Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate RR42_RS06250 RR42_RS06250 dihydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >FitnessBrowser__Cup4G11:RR42_RS06250 Length = 294 Score = 351 bits (901), Expect = e-101 Identities = 175/290 (60%), Positives = 223/290 (76%) Query: 2 IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61 I GS+VA+VTP G LD+ +L LVD+H+ EGT+ IV VGTTGES T++V+EH ++IR Sbjct: 4 INGSIVAIVTPMQEDGSLDFPALRALVDWHVAEGTDGIVIVGTTGESPTVNVDEHCELIR 63 Query: 62 RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121 V+Q RIP+IAGTG NST+EA+ LT AK GADA L V PYYNKPTQEGMY+HFR Sbjct: 64 VAVEQADKRIPIIAGTGGNSTKEAIELTAFAKQVGADASLQVVPYYNKPTQEGMYRHFRT 123 Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181 IAEAV +P +LYNVPGRT DM +T+ RL++VP IIG+KEATG++ RA ++I+ + F Sbjct: 124 IAEAVELPVVLYNVPGRTVADMQHDTILRLAQVPGIIGVKEATGNIDRAAQLIKDAPQGF 183 Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHK 241 +YSGDD TA+ LMLLGG GNISVTANVAPR M +LC AA++GDA AR I+ L+ L+K Sbjct: 184 SIYSGDDPTAIALMLLGGHGNISVTANVAPRKMHELCVAALKGDAITARRIHMELVALNK 243 Query: 242 ALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291 A+F+E+NPIPVKWAL +MG + GIRLPLT LSP H+ +R+A+ G+L Sbjct: 244 AMFVEANPIPVKWALQQMGRMQGGIRLPLTPLSPEYHDVVRKALSAAGLL 293 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: 294 Number of extensions: 9 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: 294 Length adjustment: 26 Effective length of query: 266 Effective length of database: 268 Effective search space: 71288 Effective search space used: 71288 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 RR42_RS06250 RR42_RS06250 (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.27770.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-115 370.4 0.1 2.5e-115 370.2 0.1 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS06250 RR42_RS06250 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS06250 RR42_RS06250 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.2 0.1 2.5e-115 2.5e-115 1 284 [. 6 288 .. 6 290 .. 0.99 Alignments for each domain: == domain 1 score: 370.2 bits; conditional E-value: 2.5e-115 TIGR00674 1 gvltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvp 69 g+++A++TP++edgs+df al l++ ++++g+d+iv+vGtTGEs+t +++E+ ++i+vave +++r+p lcl|FitnessBrowser__Cup4G11:RR42_RS06250 6 GSIVAIVTPMQEDGSLDFPALRALVDWHVAEGTDGIVIVGTTGESPTVNVDEHCELIRVAVEQADKRIP 74 589****************************************************************** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 +iaGtg+n+t+eaielt++a+++g+d+ l+v+PyYnkPtqeG+y+hf +iae+velP++lYnvP+Rt++ lcl|FitnessBrowser__Cup4G11:RR42_RS06250 75 IIAGTGGNSTKEAIELTAFAKQVGADASLQVVPYYNKPTQEGMYRHFRTIAEAVELPVVLYNVPGRTVA 143 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 +++ +t++rLa+ + i+++Kea+g+++r+ ++++ a++ f+++sGdD ++ ++++lG++G iSV++nva lcl|FitnessBrowser__Cup4G11:RR42_RS06250 144 DMQHDTILRLAQVPGIIGVKEATGNIDRAAQLIKDAPQGFSIYSGDDPTAIALMLLGGHGNISVTANVA 212 ********************************************************************* PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p++++e++ aal+gd ar ih +l+ l ka+f+e+NPipvK+al+ +g +++ +RlPLt+ls e + lcl|FitnessBrowser__Cup4G11:RR42_RS06250 213 PRKMHELCVAALKGDAITARRIHMELVALNKAMFVEANPIPVKWALQQMGRMQG-GIRLPLTPLSPEYH 280 ******************************************************.************** PP TIGR00674 277 eklkevlk 284 + ++++l+ lcl|FitnessBrowser__Cup4G11:RR42_RS06250 281 DVVRKALS 288 ****9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (294 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: 00:00:00.01 # Mc/sec: 7.27 // [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