Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_010961106.1 MCA_RS09110 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000008325.1:WP_010961106.1 Length = 269 Score = 316 bits (809), Expect = 4e-91 Identities = 164/265 (61%), Positives = 195/265 (73%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 IR IAG GRMG L++A LA V+L AA+ R GS ++G DAGELAG G+ V + Sbjct: 3 IRTGIAGVAGRMGGNLVRACLADPAVELTAAIARPGSPVVGRDAGELAGLSAIGLPVVGN 62 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 L V D DV IDFT PE TL HL CR G +VIGTTGF +Q I AA + IVF Sbjct: 63 LSEVSDKVDVLIDFTLPEVTLAHLESCRSAGIRLVIGTTGFSAEQRQLIAAAAEGMGIVF 122 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 A N SVGVN+ LKLL+ AA+V+G++ DIEI+EAHHRHK+DAPSGTAL MGE +A AL ++ Sbjct: 123 APNMSVGVNLALKLLDIAARVVGEHADIEIVEAHHRHKIDAPSGTALRMGEVVAKALGRN 182 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 L+DCA+Y REG TG R TIGF+T+RAGDIVGEHT MFAD GER+EITHKASSRMTFA Sbjct: 183 LQDCAIYGREGITGIRDAKTIGFSTIRAGDIVGEHTVMFADEGERIEITHKASSRMTFAK 242 Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270 GAVR+A+WL + GLFDM+DVL L Sbjct: 243 GAVRAAVWLMSQGEGLFDMQDVLGL 267 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: 255 Number of extensions: 8 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: 269 Length adjustment: 25 Effective length of query: 248 Effective length of database: 244 Effective search space: 60512 Effective search space used: 60512 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_010961106.1 MCA_RS09110 (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.21050.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-100 322.1 3.2 1.8e-100 321.9 3.2 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961106.1 MCA_RS09110 4-hydroxy-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961106.1 MCA_RS09110 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 321.9 3.2 1.8e-100 1.8e-100 2 270 .] 3 266 .. 2 266 .. 0.98 Alignments for each domain: == domain 1 score: 321.9 bits; conditional E-value: 1.8e-100 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 i+ ++aG aGrmG ++++a + + +el+aa+ r+gs+ +g+D+Gelag++ +g+pv +l+ v lcl|NCBI__GCF_000008325.1:WP_010961106.1 3 IRTGIAGVAGRMGGNLVRACLADPAVELTAAIARPGSPVVGRDAGELAGLSAIGLPVVGNLSEV----S 67 8999**********************************************************88....9 PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 +k+dvliDft+pe +l +++++ +g+rlV+GTTGfs e+++ ++++ae +++v+apN+++Gvnl l lcl|NCBI__GCF_000008325.1:WP_010961106.1 68 DKVDVLIDFTLPEVTLAHLESCRSAGIRLVIGTTGFSAEQRQLIAAAAEG--MGIVFAPNMSVGVNLAL 134 ********************************************999988..***************** PP TIGR00036 140 kllekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 kll aa+v+++ DiEi+E+HHrhK DaPSGTAl+++e++aka g++l+++a+++reg+tG r +++i lcl|NCBI__GCF_000008325.1:WP_010961106.1 135 KLLDIAARVVGEHaDIEIVEAHHRHKIDAPSGTALRMGEVVAKALGRNLQDCAIYGREGITGIRDAKTI 203 **********9877******************************************************* PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 G++++R+gd+vgehtv+Fa++Ger+eitHkassR++fakG+vra+ wl+ + e+++d++dvl+ lcl|NCBI__GCF_000008325.1:WP_010961106.1 204 GFSTIRAGDIVGEHTVMFADEGERIEITHKASSRMTFAKGAVRAAVWLMSQGEGLFDMQDVLG 266 *************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (269 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: 5.97 // [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