Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_013835599.1 THICY_RS05380 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000214825.1:WP_013835599.1 Length = 270 Score = 333 bits (855), Expect = 2e-96 Identities = 171/264 (64%), Positives = 204/264 (77%) Query: 7 RVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSL 66 R+AI GA GRMG+ L++A L G+ LGAA+ER GSSL+G DAG+L GAG GV V L Sbjct: 6 RIAILGASGRMGKYLLEAILVEPGLVLGAAVERPGSSLVGVDAGDLIGAGPQGVKVVDHL 65 Query: 67 DAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFA 126 V DDFD+ IDFTRPE TL L+ C Q K MVIGTTGFD+AG A+ +A++ I +VFA Sbjct: 66 ADVVDDFDILIDFTRPEVTLQALSLCVQANKRMVIGTTGFDQAGLAALDEASSKIPLVFA 125 Query: 127 ANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDL 186 N SVGV + LKLL+ AA+V+ D DIE+IEAHHRHK+DAPSGTAL M E +A L +DL Sbjct: 126 PNMSVGVTLTLKLLKMAAEVLNDGFDIEVIEAHHRHKIDAPSGTALRMAEVVADTLGRDL 185 Query: 187 KDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANG 246 K CAVY REG+TGER P TIGFATVRAGDIVG+HT MFA IGER+EITHKASSRMTFA G Sbjct: 186 KTCAVYGREGNTGERDPNTIGFATVRAGDIVGDHTVMFAGIGERVEITHKASSRMTFAKG 245 Query: 247 AVRSALWLSGKESGLFDMRDVLDL 270 AVR+ WL+ + +GL+DM+DVL L Sbjct: 246 AVRACGWLAERPNGLYDMQDVLGL 269 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: 284 Number of extensions: 4 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 WP_013835599.1 THICY_RS05380 (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.21624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-103 332.0 0.3 1.9e-103 331.7 0.3 1.0 1 lcl|NCBI__GCF_000214825.1:WP_013835599.1 THICY_RS05380 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214825.1:WP_013835599.1 THICY_RS05380 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 331.7 0.3 1.9e-103 1.9e-103 3 270 .] 6 268 .. 5 268 .. 0.99 Alignments for each domain: == domain 1 score: 331.7 bits; conditional E-value: 1.9e-103 TIGR00036 3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaek 71 ++a+ Ga+GrmG+ +++a+ +++l l+aa+er+gss++g D+G+l+g+g+ gv+v d+l v + lcl|NCBI__GCF_000214825.1:WP_013835599.1 6 RIAILGASGRMGKYLLEAILVEPGLVLGAAVERPGSSLVGVDAGDLIGAGPQGVKVVDHLADV----VD 70 79*********************************************************9988....9* PP TIGR00036 72 kadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllk 140 ++d+liDft+pe +l+ + +++++++r+V+GTTGf++++l++l ++++k ++lv+apN+++Gv l lk lcl|NCBI__GCF_000214825.1:WP_013835599.1 71 DFDILIDFTRPEVTLQALSLCVQANKRMVIGTTGFDQAGLAALDEASSK--IPLVFAPNMSVGVTLTLK 137 *************************************************..****************** PP TIGR00036 141 llekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG 208 ll++aa+vl+d DiE+iE+HHrhK DaPSGTAl++ae++a++ g+dlk++av++reg tGer ++iG lcl|NCBI__GCF_000214825.1:WP_013835599.1 138 LLKMAAEVLNDGfDIEVIEAHHRHKIDAPSGTALRMAEVVADTLGRDLKTCAVYGREGNTGERDPNTIG 206 ***********88******************************************************** PP TIGR00036 209 iaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 +a+vR+gd+vg+htv+Fa++Ger+eitHkassR++fakG+vra wl++ +++yd++dvl+ lcl|NCBI__GCF_000214825.1:WP_013835599.1 207 FATVRAGDIVGDHTVMFAGIGERVEITHKASSRMTFAKGAVRACGWLAERPNGLYDMQDVLG 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.24 // [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