Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_012103546.1 CKL_RS15610 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q8RBI5 (297 letters) >NCBI__GCF_000016505.1:WP_012103546.1 Length = 293 Score = 365 bits (936), Expect = e-106 Identities = 180/294 (61%), Positives = 230/294 (78%), Gaps = 1/294 (0%) Query: 1 MPVFKGSCVAIVTPFTENGVNFDKLGELIEWHIKEGTDAILICGTTGEASTMTDEEQKEA 60 M +FKGS VAIVTPF + GV+ KL EL+EWHI+ GTDAI+ICGTTGEASTMT++E+K+A Sbjct: 1 MSLFKGSGVAIVTPFNDKGVDLKKLEELLEWHIESGTDAIIICGTTGEASTMTEQERKDA 60 Query: 61 IKFTVEKVAKRIPVIAGTGSNNTAHAIELSEYAQSVGADALLVITPYYNKTTQKGLVAHF 120 IK TV+ V RIPVIAGTG+N T ++++S++A+SVG D LLVITPYYNKTTQKGL+ HF Sbjct: 61 IKLTVDVVKNRIPVIAGTGNNCTQSSVDMSKWAESVGVDGLLVITPYYNKTTQKGLIEHF 120 Query: 121 TEIARHVDIPIIIYNVPSRTSLNMLPETYLEVKKKAENVVGVKEASGDISQIAEIARIMG 180 +A V +PI++YNVP RT +N+ P+T E+ + EN+ +KEASGDISQIA++ + Sbjct: 121 KAVASGVKVPIVVYNVPGRTGMNVQPKTLKEL-CEIENIAAIKEASGDISQIAQMKALCR 179 Query: 181 KSFEIYSGNDDQVIPIMSLGGLGVISVTANIIPAKIHEMTTAYLNGDIEKARDMQLELNP 240 +IYSGNDDQVIPI+S+GG+GVISV ANIIP +H M +L G E+A +QL+ Sbjct: 180 DRIDIYSGNDDQVIPILSVGGIGVISVLANIIPKDMHNMCKLFLEGKTEEALKIQLDSFA 239 Query: 241 LNKALFIETNPIPVKTAMNLMGFGVGPLRLPLVEMSEKNLEYLKSVLRQYGLLK 294 LNKA+FIETNPIPVKTAMN++G G LRLPL +MS+ NLE LK+ L+ YGLLK Sbjct: 240 LNKAMFIETNPIPVKTAMNILGMNAGKLRLPLCDMSQANLEVLKTELKNYGLLK 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: 310 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_012103546.1 CKL_RS15610 (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.6312.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-110 352.6 1.0 6.3e-110 352.5 1.0 1.0 1 lcl|NCBI__GCF_000016505.1:WP_012103546.1 CKL_RS15610 4-hydroxy-tetrahydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016505.1:WP_012103546.1 CKL_RS15610 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.5 1.0 6.3e-110 6.3e-110 3 285 .. 8 288 .. 6 289 .. 0.98 Alignments for each domain: == domain 1 score: 352.5 bits; conditional E-value: 6.3e-110 TIGR00674 3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpvi 71 +A++TPf+++g vd+++le+l+e +ie+g+dai+++GtTGE+ t++ +E+k+ i+++v++vknr+pvi lcl|NCBI__GCF_000016505.1:WP_012103546.1 8 GVAIVTPFNDKG-VDLKKLEELLEWHIESGTDAIIICGTTGEASTMTEQERKDAIKLTVDVVKNRIPVI 75 58********99.******************************************************** PP TIGR00674 72 aGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvsl 140 aGtg n+t+ +++++k ae +gvdg+lv+tPyYnk tq+Gl++hfka+a+ v++Pi++YnvP+Rtg+++ lcl|NCBI__GCF_000016505.1:WP_012103546.1 76 AGTGNNCTQSSVDMSKWAESVGVDGLLVITPYYNKTTQKGLIEHFKAVASGVKVPIVVYNVPGRTGMNV 144 ********************************************************************* PP TIGR00674 141 epetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapk 209 +p+t+k+L e ++i aiKeasgd++++ ++ka + + ++sG+D + +il++G+ GviSV++n++pk lcl|NCBI__GCF_000016505.1:WP_012103546.1 145 QPKTLKELCEIENIAAIKEASGDISQIAQMKALCRDRIDIYSGNDDQVIPILSVGGIGVISVLANIIPK 213 ********************************************************************* PP TIGR00674 210 elkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkek 278 ++++m+k +leg+teea++i+ + l ka+fietNPipvKta+++lg+ ++ +lRlPL+ +s+ + e lcl|NCBI__GCF_000016505.1:WP_012103546.1 214 DMHNMCKLFLEGKTEEALKIQLDSFALNKAMFIETNPIPVKTAMNILGMNAG-KLRLPLCDMSQANLEV 281 ****************************************************.************9999 PP TIGR00674 279 lkevlke 285 lk lk+ lcl|NCBI__GCF_000016505.1:WP_012103546.1 282 LKTELKN 288 9987775 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.63 // [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