Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate 200320 SO_1140 dihydrodipicolinate reductase (RefSeq)
Query= CharProtDB::CH_002128 (273 letters) >FitnessBrowser__MR1:200320 Length = 270 Score = 348 bits (892), Expect = e-101 Identities = 179/266 (67%), Positives = 207/266 (77%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 +RVAI GAGGRMGR LI++A E ++LGAA+ER GSSL+G DAGELAG GK + + S Sbjct: 5 VRVAIVGAGGRMGRTLIESAYHQEHIRLGAAIERPGSSLVGVDAGELAGVGKLNIMIMDS 64 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 LD DDFDV IDFT PE ++ HL +C +H K MVIGTTGF+ A K+ I A +V Sbjct: 65 LDYATDDFDVLIDFTAPEASIVHLDWCVRHKKAMVIGTTGFNHAQKEQINAFAEQTPVVM 124 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 A N SVGVN+M KLLE AA+VMGDYTDIEIIE HHR+K DAPSGTAL MGE IA L +D Sbjct: 125 APNMSVGVNLMWKLLELAAEVMGDYTDIEIIEGHHRYKKDAPSGTALKMGEVIAKTLGRD 184 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 L+ CAVY REG TGER TIGFATVRAGD+VGEHTAMFADIGERLEITHKASSRMTFAN Sbjct: 185 LEKCAVYGREGITGERDRETIGFATVRAGDLVGEHTAMFADIGERLEITHKASSRMTFAN 244 Query: 246 GAVRSALWLSGKESGLFDMRDVLDLN 271 GA+R+A WL ++ GL+DM+ VL LN Sbjct: 245 GAMRAAHWLVEQKPGLYDMQQVLGLN 270 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: 293 Number of extensions: 15 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: 273 Length of database: 270 Length adjustment: 25 Effective length of query: 248 Effective length of database: 245 Effective search space: 60760 Effective search space used: 60760 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 200320 SO_1140 (dihydrodipicolinate reductase (RefSeq))
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.3404.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-110 353.9 2.0 3.5e-110 353.8 2.0 1.0 1 lcl|FitnessBrowser__MR1:200320 SO_1140 dihydrodipicolinate redu Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200320 SO_1140 dihydrodipicolinate reductase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.8 2.0 3.5e-110 3.5e-110 2 270 .] 5 268 .. 4 268 .. 0.99 Alignments for each domain: == domain 1 score: 353.8 bits; conditional E-value: 3.5e-110 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDft 80 ++va+ Ga+GrmGr +i+++ ++e+++l+aa+er+gss++g D+Gelag+gk+++ + d+l+ + +++dvliDft lcl|FitnessBrowser__MR1:200320 5 VRVAIVGAGGRMGRTLIESAYHQEHIRLGAAIERPGSSLVGVDAGELAGVGKLNIMIMDSLDYA----TDDFDVLIDFT 79 79***********************************************************977....9********** PP TIGR00036 81 tpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv.DiEiiE 158 pea ++ ++++ + +V+GTTGf+ +++++++++ae+ +++v+apN+++Gvnl++klle aa+v++d+ DiEiiE lcl|FitnessBrowser__MR1:200320 80 APEASIVHLDWCVRHKKAMVIGTTGFNHAQKEQINAFAEQ--TPVVMAPNMSVGVNLMWKLLELAAEVMGDYtDIEIIE 156 ****************************************..************************************* PP TIGR00036 159 lHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHk 237 HHr+KkDaPSGTAlk++e+iak+ g+dl+++av++reg+tGer +e+iG+a+vR+gd+vgeht +Fa++GerleitHk lcl|FitnessBrowser__MR1:200320 157 GHHRYKKDAPSGTALKMGEVIAKTLGRDLEKCAVYGREGITGERDRETIGFATVRAGDLVGEHTAMFADIGERLEITHK 235 ******************************************************************************* PP TIGR00036 238 assRaafakGvvrairwledkeekvydledvld 270 assR++fa+G++ra++wl++++ ++yd+++vl+ lcl|FitnessBrowser__MR1:200320 236 ASSRMTFANGAMRAAHWLVEQKPGLYDMQQVLG 268 *******************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (270 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: 00:00:00.01 # Mc/sec: 6.51 // [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