Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_011736894.1 PPRO_RS15225 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000015045.1:WP_011736894.1 Length = 290 Score = 303 bits (777), Expect = 2e-87 Identities = 146/290 (50%), Positives = 205/290 (70%), Gaps = 1/290 (0%) Query: 1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60 MF+GSIVAL+TPF++G VD E L ++++ ++NGTD I CGTTGE+ TL ++EH +VIE Sbjct: 1 MFKGSIVALVTPFRDGAVDEETLRRMVDYQIENGTDGISPCGTTGEASTLDYDEHMRVIE 60 Query: 61 FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKT 120 +++ GR+ VIAGTG N+T EA+ L+ AK++GADG L+V PYYNKP+Q GLY HF+ Sbjct: 61 IVIQQVNGRVPVIAGTGSNSTTEAIELSRKAKKLGADGVLLVSPYYNKPSQEGLYRHFRA 120 Query: 121 VAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGES 180 +A VDIP ++YN+P RT V + T+ +LA E ++IVA KE+T ++ + SE+++ G+ Sbjct: 121 IADAVDIPQVLYNVPGRTGVNMLPQTVARLA-EHDSIVAIKEATGSLQQASELMEMCGDK 179 Query: 181 FSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLF 240 V+SGDD +T PMMA GA GVISV N+MPREV L+ A EGD AR +H L ++ Sbjct: 180 IDVISGDDFITFPMMACGATGVISVVANIMPREVARLVDAFYEGDMDEARRLHLSLLNIS 239 Query: 241 KVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNL 290 +FIETNP+PVKTA ++G+C +E RLPL + + L V+K Y L Sbjct: 240 NAMFIETNPVPVKTAAALMGLCAEELRLPLAPLGDASRATLCAVMKSYGL 289 Lambda K H 0.318 0.136 0.390 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: 258 Number of extensions: 13 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: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_011736894.1 PPRO_RS15225 (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.12632.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-118 378.1 0.0 1.1e-117 377.9 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736894.1 PPRO_RS15225 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736894.1 PPRO_RS15225 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 377.9 0.0 1.1e-117 1.1e-117 1 285 [. 4 286 .. 4 287 .. 0.99 Alignments for each domain: == domain 1 score: 377.9 bits; conditional E-value: 1.1e-117 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 g+++Al+TPf++ vd ++l +++++qie+g+d+i ++GtTGE+ tL ++E+++vie++++ v++rvp lcl|NCBI__GCF_000015045.1:WP_011736894.1 4 GSIVALVTPFRDGA-VDEETLRRMVDYQIENGTDGISPCGTTGEASTLDYDEHMRVIEIVIQQVNGRVP 71 589*******9877.****************************************************** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 viaGtgsn+t+eaiel+++a+klg+dgvl+v+PyYnkP+qeGly+hf aia++v++P++lYnvP+Rtgv lcl|NCBI__GCF_000015045.1:WP_011736894.1 72 VIAGTGSNSTTEAIELSRKAKKLGADGVLLVSPYYNKPSQEGLYRHFRAIADAVDIPQVLYNVPGRTGV 140 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 ++ p+tv+rLae+ +ivaiKea+g+l+++se++++ ++++ v sGdD +t +++a+Ga+GviSV++n++ lcl|NCBI__GCF_000015045.1:WP_011736894.1 141 NMLPQTVARLAEHDSIVAIKEATGSLQQASELMEMCGDKIDVISGDDFITFPMMACGATGVISVVANIM 209 ********************************************************************* PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p+e++ +v a++egd++ear +h ll++ +a+fietNP+pvKta+al+gl+++ elRlPL++l + ++ lcl|NCBI__GCF_000015045.1:WP_011736894.1 210 PREVARLVDAFYEGDMDEARRLHLSLLNISNAMFIETNPVPVKTAAALMGLCAE-ELRLPLAPLGDASR 277 ******************************************************.************** PP TIGR00674 277 eklkevlke 285 +l +v+k+ lcl|NCBI__GCF_000015045.1:WP_011736894.1 278 ATLCAVMKS 286 *99999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (290 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: 00:00:00.01 # Mc/sec: 6.67 // [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