Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_086510469.1 BZY95_RS13640 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_002151265.1:WP_086510469.1 Length = 267 Score = 296 bits (757), Expect = 4e-85 Identities = 158/265 (59%), Positives = 183/265 (69%), Gaps = 1/265 (0%) Query: 7 RVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSL 66 R+AI G GRMGR L+ A G L + GSSL G+D GELAG GK GVT SL Sbjct: 3 RIAIVGVAGRMGRTLVNAVQEDAGATLAGGIVEPGSSLAGADIGELAGLGKLGVTAVDSL 62 Query: 67 DAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFA 126 DA+ DDFDV IDFT P TL +LAFC HGK MVIGTTG + + + VFA Sbjct: 63 DAIVDDFDVLIDFTAPRVTLANLAFCAAHGKRMVIGTTGLSDDELAELDGYRERLPFVFA 122 Query: 127 ANFSVGVNVMLKLLEKAAKVMGDYT-DIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 N SVGVN+ LKLLE AA+ +GD DIE+IEAHHRHKVD+PSGTAL MGE +A AL + Sbjct: 123 PNMSVGVNLTLKLLETAARALGDEGYDIEVIEAHHRHKVDSPSGTALKMGEVVAEALGRT 182 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 LK+ V+ R G G R IGFATVRAGDIVGEHT MFA GER+EITHKASSRMTFA Sbjct: 183 LKEHGVFERVGQCGPRDSKEIGFATVRAGDIVGEHTVMFATEGERIEITHKASSRMTFAK 242 Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270 GAVR+A W++ +ESG + M+DVL L Sbjct: 243 GAVRAARWVADQESGRYGMQDVLGL 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: 263 Number of extensions: 7 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: 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_086510469.1 BZY95_RS13640 (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.13170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-101 323.3 2.3 7.7e-101 323.1 2.3 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510469.1 BZY95_RS13640 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510469.1 BZY95_RS13640 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 323.1 2.3 7.7e-101 7.7e-101 2 270 .] 2 266 .. 1 266 [. 0.98 Alignments for each domain: == domain 1 score: 323.1 bits; conditional E-value: 7.7e-101 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 ++a+ G aGrmGr +++av+e + l++ + +gss+ g DiGelag+gk+gv+ d+l+a lcl|NCBI__GCF_002151265.1:WP_086510469.1 2 TRIAIVGVAGRMGRTLVNAVQEDAGATLAGGIVEPGSSLAGADIGELAGLGKLGVTAVDSLDAI----V 66 59*******************************9*********************888888877....9 PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 +++dvliDft p+ +l n+++++++g+r+V+GTTG+s+++l+el e+ + v+apN+++Gvnl l lcl|NCBI__GCF_002151265.1:WP_086510469.1 67 DDFDVLIDFTAPRVTLANLAFCAAHGKRMVIGTTGLSDDELAELDGYRER--LPFVFAPNMSVGVNLTL 133 **************************************************..***************** PP TIGR00036 140 kllekaakvledv..DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkee 206 klle+aa+ l+d DiE+iE+HHrhK+D+PSGTAlk++e++a+a g++lke+ v er g G r ++e lcl|NCBI__GCF_002151265.1:WP_086510469.1 134 KLLETAARALGDEgyDIEVIEAHHRHKVDSPSGTALKMGEVVAEALGRTLKEHGVFERVGQCGPRDSKE 202 **********99555****************************************************** PP TIGR00036 207 iGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 iG+a+vR+gd+vgehtv+Fa++Ger+eitHkassR++fakG+vra+rw++d+e++ y+++dvl+ lcl|NCBI__GCF_002151265.1:WP_086510469.1 203 IGFATVRAGDIVGEHTVMFATEGERIEITHKASSRMTFAKGAVRAARWVADQESGRYGMQDVLG 266 **************************************************************96 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.70 // [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