Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate Pf6N2E2_3366 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
Query= CharProtDB::CH_002128 (273 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 Length = 268 Score = 338 bits (867), Expect = 7e-98 Identities = 172/265 (64%), Positives = 205/265 (77%), Gaps = 1/265 (0%) Query: 7 RVAIAGAGGRMGRQLIQAALALEGVQ-LGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 R+A+ GA GRMG+ L++A + L AA+ R S+L+G+DAGELA G+ GV + Sbjct: 3 RIAVMGAAGRMGKALVEAVQQRSPLSGLTAAIVRPDSTLVGADAGELASLGRIGVPMSGG 62 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 L+ V D+FDV IDFT PE L +LA CR+HGK MVIGTTG D A KQ + DA DI IVF Sbjct: 63 LEKVLDEFDVLIDFTLPEVMLKNLAICRKHGKAMVIGTTGLDAAQKQLLADAGKDIPIVF 122 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 AANFSVGVN+ LKLL+ AA+V+GD DIEIIEAHHRHK+DAPSGTAL MGE IA AL +D Sbjct: 123 AANFSVGVNLSLKLLDMAARVLGDDADIEIIEAHHRHKIDAPSGTALRMGEVIADALGRD 182 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 L++ AVY R+GHTG R TIGFATVR GD+VG+HT +FA GERLEITHKASSRMTFA Sbjct: 183 LQEVAVYGRQGHTGARERSTIGFATVRGGDVVGDHTVLFATEGERLEITHKASSRMTFAK 242 Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270 GAVR+ALWL G+E GL+DM+DVLDL Sbjct: 243 GAVRAALWLDGREPGLYDMQDVLDL 267 Lambda K H 0.319 0.135 0.383 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: 277 Number of extensions: 8 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: 273 Length of database: 268 Length adjustment: 25 Effective length of query: 248 Effective length of database: 243 Effective search space: 60264 Effective search space used: 60264 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: 47 (22.7 bits)
Align candidate Pf6N2E2_3366 (4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
# 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/TIGR00036.hmm # target sequence database: /tmp/gapView.24372.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00036 [M=270] Accession: TIGR00036 Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-104 333.5 1.4 6.1e-104 333.3 1.4 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.3 1.4 6.1e-104 6.1e-104 3 270 .] 3 266 .. 1 266 [. 0.98 Alignments for each domain: == domain 1 score: 333.3 bits; conditional E-value: 6.1e-104 TIGR00036 3 kvavaGaaGrmGrevikavkeaedle.lvaalerkgsskqgkDiGelagigkvgvpveddleav 65 ++av GaaGrmG+ +++av++ l+ l+aa+ r++s ++g D+Gela++g++gvp++ le v lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 3 RIAVMGAAGRMGKALVEAVQQRSPLSgLTAAIVRPDSTLVGADAGELASLGRIGVPMSGGLEKV 66 89*******************976644***********************************88 PP TIGR00036 66 kvlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviap 129 +++dvliDft+pe +l+n++i+ ++g+ +V+GTTG++ ++++ l+d+ ++ +++v+a+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 67 ----LDEFDVLIDFTLPEVMLKNLAICRKHGKAMVIGTTGLDAAQKQLLADAGKD--IPIVFAA 124 ....89***********************************************99..******* PP TIGR00036 130 NfaiGvnlllkllekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaav 192 Nf++Gvnl lkll +aa+vl+d DiEiiE+HHrhK DaPSGTAl+++e+ia+a g+dl+e+av lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 125 NFSVGVNLSLKLLDMAARVLGDDaDIEIIEAHHRHKIDAPSGTALRMGEVIADALGRDLQEVAV 188 ********************8766**************************************** PP TIGR00036 193 eeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwle 256 ++r+g+tG+r++++iG+a+vRggdvvg+htvlFa++GerleitHkassR++fakG+vra+ wl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 189 YGRQGHTGARERSTIGFATVRGGDVVGDHTVLFATEGERLEITHKASSRMTFAKGAVRAALWLD 252 **************************************************************** PP TIGR00036 257 dkeekvydledvld 270 e ++yd++dvld lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3366 253 GREPGLYDMQDVLD 266 ************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (268 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6.84 // [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