Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_011937180.1 GURA_RS01180 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q9K1F1 (269 letters) >NCBI__GCF_000016745.1:WP_011937180.1 Length = 267 Score = 253 bits (645), Expect = 4e-72 Identities = 134/265 (50%), Positives = 179/265 (67%), Gaps = 2/265 (0%) Query: 4 LKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGLKT-GIAISDD 62 +KIA+ GA GRMG ++ A++ V+SGALE G +G DAG+ GL G+ ISDD Sbjct: 2 VKIAVCGAAGRMGGRIIAAISETEGAVVSGALERLGHPMVGQDAGFNAGLGAIGVTISDD 61 Query: 63 VDAVLAQSDVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTGIVF 122 + AV+ DVLIDFT P+ +LK+L+ C + +I+IG+TGF +A A+ +V Sbjct: 62 LTAVVQGCDVLIDFTTPKVSLKNLEVCGLNKKSIVIGSTGFTPEERALAAELAKDIPVVL 121 Query: 123 AANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIAGALGRD 182 A N SVGVN+ F +L VA++L + +D+EI+E HH+ K D+PSGTA+RMGEV+A ALGRD Sbjct: 122 APNMSVGVNVCFKVLADVAKILGDDFDVEIVEAHHKMKKDSPSGTAVRMGEVVAEALGRD 181 Query: 183 LKQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMTFAA 242 + A + REG G R IG T+R GDIVG+HT F GER+EITH+A +R F+ Sbjct: 182 YNKVANFHREGICGERTKDEIGMQTIRGGDIVGEHTVYFIGMGERIEITHRAHTRDMFSR 241 Query: 243 GAVRAAVW-VNGKTGLYDMQDVLGL 266 G+VRAA W V+ K GLYDMQDVLGL Sbjct: 242 GSVRAAKWVVSQKPGLYDMQDVLGL 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: 262 Number of extensions: 13 Number of successful extensions: 3 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_011937180.1 GURA_RS01180 (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.30235.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-96 307.3 4.4 5.8e-96 307.1 4.4 1.0 1 lcl|NCBI__GCF_000016745.1:WP_011937180.1 GURA_RS01180 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016745.1:WP_011937180.1 GURA_RS01180 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 307.1 4.4 5.8e-96 5.8e-96 1 270 [] 1 265 [. 1 265 [. 0.99 Alignments for each domain: == domain 1 score: 307.1 bits; conditional E-value: 5.8e-96 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvla 69 ++k+av GaaGrmG ++i a+ e+e+ +++aler g++ +g+D+G ag+g +gv+++ddl+av lcl|NCBI__GCF_000016745.1:WP_011937180.1 1 MVKIAVCGAAGRMGGRIIAAISETEGAVVSGALERLGHPMVGQDAGFNAGLGAIGVTISDDLTAV---- 65 589************************************************************99.... PP TIGR00036 70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138 + +dvliDfttp+ l+n++++ + + +V+G TGf+ e+++ ++la++ +++v+apN+++Gvn+ lcl|NCBI__GCF_000016745.1:WP_011937180.1 66 VQGCDVLIDFTTPKVSLKNLEVCGLNKKSIVIGSTGFTPEERALAAELAKD--IPVVLAPNMSVGVNVC 132 99***********************************************99..**************** PP TIGR00036 139 lkllekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkee 206 +k+l ++ak+l+d D+Ei+E+HH+ KkD+PSGTA++++e++a+a g+d +++a +reg+ Ger+k+e lcl|NCBI__GCF_000016745.1:WP_011937180.1 133 FKVLADVAKILGDDfDVEIVEAHHKMKKDSPSGTAVRMGEVVAEALGRDYNKVANFHREGICGERTKDE 201 ***********8766****************************************************** PP TIGR00036 207 iGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 iG++++Rggd+vgehtv+F + Ger+eitH+a+ R++f +G vra++w++ ++ ++yd++dvl+ lcl|NCBI__GCF_000016745.1:WP_011937180.1 202 IGMQTIRGGDIVGEHTVYFIGMGERIEITHRAHTRDMFSRGSVRAAKWVVSQKPGLYDMQDVLG 265 **************************************************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.84 // [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