Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate GFF1410 PS417_07165 dihydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__WCS417:GFF1410 Length = 292 Score = 472 bits (1215), Expect = e-138 Identities = 239/291 (82%), Positives = 260/291 (89%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 MIAGSMVALVTP DAQG LDWDSL KLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI Sbjct: 1 MIAGSMVALVTPMDAQGHLDWDSLGKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120 VV +V GRI VIAGTGANSTREA+ LT+ AK GADACLLVTPYYNKPTQEG+YQHFR Sbjct: 61 EFVVKRVAGRIAVIAGTGANSTREAIELTKNAKKAGADACLLVTPYYNKPTQEGLYQHFR 120 Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180 IAEAV IPQILYNVPGRT+CDM TV RLS VPNIIGIKEATGDLQRAK+++ V D Sbjct: 121 AIAEAVDIPQILYNVPGRTACDMQAATVIRLSTVPNIIGIKEATGDLQRAKDILAGVSSD 180 Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240 FLVYSGDDATAVEL+LLGGKGNISVTANVAPRAMS++CAAA+ GDA ARAI+++LMPL+ Sbjct: 181 FLVYSGDDATAVELILLGGKGNISVTANVAPRAMSEMCAAAIAGDAVTARAIHEKLMPLN 240 Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291 K LFIESNPIPVKWAL EMG++P+GIRLPLT LS CHEPLRQA+RQ+GVL Sbjct: 241 KTLFIESNPIPVKWALTEMGMMPDGIRLPLTRLSEACHEPLRQALRQSGVL 291 Lambda K H 0.319 0.134 0.393 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: 352 Number of extensions: 8 Number of successful extensions: 1 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: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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 GFF1410 PS417_07165 (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.8934.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-119 384.0 0.1 1.8e-119 383.8 0.1 1.0 1 lcl|FitnessBrowser__WCS417:GFF1410 PS417_07165 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF1410 PS417_07165 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.8 0.1 1.8e-119 1.8e-119 2 285 .. 5 287 .. 4 288 .. 0.99 Alignments for each domain: == domain 1 score: 383.8 bits; conditional E-value: 1.8e-119 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgs 76 +++Al+TP++++g++d ++l kl+++++++g++aiv+vGtTGEsatL +eE+++vie++v+ v++r+ viaGtg+ lcl|FitnessBrowser__WCS417:GFF1410 5 SMVALVTPMDAQGHLDWDSLGKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIEFVVKRVAGRIAVIAGTGA 79 799************************************************************************ PP TIGR00674 77 nateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaee 151 n+t+eaieltk a+k+g+d++l+vtPyYnkPtqeGly+hf aiae+v++P+ilYnvP+Rt+++++ tv+rL++ lcl|FitnessBrowser__WCS417:GFF1410 80 NSTREAIELTKNAKKAGADACLLVTPYYNKPTQEGLYQHFRAIAEAVDIPQILYNVPGRTACDMQAATVIRLSTV 154 *************************************************************************** PP TIGR00674 152 veivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteea 226 ++i++iKea+gdl+r++ i a ++ df v+sGdDa++ e+++lG+kG iSV++nvap+ ++em++aa++gd a lcl|FitnessBrowser__WCS417:GFF1410 155 PNIIGIKEATGDLQRAKDILAGVSSDFLVYSGDDATAVELILLGGKGNISVTANVAPRAMSEMCAAAIAGDAVTA 229 *************************************************************************** PP TIGR00674 227 reihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 r ih+kl++l k+lfie+NPipvK+al+ +g++ +RlPLt lse +e l+++l++ lcl|FitnessBrowser__WCS417:GFF1410 230 RAIHEKLMPLNKTLFIESNPIPVKWALTEMGMMPD-GIRLPLTRLSEACHEPLRQALRQ 287 *********************************99.9*************999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (292 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: 00:00:00.01 # Mc/sec: 6.56 // [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