Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011734001.1 PPRO_RS00225 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000015045.1:WP_011734001.1 Length = 365 Score = 493 bits (1269), Expect = e-144 Identities = 245/368 (66%), Positives = 290/368 (78%), Gaps = 4/368 (1%) Query: 3 RVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDE 62 +VGL+GWRGMVGSVL+QRM EE DFD IEP+FFTTS G P D L DA + +E Sbjct: 2 KVGLVGWRGMVGSVLLQRMREENDFDGIEPLFFTTSQQGQPAP---MDRGVLIDALNFEE 58 Query: 63 LKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQA 122 LK D+I+TCQGG YT++ +LR GW GYWIDAAS+LRME D+VIVLDPVNR VID A Sbjct: 59 LKKQDIIVTCQGGGYTTKAHAELRRQGWDGYWIDAASTLRMERDSVIVLDPVNRDVIDAA 118 Query: 123 LDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAA 182 L G +++IGGNCTVSLMLMALGGLF AGLVEW+S+MTYQAASGAGA NMRELL QMG Sbjct: 119 LANGQKDFIGGNCTVSLMLMALGGLFRAGLVEWVSSMTYQAASGAGAPNMRELLNQMGML 178 Query: 183 HASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242 VAD LA P+SAILDID +V T+R ++ PT+ FG PL G+++PWID E+ +GQSREE Sbjct: 179 RDCVADQLATPSSAILDIDCQVTATMRGDSLPTKAFGYPLAGNVLPWIDSEVEDGQSREE 238 Query: 243 WKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPW 302 WK ETNKIL PIPVDG+CVRVG+MRCHSQALTIKLN+D+P+ DIE LI+ N W Sbjct: 239 WKGFVETNKILGT-TTPIPVDGLCVRVGSMRCHSQALTIKLNRDLPIADIESLIAHDNQW 297 Query: 303 VKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRR 362 V LVPN + S+ LTPAA+ GTL+VP+GR+RK+ G +Y+ AFT GDQLLWGAAEPLRR Sbjct: 298 VDLVPNTKAESLSRLTPAAIAGTLTVPIGRVRKMKQGPEYISAFTCGDQLLWGAAEPLRR 357 Query: 363 MLRILLER 370 MLRIL+ER Sbjct: 358 MLRILMER 365 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: 493 Number of extensions: 13 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: 370 Length of database: 365 Length adjustment: 30 Effective length of query: 340 Effective length of database: 335 Effective search space: 113900 Effective search space used: 113900 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: 49 (23.5 bits)
Align candidate WP_011734001.1 PPRO_RS00225 (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.1704.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-182 592.1 0.0 2.1e-182 592.0 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011734001.1 PPRO_RS00225 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011734001.1 PPRO_RS00225 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 592.0 0.0 2.1e-182 2.1e-182 1 366 [] 1 363 [. 1 363 [. 0.99 Alignments for each domain: == domain 1 score: 592.0 bits; conditional E-value: 2.1e-182 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 +kvglvgwrgmvgsvll+rm+ee+dfd i+p+ff+tsq gq ap+ ++l da +++ lk+ dii+ lcl|NCBI__GCF_000015045.1:WP_011734001.1 1 MKVGLVGWRGMVGSVLLQRMREENDFDGIEPLFFTTSQQGQPAPMD---RGVLIDALNFEELKKQDIIV 66 69******************************************75...4689**************** PP TIGR01745 70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138 tcqgg yt++ + +lr++gw+gywidaas+lrm+ d+vi+ldpvn dvi+ a+++g ++f+ggnctvsl lcl|NCBI__GCF_000015045.1:WP_011734001.1 67 TCQGGGYTTKAHAELRRQGWDGYWIDAASTLRMERDSVIVLDPVNRDVIDAALANGQKDFIGGNCTVSL 135 ********************************************************************* PP TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207 +lm+lgglfr +lvewvs++tyqaasg+ga mrell+qmg+l v+++la+pssail+i+ +vt ++ lcl|NCBI__GCF_000015045.1:WP_011734001.1 136 MLMALGGLFRAGLVEWVSSMTYQAASGAGAPNMRELLNQMGMLRDCVADQLATPSSAILDIDCQVTATM 204 ********************************************************************* PP TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqa 276 r + lp++ f+ plag+++pwid ++++gqsreewkg etnkilgt++ i+vdglcvr+g++rchsqa lcl|NCBI__GCF_000015045.1:WP_011734001.1 205 RGDSLPTKAFGYPLAGNVLPWIDSEVEDGQSREEWKGFVETNKILGTTTPIPVDGLCVRVGSMRCHSQA 273 ********************************************************************* PP TIGR01745 277 ltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaft 345 ltikl++d+++ +ie++i+ +n+wv++vpn + +l +ltpaa++gtl++p+gr+rk++ g+ey+saft lcl|NCBI__GCF_000015045.1:WP_011734001.1 274 LTIKLNRDLPIADIESLIAHDNQWVDLVPNTKAESLSRLTPAAIAGTLTVPIGRVRKMKQGPEYISAFT 342 ********************************************************************* PP TIGR01745 346 vgdqllwgaaeplrrmlrill 366 gdqllwgaaeplrrmlril+ lcl|NCBI__GCF_000015045.1:WP_011734001.1 343 CGDQLLWGAAEPLRRMLRILM 363 *******************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (365 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: 6.84 // [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