Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_013092939.1 BC1002_RS25770 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000092885.1:WP_013092939.1 Length = 373 Score = 543 bits (1398), Expect = e-159 Identities = 263/371 (70%), Positives = 307/371 (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 D I++CQGGDYT+EVFPKLR GW GYWIDAASSLRM+DDAVI+LDPVN VI AL Sbjct: 63 KKCDAIISCQGGDYTNEVFPKLRAVGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNAL 122 Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183 G +N+IGGNCTVSLMLMALGGLF LV+WM+AMTYQAASGAGAQNMRELL QMG H Sbjct: 123 VKGQKNFIGGNCTVSLMLMALGGLFRENLVDWMTAMTYQAASGAGAQNMRELLSQMGTLH 182 Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243 +V ++LA+PASAILDIDR+V E + S++ PT+HFG PL GSLIPWIDK+L NG S+EEW Sbjct: 183 GAVKNELADPASAILDIDRRVLEAMNSDSMPTDHFGVPLAGSLIPWIDKDLGNGMSKEEW 242 Query: 244 KAQAETNKILAR----FKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299 K AETNKIL + IPVDG+CVR+GAMRCHSQALTIKLNKDVPL ++ +++ Sbjct: 243 KGGAETNKILGKPAMGTPGAIPVDGLCVRIGAMRCHSQALTIKLNKDVPLDEVNSILASG 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: 537 Number of extensions: 11 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 WP_013092939.1 BC1002_RS25770 (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.3831840.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-198 642.8 0.3 8.4e-198 642.6 0.3 1.0 1 NCBI__GCF_000092885.1:WP_013092939.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000092885.1:WP_013092939.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 642.6 0.3 8.4e-198 8.4e-198 1 365 [. 1 370 [. 1 371 [. 0.98 Alignments for each domain: == domain 1 score: 642.6 bits; conditional E-value: 8.4e-198 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqg 73 ++vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g++aps+ak ++ l+da i+ lk++d ii+cqg NCBI__GCF_000092885.1:WP_013092939.1 1 MNVGLVGWRGMVGSVLMQRMQQEGDFDLIEPVFFSTSNAGGNAPSFAKNETKLKDATSIEDLKKCDAIISCQG 73 68*********************************************************************** PP TIGR01745 74 gdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslggl 146 gdyt+e++pklr+ gw+gywidaasslrmkddaviildpvnldvik+a+ kg ++f+ggnctvsl+lm+lggl NCBI__GCF_000092885.1:WP_013092939.1 74 GDYTNEVFPKLRAVGWNGYWIDAASSLRMKDDAVIILDPVNLDVIKNALVKGQKNFIGGNCTVSLMLMALGGL 146 ************************************************************************* PP TIGR01745 147 frdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsv 219 fr++lv+w++++tyqaasg+ga+ mrell+qmg+l++ v++ela p+sail+i+r+v + + s+ +p+++f+v NCBI__GCF_000092885.1:WP_013092939.1 147 FRENLVDWMTAMTYQAASGAGAQNMRELLSQMGTLHGAVKNELADPASAILDIDRRVLEAMNSDSMPTDHFGV 219 ************************************************************************* PP TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvrigalrchsqaltiklkkdvsl 287 plagslipwidk+l ng s+eewkg aetnkilg t +i+vdglcvriga+rchsqaltikl+kdv+l NCBI__GCF_000092885.1:WP_013092939.1 220 PLAGSLIPWIDKDLGNGMSKEEWKGGAETNKILGkpamgTPGAIPVDGLCVRIGAMRCHSQALTIKLNKDVPL 292 ********************************96333337789****************************** PP TIGR01745 288 eeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrr 360 +e+++i++++n+wvkvvpnere ++r+l+pa vtgtl++pvgr+rkl mg eylsaftvgdqllwgaaeplrr NCBI__GCF_000092885.1:WP_013092939.1 293 DEVNSILASGNDWVKVVPNEREASMRDLSPAVVTGTLTVPVGRVRKLAMGGEYLSAFTVGDQLLWGAAEPLRR 365 ************************************************************************* PP TIGR01745 361 mlril 365 mlri+ NCBI__GCF_000092885.1:WP_013092939.1 366 MLRIV 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 23.50 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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