Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Synpcc7942_0853 Synpcc7942_0853 L,L-diaminopimelate aminotransferase
Query= BRENDA::Q3MAL4 (411 letters) >FitnessBrowser__SynE:Synpcc7942_0853 Length = 411 Score = 708 bits (1827), Expect = 0.0 Identities = 342/405 (84%), Positives = 376/405 (92%) Query: 1 MATINDNYLKLKAGYLFPEIARRVNAFAEANPDAKIIRLGIGDVTEPLPEACRTAMIQAV 60 MATINDNYLKLKAGYLFPEIARRVNAFA++NP+A IIRLGIGDVTEPLP ACR AMIQAV Sbjct: 1 MATINDNYLKLKAGYLFPEIARRVNAFAQSNPEAAIIRLGIGDVTEPLPVACRQAMIQAV 60 Query: 61 EEMGDRSSFKGYGPEQGYAWLREKIATQDFQARGADVDASEIFISDGSKCDTGNILDIFG 120 E+MG R +FKGYGPEQGYAWLREKIA DFQ+RG +VDASEIFISDGSKCD GNILDIFG Sbjct: 61 EDMGQRENFKGYGPEQGYAWLREKIAAHDFQSRGCEVDASEIFISDGSKCDCGNILDIFG 120 Query: 121 DNNIIAVTDPVYPVYVDTNVMAGHTGVANDKGEFEGLVYLPVTAENNFTAEIPSQKVDLI 180 +NN IAVTDPVYPVYVDTNVMAGHTG AND+GE++GLVYLP++AENNFTAEIPS+KVDLI Sbjct: 121 NNNRIAVTDPVYPVYVDTNVMAGHTGDANDRGEYDGLVYLPISAENNFTAEIPSEKVDLI 180 Query: 181 YLCFPNNPTGATATKEHLQAWVDYAKAHNSIIFFDAAYESYITDPSLPHSIYEIEGAREV 240 YLCFPNNPTGA A++E+LQAWVDYA+A+ +II FDAAYE++ITDP++PHSI+EI GAR+ Sbjct: 181 YLCFPNNPTGAVASREYLQAWVDYARANGAIILFDAAYEAFITDPAIPHSIFEIPGARDC 240 Query: 241 AIEFRSFSKNAGFTGTRCALTVVPKTLKAKAADGSDVELWKLWNRRQSTKFNGVSYIVQR 300 AIEFRSFSKNAGFTGTRCA TVVPK LK KAADGS+VELW LWNRRQSTKFNGVSYIVQR Sbjct: 241 AIEFRSFSKNAGFTGTRCAFTVVPKGLKGKAADGSEVELWGLWNRRQSTKFNGVSYIVQR 300 Query: 301 GAEAVYSEAGQAQVKALVSFYLDNAKIIREKLTAAGLSVYGGVNAPYVWVKTPNGLSSWD 360 GAEAVYS GQAQ+K LV+FYL+NA+IIRE+LTAAGL V+GGVNAPYVWVKTP GL+SWD Sbjct: 301 GAEAVYSAEGQAQIKELVAFYLENARIIREELTAAGLDVHGGVNAPYVWVKTPAGLTSWD 360 Query: 361 FFDKLLQTVNVVGTPGSGFGAAGEGYFRISAFNSRENVEEAMQRI 405 FFDKLLQ NVVGTPGSGFGAAGEGYFRISAFNSRENV AMQRI Sbjct: 361 FFDKLLQVCNVVGTPGSGFGAAGEGYFRISAFNSRENVVTAMQRI 405 Lambda K H 0.317 0.134 0.397 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: 665 Number of extensions: 21 Number of successful extensions: 1 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: 411 Length of database: 411 Length adjustment: 31 Effective length of query: 380 Effective length of database: 380 Effective search space: 144400 Effective search space used: 144400 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate Synpcc7942_0853 Synpcc7942_0853 (L,L-diaminopimelate aminotransferase)
to HMM TIGR03542 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))
