Align succinyldiaminopimelate transaminase (EC 2.6.1.17); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_084704115.1 BS73_RS16265 succinyldiaminopimelate transaminase
Query= BRENDA::Q82IK5 (364 letters) >NCBI__GCF_000744815.1:WP_084704115.1 Length = 390 Score = 548 bits (1411), Expect = e-160 Identities = 274/365 (75%), Positives = 304/365 (83%), Gaps = 5/365 (1%) Query: 4 VSDRLPTFPWDKLEPYKARAAAHPDGIVDLSVGTPVDPVPELIQKALVAAADSPGYPTVW 63 VS LP FPWD+LEPYK RA HPDGIVDLS+GTPVDPVP LIQ+AL AD+PGYPTVW Sbjct: 22 VSALLPQFPWDRLEPYKKRALEHPDGIVDLSIGTPVDPVPALIQEALREHADTPGYPTVW 81 Query: 64 GTPELRDALTGWVERRLGARGVTHHHVLPIVGSKELVAWLPTQLGLGPGDKVAHPRLAYP 123 GT RDA+ GW RRLGA + H VLP+VGSKELVAWLPTQLGLGPGD VA+P+LAYP Sbjct: 82 GTRAYRDAILGWAGRRLGATALDEHGVLPVVGSKELVAWLPTQLGLGPGDVVAYPQLAYP 141 Query: 124 TYEVGARLARADHVVY-DDPTELDP---TGLKLLWLNSPSNPTGKVLSKAELTRIVAWAR 179 TYEVGARLARAD+ Y DDP ELD + L+LLWLNSPSNPTG+VL+ L IV WAR Sbjct: 142 TYEVGARLARADYASYVDDPRELDADVVSRLRLLWLNSPSNPTGRVLAADRLREIVEWAR 201 Query: 180 EHGILVFSDECYLELGWEADPVSVLHPDVCGGSYEGIVSVHSLSKRSNLAGYRAAFLAGD 239 E G+LV SDECYLELGWEADPVS+LHP+V GGSYEG+V+VHSLSKRSNLAGYRAAFL GD Sbjct: 202 ERGVLVVSDECYLELGWEADPVSILHPEVSGGSYEGLVAVHSLSKRSNLAGYRAAFLLGD 261 Query: 240 PAVLGPLLQIRKHGGMMTSAPTQAAVVAALGDDAHVREQRERYAARRTALRDALLSHGFR 299 +L LLQ+RKHGGMMT AP QAA ALGDDAHV EQRERYA RRTALR+AL ++GFR Sbjct: 262 DGLLHELLQVRKHGGMMTPAPVQAAAAVALGDDAHVAEQRERYARRRTALREALEAYGFR 321 Query: 300 IEHSEASLYLWATRGESCWDTVAHLADLGILVAPGDFYGS-AGEQFVRVALTATDERVAA 358 ++HSEASLYLW+TR ESCWDTVA LADLGILVAPG+FYG+ AG + VRVA TATDERV A Sbjct: 322 VDHSEASLYLWSTRDESCWDTVAALADLGILVAPGEFYGAEAGSRHVRVAFTATDERVDA 381 Query: 359 AVRRL 363 AV RL Sbjct: 382 AVIRL 386 Lambda K H 0.319 0.135 0.420 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: 615 Number of extensions: 26 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: 364 Length of database: 390 Length adjustment: 30 Effective length of query: 334 Effective length of database: 360 Effective search space: 120240 Effective search space used: 120240 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: 50 (23.9 bits)
Align candidate WP_084704115.1 BS73_RS16265 (succinyldiaminopimelate transaminase)
to HMM TIGR03539 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))
# 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/TIGR03539.hmm # target sequence database: /tmp/gapView.3923009.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03539 [M=357] Accession: TIGR03539 Description: DapC_actino: succinyldiaminopimelate transaminase 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-180 586.3 0.7 1.2e-180 586.1 0.7 1.0 1 NCBI__GCF_000744815.1:WP_084704115.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_084704115.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 586.1 0.7 1.2e-180 1.2e-180 1 357 [] 26 387 .. 26 387 .. 0.98 Alignments for each domain: == domain 1 score: 586.1 bits; conditional E-value: 1.2e-180 TIGR03539 1 lPdfPWdklaeakakaashpdGivdlsvGtPvdpvpalirealaeaadapgyPqtaGteelreaivdalerrl 73 lP+fPWd+l+++k++a +hpdGivdls+GtPvdpvpali+eal e ad+pgyP+++Gt++ r+ai+++ rrl NCBI__GCF_000744815.1:WP_084704115.1 26 LPQFPWDRLEPYKKRALEHPDGIVDLSIGTPVDPVPALIQEALREHADTPGYPTVWGTRAYRDAILGWAGRRL 98 8************************************************************************ PP TIGR03539 74 gvkgldeeavlPviGtkelvallPtllGlgagdtvviPevayPtyevgarlagaeava.addlteldp...ek 142 g+++lde+ vlPv+G+kelva+lPt+lGlg+gd+v+ P++ayPtyevgarla+a+ + +dd++eld ++ NCBI__GCF_000744815.1:WP_084704115.1 99 GATALDEHGVLPVVGSKELVAWLPTQLGLGPGDVVAYPQLAYPTYEVGARLARADYASyVDDPRELDAdvvSR 171 ******************************************************987527******9966668 PP TIGR03539 143 vkliwlnsPanPtGrvlsveelrkvvalarergvvvasdecylelgWegeavsvldpevcggdlegllavhsl 215 ++l+wlnsP+nPtGrvl ++lr++v++arergv+v+sdecylelgWe+++vs+l+pev+gg++egl+avhsl NCBI__GCF_000744815.1:WP_084704115.1 172 LRLLWLNSPSNPTGRVLAADRLREIVEWARERGVLVVSDECYLELGWEADPVSILHPEVSGGSYEGLVAVHSL 244 89*********************************************************************** PP TIGR03539 216 skrsnlagyragfvaGdealvaellevrkhaGlmvpaPvqaamvaaladdehvaeqkeryaarrellkaalek 288 skrsnlagyra+f+ Gd+ l++ell+vrkh+G+m+paPvqaa ++al+dd+hvaeq+erya+rr++l++ale+ NCBI__GCF_000744815.1:WP_084704115.1 245 SKRSNLAGYRAAFLLGDDGLLHELLQVRKHGGMMTPAPVQAAAAVALGDDAHVAEQRERYARRRTALREALEA 317 ************************************************************************* PP TIGR03539 289 aGfriehseaglylWatrgedaretvdrlaelGilvaPGdfyg.eagkefvrvaltatderiaaaverlt 357 +Gfr++hsea+lylW+tr+e++++tv++la+lGilvaPG+fyg eag+++vrva+tatder++aav rlt NCBI__GCF_000744815.1:WP_084704115.1 318 YGFRVDHSEASLYLWSTRDESCWDTVAALADLGILVAPGEFYGaEAGSRHVRVAFTATDERVDAAVIRLT 387 ******************************************934689********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (357 nodes) Target sequences: 1 (390 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: 00:00:00.00 # Mc/sec: 14.18 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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