Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_090219124.1 CV091_RS12385 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_002796795.1:WP_090219124.1 Length = 269 Score = 313 bits (801), Expect = 3e-90 Identities = 156/265 (58%), Positives = 196/265 (73%), Gaps = 1/265 (0%) Query: 2 GLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDDP 61 G+V+ GA GRMGQ LI+T+ + A+LVGA+ER G ++G+D G G +GV +T D Sbjct: 6 GIVITGASGRMGQMLIKTVLDSDKARLVGAVEREGHDWVGQDIGAAMGGADVGVTVTSDA 65 Query: 62 LPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVKS 121 L FAKA V+DFT+PAA++EF+ LAAQAR VHVIGTTG + E+ ++ +ARHA IV++ Sbjct: 66 LEAFAKAQAVIDFTAPAATIEFSKLAAQARAVHVIGTTGMTEEEIAQLEPSARHAVIVRA 125 Query: 122 GNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDIA 181 GNMSLGVNLL L +K A AL +DFDIE++E HH HKVDAPSGTAL+LGEAAA GR ++ Sbjct: 126 GNMSLGVNLLVQLTKKVAAALD-DDFDIEVIEAHHHHKVDAPSGTALMLGEAAAEGRGVS 184 Query: 182 LADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFAR 241 L D RDG TG R+ G IGF +RGG ++G+H V+ A GER+VL H A DR+IFAR Sbjct: 185 LKDVRDSGRDGITGARKKGDIGFTAIRGGDIVGEHDVLFAAAGERIVLRHMATDRAIFAR 244 Query: 242 GAIKAALWAHGKKPGLYSMLDVLGL 266 GA+KAALW GK PG Y MLDVLGL Sbjct: 245 GALKAALWGQGKTPGEYDMLDVLGL 269 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: 273 Number of extensions: 12 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: 269 Length adjustment: 25 Effective length of query: 243 Effective length of database: 244 Effective search space: 59292 Effective search space used: 59292 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_090219124.1 CV091_RS12385 (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.3550664.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-83 265.7 7.8 2.9e-83 265.5 7.8 1.0 1 NCBI__GCF_002796795.1:WP_090219124.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002796795.1:WP_090219124.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.5 7.8 2.9e-83 2.9e-83 4 270 .] 7 268 .. 5 268 .. 0.97 Alignments for each domain: == domain 1 score: 265.5 bits; conditional E-value: 2.9e-83 TIGR00036 4 vavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvl 76 ++++Ga+GrmG+ +ik+v ++++ +lv+a+er+g++ +g+DiG +g + vgv+v++d + ka+ + NCBI__GCF_002796795.1:WP_090219124.1 7 IVITGASGRMGQMLIKTVLDSDKARLVGAVEREGHDWVGQDIGAAMGGADVGVTVTSDALEA----FAKAQAV 75 89*****************************************************9876544....5788899 PP TIGR00036 77 iDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvl 149 iDft p a+ e k+a+++ V+GTTG++ee++++l+ a + + +v a N+++Gvnll++l++k+a l NCBI__GCF_002796795.1:WP_090219124.1 76 IDFTAPAATIEFSKLAAQARAVHVIGTTGMTEEEIAQLEPSARH--AVIVRAGNMSLGVNLLVQLTKKVAAAL 146 ******************************************99..999************************ PP TIGR00036 150 edv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgeh 221 +d DiE+iE+HH+hK+DaPSGTAl l+e+ a+ rg lk++ ++r+g+tG+rkk +iG++a+Rggd+vgeh NCBI__GCF_002796795.1:WP_090219124.1 147 DDDfDIEVIEAHHHHKVDAPSGTALMLGEAAAEGRGVSLKDVRDSGRDGITGARKKGDIGFTAIRGGDIVGEH 219 8766********************************************************************* PP TIGR00036 222 tvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 vlFa Ger+ ++H a++Ra+fa+G+++a+ w + k + yd+ dvl+ NCBI__GCF_002796795.1:WP_090219124.1 220 DVLFAAAGERIVLRHMATDRAIFARGALKAALWGQGKTPGEYDMLDVLG 268 ***********************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (269 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: 22.16 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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