Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_018234074.1 THITHI_RS0115800 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000378965.1:WP_018234074.1 Length = 267 Score = 353 bits (906), Expect = e-102 Identities = 179/263 (68%), Positives = 207/263 (78%) Query: 8 VAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLD 67 +AI GAGGRMGR LI+A EG+ L A E+ GS+LLGSDAGELAG G+ GVT+ Sbjct: 4 IAIVGAGGRMGRTLIEAVQQAEGLVLTVATEQPGSTLLGSDAGELAGVGRLGVTITDDPA 63 Query: 68 AVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFAA 127 A D FDV IDFTRPEGTL HL CR+ G+ MVIGTTGF E KQAIR+AA +I +VFA Sbjct: 64 ARADAFDVLIDFTRPEGTLKHLEICREAGRAMVIGTTGFSEDQKQAIREAAKEIPVVFAP 123 Query: 128 NFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLK 187 N SVGVN+ LKLL+ AA+V+GD DIE+IEAHHRHKVDAPSGTAL MGE +A AL +DL Sbjct: 124 NMSVGVNLCLKLLDLAARVLGDEVDIEVIEAHHRHKVDAPSGTALHMGEVVAGALGRDLA 183 Query: 188 DCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGA 247 +CAVY REGHTGER TIGF T+RAGDIVGEHT MFA GER+EITHKASSRMTFA GA Sbjct: 184 ECAVYGREGHTGERDRRTIGFETIRAGDIVGEHTVMFAGPGERVEITHKASSRMTFARGA 243 Query: 248 VRSALWLSGKESGLFDMRDVLDL 270 VR+A WL + +GL+DM+DVL+L Sbjct: 244 VRAAAWLKDRAAGLYDMQDVLNL 266 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: 273 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: 273 Length of database: 267 Length adjustment: 25 Effective length of query: 248 Effective length of database: 242 Effective search space: 60016 Effective search space used: 60016 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 WP_018234074.1 THITHI_RS0115800 (4-hydroxy-tetrahydrodipicolinate 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.7891.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-109 350.2 2.7 4.9e-109 350.0 2.7 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018234074.1 THITHI_RS0115800 4-hydroxy-tetra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018234074.1 THITHI_RS0115800 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.0 2.7 4.9e-109 4.9e-109 3 269 .. 3 264 .. 1 265 [. 0.99 Alignments for each domain: == domain 1 score: 350.0 bits; conditional E-value: 4.9e-109 TIGR00036 3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaek 71 ++a+ Ga+GrmGr +i+av++ae+l l+ a e++gs + g+D+Gelag+g++gv+++dd a + lcl|NCBI__GCF_000378965.1:WP_018234074.1 3 NIAIVGAGGRMGRTLIEAVQQAEGLVLTVATEQPGSTLLGSDAGELAGVGRLGVTITDDPAAR----AD 67 69*********************************************************9988....9* PP TIGR00036 72 kadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllk 140 ++dvliDft+pe++l++++i+ e+g +V+GTTGfse+++++++++a++ +++v+apN+++Gvnl lk lcl|NCBI__GCF_000378965.1:WP_018234074.1 68 AFDVLIDFTRPEGTLKHLEICREAGRAMVIGTTGFSEDQKQAIREAAKE--IPVVFAPNMSVGVNLCLK 134 *************************************************..****************** PP TIGR00036 141 llekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG 208 ll aa+vl+d DiE+iE+HHrhK+DaPSGTAl+++e++a a g+dl e+av++reg+tGer + +iG lcl|NCBI__GCF_000378965.1:WP_018234074.1 135 LLDLAARVLGDEvDIEVIEAHHRHKVDAPSGTALHMGEVVAGALGRDLAECAVYGREGHTGERDRRTIG 203 *********9877******************************************************** PP TIGR00036 209 iaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269 + ++R+gd+vgehtv+Fa+ Ger+eitHkassR++fa+G+vra+ wl+d ++++yd++dvl lcl|NCBI__GCF_000378965.1:WP_018234074.1 204 FETIRAGDIVGEHTVMFAGPGERVEITHKASSRMTFARGAVRAAAWLKDRAAGLYDMQDVL 264 ************************************************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (267 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: 00:00:00.00 # Mc/sec: 8.11 // [ok]
This GapMind analysis is from Apr 10 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