Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate Pf6N2E2_67 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 Length = 370 Score = 687 bits (1773), Expect = 0.0 Identities = 334/370 (90%), Positives = 357/370 (96%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 MKRVGLIGWRGMVGSVLMQRMLEE+DFDLIEPVFFTTSNVGGQGP VGKDI LKDAYSI Sbjct: 1 MKRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIGALKDAYSI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 +ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRM+DDAVI+LDPVNRKVID Sbjct: 61 EELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVID 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 Q LDAGT+NYIGGNCTVSLMLM LGGLF+AGLVEWMSAMTYQAASGAGAQNMREL+KQMG Sbjct: 121 QQLDAGTKNYIGGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 A HA+VADDLANPASAILDIDRKVAE +RS+A+PTE+FG PL GSLIPWIDKELPNGQSR Sbjct: 181 ATHAAVADDLANPASAILDIDRKVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSR 240 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWKAQAETNKIL RFK+PIPVDGICVR+GAMRCHSQALTIKLNKDVP+ DIEGLISQHN Sbjct: 241 EEWKAQAETNKILGRFKSPIPVDGICVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHN 300 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 PWVKLVPN+RE+S++EL+P VTGTL+VPVGRLRKLNMGSQ++GAFTVGDQLLWGAAEPL Sbjct: 301 PWVKLVPNNREISMQELSPTKVTGTLNVPVGRLRKLNMGSQFVGAFTVGDQLLWGAAEPL 360 Query: 361 RRMLRILLER 370 RRMLRILLER Sbjct: 361 RRMLRILLER 370 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: 646 Number of extensions: 15 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: 370 Length of database: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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 Pf6N2E2_67 (Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
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.26190.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-200 651.0 0.1 2.7e-200 650.8 0.1 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 Aspartate-semialdehyde dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 650.8 0.1 2.7e-200 2.7e-200 1 366 [] 2 368 .. 2 368 .. 0.99 Alignments for each domain: == domain 1 score: 650.8 bits; conditional E-value: 2.7e-200 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeld 66 k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++ps++k ++l+day i+ lk ld lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 2 KRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIGALKDAYSIEELKTLD 67 68**************************************************************** PP TIGR01745 67 iiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvgg 132 +i+tcqggdyt+e++pklr+agw+gywidaasslrm+ddaviildpvn +vi++ ++ g+++++gg lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 68 VILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIILDPVNRKVIDQQLDAGTKNYIGG 133 ****************************************************************** PP TIGR01745 133 nctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaile 198 nctvsl+lm+lgglf+ +lvew+s++tyqaasg+ga+ mrel+kqmg + v+++la+p+sail+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 134 NCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMGATHAAVADDLANPASAILD 199 ****************************************************************** PP TIGR01745 199 ierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgt.kdtilvdgl 263 i+rkv++ +rs+ p+enf+vplagslipwidk+l ngqsreewk qaetnkilg k+ i+vdg+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 200 IDRKVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSREEWKAQAETNKILGRfKSPIPVDGI 265 ******************************************************964788****** PP TIGR01745 264 cvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvg 329 cvriga+rchsqaltikl+kdv++ +ie +i +hn+wvk+vpn+rei+++el+p+ vtgtl++pvg lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 266 CVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHNPWVKLVPNNREISMQELSPTKVTGTLNVPVG 331 ****************************************************************** PP TIGR01745 330 rlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366 rlrklnmg +++ aftvgdqllwgaaeplrrmlrill lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_67 332 RLRKLNMGSQFVGAFTVGDQLLWGAAEPLRRMLRILL 368 ***********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (370 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: 11.90 // [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