Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_006748154.1 THITH_RS10440 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000227685.2:WP_006748154.1 Length = 341 Score = 442 bits (1136), Expect = e-129 Identities = 225/337 (66%), Positives = 264/337 (78%), Gaps = 3/337 (0%) Query: 3 QQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEF 62 ++F+VA+ GATGAVGETML +L ER FPV + LASERS GKT F + + V+++ F Sbjct: 4 KKFDVAVVGATGAVGETMLAILAERAFPVGTVHALASERSAGKTVAFGNRELVVEDLATF 63 Query: 63 DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122 D+S+V I LFS G +SA +AP AA AG VVIDNTS FRYD DIPL+VPEVNP A+A +R Sbjct: 64 DFSKVQIGLFSPGASVSAVYAPKAAAAGCVVIDNTSQFRYDDDIPLIVPEVNPAAVASYR 123 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 NR IIANPNCSTIQMLVALKPIYDAVGIERINV TYQ+VSG GK IDELA QTA LLNG Sbjct: 124 NRGIIANPNCSTIQMLVALKPIYDAVGIERINVATYQAVSGTGKDAIDELAQQTAALLNG 183 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 P E + + +QIAFN +P ID FMDNGYTKEEMKMVWET+KIF D SIMVNPT VRVPVF Sbjct: 184 KPVECSVYPKQIAFNVLPHIDAFMDNGYTKEEMKMVWETRKIFEDDSIMVNPTTVRVPVF 243 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF--RG-ADFPTQVRDAGGKDHVLVGRVR 299 YGH+EAVH+ETR I AE +LEQ G+E+ RG +PT V ++ G+D V VGR+R Sbjct: 244 YGHSEAVHIETREKISAETARALLEQAPGVEVLDSRGPGGYPTAVTESSGRDGVFVGRIR 303 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 DISH G++LWVV+DNVRKGAA N +QIAELLVR+Y Sbjct: 304 EDISHPRGLDLWVVSDNVRKGAALNTIQIAELLVREY 340 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: 360 Number of extensions: 7 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: 341 Length adjustment: 28 Effective length of query: 309 Effective length of database: 313 Effective search space: 96717 Effective search space used: 96717 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_006748154.1 THITH_RS10440 (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.13829.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-137 443.9 0.1 2.1e-137 443.7 0.1 1.0 1 lcl|NCBI__GCF_000227685.2:WP_006748154.1 THITH_RS10440 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000227685.2:WP_006748154.1 THITH_RS10440 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.7 0.1 2.1e-137 2.1e-137 2 338 .. 8 338 .. 7 339 .. 0.98 Alignments for each domain: == domain 1 score: 443.7 bits; conditional E-value: 2.1e-137 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 va+vGatGavG+++l +L+er fp+ ++ +lasersaGk v+f ++el ve++ +++f++++i lfs G lcl|NCBI__GCF_000227685.2:WP_006748154.1 8 VAVVGATGAVGETMLAILAERAFPVGTVHALASERSAGKTVAFGNRELVVEDLATFDFSKVQIGLFSPG 76 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 +svs ++apkaa+ag++viDnts fr d+d+PL+vpevn + ++ +++giianPnCstiq++v+Lkp+ lcl|NCBI__GCF_000227685.2:WP_006748154.1 77 ASVSAVYAPKAAAAGCVVIDNTSQFRYDDDIPLIVPEVNPAAVASYRNRGIIANPNCSTIQMLVALKPI 145 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +d+++++r+ v+tYqavsG+Gk++++eL++qt a l+gk e + ++kqiafn++p+id ++ lcl|NCBI__GCF_000227685.2:WP_006748154.1 146 YDAVGIERINVATYQAVSGTGKDAIDELAQQTAALLNGKPVE-------CSVYPKQIAFNVLPHIDAFM 207 ************************************998766.......699***************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 ++Gytkee+k+++etrki++++ + v t+vrvPvf+ghse+v+ie+ +++s+e ++ lL++apgv v+ lcl|NCBI__GCF_000227685.2:WP_006748154.1 208 DNGYTKEEMKMVWETRKIFEDDSIMVNPTTVRVPVFYGHSEAVHIETREKISAETARALLEQAPGVEVL 276 ********************************************************************* PP TIGR01296 278 ddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 d ypt + e +g+d vfvgrir+D+s+ +gl+l+vv+Dn+rkGaaln++qiaell++ lcl|NCBI__GCF_000227685.2:WP_006748154.1 277 DSRGPGGYPTAVtESSGRDGVFVGRIREDISHPRGLDLWVVSDNVRKGAALNTIQIAELLVR 338 **********983689*******************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (341 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: 00:00:00.01 # Mc/sec: 10.40 // [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