Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_012709958.1 NGR_RS28555 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_000018545.1:WP_012709958.1 Length = 272 Score = 393 bits (1010), Expect = e-114 Identities = 198/267 (74%), Positives = 223/267 (83%) Query: 1 MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60 M LVVVGA GRMGQTLIRT+ G +L AIERS SPF+G+DAGE+ G+G +GV ITD Sbjct: 6 MKLVVVGAAGRMGQTLIRTVHEAAGVRLHAAIERSNSPFIGRDAGELAGLGPIGVPITDK 65 Query: 61 PLPVFAKAHGVLDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATIVK 120 PL F +A GVLDFT+PA +VEFAGLAAQARIVHVIGTTGCSA+D+ KIRAAARHA +VK Sbjct: 66 PLEAFVEAEGVLDFTAPAGTVEFAGLAAQARIVHVIGTTGCSADDEAKIRAAARHARVVK 125 Query: 121 SGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGRDI 180 SGNMSLGVNLL VL + AA AL +D+DIEILEMHHRHKVDAPSGTALLLGEAAA+GR I Sbjct: 126 SGNMSLGVNLLGVLTETAARALSAKDWDIEILEMHHRHKVDAPSGTALLLGEAAAKGRGI 185 Query: 181 ALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSIFA 240 LAD +V+VRDG+TGPR G IGFATLRGG V+G+HSVILAG GE V LSH A DRSIFA Sbjct: 186 DLADQAVKVRDGHTGPRPQGTIGFATLRGGLVVGEHSVILAGEGELVTLSHSATDRSIFA 245 Query: 241 RGAIKAALWAHGKKPGLYSMLDVLGLN 267 RGA+ AALW +KPG Y+MLDVLGLN Sbjct: 246 RGAVAAALWGRSQKPGFYTMLDVLGLN 272 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: 306 Number of extensions: 10 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: 268 Length of database: 272 Length adjustment: 25 Effective length of query: 243 Effective length of database: 247 Effective search space: 60021 Effective search space used: 60021 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_012709958.1 NGR_RS28555 (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.3550512.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-82 262.7 0.8 2.3e-82 262.5 0.8 1.0 1 NCBI__GCF_000018545.1:WP_012709958.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000018545.1:WP_012709958.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.5 0.8 2.3e-82 2.3e-82 2 270 .] 6 270 .. 5 270 .. 0.96 Alignments for each domain: == domain 1 score: 262.5 bits; conditional E-value: 2.3e-82 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkad 74 +k++v GaaGrmG+ +i++v+ea +++l aa+er +s+ g+D+Gelag+g++gvp++d+ + +a+ NCBI__GCF_000018545.1:WP_012709958.1 6 MKLVVVGAAGRMGQTLIRTVHEAAGVRLHAAIERSNSPFIGRDAGELAGLGPIGVPITDKPLEA----FVEAE 74 89*******************************************************9985533....35667 PP TIGR00036 75 vliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaak 147 ++Dft p +++e + +a+++ + V+GTTG s +d ++++++a + +++v + N+++Gvnll l+e+aa+ NCBI__GCF_000018545.1:WP_012709958.1 75 GVLDFTAPAGTVEFAGLAAQARIVHVIGTTGCSADDEAKIRAAARH--ARVVKSGNMSLGVNLLGVLTETAAR 145 778******************************************9..9***********************9 PP TIGR00036 148 vl..edvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvv 218 l +d+DiEi+E+HHrhK+DaPSGTAl l+e+ ak rg dl ++av+ r+g+tG r + +iG+a++Rgg vv NCBI__GCF_000018545.1:WP_012709958.1 146 ALsaKDWDIEILEMHHRHKVDAPSGTALLLGEAAAKGRGIDLADQAVKVRDGHTGPRPQGTIGFATLRGGLVV 218 9844699****************************************************************** PP TIGR00036 219 gehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 geh+v+ a++Ge ++++H a++R++fa+G+v a+ w ++ ++y++ dvl+ NCBI__GCF_000018545.1:WP_012709958.1 219 GEHSVILAGEGELVTLSHSATDRSIFARGAVAAALWGRSQKPGFYTMLDVLG 270 **************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (272 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: 00:00:00.00 # Mc/sec: 11.95 // [ok]
This GapMind analysis is from Jul 25 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