Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate GFF3239 PGA1_c32920 dihydrodipicolinate reductase DapB
Query= BRENDA::Q2YJN7 (268 letters) >FitnessBrowser__Phaeo:GFF3239 Length = 273 Score = 306 bits (785), Expect = 2e-88 Identities = 154/265 (58%), Positives = 194/265 (73%), Gaps = 1/265 (0%) Query: 2 GLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDP 61 G+V+ GA GRMGQ LI+TI A LVGA+ER G ++G+D G G +G+ +TDD Sbjct: 10 GIVITGASGRMGQMLIKTIADHPRAHLVGAVEREGHDWVGQDVGLAMGGSEIGITVTDDA 69 Query: 62 LPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121 FAKA V+DFTSP A++ FAG+AA+A +VHVIGTTG + ++ A+RH+ +++ Sbjct: 70 PAAFAKAQAVIDFTSPEATIAFAGMAAEAGVVHVIGTTGMNDAQIVQLEPASRHSVQMRA 129 Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181 GNMSLGVNLL L +K A AL EDFDIE++E HH HKVDAPSGTAL+LGEAAA GR + Sbjct: 130 GNMSLGVNLLVQLTKKVAAALD-EDFDIEVIEAHHHHKVDAPSGTALMLGEAAAEGRGVT 188 Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241 L+D S RDG TG R+ G IGF+ +RGG ++G+H V+ AG GER+VL H A DR+IFAR Sbjct: 189 LSDVSDSGRDGITGARKRGDIGFSAIRGGDIVGEHDVLFAGQGERIVLRHLATDRAIFAR 248 Query: 242 GAIKAALWAHGKKPGLYSMLDVLGL 266 GAIKAALW GK+PG Y MLDVLGL Sbjct: 249 GAIKAALWGQGKEPGQYDMLDVLGL 273 Lambda K H 0.318 0.136 0.387 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: 281 Number of extensions: 14 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: 268 Length of database: 273 Length adjustment: 25 Effective length of query: 243 Effective length of database: 248 Effective search space: 60264 Effective search space used: 60264 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 GFF3239 PGA1_c32920 (dihydrodipicolinate reductase DapB)
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.28435.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-84 267.8 6.0 6.8e-84 267.5 6.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3239 PGA1_c32920 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3239 PGA1_c32920 dihydrodipicolinate reductase DapB # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.5 6.0 6.8e-84 6.8e-84 4 270 .] 11 272 .. 9 272 .. 0.97 Alignments for each domain: == domain 1 score: 267.5 bits; conditional E-value: 6.8e-84 TIGR00036 4 vavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDf 79 ++++Ga+GrmG+ +ik++++++ +lv+a+er+g++ +g+D+G +g +++g++v+dd a+ ka+ +iDf lcl|FitnessBrowser__Phaeo:GFF3239 11 IVITGASGRMGQMLIKTIADHPRAHLVGAVEREGHDWVGQDVGLAMGGSEIGITVTDDAPAA----FAKAQAVIDF 82 89********************************************************9987....778899**** PP TIGR00036 80 ttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvle.dvDi 154 t pea+ + +a+e+gv V+GTTG++++++ +l+ ++ + +v + a N+++Gvnll++l++k+a l+ d+Di lcl|FitnessBrowser__Phaeo:GFF3239 83 TSPEATIAFAGMAAEAGVVHVIGTTGMNDAQIVQLEPASRH-SV-QMRAGNMSLGVNLLVQLTKKVAAALDeDFDI 156 *************************************9999.55.569*****************999997256** PP TIGR00036 155 EiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGe 230 E+iE+HH+hK+DaPSGTAl l+e+ a+ rg +l+++ ++r+g+tG+rk+ +iG++a+Rggd+vgeh vlFa++Ge lcl|FitnessBrowser__Phaeo:GFF3239 157 EVIEAHHHHKVDAPSGTALMLGEAAAEGRGVTLSDVSDSGRDGITGARKRGDIGFSAIRGGDIVGEHDVLFAGQGE 232 **************************************************************************** PP TIGR00036 231 rleitHkassRaafakGvvrairwledkeekvydledvld 270 r+ ++H a++Ra+fa+G+++a+ w + ke + yd+ dvl+ lcl|FitnessBrowser__Phaeo:GFF3239 233 RIVLRHLATDRAIFARGAIKAALWGQGKEPGQYDMLDVLG 272 **************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (273 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: 7.90 // [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