Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_029933938.1 N746_RS0103290 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000711195.1:WP_029933938.1 Length = 339 Score = 426 bits (1094), Expect = e-124 Identities = 214/337 (63%), Positives = 262/337 (77%), Gaps = 3/337 (0%) Query: 3 QQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEF 62 ++F+VA+ GATGAVGET+L+VL+ER FP+ L+ LAS RS GK F G+ V V ++E+F Sbjct: 2 RKFDVAVVGATGAVGETILKVLEERNFPIGNLYPLASSRSAGKKIEFKGEWVEVLDLEKF 61 Query: 63 DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122 D+S+ I LFS G +SA +AP AAEAG VV+DNTS FRYD +IPLVVPEVNP+AIA ++ Sbjct: 62 DFSKAQIGLFSPGASVSAIYAPKAAEAGCVVVDNTSQFRYDDEIPLVVPEVNPDAIAGYK 121 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 R IIANPNCSTIQM+VALKPIYDAVGIERINV TYQ+VSG GK I+ELA QTA +LN Sbjct: 122 KRGIIANPNCSTIQMMVALKPIYDAVGIERINVATYQAVSGTGKEAIEELAKQTANILNL 181 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 P E + +QIAFNCIPQID FM+NGYTKEEMKMVWET+KIF D SI VNPT VRVPVF Sbjct: 182 KPVEIEVYPKQIAFNCIPQIDVFMENGYTKEEMKMVWETKKIFGDESIKVNPTAVRVPVF 241 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVR 299 +GH+EAVH+ET+ I A+Q ++L+++ G I+ +PT V DA + V VGR+R Sbjct: 242 FGHSEAVHIETKQKITAQQARELLQKSPGLVVIDEHADGGYPTAVSDAADTNPVYVGRIR 301 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 DI+ G+NLWVVADNVRKGAATN VQIAE+L+ Y Sbjct: 302 EDITVERGLNLWVVADNVRKGAATNTVQIAEVLIEKY 338 Lambda K H 0.319 0.135 0.395 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: 369 Number of extensions: 13 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: 337 Length of database: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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_029933938.1 N746_RS0103290 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (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/TIGR01296.hmm # target sequence database: /tmp/gapView.3697257.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01296 [M=339] Accession: TIGR01296 Description: asd_B: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-138 447.2 1.3 2.1e-138 447.0 1.3 1.0 1 NCBI__GCF_000711195.1:WP_029933938.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000711195.1:WP_029933938.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.0 1.3 2.1e-138 2.1e-138 2 338 .. 6 336 .. 5 337 .. 0.98 Alignments for each domain: == domain 1 score: 447.0 bits; conditional E-value: 2.1e-138 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvs 74 va+vGatGavG+++lkvLeernfpi +l++las+rsaGkk++fkg+ +ev ++ek++f++ +i lfs G+svs NCBI__GCF_000711195.1:WP_029933938.1 6 VAVVGATGAVGETILKVLEERNFPIGNLYPLASSRSAGKKIEFKGEWVEVLDLEKFDFSKAQIGLFSPGASVS 78 9************************************************************************ PP TIGR01296 75 kefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkr 147 +apkaa+ag++v+Dnts fr d+++PLvvpevn + ++ kk+giianPnCstiq++v+Lkp++d+++++r NCBI__GCF_000711195.1:WP_029933938.1 79 AIYAPKAAEAGCVVVDNTSQFRYDDEIPLVVPEVNPDAIAGYKKRGIIANPNCSTIQMMVALKPIYDAVGIER 151 ************************************************************************* PP TIGR01296 148 vvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkll 220 + v+tYqavsG+Gk+++eeL++qt +l+ k e + ++kqiafn ip+id ++e+Gytkee+k++ NCBI__GCF_000711195.1:WP_029933938.1 152 INVATYQAVSGTGKEAIEELAKQTANILNLKPVEI-------EVYPKQIAFNCIPQIDVFMENGYTKEEMKMV 217 ***************************99987765.......89***************************** PP TIGR01296 221 fetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eav 292 +et+ki+g+e +kv t+vrvPvf ghse+v+ie+++++++++++elL+++pg+vvid+ + ypt + +a+ NCBI__GCF_000711195.1:WP_029933938.1 218 WETKKIFGDESIKVNPTAVRVPVFFGHSEAVHIETKQKITAQQARELLQKSPGLVVIDEHADGGYPTAVsDAA 290 *******************************************************************984699 PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +++ v+vgrir+D++ e+gl+l+vvaDn+rkGaa+n+vqiae li+ NCBI__GCF_000711195.1:WP_029933938.1 291 DTNPVYVGRIREDITVERGLNLWVVADNVRKGAATNTVQIAEVLIE 336 9******************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (339 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: 27.60 // [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