Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_018123597.1 B149_RS0102570 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q8RBI5 (297 letters) >NCBI__GCF_000375485.1:WP_018123597.1 Length = 293 Score = 276 bits (705), Expect = 5e-79 Identities = 139/291 (47%), Positives = 193/291 (66%), Gaps = 1/291 (0%) Query: 4 FKGSCVAIVTPFTENGVNFDKLGELIEWHIKEGTDAILICGTTGEASTMTDEEQKEAIKF 63 F G+ A+ TPF N ++ D + I+W I++G D ++ CGTTGEA+TMT EEQ I+ Sbjct: 3 FTGAYTALSTPFVNNEIDEDAYRKFIDWQIEQGIDGLVPCGTTGEAATMTHEEQGRIIRI 62 Query: 64 TVEKVAKRIPVIAGTGSNNTAHAIELSEYAQSVGADALLVITPYYNKTTQKGLVAHFTEI 123 VE+ R+PVIAG GSN+T A+EL+ A+ GAD L+ITPYYNK T GLV HF I Sbjct: 63 CVEQAKGRVPVIAGAGSNSTKEAVELTRLAKDAGADGALLITPYYNKPTPNGLVQHFRAI 122 Query: 124 ARHVDIPIIIYNVPSRTSLNMLPETYLEVKKKAENVVGVKEASGDISQIAEIARIMGKSF 183 A+ +PII+YNVP RT LN PET +K VVGVKEAS D+ Q AE+ GK F Sbjct: 123 AKDASMPIIVYNVPGRTGLNCTPETLKRIKDAVPEVVGVKEASADLKQCAEVIENCGKDF 182 Query: 184 EIYSGNDDQVIPIMSLGGLGVISVTANIIPAKIHEMTTAYLNGDIEKARDMQLELNPLNK 243 ++ SG+D +P+++ GG G ISV +NI+PA++ M A+ D+E A D+ L+L P+ + Sbjct: 183 QMLSGDDFTTLPLLAAGGCGAISVVSNIMPAEMAGMCKAFRERDMETALDLSLKLAPVCR 242 Query: 244 ALFIETNPIPVKTAMNLMG-FGVGPLRLPLVEMSEKNLEYLKSVLRQYGLL 293 A+F+ETNPIPVKT+++ MG F RLP+V + +N L+ +L++ GLL Sbjct: 243 AMFLETNPIPVKTSLHKMGLFPNLEFRLPMVPLEPENDPKLEDMLKEAGLL 293 Lambda K H 0.315 0.134 0.373 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: 260 Number of extensions: 8 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: 297 Length of database: 293 Length adjustment: 26 Effective length of query: 271 Effective length of database: 267 Effective search space: 72357 Effective search space used: 72357 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: 48 (23.1 bits)
Align candidate WP_018123597.1 B149_RS0102570 (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.9798.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-109 350.8 0.0 2.3e-109 350.7 0.0 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018123597.1 B149_RS0102570 4-hydroxy-tetrahy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000375485.1:WP_018123597.1 B149_RS0102570 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.7 0.0 2.3e-109 2.3e-109 2 285 .. 6 289 .. 5 290 .. 0.99 Alignments for each domain: == domain 1 score: 350.7 bits; conditional E-value: 2.3e-109 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 +tAl TPf +++ +d +a+ k i+ qie+g+d++v++GtTGE+at+++eE+ ++i++ ve +k+rvpv lcl|NCBI__GCF_000375485.1:WP_018123597.1 6 AYTALSTPFVNNE-IDEDAYRKFIDWQIEQGIDGLVPCGTTGEAATMTHEEQGRIIRICVEQAKGRVPV 73 589********99.******************************************************* PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 iaG+gsn+t+ea+elt+ a+++g+dg+l++tPyYnkPt +Gl++hf aia+ +++Pii+YnvP+Rtg + lcl|NCBI__GCF_000375485.1:WP_018123597.1 74 IAGAGSNSTKEAVELTRLAKDAGADGALLITPYYNKPTPNGLVQHFRAIAKDASMPIIVYNVPGRTGLN 142 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnva 207 +pet+kr+ + v+ +v++Keas dl+++ e+++ ++df++lsGdD +tl++la G++G iSV+sn++ lcl|NCBI__GCF_000375485.1:WP_018123597.1 143 CTPETLKRIKDAVPeVVGVKEASADLKQCAEVIENCGKDFQMLSGDDFTTLPLLAAGGCGAISVVSNIM 211 **********99888****************************************************** PP TIGR00674 208 pkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekk 276 p e++ m+ka+ e d+e a+ + kl ++++a+f+etNPipvKt l+ +gl + e+RlP+++l+ e+ lcl|NCBI__GCF_000375485.1:WP_018123597.1 212 PAEMAGMCKAFRERDMETALDLSLKLAPVCRAMFLETNPIPVKTSLHKMGLFPNLEFRLPMVPLEPEND 280 ********************************************************************* PP TIGR00674 277 eklkevlke 285 kl+++lke lcl|NCBI__GCF_000375485.1:WP_018123597.1 281 PKLEDMLKE 289 ******997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (293 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: 10.39 // [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