Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate PfGW456L13_4507 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 Length = 292 Score = 466 bits (1200), Expect = e-136 Identities = 234/291 (80%), Positives = 256/291 (87%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 MIAGSMVALVTP DAQGRLDWDSL+KLVDFHL+ GT+AIVAVGTTGESATLDV EHI+VI Sbjct: 1 MIAGSMVALVTPMDAQGRLDWDSLSKLVDFHLENGTHAIVAVGTTGESATLDVNEHIEVI 60 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120 R VV QV GRIPVIAGTGANSTREAV LT AK GADACLLV PYYNKPTQEG+Y HF+ Sbjct: 61 RAVVKQVNGRIPVIAGTGANSTREAVELTRNAKEAGADACLLVVPYYNKPTQEGLYLHFK 120 Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180 HIAE+V IPQILYNVPGRTSCDM ETV RLS VPNIIGIKEATGDL+RAK +++ V KD Sbjct: 121 HIAESVDIPQILYNVPGRTSCDMQAETVIRLSTVPNIIGIKEATGDLKRAKAILDGVSKD 180 Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240 F+V SGDD TAVEL+L+GGKGNISVTANVAPR M+DLC AA++GDA ARAIN++LMPLH Sbjct: 181 FIVLSGDDPTAVELILMGGKGNISVTANVAPREMADLCEAALKGDAETARAINEKLMPLH 240 Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291 K LFIE+NPIPVKWAL EMGL+ EGIRLPLTWLS CHE LR A+RQ GVL Sbjct: 241 KDLFIEANPIPVKWALVEMGLMHEGIRLPLTWLSAPCHETLRTALRQCGVL 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: 329 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 PfGW456L13_4507 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
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.30226.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-117 377.8 0.0 1.4e-117 377.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 377.6 0.0 1.4e-117 1.4e-117 2 285 .. 5 287 .. 4 288 .. 0.99 Alignments for each domain: == domain 1 score: 377.6 bits; conditional E-value: 1.4e-117 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkv 56 +++Al+TP++++g +d ++l+kl+++++e+g+ aiv+vGtTGEsatL ++E+++v lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 5 SMVALVTPMDAQGRLDWDSLSKLVDFHLENGTHAIVAVGTTGESATLDVNEHIEV 59 799**************************************************** PP TIGR00674 57 ievavelvknrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeG 111 i+ +v+ v++r+pviaGtg+n+t+ea+elt+ a+++g+d++l+v+PyYnkPtqeG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 60 IRAVVKQVNGRIPVIAGTGANSTREAVELTRNAKEAGADACLLVVPYYNKPTQEG 114 ******************************************************* PP TIGR00674 112 lykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeveivaiKeasgdler 166 ly hfk iae+v++P+ilYnvP+Rt+++++ etv+rL++ ++i++iKea+gdl+r lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 115 LYLHFKHIAESVDIPQILYNVPGRTSCDMQAETVIRLSTVPNIIGIKEATGDLKR 169 ******************************************************* PP TIGR00674 167 vseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaaleg 221 ++ i +++df vlsGdD ++ e++++G+kG iSV++nvap+e++++++aal+g lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 170 AKAILDGVSKDFIVLSGDDPTAVELILMGGKGNISVTANVAPREMADLCEAALKG 224 ******************************************************* PP TIGR00674 222 dteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 d e ar i++kl++l+k lfie+NPipvK+al +gl+++ +RlPLt ls + lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 225 DAETARAINEKLMPLHKDLFIEANPIPVKWALVEMGLMHE-GIRLPLTWLSAPCH 278 **************************************99.***********999 PP TIGR00674 277 eklkevlke 285 e+l+ +l++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4507 279 ETLRTALRQ 287 999998875 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: 00:00:00.00 # Mc/sec: 9.29 // [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