTRVVCEQVRQLDRFDLAGYLVPPPYYLRPGDEGIAWHVERVADATWRPLMLYNVPKRTGCNMSPA 152 ********************************************************************* PP TIGR00674 144 tvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelk 212 +v+rLa+++++va+Ke+ + + + ++ ++v++G+Da +l+ l+ G+ Gv+ +++ p+++ lcl|FitnessBrowser__Cup4G11:RR42_RS17475 153 LVQRLAAHPRVVAVKECDA--AGLRALAG--NDRLAVFCGEDAAMLDHLLAGGGGVVPACAHIRPDLFV 217 *****************88..33333433..4579********************************** PP TIGR00674 213 emvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklke 281 +++ +++g+++ ar + + l +l++ lf e+NP pvK alal gl+ + e+R PL+++s+ +e+l++ lcl|FitnessBrowser__Cup4G11:RR42_RS17475 218 RLLQLVAQGRVAAARALFASLAPLISLLFSEPNPAPVKSALALCGLASS-EVRRPLVPASRALRERLDQ 285 ************************************************9.******************* PP TIGR00674 282 vlke 285 v+++ lcl|FitnessBrowser__Cup4G11:RR42_RS17475 286 VIAS 289 9976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (303 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.96 // [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