Align dihydrodipicolinate reductase subunit (EC 1.17.1.8) (characterized)
to candidate WP_069665198.1 BCR25_RS19050 4-hydroxy-tetrahydrodipicolinate reductase
Query= metacyc::MONOMER-6568 (267 letters) >NCBI__GCF_001730305.1:WP_069665198.1 Length = 262 Score = 285 bits (728), Expect = 9e-82 Identities = 143/262 (54%), Positives = 197/262 (75%), Gaps = 2/262 (0%) Query: 6 IKLVIAGPRGRMGQEAVKLAERTPHFDLVGAIDHTYDQQKLSDVMPVES-DAFIYTDIHA 64 IK+++AG +G+MG A K+ F+LVG +D ++ L ++ + D I+ Sbjct: 2 IKILVAGFKGKMGATATKMVIDHEGFELVGVLDPFEEKDNLQELPEYATLDVPIFKTKEE 61 Query: 65 CFTETQPDVLIDLTTPEIGKVHTKIALEHGVRPVVGTTGFSEADLKELTSLTEEKGIGAI 124 + QPDV ID T P++ +T+ A+EH + PVVGTTG +E L+ELT+ +EE +G + Sbjct: 62 VIS-VQPDVWIDFTIPKVAYENTRFAIEHHISPVVGTTGLTEEQLEELTARSEELQVGGL 120 Query: 125 IAPNFALGAILMMKFSKMAANYFEDVEIIELHHDQKLDAPSGTALKTAEMISEVRKEKQQ 184 IAPNFA+GA+LMM+F++ AA YF DVEIIELHHD KLDAPSGTA+KTAEM+SEVRK+K Q Sbjct: 121 IAPNFAVGAVLMMQFAQKAAEYFPDVEIIELHHDNKLDAPSGTAIKTAEMMSEVRKKKTQ 180 Query: 185 GHPDEKEILPGARGAEQNGIRLHSVRLPGLIAHQEVMFGMDGQTLQIRHDSYNRASFMSG 244 GHP+EKE+L GARGA+ +G+++HSVRLPGLIAHQ+V FG G+ L IRHDSY+R+SFM+G Sbjct: 181 GHPEEKELLAGARGADFDGMKIHSVRLPGLIAHQQVQFGGIGEGLTIRHDSYDRSSFMTG 240 Query: 245 VKLSVEQVMKIDQLVYGLENII 266 V L E+V++++ LVYGLEN++ Sbjct: 241 VALGCEKVVQLNTLVYGLENLL 262 Lambda K H 0.317 0.135 0.379 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: 247 Number of extensions: 7 Number of successful extensions: 2 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: 267 Length of database: 262 Length adjustment: 25 Effective length of query: 242 Effective length of database: 237 Effective search space: 57354 Effective search space used: 57354 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_069665198.1 BCR25_RS19050 (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.3404841.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-83 264.0 0.2 9.5e-83 263.8 0.2 1.0 1 NCBI__GCF_001730305.1:WP_069665198.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069665198.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 263.8 0.2 9.5e-83 9.5e-83 1 269 [. 1 262 [] 1 262 [] 0.96 Alignments for each domain: == domain 1 score: 263.8 bits; conditional E-value: 9.5e-83 TIGR00036 1 likvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekka 73 +ik+ vaG +G+mG + k v ++e++elv++l+ + ++ ++ el + + ++vp+ + e v ++ NCBI__GCF_001730305.1:WP_069665198.1 1 MIKILVAGFKGKMGATATKMVIDHEGFELVGVLD-PFEE--KDNLQELPEYATLDVPIFKTKEEV---ISVQP 67 69********************************.3333..34678***********99888865...7899* PP TIGR00036 74 dvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaa 146 dv iDft+p+ ++en+++a+e+ + +VvGTTG++ee+l+el++ +e+ +v+ +iapNfa+G++l++++++kaa NCBI__GCF_001730305.1:WP_069665198.1 68 DVWIDFTIPKVAYENTRFAIEHHISPVVGTTGLTEEQLEELTARSEELQVGGLIAPNFAVGAVLMMQFAQKAA 140 ************************************************************************* PP TIGR00036 147 kvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiG..iaavRggdv 217 +++ dv EiiElHH++K DaPSGTA+k+ae+++++r+ ++ + + ee+e l+G+r+++ G i++vR++++ NCBI__GCF_001730305.1:WP_069665198.1 141 EYFPDV--EIIELHHDNKLDAPSGTAIKTAEMMSEVRK-KKTQGHPEEKELLAGARGADFDGmkIHSVRLPGL 210 ****99..******************************.59999******************99********* PP TIGR00036 218 vgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvl 269 +++++v F+++Ge l+i+H++++R++f++Gv ++ +++++++++vy+le++l NCBI__GCF_001730305.1:WP_069665198.1 211 IAHQQVQFGGIGEGLTIRHDSYDRSSFMTGVALGCEKVVQLNTLVYGLENLL 262 *************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (262 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: 15.37 // [ok]
This GapMind analysis is from Jul 26 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