# 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/TIGR03542.hmm # target sequence database: /tmp/gapView.30052.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03542 [M=402] Accession: TIGR03542 Description: DAPAT_plant: LL-diaminopimelate aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-189 613.7 0.0 8.4e-189 613.5 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0853 Synpcc7942_0853 L,L-diaminopimel Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0853 Synpcc7942_0853 L,L-diaminopimelate aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 613.5 0.0 8.4e-189 8.4e-189 2 400 .. 3 407 .. 2 409 .. 0.98 Alignments for each domain: == domain 1 score: 613.5 bits; conditional E-value: 8.4e-189 TIGR03542 2 kvnehflklkssylfseiakkvkefrkknpeadiirlgiGdvtqPlakaviealkeaveelaseetfrG 70 ++n+++lklk++ylf+eia++v+ f+++npea iirlgiGdvt+Pl+ a+ +a+ +ave++ ++e+f+G lcl|FitnessBrowser__SynE:Synpcc7942_0853 3 TINDNYLKLKAGYLFPEIARRVNAFAQSNPEAAIIRLGIGDVTEPLPVACRQAMIQAVEDMGQRENFKG 71 68******************************************************************* PP TIGR03542 71 yGpeqGldllreaiaeeeykgr...idpeeifisdGakcdvarllelfgsdktvavqdPvyPvyvdsav 136 yGpeqG+ +lre+ia +++++r +d++eifisdG+kcd++++l++fg+++ +av+dPvyPvyvd++v lcl|FitnessBrowser__SynE:Synpcc7942_0853 72 YGPEQGYAWLREKIAAHDFQSRgceVDASEIFISDGSKCDCGNILDIFGNNNRIAVTDPVYPVYVDTNV 140 ***********************9********************************************* PP TIGR03542 137 laGragvldddgkykkivylpctkenefiPelpeekkvdiiylCsPnnPtGtvltkeqlkelvdyaken 205 +aG++g ++d g+y +vylp +en+f e+p+ek vd+iylC+PnnPtG+v+++e l+++vdya++n lcl|FitnessBrowser__SynE:Synpcc7942_0853 141 MAGHTGDANDRGEYDGLVYLPISAENNFTAEIPSEK-VDLIYLCFPNNPTGAVASREYLQAWVDYARAN 208 ***********************************9.******************************** PP TIGR03542 206 dslilfdaayeafisdpslPksiyeiegakecaieirsfsktlGftGvrlgytvvPkelkvedg....e 270 +++ilfdaayeafi+dp++P+si+ei+ga+ caie+rsfsk++GftG+r+++tvvPk lk + + lcl|FitnessBrowser__SynE:Synpcc7942_0853 209 GAIILFDAAYEAFITDPAIPHSIFEIPGARDCAIEFRSFSKNAGFTGTRCAFTVVPKGLKGKAAdgseV 277 ***********************************************************9765555666 PP TIGR03542 271 slkklWerllctkfnGaslivqraaeavlakeglqqikeaisyymenarilrkaleaaglkvyGGenaP 339 +l lW+r+++tkfnG+s+ivqr+aeav++ eg+ qike+++ y+enari+r++l+aagl v+GG+naP lcl|FitnessBrowser__SynE:Synpcc7942_0853 278 ELWGLWNRRQSTKFNGVSYIVQRGAEAVYSAEGQAQIKELVAFYLENARIIREELTAAGLDVHGGVNAP 346 7889***************************************************************** PP TIGR03542 340 ylWvklpegissedffdkllkeaevvgtPGsGfGssGeGfvrlsalgkredivealerike 400 y+Wvk+p+g++s+dffdkll+ ++vvgtPGsGfG++GeG++r+sa+++re++v+a++ri++ lcl|FitnessBrowser__SynE:Synpcc7942_0853 347 YVWVKTPAGLTSWDFFDKLLQVCNVVGTPGSGFGAAGEGYFRISAFNSRENVVTAMQRIRS 407 ***********************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (402 nodes) Target sequences: 1 (411 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.18 // [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