Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_012966505.1 FERP_RS10190 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000025505.1:WP_012966505.1 Length = 253 Score = 193 bits (490), Expect = 4e-54 Identities = 116/265 (43%), Positives = 161/265 (60%), Gaps = 16/265 (6%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 + V + GA GRMGR +++ A+ + A RE +G DAGELAG GK G +Q Sbjct: 1 MNVCVNGAAGRMGRLVVKNAVEANHKVVQAFDVRE----IGKDAGELAGVGKIGTLIQEM 56 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 D + DV IDF+ PE T+ + + +VIGTTGF++ K+ I +A+ I IV Sbjct: 57 SDL---NCDVAIDFSVPEATIKLVELALKSNTKLVIGTTGFNDEQKRVIEEASKKIPIVM 113 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 + NFSVGVNV K++E+A+K++ DY D+EI+E HHR K DAPSGTAL E + + + + Sbjct: 114 SPNFSVGVNVFWKIIEEASKLLRDY-DVEILEIHHRFKRDAPSGTALKAAEIVKNEIGVE 172 Query: 186 LKDCAVYSREGHTGERVPG-TIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFA 244 V+ G +GE + G IG +R GD+VGEH MF GER+EI HKA SR FA Sbjct: 173 K---LVF---GRSGECLRGDEIGVMAIRGGDVVGEHYVMFIGFGERIEINHKAWSREIFA 226 Query: 245 NGAVRSALWLSGKES-GLFDMRDVL 268 GA+++A W+ + GL+ MRDVL Sbjct: 227 RGAIKAAEWVMNVDKPGLYGMRDVL 251 Lambda K H 0.319 0.135 0.383 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: 221 Number of extensions: 20 Number of successful extensions: 5 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: 273 Length of database: 253 Length adjustment: 25 Effective length of query: 248 Effective length of database: 228 Effective search space: 56544 Effective search space used: 56544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_012966505.1 FERP_RS10190 (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.16749.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-92 294.3 3.3 5.2e-92 294.2 3.3 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012966505.1 FERP_RS10190 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012966505.1 FERP_RS10190 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 294.2 3.3 5.2e-92 5.2e-92 2 270 .] 1 252 [. 1 252 [. 0.95 Alignments for each domain: == domain 1 score: 294.2 bits; conditional E-value: 5.2e-92 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 ++v v+GaaGrmGr v+k++ ea + ++v+a++ + gkD+Gelag+gk+g +++ +++ lcl|NCBI__GCF_000025505.1:WP_012966505.1 1 MNVCVNGAAGRMGRLVVKNAVEA-NHKVVQAFD---VREIGKDAGELAGVGKIGTLIQEMSDL------ 59 789******************95.569******...599****************88877775...... PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 ++dv iDf++pea+ + v++al+ + +lV+GTTGf++e+++ ++++++k +++v++pNf++Gvn+++ lcl|NCBI__GCF_000025505.1:WP_012966505.1 60 -NCDVAIDFSVPEATIKLVELALKSNTKLVIGTTGFNDEQKRVIEEASKK--IPIVMSPNFSVGVNVFW 125 .5************************************************..***************** PP TIGR00036 140 kllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG 208 k++e+a+k l+d+D+Ei+E+HHr K+DaPSGTAlk+aei+++ g e++v +r+g r +eiG lcl|NCBI__GCF_000025505.1:WP_012966505.1 126 KIIEEASKLLRDYDVEILEIHHRFKRDAPSGTALKAAEIVKNEIG---VEKLVFGRSGEC-LR-GDEIG 189 ******************************************999...577888888877.66.799** PP TIGR00036 209 iaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkee.kvydledvld 270 ++a+Rggdvvgeh v+F + Ger+ei+Hka sR++fa+G+++a++w++++++ ++y+++dvl+ lcl|NCBI__GCF_000025505.1:WP_012966505.1 190 VMAIRGGDVVGEHYVMFIGFGERIEINHKAWSREIFARGAIKAAEWVMNVDKpGLYGMRDVLG 252 ***************************************************99********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (253 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 9.94 // [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