Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_012474043.1 CPHAMN1_RS02975 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000020545.1:WP_012474043.1 Length = 297 Score = 289 bits (739), Expect = 6e-83 Identities = 140/288 (48%), Positives = 199/288 (69%), Gaps = 1/288 (0%) Query: 4 GSIVALITPFKEG-EVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFA 62 GS VAL+TPF++ VD EA+ L+ FH+ GTD ++ CGTTGESPTLT +E ++IE Sbjct: 8 GSAVALVTPFRQDMSVDREAIRRLVHFHIAAGTDILIPCGTTGESPTLTADEQTEIIEIV 67 Query: 63 VKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVA 122 + A ++ V AG G NAT EAV L ++A++ GA L V PYYNKP+Q G Y+H++ +A Sbjct: 68 REEAGNKMLVAAGAGTNATEEAVSLASNAQKAGAQALLSVAPYYNKPSQEGYYQHYRRIA 127 Query: 123 QEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFS 182 + V IP+I+YN+P RT + +T+ +LA +CENI A KE++ NM +I E++ + FS Sbjct: 128 EAVSIPVIVYNVPGRTGSNVHAETILRLAHDCENIAAVKEASDNMAQIMELLASRPDDFS 187 Query: 183 VLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKV 242 V++G+DSL LP MALG GVISVA N++P EVK+L+ EGD +AR IH L LF + Sbjct: 188 VMTGEDSLILPFMALGGDGVISVAANLLPAEVKQLVTEMHEGDLEKARVIHNRLRRLFSL 247 Query: 243 LFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNL 290 FIE+NP+PVK + ++GM E+ +RLPL + PEN+ K++E L+ L Sbjct: 248 NFIESNPVPVKYSLSLMGMIEEVYRLPLVALQPENKEKIKEELRNLGL 295 Lambda K H 0.318 0.136 0.390 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: 251 Number of extensions: 11 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: 294 Length of database: 297 Length adjustment: 26 Effective length of query: 268 Effective length of database: 271 Effective search space: 72628 Effective search space used: 72628 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_012474043.1 CPHAMN1_RS02975 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.3510.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-110 353.3 0.1 3.9e-110 353.2 0.1 1.0 1 lcl|NCBI__GCF_000020545.1:WP_012474043.1 CPHAMN1_RS02975 4-hydroxy-tetrah Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_012474043.1 CPHAMN1_RS02975 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.2 0.1 3.9e-110 3.9e-110 2 285 .. 9 292 .. 8 293 .. 0.99 Alignments for each domain: == domain 1 score: 353.2 bits; conditional E-value: 3.9e-110 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 + +Al+TPf++d svd +a+ +l++++i++g+d ++++GtTGEs+tL+ +E++++ie++ e + n++ v lcl|NCBI__GCF_000020545.1:WP_012474043.1 9 SAVALVTPFRQDMSVDREAIRRLVHFHIAAGTDILIPCGTTGESPTLTADEQTEIIEIVREEAGNKMLV 77 689****************************************************************** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 aG+g+nateea++l++ a+k+g++++l+v+PyYnkP+qeG y+h+ +iae+v++P+i+YnvP+Rtg + lcl|NCBI__GCF_000020545.1:WP_012474043.1 78 AAGAGTNATEEAVSLASNAQKAGAQALLSVAPYYNKPSQEGYYQHYRRIAEAVSIPVIVYNVPGRTGSN 146 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 ++ et++rLa+++e i a+Keas ++++++e+ a ++df+v++G+D+l l+++alG+ GviSVa+n++ lcl|NCBI__GCF_000020545.1:WP_012474043.1 147 VHAETILRLAHDCEnIAAVKEASDNMAQIMELLASRPDDFSVMTGEDSLILPFMALGGDGVISVAANLL 215 *************99****************************************************** PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p e+k++v+++ egd e+ar+ih++l +lf+ fie+NP+pvK+ l l+g+ie+ +RlPL++l+ e+k lcl|NCBI__GCF_000020545.1:WP_012474043.1 216 PAEVKQLVTEMHEGDLEKARVIHNRLRRLFSLNFIESNPVPVKYSLSLMGMIEE-VYRLPLVALQPENK 283 ******************************************************.************** PP TIGR00674 277 eklkevlke 285 ek+ke l++ lcl|NCBI__GCF_000020545.1:WP_012474043.1 284 EKIKEELRN 292 ***998875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (297 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: 00:00:00.01 # Mc/sec: 8.25 // [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