Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_050463053.1 AKL27_RS11950 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_001189915.1:WP_050463053.1 Length = 368 Score = 530 bits (1365), Expect = e-155 Identities = 259/370 (70%), Positives = 303/370 (81%), Gaps = 2/370 (0%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 MK VGL+GWRGMVGSVLMQRM +E DFD IEPVFF+TSN GG+ P K LKDA SI Sbjct: 1 MKLVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKTATTLKDANSI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 DELK D+I+T QGGDYT+E+FPKLR AGW GYWIDAAS+LRM+DDAVIVLDPVN+ VI Sbjct: 61 DELKKCDIIITAQGGDYTTEIFPKLRAAGWNGYWIDAASTLRMKDDAVIVLDPVNQDVIG 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 +A+ G +NYIGGNCT S++LM +GGLF GLVEW+S+MTYQAASG GA +MRELLK MG Sbjct: 121 EAMARGVKNYIGGNCTNSILLMGVGGLFKHGLVEWVSSMTYQAASGGGANHMRELLKGMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 H +VAD+LA P+SAILDIDRKVA T+R E+ PTE FGAPL G LIPWID +L NGQS+ Sbjct: 181 VIHDAVADELATPSSAILDIDRKVANTIR-ESVPTEFFGAPLAGGLIPWIDAQLENGQSK 239 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWK QAE NKIL PIPVDG+CVRVGAMRCHS ALTIKL +D+PL +IE +I N Sbjct: 240 EEWKGQAEVNKILGN-AQPIPVDGLCVRVGAMRCHSLALTIKLKRDLPLAEIESIIRDGN 298 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 WVK VPN R V+V+ELTPA++TG+L + VGR+RKLN G +Y+ AF +GDQLLWGAAEPL Sbjct: 299 QWVKWVPNDRAVTVKELTPASITGSLEIGVGRVRKLNQGPEYISAFVIGDQLLWGAAEPL 358 Query: 361 RRMLRILLER 370 RRMLRI+LE+ Sbjct: 359 RRMLRIILEK 368 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: 516 Number of extensions: 14 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: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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_050463053.1 AKL27_RS11950 (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.25503.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-210 683.1 0.3 4.7e-210 682.9 0.3 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463053.1 AKL27_RS11950 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463053.1 AKL27_RS11950 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 682.9 0.3 4.7e-210 4.7e-210 2 365 .. 3 365 .. 2 366 .. 0.99 Alignments for each domain: == domain 1 score: 682.9 bits; conditional E-value: 4.7e-210 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g+kaps+ak++++l+da+ id lk++diiit lcl|NCBI__GCF_001189915.1:WP_050463053.1 3 LVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKTATTLKDANSIDELKKCDIIIT 71 69******************************************************************* PP TIGR01745 71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139 qggdyt+ei+pklr+agw+gywidaas+lrmkddavi+ldpvn+dvi +a+++g+++++ggnct+s+l lcl|NCBI__GCF_001189915.1:WP_050463053.1 72 AQGGDYTTEIFPKLRAAGWNGYWIDAASTLRMKDDAVIVLDPVNQDVIGEAMARGVKNYIGGNCTNSIL 140 ********************************************************************* PP TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208 lm++gglf+++lvewvs++tyqaasggga+hmrellk+mgv++ v++ela+pssail+i+rkv++++r lcl|NCBI__GCF_001189915.1:WP_050463053.1 141 LMGVGGLFKHGLVEWVSSMTYQAASGGGANHMRELLKGMGVIHDAVADELATPSSAILDIDRKVANTIR 209 ********************************************************************* PP TIGR01745 209 seelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqal 277 e +p+e+f++plag+lipwid ql+ngqs+eewkgqae+nkilg ++ i+vdglcvr+ga+rchs+al lcl|NCBI__GCF_001189915.1:WP_050463053.1 210 -ESVPTEFFGAPLAGGLIPWIDAQLENGQSKEEWKGQAEVNKILGNAQPIPVDGLCVRVGAMRCHSLAL 277 .9******************************************************************* PP TIGR01745 278 tiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftv 346 tiklk+d++l eie+iir++n+wvk+vpn+r +t++eltpa++tg+l+i+vgr+rkln g+ey+saf++ lcl|NCBI__GCF_001189915.1:WP_050463053.1 278 TIKLKRDLPLAEIESIIRDGNQWVKWVPNDRAVTVKELTPASITGSLEIGVGRVRKLNQGPEYISAFVI 346 ********************************************************************* PP TIGR01745 347 gdqllwgaaeplrrmlril 365 gdqllwgaaeplrrmlri+ lcl|NCBI__GCF_001189915.1:WP_050463053.1 347 GDQLLWGAAEPLRRMLRII 365 *****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (368 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: 10.15 // [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