Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_014450265.1 LFE_RS10835 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q2YJN7 (268 letters) >NCBI__GCF_000284315.1:WP_014450265.1 Length = 273 Score = 201 bits (511), Expect = 1e-56 Identities = 116/268 (43%), Positives = 161/268 (60%), Gaps = 4/268 (1%) Query: 1 MGLVVVGAGGRMGQTLIRTIQSIEGAKLVGAIERSGSPFLGKDAGEVTGIGTLGVAITDD 60 +G+V+VGA GRMG+ +++ + G L GAI S P GK A GI G + Sbjct: 6 LGVVMVGASGRMGREILQVLSRESGVSLHGAIVESSDPLSGKPAPFHPGINCRGELTVSE 65 Query: 61 PLPVFAKAHGV--LDFTSPAASVEFAGLAAQARIVHVIGTTGCSAEDDEKIRAAARHATI 118 + + +DFT+ ++++ A L A+A + VIGTTG SA + E++ + + + Sbjct: 66 LRRGAGEGMPIVGIDFTNVSSTLSTARLFAEAGVPLVIGTTGFSAPEKEELFSHSAKIPL 125 Query: 119 VKSGNMSLGVNLLSVLVQKAAEALGPEDFDIEILEMHHRHKVDAPSGTALLLGEAAARGR 178 + + NMSLG++LL+ LV++ + AL FD EI+E+HH+ K DAPSGTAL LGEA A GR Sbjct: 126 LLAPNMSLGIHLLAHLVRQVSRAL--PGFDAEIVEVHHQKKKDAPSGTALFLGEAVASGR 183 Query: 179 DIALADNSVRVRDGYTGPRETGAIGFATLRGGSVIGDHSVILAGTGERVVLSHHAEDRSI 238 LAD V R+G G R IG +RGG V+GDH+V G GER+ L+H A R Sbjct: 184 GENLADRGVYSREGMVGERIPDTIGIMAVRGGDVVGDHTVHFLGMGERLELTHRASSRET 243 Query: 239 FARGAIKAALWAHGKKPGLYSMLDVLGL 266 FARGA++AA W KKPG Y M DVLG+ Sbjct: 244 FARGAVEAARWLALKKPGFYQMEDVLGI 271 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: 235 Number of extensions: 12 Number of successful extensions: 3 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 WP_014450265.1 LFE_RS10835 (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.13109.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-79 252.1 0.0 4.1e-79 251.9 0.0 1.0 1 lcl|NCBI__GCF_000284315.1:WP_014450265.1 LFE_RS10835 4-hydroxy-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000284315.1:WP_014450265.1 LFE_RS10835 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.9 0.0 4.1e-79 4.1e-79 4 270 .] 8 270 .. 5 270 .. 0.95 Alignments for each domain: == domain 1 score: 251.9 bits; conditional E-value: 4.1e-79 TIGR00036 4 vavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekk 72 v++ Ga+GrmGre+++ + ++ +++l +a+ + ++ gk + gi g + +e+ + e lcl|NCBI__GCF_000284315.1:WP_014450265.1 8 VVMVGASGRMGREILQVLSRESGVSLHGAIVESSDPLSGKPAPFHPGINCRGE--LTVSELRRGAGEGM 74 8999***************************9999*****9888888876655..23334444568999 PP TIGR00036 73 advliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkl 141 + v iDft +++l+++++ +e+gv lV+GTTGfs +++el + ++k ++l++apN+++G+ ll +l lcl|NCBI__GCF_000284315.1:WP_014450265.1 75 PIVGIDFTNVSSTLSTARLFAEAGVPLVIGTTGFSAPEKEELFSHSAK--IPLLLAPNMSLGIHLLAHL 141 *********************************************999..******************* PP TIGR00036 142 lekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGia 210 ++++++ l +D+Ei+E+HH++KkDaPSGTAl l+e++a rg++l + v++reg+ Ger ++iGi+ lcl|NCBI__GCF_000284315.1:WP_014450265.1 142 VRQVSRALPGFDAEIVEVHHQKKKDAPSGTALFLGEAVASGRGENLADRGVYSREGMVGERIPDTIGIM 210 ********************************************************************* PP TIGR00036 211 avRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 avRggdvvg+htv F + Gerle+tH+assR++fa+G+v+a+rwl+ k+ ++y++edvl+ lcl|NCBI__GCF_000284315.1:WP_014450265.1 211 AVRGGDVVGDHTVHFLGMGERLELTHRASSRETFARGAVEAARWLALKKPGFYQMEDVLG 270 **********************************************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.57 // [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