Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate WP_083442179.1 NITAL_RS12925 4-hydroxy-tetrahydrodipicolinate synthase
Query= metacyc::MONOMER-6565 (289 letters) >NCBI__GCF_000969705.1:WP_083442179.1 Length = 295 Score = 233 bits (593), Expect = 5e-66 Identities = 121/266 (45%), Positives = 178/266 (66%), Gaps = 6/266 (2%) Query: 10 MVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVALIQYSVKEAA 69 M+TPF + +D L D+L++NGTD+++V GTTGESPTL EE L+ +VK+A Sbjct: 1 MITPFTSDGALDLDGAQTLADHLVSNGTDTVLVHGTTGESPTLLGEEMWELLA-AVKDAV 59 Query: 70 G-RAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHFRAIAEETS 128 G RA ++ G+GSN T +I+ T++A E GAD++++VTPYYNKP Q G+ RHFRA+AE T Sbjct: 60 GDRANVMMGSGSNATATAIRSTQRATEMGADSLLVVTPYYNKPDQRGLVRHFRAVAEVTD 119 Query: 129 LPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAET---PEDFAVY 185 LP++LY++ RTA ++ T + LAE+PNI+ K+ASG+ + ++ T P F V+ Sbjct: 120 LPIVLYDIKPRTATAIEVSTMVDLAEVPNIVGTKDASGEWAKVGDVLVATEGAPGGFGVW 179 Query: 186 SGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPLMKGLF 245 SG D L +++ GA G++SVA+H++G E+ EMI + + +A +H LPL + LF Sbjct: 180 SGADEFNLGSIATGATGVISVAAHLVGRELAEMIDVFAT-DPLRARQLHLACLPLHRALF 238 Query: 246 AAPNPSPLKTALQLKGLDVGSVRLPL 271 A P+P+PLK A+ GL G VRLPL Sbjct: 239 AEPSPAPLKAAMNELGLPAGPVRLPL 264 Lambda K H 0.313 0.131 0.357 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: 239 Number of extensions: 8 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: 289 Length of database: 295 Length adjustment: 26 Effective length of query: 263 Effective length of database: 269 Effective search space: 70747 Effective search space used: 70747 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_083442179.1 NITAL_RS12925 (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.30572.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-84 269.7 0.0 1.2e-84 269.5 0.0 1.0 1 lcl|NCBI__GCF_000969705.1:WP_083442179.1 NITAL_RS12925 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000969705.1:WP_083442179.1 NITAL_RS12925 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 269.5 0.0 1.2e-84 1.2e-84 6 284 .. 1 280 [. 1 282 [. 0.96 Alignments for each domain: == domain 1 score: 269.5 bits; conditional E-value: 1.2e-84 TIGR00674 6 liTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 +iTPf +dg +d++ ++l ++++++g+d+++v GtTGEs+tL eE +++ + + v +r +v+ G lcl|NCBI__GCF_000969705.1:WP_083442179.1 1 MITPFTSDGALDLDGAQTLADHLVSNGTDTVLVHGTTGESPTLLGEEMWELLAAVKDAVGDRANVMMGS 69 8******************************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepe 143 gsnat+ ai+ t++a ++g+d++lvvtPyYnkP q+Gl++hf a+ae+++lPi+lY++ Rt++ +e+ lcl|NCBI__GCF_000969705.1:WP_083442179.1 70 GSNATATAIRSTQRATEMGADSLLVVTPYYNKPDQRGLVRHFRAVAEVTDLPIVLYDIKPRTATAIEVS 138 ********************************************************************* PP TIGR00674 144 tvkrLaeeveivaiKeasgdlervseik...aeakedfkvlsGdDaltleilalGakGviSVasnvapk 209 t+ Lae ++iv+ K+asg+ ++v + + a+ f v+sG D+++l +a+Ga+GviSVa++++++ lcl|NCBI__GCF_000969705.1:WP_083442179.1 139 TMVDLAEVPNIVGTKDASGEWAKVGDVLvatEGAPGGFGVWSGADEFNLGSIATGATGVISVAAHLVGR 207 ********************99998765111445789******************************** PP TIGR00674 210 elkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkek 278 el+em+ ++ d +ar++h l+l++alf e+ P p+K+a++ lgl+++ +RlPL+e+s e++++ lcl|NCBI__GCF_000969705.1:WP_083442179.1 208 ELAEMIDVFA-TDPLRARQLHLACLPLHRALFAEPSPAPLKAAMNELGLPAG-PVRLPLAEASPEATRT 274 ******9965.6788999**********************************.9*************99 PP TIGR00674 279 lkevlk 284 + ++l+ lcl|NCBI__GCF_000969705.1:WP_083442179.1 275 VLDALE 280 988876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (295 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: 9.97 // [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