Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO353_17670 AO353_17670 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17670 Length = 292 Score = 479 bits (1233), Expect = e-140 Identities = 241/291 (82%), Positives = 261/291 (89%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 MIAGSMVALVTP DAQGRLDWDSL+KLVDFHLQ GT+AIVAVGTTGESATLDV EHI+VI Sbjct: 1 MIAGSMVALVTPMDAQGRLDWDSLSKLVDFHLQNGTHAIVAVGTTGESATLDVNEHIEVI 60 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFR 120 RRVV QV GRIPVIAGTGANSTREA+ LT AK+ GADACLLVTPYYNKPTQEG+Y HF+ Sbjct: 61 RRVVKQVNGRIPVIAGTGANSTREAIELTTNAKTAGADACLLVTPYYNKPTQEGLYLHFK 120 Query: 121 HIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKD 180 IAEAV IPQILYNVPGRT+CDM ETV RLS V NIIGIKEATGDL RAK +++ V KD Sbjct: 121 TIAEAVDIPQILYNVPGRTACDMQAETVIRLSTVKNIIGIKEATGDLSRAKAILDGVSKD 180 Query: 181 FLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLH 240 FLV SGDDATAVEL+LLGGKGNISVTANVAPR MSDLC AA+ GDA ARAI+++LMPL+ Sbjct: 181 FLVISGDDATAVELILLGGKGNISVTANVAPRDMSDLCIAALNGDAVKARAIHEKLMPLN 240 Query: 241 KALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291 K LFIESNPIPVKWALHEMGL+P+GIRLPLTWLS CHEPLRQAMRQ+GVL Sbjct: 241 KTLFIESNPIPVKWALHEMGLMPDGIRLPLTWLSEACHEPLRQAMRQSGVL 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: 344 Number of extensions: 6 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 AO353_17670 AO353_17670 (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.22981.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-117 375.8 0.0 5.5e-117 375.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 AO353_17670 4-hydroxy-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 AO353_17670 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 375.6 0.0 5.5e-117 5.5e-117 2 284 .. 5 286 .. 4 288 .. 0.99 Alignments for each domain: == domain 1 score: 375.6 bits; conditional E-value: 5.5e-117 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn 66 +++Al+TP++++g +d ++l+kl+++++++g+ aiv+vGtTGEsatL ++E+++vi+ +v+ v++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 5 SMVALVTPMDAQGRLDWDSLSKLVDFHLQNGTHAIVAVGTTGESATLDVNEHIEVIRRVVKQVNG 69 799************************************************************** PP TIGR00674 67 rvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYn 131 r+pviaGtg+n+t+eaielt+ a+ +g+d++l+vtPyYnkPtqeGly hfk+iae+v++P+ilYn lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 70 RIPVIAGTGANSTREAIELTTNAKTAGADACLLVTPYYNKPTQEGLYLHFKTIAEAVDIPQILYN 134 ***************************************************************** PP TIGR00674 132 vPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGa 196 vP+Rt+++++ etv+rL++ ++i++iKea+gdl+r++ i +++df v sGdDa++ e+++lG+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 135 VPGRTACDMQAETVIRLSTVKNIIGIKEATGDLSRAKAILDGVSKDFLVISGDDATAVELILLGG 199 ***************************************************************** PP TIGR00674 197 kGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliek 261 kG iSV++nvap+++++++ aal+gd +ar ih+kl++l k+lfie+NPipvK+al+ +gl+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 200 KGNISVTANVAPRDMSDLCIAALNGDAVKARAIHEKLMPLNKTLFIESNPIPVKWALHEMGLMPD 264 ***************************************************************99 PP TIGR00674 262 delRlPLtelseekkeklkevlk 284 +RlPLt lse +e l+++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_17670 265 -GIRLPLTWLSEACHEPLRQAMR 286 .9**********99999998876 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.81 // [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