Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_012674160.1 SULAZ_RS07200 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q9K1F1 (269 letters) >NCBI__GCF_000021545.1:WP_012674160.1 Length = 267 Score = 209 bits (532), Expect = 5e-59 Identities = 121/268 (45%), Positives = 162/268 (60%), Gaps = 7/268 (2%) Query: 4 LKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGLKTGIA-ISDD 62 L++ I+G GRMGR + +N PD ++ +E L G + K A I+ D Sbjct: 2 LRLGISGVMGRMGRTIANLASNDPDISITAGIESPDCAHLHNTIGELINKKDLTAPITSD 61 Query: 63 VDAVLAQSDVLIDFT-RPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTGIV 121 + V+ Q DVLIDF E L HL+ + +IGTTGF D I +++ IV Sbjct: 62 LSQVIDQIDVLIDFAANQEAVLGHLRILAADKKAAVIGTTGFLDYQLQEIKEISKEIPIV 121 Query: 122 FAANFSVGVNLTFHILDTVARVLNE-GYDIEIIEGHHRHKVDAPSGTALRMGEVIAGALG 180 A N S+GVNL F +++ ARVL + G+DIE++E HHR+K DAPSGTA+++ +++ G Sbjct: 122 LAPNMSIGVNLLFKLVEKAARVLKDKGFDIEVVEMHHRYKKDAPSGTAMKIVDILKRETG 181 Query: 181 RDLKQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMTF 240 + VYGREG TG R IG +R GD+VGDHT +FA+ GER+E+THKASSR F Sbjct: 182 IEK---IVYGREGITGERSSKEIGVFALRGGDVVGDHTVIFASMGERIELTHKASSRDIF 238 Query: 241 AAGAVRAAVWVNGK-TGLYDMQDVLGLN 267 A GA+ AA WV K GLYDM DVLGLN Sbjct: 239 AKGAIEAAKWVKDKPAGLYDMIDVLGLN 266 Lambda K H 0.318 0.136 0.392 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: 242 Number of extensions: 11 Number of successful extensions: 6 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: 269 Length of database: 267 Length adjustment: 25 Effective length of query: 244 Effective length of database: 242 Effective search space: 59048 Effective search space used: 59048 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_012674160.1 SULAZ_RS07200 (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.41937.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-90 287.5 3.2 6.5e-90 287.3 3.2 1.0 1 NCBI__GCF_000021545.1:WP_012674160.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000021545.1:WP_012674160.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 287.3 3.2 6.5e-90 6.5e-90 1 270 [] 1 264 [. 1 264 [. 0.97 Alignments for each domain: == domain 1 score: 287.3 bits; conditional E-value: 6.5e-90 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekka 73 +++++++G +GrmGr + + + + +d++++a +e ++ + + iGel++ + p+++dl+ v ++ NCBI__GCF_000021545.1:WP_012674160.1 1 MLRLGISGVMGRMGRTIANLASNDPDISITAGIESPDCAHLHNTIGELINKKDLTAPITSDLSQV----IDQI 69 5899***********************************************************88....89** PP TIGR00036 74 dvliDftt.peavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllklleka 145 dvliDf+ eavl +++i+++ + V+GTTGf + +l+e+k+++++ +++v+apN++iGvnll+kl+eka NCBI__GCF_000021545.1:WP_012674160.1 70 DVLIDFAAnQEAVLGHLRILAADKKAAVIGTTGFLDYQLQEIKEISKE--IPIVLAPNMSIGVNLLFKLVEKA 140 ******86258999**********************************..*********************** PP TIGR00036 146 akvledv..DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggd 216 a+vl+d DiE++E+HHr+KkDaPSGTA+k+ +i+++ +g e+ v++reg+tGer+++eiG++a+Rggd NCBI__GCF_000021545.1:WP_012674160.1 141 ARVLKDKgfDIEVVEMHHRYKKDAPSGTAMKIVDILKRETG---IEKIVYGREGITGERSSKEIGVFALRGGD 210 ******888****************************9999...5789************************* PP TIGR00036 217 vvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 vvg+htv+Fas Ger+e+tHkassR++fakG+++a++w++dk +++yd+ dvl+ NCBI__GCF_000021545.1:WP_012674160.1 211 VVGDHTVIFASMGERIELTHKASSRDIFAKGAIEAAKWVKDKPAGLYDMIDVLG 264 ****************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (267 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: 14.64 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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