Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate RR42_RS18515 RR42_RS18515 dihydrodipicolinate reductase
Query= BRENDA::Q3MFY8 (278 letters) >FitnessBrowser__Cup4G11:RR42_RS18515 Length = 269 Score = 134 bits (337), Expect = 2e-36 Identities = 94/273 (34%), Positives = 140/273 (51%), Gaps = 12/273 (4%) Query: 7 IPVIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPITNQ 66 I V V G G G E+ + +A A D+ L+ + +G LA L+ P Sbjct: 5 IRVAVGGVTGWAGGELARGVAHADDMTLVAGLS-----RGAAGQALAALTAHKGTPGV-- 57 Query: 67 LEPMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNLADF 126 + + QG V V++T PD N+ A+A G VVGT+GLS + Sbjct: 58 ---AVASIDELAQGAFDVYVEYTKPDIAKRNILQALAKGAHVVVGTSGLSDEDYAEIDAA 114 Query: 127 AEKASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTAELL 186 A +A G L NF+I +VLLQ+ A A+++ +H EII+ K D PSGT + A L Sbjct: 115 ARQARRGVLACGNFAITVVLLQKFAEMAARHLEHWEIIDYAKAGKIDVPSGTVRELAYRL 174 Query: 187 AELGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTLRHD 246 ++ + + +++ + RG+ G ++H+VRLPG EVIFGA GQ L+H+ Sbjct: 175 GQVREARQAVPIDQVKGPKETRGATM-SGSQVHAVRLPGYQLGVEVIFGADGQRLHLKHE 233 Query: 247 TSDRA-CYMPGVLLAIRKVLQLKSLVYGLEKIL 278 + D + Y+ G LLAIRKV L LV GL+K++ Sbjct: 234 SGDGSKPYVSGALLAIRKVHALTGLVRGLDKVM 266 Lambda K H 0.317 0.136 0.386 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: 205 Number of extensions: 11 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: 278 Length of database: 269 Length adjustment: 25 Effective length of query: 253 Effective length of database: 244 Effective search space: 61732 Effective search space used: 61732 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 (21.6 bits) S2: 47 (22.7 bits)
Align candidate RR42_RS18515 RR42_RS18515 (dihydrodipicolinate 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.24471.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-46 143.1 1.5 6.7e-46 143.0 1.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS18515 RR42_RS18515 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18515 RR42_RS18515 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 143.0 1.5 6.7e-46 6.7e-46 2 269 .. 5 266 .. 4 267 .. 0.92 Alignments for each domain: == domain 1 score: 143.0 bits; conditional E-value: 6.7e-46 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelag.igkvgvpveddleavkvla 69 i+vav G +G G e+ + v++a+d+ lva l r g+ + l+ g gv+v + e la lcl|FitnessBrowser__Cup4G11:RR42_RS18515 5 IRVAVGGVTGWAGGELARGVAHADDMTLVAGLSR---GAAGQALAALTAhKGTPGVAVASIDE----LA 66 9********************************7...55566666776514566776666555....66 PP TIGR00036 70 ekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnll 138 + ++dv +++t+p++++ n+ al+kg ++VvGT G+s+ed +e+ ++a ++ +++ Nfai v+ll lcl|FitnessBrowser__Cup4G11:RR42_RS18515 67 QGAFDVYVEYTKPDIAKRNILQALAKGAHVVVGTSGLSDEDYAEIDAAARQARRGVLACGNFAITVVLL 135 ********************************************************************* PP TIGR00036 139 lkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 +k++e+aa+ le++ Eii+ K D+PSGT +la + ++r+ +++ +++ +g + r++ lcl|FitnessBrowser__Cup4G11:RR42_RS18515 136 QKFAEMAARHLEHW--EIIDYAKAGKIDVPSGTVRELAYRLGQVRE-ARQAVPIDQVKGPKETRGATMS 201 **************..******************************.6888889999999999999999 PP TIGR00036 208 G..iaavRggdvvgehtvlFasdGerleitHkassR.aafakGvvrairwledkeekvydledvl 269 G ++avR+++ +v+F+ dG+rl+++H++ + + +++G+++air+++ + +v +l++v+ lcl|FitnessBrowser__Cup4G11:RR42_RS18515 202 GsqVHAVRLPGYQLGVEVIFGADGQRLHLKHESGDGsKPYVSGALLAIRKVHALTGLVRGLDKVM 266 999*****************************9986267****************9999999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (269 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: 10.73 // [ok]
This GapMind analysis is from Apr 09 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