Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate GFF937 Psest_0966 dihydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >FitnessBrowser__psRCH2:GFF937 Length = 268 Score = 318 bits (816), Expect = 6e-92 Identities = 167/265 (63%), Positives = 198/265 (74%), Gaps = 1/265 (0%) Query: 7 RVAIAGAGGRMGRQLIQAALALEGVQ-LGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 R+A+ GA GRMG+ LI+A G L AA++R S+L+G+DAGELA G+ GV + Sbjct: 3 RIAVTGAAGRMGKTLIEAVQQTGGAAGLTAAIDRPDSTLVGADAGELAAIGRLGVPLTGE 62 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 L D+FDV IDFT P TL +L CR+ GK MVIGTTGF K+ + AA +I IVF Sbjct: 63 LARAVDEFDVLIDFTHPSVTLKNLEVCRRAGKAMVIGTTGFSPEEKERLAAAAREIPIVF 122 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 AANFSVGVN+ LKLL+ AA+V+GD DIEIIEAHHRHKVDAPSGTAL MGE IA AL +D Sbjct: 123 AANFSVGVNLCLKLLDTAARVLGDDVDIEIIEAHHRHKVDAPSGTALRMGEVIAEALGRD 182 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 L+ AVY REG TG R TIGFATVRAGD+VG+HT +FA GER+EITHKASSRMTFA Sbjct: 183 LQKVAVYGREGQTGARQRETIGFATVRAGDVVGDHTVLFAADGERVEITHKASSRMTFAK 242 Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270 GAVR+ALWL K +GL+DM+DVL L Sbjct: 243 GAVRAALWLDEKPAGLYDMQDVLGL 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: 262 Number of extensions: 11 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 GFF937 Psest_0966 (dihydrodipicolinate reductase)
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.30701.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-107 343.7 2.3 4.5e-107 343.6 2.3 1.0 1 lcl|FitnessBrowser__psRCH2:GFF937 Psest_0966 dihydrodipicolinate r Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF937 Psest_0966 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 343.6 2.3 4.5e-107 4.5e-107 3 270 .] 3 266 .. 1 266 [. 0.97 Alignments for each domain: == domain 1 score: 343.6 bits; conditional E-value: 4.5e-107 TIGR00036 3 kvavaGaaGrmGrevikavkea.edlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvli 77 ++av+GaaGrmG+ +i+av+++ l+aa++r++s ++g D+Gela ig++gvp++ +l + +++dvli lcl|FitnessBrowser__psRCH2:GFF937 3 RIAVTGAAGRMGKTLIEAVQQTgGAAGLTAAIDRPDSTLVGADAGELAAIGRLGVPLTGELARA----VDEFDVLI 74 89*******************944567********************************99977....9******* PP TIGR00036 78 DfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv. 152 Dft+p+ +l+n++++ ++g+ +V+GTTGfs e++++l+++a + +++v+a+Nf++Gvnl lkll +aa+vl+d lcl|FitnessBrowser__psRCH2:GFF937 75 DFTHPSVTLKNLEVCRRAGKAMVIGTTGFSPEEKERLAAAARE--IPIVFAANFSVGVNLCLKLLDTAARVLGDDv 148 *******************************************..***************************8644 PP TIGR00036 153 DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasd 228 DiEiiE+HHrhK+DaPSGTAl+++e+ia+a g+dl+++av++reg tG+r++e+iG+a+vR+gdvvg+htvlFa d lcl|FitnessBrowser__psRCH2:GFF937 149 DIEIIEAHHRHKVDAPSGTALRMGEVIAEALGRDLQKVAVYGREGQTGARQRETIGFATVRAGDVVGDHTVLFAAD 224 **************************************************************************** PP TIGR00036 229 GerleitHkassRaafakGvvrairwledkeekvydledvld 270 Ger+eitHkassR++fakG+vra+ wl +k +++yd++dvl+ lcl|FitnessBrowser__psRCH2:GFF937 225 GERVEITHKASSRMTFAKGAVRAALWLDEKPAGLYDMQDVLG 266 ****************************************96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.69 // [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