Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_013684583.1 ARCVE_RS09630 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_000194625.1:WP_013684583.1 Length = 259 Score = 198 bits (504), Expect = 9e-56 Identities = 120/268 (44%), Positives = 160/268 (59%), Gaps = 13/268 (4%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALE-REGSSLLGSDAGELAGAGKTGVTV-Q 63 IRVA+AGA GRMGR +I+ + + ++L A + RE +G DAGELAG GKTGV+V Sbjct: 2 IRVAVAGAAGRMGRLIIKNVVEDKELELAQAFDVRE----VGKDAGELAGVGKTGVSVIH 57 Query: 64 SSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAI 123 +S K D DV +DFT + ++ Q G +V+GTTGF E K+ I + + Sbjct: 58 ASEMEEKLDADVLVDFTTASAAVENIRIASQKGVKLVVGTTGFTEEQKKQIEEYCKAVPA 117 Query: 124 VFAANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALD 183 V + NFSVGVNV KLLE AA + +Y D+EI+E HHR K DAPSGTA+ E I + Sbjct: 118 VVSPNFSVGVNVFWKLLEAAASYLSNY-DVEIVEIHHRFKRDAPSGTAVKAAEVIKSVIG 176 Query: 184 KDLKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTF 243 + V R G IG VR GD+VGEHT F +GER+EITH+A SR F Sbjct: 177 ERE---VVTGRSGECPR--SDEIGVFAVRGGDVVGEHTVFFIGMGERVEITHRAWSRQAF 231 Query: 244 ANGAVRSALWLSG-KESGLFDMRDVLDL 270 A GA+++ W++G + G++ M DVL L Sbjct: 232 AGGAIKAVKWIAGINKPGIYGMADVLGL 259 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: 233 Number of extensions: 13 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: 259 Length adjustment: 25 Effective length of query: 248 Effective length of database: 234 Effective search space: 58032 Effective search space used: 58032 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_013684583.1 ARCVE_RS09630 (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.8007.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-102 327.4 6.0 4.4e-102 327.2 6.0 1.0 1 lcl|NCBI__GCF_000194625.1:WP_013684583.1 ARCVE_RS09630 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000194625.1:WP_013684583.1 ARCVE_RS09630 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 327.2 6.0 4.4e-102 4.4e-102 1 270 [] 1 258 [. 1 258 [. 0.98 Alignments for each domain: == domain 1 score: 327.2 bits; conditional E-value: 4.4e-102 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla 69 +i+vavaGaaGrmGr +ik+v e ++lel++a++ ++gkD+Gelag+gk+gv+v +++e++ lcl|NCBI__GCF_000194625.1:WP_013684583.1 1 MIRVAVAGAAGRMGRLIIKNVVEDKELELAQAFD---VREVGKDAGELAGVGKTGVSVIHASEME---E 63 69********************************...59*****************999998877...7 PP TIGR00036 70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138 + +advl+Dftt++a++en++ia +kgv+lVvGTTGf+ee++k++++ + v++v++pNf++Gvn++ lcl|NCBI__GCF_000194625.1:WP_013684583.1 64 KLDADVLVDFTTASAAVENIRIASQKGVKLVVGTTGFTEEQKKQIEEYCKA--VPAVVSPNFSVGVNVF 130 99***********************************************99..**************** PP TIGR00036 139 lkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 +klle aa +l+++D+Ei+E+HHr K+DaPSGTA+k+ae+i+ + g ++++v++r+g r ++ei lcl|NCBI__GCF_000194625.1:WP_013684583.1 131 WKLLEAAASYLSNYDVEIVEIHHRFKRDAPSGTAVKAAEVIKSVIG---EREVVTGRSGEC-PR-SDEI 194 **********************************************...7899******98.88.8*** PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkee.kvydledvld 270 G++avRggdvvgehtv+F + Ger+eitH+a sR+afa G+++a++w++ +++ ++y++ dvl+ lcl|NCBI__GCF_000194625.1:WP_013684583.1 195 GVFAVRGGDVVGEHTVFFIGMGERVEITHRAWSRQAFAGGAIKAVKWIAGINKpGIYGMADVLG 258 ***************************************************999********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (259 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: 00:00:00.00 # Mc/sec: 8.38 // [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