Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate PfGW456L13_3944 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 Length = 370 Score = 685 bits (1768), Expect = 0.0 Identities = 333/370 (90%), Positives = 357/370 (96%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 MKRVGLIGWRGMVGSVLMQRMLEE+DFDLIEPVFFTTSNVGGQGP VGKDIAPLKDAYSI Sbjct: 1 MKRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIAPLKDAYSI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 +ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRM+DDAVIVLDPVNRKVID Sbjct: 61 EELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRKVID 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 Q LDAGT+NYIGGNCTVSLMLM LGGLF+AGLVEWMSAMTYQAASGAGAQNMREL+KQMG Sbjct: 121 QQLDAGTKNYIGGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 A HA+VAD LA+PASAILDIDR+VAE +RS+A+PTE+FG PL GSLIPWIDKELPNGQSR Sbjct: 181 ATHAAVADQLADPASAILDIDRRVAEAMRSDAYPTENFGVPLAGSLIPWIDKELPNGQSR 240 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWKAQAETNKIL RFK+PIPVDGICVR+GAMRCHSQALTIKLNKDVP+ DIEGLISQHN Sbjct: 241 EEWKAQAETNKILGRFKSPIPVDGICVRIGAMRCHSQALTIKLNKDVPIADIEGLISQHN 300 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 PWVKLVPN+RE S++EL+P VTGTL++PVGRLRKLNMGSQ++GAFTVGDQLLWGAAEPL Sbjct: 301 PWVKLVPNNRETSIQELSPNKVTGTLNIPVGRLRKLNMGSQFVGAFTVGDQLLWGAAEPL 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: 637 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 PfGW456L13_3944 (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.3965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-199 645.7 0.0 1.1e-198 645.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 Aspartate-semialdehyde dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 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 ! 645.5 0.0 1.1e-198 1.1e-198 1 366 [] 2 368 .. 2 368 .. 0.99 Alignments for each domain: == domain 1 score: 645.5 bits; conditional E-value: 1.1e-198 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailed 55 k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++ps++k a+l+d lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 2 KRVGLIGWRGMVGSVLMQRMLEEQDFDLIEPVFFTTSNVGGQGPSVGKDIAPLKD 56 68***************************************************** PP TIGR01745 56 aydidalkeldiiitcqggdytkeiypklrkagwkgywidaasslrmkddaviil 110 ay i+ lk ld+i+tcqggdyt+e++pklr+agw+gywidaasslrm+ddavi+l lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 57 AYSIEELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMQDDAVIVL 111 ******************************************************* PP TIGR01745 111 dpvnldvikdavnkgirtfvggnctvslllmslgglfrdelvewvsvatyqaasg 165 dpvn +vi++ ++ g+++++ggnctvsl+lm+lgglf+ +lvew+s++tyqaasg lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 112 DPVNRKVIDQQLDAGTKNYIGGNCTVSLMLMGLGGLFEAGLVEWMSAMTYQAASG 166 ******************************************************* PP TIGR01745 166 ggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvp 220 +ga+ mrel+kqmg + v+++la p+sail+i+r+v++ +rs+ p+enf+vp lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 167 AGAQNMRELIKQMGATHAAVADQLADPASAILDIDRRVAEAMRSDAYPTENFGVP 221 ******************************************************* PP TIGR01745 221 lagslipwidkqldngqsreewkgqaetnkilgt.kdtilvdglcvrigalrchs 274 lagslipwidk+l ngqsreewk qaetnkilg k+ i+vdg+cvriga+rchs lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 222 LAGSLIPWIDKELPNGQSREEWKAQAETNKILGRfKSPIPVDGICVRIGAMRCHS 276 ********************************964788***************** PP TIGR01745 275 qaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvg 329 qaltikl+kdv++ +ie +i +hn+wvk+vpn+re +++el+p vtgtl+ipvg lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 277 QALTIKLNKDVPIADIEGLISQHNPWVKLVPNNRETSIQELSPNKVTGTLNIPVG 331 ******************************************************* PP TIGR01745 330 rlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366 rlrklnmg +++ aftvgdqllwgaaeplrrmlrill lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3944 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.82 // [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