Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate N515DRAFT_2152 N515DRAFT_2152 dihydrodipicolinate reductase
Query= BRENDA::Q3MFY8 (278 letters) >FitnessBrowser__Dyella79:N515DRAFT_2152 Length = 267 Score = 141 bits (355), Expect = 2e-38 Identities = 98/272 (36%), Positives = 140/272 (51%), Gaps = 13/272 (4%) Query: 9 VIVNGAAGKMGREVVKAIAQAPDLNLLGAIDSSPEHQGKDAGELAGLSEPLEVPITNQLE 68 V + GA G G E+ + +A A L L+ A+ S +H G + G E L+ P+ Sbjct: 5 VCLAGATGWAGSELARGLAVADGLKLVSAV--SRKHAGATLAQALG-DERLDAPV----- 56 Query: 69 PMLGYVAGERQGPPGVIVDFTHPDSVYDNVRSAIAYGIRPVVGTTGLSPAQIQNLADFAE 128 A P V +++T PDS N+ +A+ +G VVGT+GLS + + A Sbjct: 57 --FATAAEALSKPVDVFMEYTRPDSAKANILAALEHGAHVVVGTSGLSDEDYARIDEAAR 114 Query: 129 KASTGCLIIPNFSIGMVLLQQAAVTASQYFDHVEIIELHHNQKADAPSGTAIQTAELLAE 188 L NF++ MVLLQ+ A A++Y EII+ + K DAPSGT + A L + Sbjct: 115 AKGRAVLACGNFALTMVLLQKFAEQAAKYIPSWEIIDYAYEGKPDAPSGTVRELAGRLGK 174 Query: 189 LGKTFNSAIVEETEKIPGARGSLAGEGIRIHSVRLPGLIAHQEVIFGAPGQIYTLRHDTS 248 + + +E+T + RG G G ++H+VRLPG + EVIFG P Q TLRH+ Sbjct: 175 VRQPEPGLPLEKTNGVRETRGGTLG-GAQVHAVRLPGFVLGAEVIFGMPDQTLTLRHNAG 233 Query: 249 DRA-CYMPGVLLAIRKVLQL-KSLVYGLEKIL 278 A Y+ G LLAIRKV L L GL+K+L Sbjct: 234 SSAKPYVDGALLAIRKVSGLAPGLHRGLDKVL 265 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: 215 Number of extensions: 9 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: 267 Length adjustment: 25 Effective length of query: 253 Effective length of database: 242 Effective search space: 61226 Effective search space used: 61226 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 N515DRAFT_2152 N515DRAFT_2152 (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.19925.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-46 144.5 0.0 2.5e-46 144.4 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 N515DRAFT_2152 dihydrodipicolina Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 N515DRAFT_2152 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 144.4 0.0 2.5e-46 2.5e-46 2 269 .. 3 265 .. 2 266 .. 0.90 Alignments for each domain: == domain 1 score: 144.4 bits; conditional E-value: 2.5e-46 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkv 67 ++v +aGa+G G+e+ + ++ a++l+lv+a+ r ++ g + + g +++ pv + + lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 3 LNVCLAGATGWAGSELARGLAVADGLKLVSAVSR---KHAGATLAQALGDERLDAPVFATAAEA-- 63 7899*****************************7...777888899999999999998776644.. PP TIGR00036 68 laekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfai 133 k +dv++++t+p++++ n+ +ale+g ++VvGT G+s+ed +++ ++a kg a++ Nfa+ lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 64 -LSKPVDVFMEYTRPDSAKANILAALEHGAHVVVGTSGLSDEDYARIDEAARAKGRAVLACGNFAL 128 .6899************************************************************* PP TIGR00036 134 GvnlllkllekaakvledvDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveereglt 199 ++ll+k++e+aak++ + Eii+ + K DaPSGT +la + k+r+ + e+ +g++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 129 TMVLLQKFAEQAAKYIPSW--EIIDYAYEGKPDAPSGTVRELAGRLGKVRQ-PEPGLPLEKTNGVR 191 *******************..*****************************9.34444456667899 PP TIGR00036 200 GerkkeeiG..iaavRggdvvgehtvlFasdGerleitHka.ssRaafakGvvrairwledkeekv 262 r+ G ++avR+++ v +v+F++ ++l+++H+a ss + ++ G+++air+++ ++ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 192 ETRGGTLGGaqVHAVRLPGFVLGAEVIFGMPDQTLTLRHNAgSSAKPYVDGALLAIRKVSGLAPGL 257 78866666699*****************************9445678*************999865 PP TIGR00036 263 y.dledvl 269 + +l++vl lcl|FitnessBrowser__Dyella79:N515DRAFT_2152 258 HrGLDKVL 265 42566666 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.09 // [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