Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate WP_093396407.1 BM091_RS13070 4-hydroxy-tetrahydrodipicolinate reductase
Query= CharProtDB::CH_002128 (273 letters) >NCBI__GCF_900114975.1:WP_093396407.1 Length = 267 Score = 234 bits (596), Expect = 2e-66 Identities = 123/265 (46%), Positives = 165/265 (62%) Query: 6 IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65 IRVA+AG GRMG ++ Q E + L ER+ L+G G+ V S Sbjct: 2 IRVAVAGIAGRMGSRIAQLVSEAEDLTLVGCWERKDHPLVGKPLKSAVAWAPEGLMVSES 61 Query: 66 LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125 + ++ +V IDFT PE T+ H C G VIGTTG E ++ + + A I +V Sbjct: 62 PEKAVENAEVVIDFTVPEATVEHAKICASMGICAVIGTTGLSETDRKILEECARKIPMVV 121 Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185 A N SVGVNV+ +L+E AA+++G DIEI+EAHHR K DAPSGTA+ +G+ +A A + Sbjct: 122 APNMSVGVNVLFRLVEFAARLLGPDFDIEIVEAHHRFKKDAPSGTAIKLGQILADATGRS 181 Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245 + AVY R+G GER P IG +RAGDIVGEHT +FA +GER+EITH+A SR FA Sbjct: 182 WDNSAVYVRKGIVGERKPEEIGIQVLRAGDIVGEHTVLFASLGERIEITHRAHSRDNFAR 241 Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270 GA+R+A W+ GK GL+DM++VL L Sbjct: 242 GALRAARWVVGKAPGLYDMQNVLGL 266 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: 222 Number of extensions: 9 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: 267 Length adjustment: 25 Effective length of query: 248 Effective length of database: 242 Effective search space: 60016 Effective search space used: 60016 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_093396407.1 BM091_RS13070 (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.1737119.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-95 306.0 0.1 1.5e-95 305.8 0.1 1.0 1 NCBI__GCF_900114975.1:WP_093396407.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900114975.1:WP_093396407.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 305.8 0.1 1.5e-95 1.5e-95 1 270 [] 1 265 [. 1 265 [. 0.98 Alignments for each domain: == domain 1 score: 305.8 bits; conditional E-value: 1.5e-95 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekka 73 +i+vavaG aGrmG+++ + v eaedl lv+ erk+++++gk + + ++ g+ v+++ e + ++a NCBI__GCF_900114975.1:WP_093396407.1 1 MIRVAVAGIAGRMGSRIAQLVSEAEDLTLVGCWERKDHPLVGKPLKSAVAWAPEGLMVSESPEKA----VENA 69 69********************************************************9999977....999* PP TIGR00036 74 dvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaa 146 +v+iDft+pea++e++ki++ g+ V+GTTG+se d+k l+++a k +++v+apN+++Gvn+l++l+e aa NCBI__GCF_900114975.1:WP_093396407.1 70 EVVIDFTVPEATVEHAKICASMGICAVIGTTGLSETDRKILEECARK--IPMVVAPNMSVGVNVLFRLVEFAA 140 ***********************************************..************************ PP TIGR00036 147 kvle.dvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvv 218 + l+ d+DiEi+E+HHr KkDaPSGTA+kl++i+a+a+g+ ++ av+ r+g+ Gerk eeiGi+ +R+gd+v NCBI__GCF_900114975.1:WP_093396407.1 141 RLLGpDFDIEIVEAHHRFKKDAPSGTAIKLGQILADATGRSWDNSAVYVRKGIVGERKPEEIGIQVLRAGDIV 213 ***8688****************************************************************** PP TIGR00036 219 gehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 gehtvlFas Ger+eitH+a+sR+ fa+G++ra+rw++ k+ ++yd+++vl+ NCBI__GCF_900114975.1:WP_093396407.1 214 GEHTVLFASLGERIEITHRAHSRDNFARGALRAARWVVGKAPGLYDMQNVLG 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 23.45 // [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