Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; Protein MosA; EC 4.3.3.7 (characterized)
to candidate AZOBR_RS08420 AZOBR_RS08420 dihydrodipicolinate synthase
Query= SwissProt::Q07607 (292 letters) >FitnessBrowser__azobra:AZOBR_RS08420 Length = 291 Score = 329 bits (844), Expect = 4e-95 Identities = 163/291 (56%), Positives = 208/291 (71%), Gaps = 1/291 (0%) Query: 1 MFEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVE 60 M GSI AL+TPF + ++DE A VEWQ+ +G+ GLVPCGTTGESPTLS EH +VVE Sbjct: 1 MLYGSIVALLTPFKNGKVDEAAFQSFVEWQVAQGTHGLVPCGTTGESPTLSHEEHNRVVE 60 Query: 61 ITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKA 120 + I+ A G+VPV+AG GSNST EAI+ +HA+ AGA L+V+PYYNKPTQEG+YQHFKA Sbjct: 61 LCIEAAGGKVPVVAGTGSNSTEEAISLTQHAKKAGAAAALVVTPYYNKPTQEGLYQHFKA 120 Query: 121 IDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACGED 180 I A+ +PI++YNIPGRS +++ V T+AR+ + PN+ GVKDAT +L RP G D Sbjct: 121 IHDAADLPIVIYNIPGRSVVDMSVATMARLAK-LPNIIGVKDATADLARPVRLLQDVGPD 179 Query: 181 FNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLH 240 F L+GED TAL + A GG GCISVTAN+APA CA Q A GD A A K +D L PLH Sbjct: 180 FIQLSGEDATALAFNAQGGVGCISVTANIAPAQCAAMQDAWRKGDLATAYKYRDLLTPLH 239 Query: 241 RALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGIL 291 ++F+ET+PA KYA LG+ ++RLPLV S S + + DAM+ AG+L Sbjct: 240 DSMFVETSPAPVKYAASLLGKSSDEVRLPLVAASESTRTTVRDAMKKAGLL 290 Lambda K H 0.319 0.136 0.402 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: 290 Number of extensions: 11 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: 292 Length of database: 291 Length adjustment: 26 Effective length of query: 266 Effective length of database: 265 Effective search space: 70490 Effective search space used: 70490 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate AZOBR_RS08420 AZOBR_RS08420 (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.22115.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-106 340.0 0.0 4.6e-106 339.8 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS08420 AZOBR_RS08420 dihydrodipicolinat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS08420 AZOBR_RS08420 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.8 0.0 4.6e-106 4.6e-106 1 285 [. 4 286 .. 4 287 .. 0.99 Alignments for each domain: == domain 1 score: 339.8 bits; conditional E-value: 4.6e-106 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 g+++Al+TPfk+ + vd aa+++ +e q+++g+ ++v++GtTGEs+tLs+eE+++v+e+ +e + ++vp lcl|FitnessBrowser__azobra:AZOBR_RS08420 4 GSIVALLTPFKNGK-VDEAAFQSFVEWQVAQGTHGLVPCGTTGESPTLSHEEHNRVVELCIEAAGGKVP 71 589********998.****************************************************** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 v+aGtgsn+teeai+lt++a+k+g++++lvvtPyYnkPtqeGly+hfkai+++++lPi++Yn+P+R++v lcl|FitnessBrowser__azobra:AZOBR_RS08420 72 VVAGTGSNSTEEAISLTQHAKKAGAAAALVVTPYYNKPTQEGLYQHFKAIHDAADLPIVIYNIPGRSVV 140 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 ++++ t++rLa+ ++i+++K+a+ dl+r +++ + ++ df lsG+Da++l++ a+G+ G iSV++n+a lcl|FitnessBrowser__azobra:AZOBR_RS08420 141 DMSVATMARLAKLPNIIGVKDATADLARPVRLLQDVGPDFIQLSGEDATALAFNAQGGVGCISVTANIA 209 ********************************************************************* PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p +++ m a+ +gd + a + + l++l++ +f+et P pvK+a+ llg e+RlPL+++se+++ lcl|FitnessBrowser__azobra:AZOBR_RS08420 210 PAQCAAMQDAWRKGDLATAYKYRDLLTPLHDSMFVETSPAPVKYAASLLGKSSD-EVRLPLVAASESTR 277 **************************************************9988.************** PP TIGR00674 277 eklkevlke 285 +++++++k+ lcl|FitnessBrowser__azobra:AZOBR_RS08420 278 TTVRDAMKK 286 *****9986 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: 00:00:00.00 # Mc/sec: 8.75 // [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