Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_013519947.1 ALIDE2_RS06505 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000204645.1:WP_013519947.1 Length = 370 Score = 503 bits (1296), Expect = e-147 Identities = 248/365 (67%), Positives = 292/365 (80%), Gaps = 2/365 (0%) Query: 4 VGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDEL 63 VGL+GWRGMVGSVLM RM E DFDLIEPVFF+TSN GG+ P + + LKDA + EL Sbjct: 6 VGLVGWRGMVGSVLMDRMQAEGDFDLIEPVFFSTSNAGGKAPAMARTHTQLKDANDVAEL 65 Query: 64 KTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQAL 123 D+++TCQGGDYT EVFP++R AGW+G+WIDAAS+LRMEDDAVIVLDPVN +I L Sbjct: 66 AKCDIVITCQGGDYTKEVFPRIRAAGWKGHWIDAASALRMEDDAVIVLDPVNDGLIKSRL 125 Query: 124 DAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAAH 183 AG RN+IGGNCT S++LM L GLF A LVEW+S+MTYQAASG GA +MRELLK MG + Sbjct: 126 AAGGRNWIGGNCTNSILLMGLAGLFKADLVEWVSSMTYQAASGGGANHMRELLKGMGVIY 185 Query: 184 ASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREEW 243 SVA +LA PASAIL+IDRKVA T+R + PTE FGAPL G LIPWID +LPNGQS+EEW Sbjct: 186 GSVAGELATPASAILEIDRKVAATIRQDV-PTEFFGAPLAGGLIPWIDSQLPNGQSKEEW 244 Query: 244 KAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPWV 303 K QAE NKIL IPVDG+CVR+GAMRCHS ALT+KL +D+PL +IE LI NPWV Sbjct: 245 KGQAEVNKILGT-PATIPVDGLCVRIGAMRCHSLALTLKLKRDLPLAEIESLIKGGNPWV 303 Query: 304 KLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRRM 363 K V N + ++++ELTPAA+TG L V VGR+RKLNMG +Y+ AF +GDQLLWGAAEPLRRM Sbjct: 304 KFVANDKALTLQELTPAAITGGLQVGVGRVRKLNMGPEYVSAFVIGDQLLWGAAEPLRRM 363 Query: 364 LRILL 368 LRILL Sbjct: 364 LRILL 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: 513 Number of extensions: 22 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: 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 WP_013519947.1 ALIDE2_RS06505 (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.15113.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-201 653.2 0.1 6.2e-201 652.9 0.1 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013519947.1 ALIDE2_RS06505 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013519947.1 ALIDE2_RS06505 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 652.9 0.1 6.2e-201 6.2e-201 2 366 .] 5 368 .. 4 368 .. 1.00 Alignments for each domain: == domain 1 score: 652.9 bits; conditional E-value: 6.2e-201 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 vglvgwrgmvgsvl++rmq e dfd+i+pvffsts++g+kap++a+++++l+da+d+ l ++di+it lcl|NCBI__GCF_000204645.1:WP_013519947.1 5 LVGLVGWRGMVGSVLMDRMQAEGDFDLIEPVFFSTSNAGGKAPAMARTHTQLKDANDVAELAKCDIVIT 73 59******************************************************************* PP TIGR01745 71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139 cqggdytke++p++r+agwkg+widaas+lrm+ddavi+ldpvn +ik ++ g r+++ggnct+s+l lcl|NCBI__GCF_000204645.1:WP_013519947.1 74 CQGGDYTKEVFPRIRAAGWKGHWIDAASALRMEDDAVIVLDPVNDGLIKSRLAAGGRNWIGGNCTNSIL 142 ********************************************************************* PP TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208 lm+l glf+ +lvewvs++tyqaasggga+hmrellk+mgv+y++v+ ela+p+sailei+rkv+ ++r lcl|NCBI__GCF_000204645.1:WP_013519947.1 143 LMGLAGLFKADLVEWVSSMTYQAASGGGANHMRELLKGMGVIYGSVAGELATPASAILEIDRKVAATIR 211 ********************************************************************* PP TIGR01745 209 seelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqal 277 +++p+e+f++plag+lipwid ql ngqs+eewkgqae+nkilgt ti+vdglcvriga+rchs+al lcl|NCBI__GCF_000204645.1:WP_013519947.1 212 -QDVPTEFFGAPLAGGLIPWIDSQLPNGQSKEEWKGQAEVNKILGTPATIPVDGLCVRIGAMRCHSLAL 279 .9******************************************************************* PP TIGR01745 278 tiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftv 346 t+klk+d++l eie++i+ +n+wvk+v n++ tl+eltpaa+tg+l+++vgr+rklnmg+ey+saf++ lcl|NCBI__GCF_000204645.1:WP_013519947.1 280 TLKLKRDLPLAEIESLIKGGNPWVKFVANDKALTLQELTPAAITGGLQVGVGRVRKLNMGPEYVSAFVI 348 ********************************************************************* PP TIGR01745 347 gdqllwgaaeplrrmlrill 366 gdqllwgaaeplrrmlrill lcl|NCBI__GCF_000204645.1:WP_013519947.1 349 GDQLLWGAAEPLRRMLRILL 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: 7.78 // [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