Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate H281DRAFT_06071 H281DRAFT_06071 aspartate semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__Burk376:H281DRAFT_06071 Length = 373 Score = 535 bits (1377), Expect = e-156 Identities = 259/371 (69%), Positives = 306/371 (82%), Gaps = 4/371 (1%) Query: 4 VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63 VGL+GWRGMVGSVLMQRM +E DFDLIEPVFF+TSN GG P K+ LKDA SI++L Sbjct: 3 VGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDL 62 Query: 64 KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123 K + I++CQGGDYT+EVFPKLR AGW GYWIDAASSLRM+DDAVI+LDPVN VI AL Sbjct: 63 KKCEAIISCQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNAL 122 Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183 G +N+IGGNCTVSLMLMALGGLF LV+WM+AMTYQAASGAGAQNMRELL+QMG + Sbjct: 123 VKGQKNFIGGNCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLQQMGTLY 182 Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243 + +DLA+P+SAILDIDR+V + S+ PT++FG PL GSLIPWIDK+L NG S+EEW Sbjct: 183 GAAKEDLADPSSAILDIDRRVLSAMNSDRMPTDNFGVPLAGSLIPWIDKDLGNGMSKEEW 242 Query: 244 KAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299 K AETNKIL + IPVDG+CVR+GAMRCHSQALTIKLNKDVPL ++ +++ Sbjct: 243 KGGAETNKILGKPAMGTPGSIPVDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASG 302 Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359 N WVK+VPN RE S+R+L+PA VTGTL+VPVGR+RKL MG +YL AFTVGDQLLWGAAEP Sbjct: 303 NDWVKVVPNEREASMRDLSPAVVTGTLTVPVGRVRKLAMGGEYLSAFTVGDQLLWGAAEP 362 Query: 360 LRRMLRILLER 370 LRRMLRI+L++ Sbjct: 363 LRRMLRIVLDK 373 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: 542 Number of extensions: 12 Number of successful extensions: 2 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: 373 Length adjustment: 30 Effective length of query: 340 Effective length of database: 343 Effective search space: 116620 Effective search space used: 116620 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 H281DRAFT_06071 H281DRAFT_06071 (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.22879.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-198 642.7 0.3 9.1e-198 642.5 0.3 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06071 H281DRAFT_06071 aspartate semial Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06071 H281DRAFT_06071 aspartate semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 642.5 0.3 9.1e-198 9.1e-198 1 365 [. 1 370 [. 1 371 [. 0.98 Alignments for each domain: == domain 1 score: 642.5 bits; conditional E-value: 9.1e-198 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeld 66 ++vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g++aps+ak ++ l+da i+ lk+++ lcl|FitnessBrowser__Burk376:H281DRAFT_06071 1 MNVGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDLKKCE 66 68**************************************************************** PP TIGR01745 67 iiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvgg 132 ii+cqggdyt+e++pklr+agw+gywidaasslrmkddaviildpvnldvik+a+ kg ++f+gg lcl|FitnessBrowser__Burk376:H281DRAFT_06071 67 AIISCQGGDYTNEVFPKLRAAGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNALVKGQKNFIGG 132 ****************************************************************** PP TIGR01745 133 nctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaile 198 nctvsl+lm+lgglfr++lv+w++++tyqaasg+ga+ mrell+qmg+ly+ +e+la pssail+ lcl|FitnessBrowser__Burk376:H281DRAFT_06071 133 NCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLQQMGTLYGAAKEDLADPSSAILD 198 ****************************************************************** PP TIGR01745 199 ierkvtklsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.....tkdtil 259 i+r+v + s+ +p++nf+vplagslipwidk+l ng s+eewkg aetnkilg t i+ lcl|FitnessBrowser__Burk376:H281DRAFT_06071 199 IDRRVLSAMNSDRMPTDNFGVPLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGkpamgTPGSIP 264 *****************************************************96333337789** PP TIGR01745 260 vdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtld 325 vdglcvriga+rchsqaltikl+kdv+l+e+++i++++n+wvkvvpnere ++r+l+pa vtgtl+ lcl|FitnessBrowser__Burk376:H281DRAFT_06071 265 VDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASGNDWVKVVPNEREASMRDLSPAVVTGTLT 330 ****************************************************************** PP TIGR01745 326 ipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365 +pvgr+rkl mg eylsaftvgdqllwgaaeplrrmlri+ lcl|FitnessBrowser__Burk376:H281DRAFT_06071 331 VPVGRVRKLAMGGEYLSAFTVGDQLLWGAAEPLRRMLRIV 370 **************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (373 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: 9.06 // [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