Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_011306167.1 MBAR_RS06165 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q9K1F1 (269 letters) >NCBI__GCF_000195895.1:WP_011306167.1 Length = 263 Score = 188 bits (478), Expect = 9e-53 Identities = 129/271 (47%), Positives = 162/271 (59%), Gaps = 17/271 (6%) Query: 4 LKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAG-YAVGLKTGIAISD- 61 + +A+ GA GRMG ++VE V N D L A + S G DAG +A K G+ ISD Sbjct: 2 INVAVLGACGRMGSLIVENVINSKDMQLVAAFDIS---YFGRDAGEFARVGKLGVQISDV 58 Query: 62 -DVDAVLAQS--DVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKT 118 +++ VL +S DVLIDFT T+ + VN+IIGTTG +A I A ++ Sbjct: 59 KNLETVLKESKADVLIDFTAAGATVVNAPIAARAGVNLIIGTTGLTPEQRAVIDEAIQEG 118 Query: 119 GI--VFAANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIA 176 + V + N+SVGVN+ F I+ A+ L + YDIEIIE HH K DAPSGTALR ++I+ Sbjct: 119 QVSAVISPNYSVGVNVFFKIIREAAKYLAD-YDIEIIEAHHNQKKDAPSGTALRAADIIS 177 Query: 177 GALGRDLKQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASS 236 A+G + VYGREG PR IG VRAGDI GDH LFA + ER+EI H A S Sbjct: 178 EAVGG---REYVYGREG-IAPRGKE-IGIHGVRAGDITGDHIVLFAGNSERIEIKHIAHS 232 Query: 237 RMTFAAGAVRAAVWV-NGKTGLYDMQDVLGL 266 R FA GAVRAA WV K G+Y M DVLGL Sbjct: 233 RQIFAKGAVRAAEWVCRQKPGIYSMDDVLGL 263 Lambda K H 0.318 0.136 0.392 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: 225 Number of extensions: 17 Number of successful extensions: 6 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: 269 Length of database: 263 Length adjustment: 25 Effective length of query: 244 Effective length of database: 238 Effective search space: 58072 Effective search space used: 58072 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_011306167.1 MBAR_RS06165 (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.20927.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-99 319.3 3.8 1.2e-99 319.2 3.8 1.0 1 lcl|NCBI__GCF_000195895.1:WP_011306167.1 MBAR_RS06165 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011306167.1 MBAR_RS06165 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 319.2 3.8 1.2e-99 1.2e-99 1 270 [] 1 262 [. 1 262 [. 0.99 Alignments for each domain: == domain 1 score: 319.2 bits; conditional E-value: 1.2e-99 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla 69 +i+vav Ga+GrmG+ ++++v +++d++lvaa++ +s g+D+Ge+a +gk+gv+++d ++++vl+ lcl|NCBI__GCF_000195895.1:WP_011306167.1 1 MINVAVLGACGRMGSLIVENVINSKDMQLVAAFD---ISYFGRDAGEFARVGKLGVQISDVKNLETVLK 66 699*******************************...7******************************* PP TIGR00036 70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138 e+kadvliDft + a++ n+ ia+++gv+l++GTTG++ e+++ + +++++ +v++vi+pN+++Gvn++ lcl|NCBI__GCF_000195895.1:WP_011306167.1 67 ESKADVLIDFTAAGATVVNAPIAARAGVNLIIGTTGLTPEQRAVIDEAIQEGQVSAVISPNYSVGVNVF 135 ********************************************************************* PP TIGR00036 139 lkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 +k++++aak+l d+DiEiiE+HH++KkDaPSGTAl++a+ii++a g ++ v++reg++ r +ei lcl|NCBI__GCF_000195895.1:WP_011306167.1 136 FKIIREAAKYLADYDIEIIEAHHNQKKDAPSGTALRAADIISEAVG---GREYVYGREGIA-PR-GKEI 199 *********************************************9...6799********.88.899* PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 Gi++vR+gd+ g+h vlFa++ er+ei+H a+sR++fakG+vra++w+ ++ ++y ++dvl+ lcl|NCBI__GCF_000195895.1:WP_011306167.1 200 GIHGVRAGDITGDHIVLFAGNSERIEIKHIAHSRQIFAKGAVRAAEWVCRQKPGIYSMDDVLG 262 *************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (263 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: 6.22 // [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