Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate BWI76_RS04460 BWI76_RS04460 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >FitnessBrowser__Koxy:BWI76_RS04460 Length = 273 Score = 489 bits (1259), Expect = e-143 Identities = 247/273 (90%), Positives = 261/273 (95%) Query: 1 MHDANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGV 60 MHDA IRVAIAGAGGRMGRQLIQA ++G LGAALEREGSSLLGSDAGELAGAGK GV Sbjct: 1 MHDAQIRVAIAGAGGRMGRQLIQAVQQMDGAALGAALEREGSSLLGSDAGELAGAGKAGV 60 Query: 61 TVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAAD 120 VQSSL+AVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFD+AGKQAIR+A+ + Sbjct: 61 VVQSSLEAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDDAGKQAIREASQE 120 Query: 121 IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAH 180 IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIA Sbjct: 121 IAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAG 180 Query: 181 ALDKDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSR 240 ALDKDLK CAVYSREG+TGERVPGTIGFATVRAGDIVGEHTAMFADIGER+EI+HKASSR Sbjct: 181 ALDKDLKACAVYSREGYTGERVPGTIGFATVRAGDIVGEHTAMFADIGERIEISHKASSR 240 Query: 241 MTFANGAVRSALWLSGKESGLFDMRDVLDLNNL 273 MTFANGAVRSALWL GK++GLFDMRDVL+LN+L Sbjct: 241 MTFANGAVRSALWLKGKKNGLFDMRDVLELNSL 273 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: 387 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: 273 Length of database: 273 Length adjustment: 25 Effective length of query: 248 Effective length of database: 248 Effective search space: 61504 Effective search space used: 61504 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 BWI76_RS04460 BWI76_RS04460 (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.19917.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-114 367.2 5.5 3.2e-114 367.0 5.5 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS04460 BWI76_RS04460 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS04460 BWI76_RS04460 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 367.0 5.5 3.2e-114 3.2e-114 2 270 .] 6 269 .. 5 269 .. 0.99 Alignments for each domain: == domain 1 score: 367.0 bits; conditional E-value: 3.2e-114 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekk 72 i+va+aGa+GrmGr++i+av++ ++ +l+aaler+gss+ g+D+Gelag+gk+gv v+++leav +++ lcl|FitnessBrowser__Koxy:BWI76_RS04460 6 IRVAIAGAGGRMGRQLIQAVQQMDGAALGAALEREGSSLLGSDAGELAGAGKAGVVVQSSLEAV----KDD 72 9*************************************************************99....*** PP TIGR00036 73 advliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllklle 143 +dv+iDft+pe++l++++++ ++g+ +V+GTTGf++++++++++++++ +a+v+a+Nf++Gvn++lklle lcl|FitnessBrowser__Koxy:BWI76_RS04460 73 FDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDDAGKQAIREASQE--IAIVFAANFSVGVNVMLKLLE 141 ************************************************..********************* PP TIGR00036 144 kaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavR 213 kaakv++d+ DiEiiE+HHrhK+DaPSGTAl+++e+ia a +kdlk++av++reg tGer +iG+a+vR lcl|FitnessBrowser__Koxy:BWI76_RS04460 142 KAAKVMGDYtDIEIIEAHHRHKVDAPSGTALAMGEAIAGALDKDLKACAVYSREGYTGERVPGTIGFATVR 212 *********************************************************************** PP TIGR00036 214 ggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 +gd+vgeht +Fa++Ger+ei+HkassR++fa+G+vr++ wl+ k+++++d++dvl+ lcl|FitnessBrowser__Koxy:BWI76_RS04460 213 AGDIVGEHTAMFADIGERIEISHKASSRMTFANGAVRSALWLKGKKNGLFDMRDVLE 269 *******************************************************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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.73 // [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