Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_027456320.1 K420_RS0100500 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000519045.1:WP_027456320.1 Length = 377 Score = 516 bits (1328), Expect = e-151 Identities = 260/376 (69%), Positives = 303/376 (80%), Gaps = 7/376 (1%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIA--PLKDAY 58 MK+VGL+GWRGMVGSVLMQRM+EE DF I+PV+F+TS GG+ P G A PL+DA Sbjct: 1 MKKVGLVGWRGMVGSVLMQRMVEEGDFAHIDPVYFSTSAAGGKAPVFGGKEASLPLQDAS 60 Query: 59 SIDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKV 118 SI+ LK D+++TCQGGDYT +VFPKLR AGW G+WIDAAS+LRM DDAVI+LDPVN V Sbjct: 61 SIEALKACDIVITCQGGDYTKDVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNMNV 120 Query: 119 IDQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQ 178 I +L G +N+IGGNCTVSLMLM LGGLF LVEW ++MTYQAASGAGAQNMREL+ Q Sbjct: 121 IKDSLAKGGKNWIGGNCTVSLMLMGLGGLFQNDLVEWATSMTYQAASGAGAQNMRELISQ 180 Query: 179 MGAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHF-GAPLGGSLIPWIDKELPNG 237 MG H SV D LA+PASAILDIDRKVAET+RS+ FP ++F PL GSLIPWID + G Sbjct: 181 MGVIHDSVKDLLADPASAILDIDRKVAETIRSDGFPKKNFRNTPLAGSLIPWIDVPVEGG 240 Query: 238 QSREEWKAQAETNKILAR--FK--NPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIE 293 QS+EEWK AE NKIL R FK IP+DG+CVR+GAMRCHSQALTIKL KDVPL +I Sbjct: 241 QSKEEWKGGAECNKILGRPAFKTVGSIPIDGLCVRIGAMRCHSQALTIKLKKDVPLDEIS 300 Query: 294 GLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLL 353 ++++ N W K+VPN RE+S RELTPAAVTGTL+VPVGRL K+ MG +YL AFT GDQLL Sbjct: 301 DMLAKANQWAKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMGPEYLAAFTCGDQLL 360 Query: 354 WGAAEPLRRMLRILLE 369 WGAAEPLRRMLRILL+ Sbjct: 361 WGAAEPLRRMLRILLD 376 Lambda K H 0.319 0.136 0.409 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: 545 Number of extensions: 11 Number of successful extensions: 4 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: 370 Length of database: 377 Length adjustment: 30 Effective length of query: 340 Effective length of database: 347 Effective search space: 117980 Effective search space used: 117980 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_027456320.1 K420_RS0100500 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
# 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/TIGR01745.hmm # target sequence database: /tmp/gapView.24688.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01745 [M=366] Accession: TIGR01745 Description: asd_gamma: aspartate-semialdehyde dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-193 627.3 0.1 4.4e-193 627.1 0.1 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456320.1 K420_RS0100500 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027456320.1 K420_RS0100500 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 627.1 0.1 4.4e-193 4.4e-193 1 366 [] 2 375 .. 2 375 .. 0.98 Alignments for each domain: == domain 1 score: 627.1 bits; conditional E-value: 4.4e-193 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa..iledaydidalkeldi 67 kkvglvgwrgmvgsvl++rm+ee df +i+pv+fsts +g+kap++++ +a +l+da i+alk++di lcl|NCBI__GCF_000519045.1:WP_027456320.1 2 KKVGLVGWRGMVGSVLMQRMVEEGDFAHIDPVYFSTSAAGGKAPVFGGKEAslPLQDASSIEALKACDI 70 69********************************************988775689************** PP TIGR01745 68 iitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctv 136 +itcqggdytk+++pklr+agw+g+widaas+lrm ddaviildpvn++vikd+++kg ++++ggnctv lcl|NCBI__GCF_000519045.1:WP_027456320.1 71 VITCQGGDYTKDVFPKLRAAGWNGHWIDAASALRMADDAVIILDPVNMNVIKDSLAKGGKNWIGGNCTV 139 ********************************************************************* PP TIGR01745 137 slllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtk 205 sl+lm+lgglf+++lvew +++tyqaasg+ga+ mrel++qmgv++ +v++ la p+sail+i+rkv++ lcl|NCBI__GCF_000519045.1:WP_027456320.1 140 SLMLMGLGGLFQNDLVEWATSMTYQAASGAGAQNMRELISQMGVIHDSVKDLLADPASAILDIDRKVAE 208 ********************************************************************* PP TIGR01745 206 lsrseelpvenf.svplagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrig 268 ++rs+ +p +nf ++plagslipwid ++ gqs+eewkg ae nkilg t i++dglcvrig lcl|NCBI__GCF_000519045.1:WP_027456320.1 209 TIRSDGFPKKNFrNTPLAGSLIPWIDVPVEGGQSKEEWKGGAECNKILGrpafkTVGSIPIDGLCVRIG 277 ************558********************************98555446778*********** PP TIGR01745 269 alrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmg 337 a+rchsqaltiklkkdv+l+ei +++++ n+w+kvvpnerei++reltpaavtgtl++pvgrl k+ mg lcl|NCBI__GCF_000519045.1:WP_027456320.1 278 AMRCHSQALTIKLKKDVPLDEISDMLAKANQWAKVVPNEREISERELTPAAVTGTLTVPVGRLHKMAMG 346 ********************************************************************* PP TIGR01745 338 keylsaftvgdqllwgaaeplrrmlrill 366 +eyl+aft gdqllwgaaeplrrmlrill lcl|NCBI__GCF_000519045.1:WP_027456320.1 347 PEYLAAFTCGDQLLWGAAEPLRRMLRILL 375 ***************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (377 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: 9.68 // [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