Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_028485423.1 A377_RS0109010 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000384235.1:WP_028485423.1 Length = 340 Score = 434 bits (1116), Expect = e-126 Identities = 211/339 (62%), Positives = 268/339 (79%), Gaps = 3/339 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 M++Q+++A+ GATGAVGET+L+VL+ER+FPV L+ LAS RS GK FNG V +Q++ Sbjct: 1 MTKQYDIAVVGATGAVGETILKVLEERDFPVRNLYPLASSRSAGKKIEFNGSWVEIQDLA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FD+S+V I LFS GG +S ++AP AA AG VV+DNTS FRYD D+PL+VPEVNP+A+A Sbjct: 61 TFDFSKVQIGLFSPGGSVSREYAPKAAAAGCVVVDNTSEFRYDKDVPLIVPEVNPDAVAG 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 + RNIIANPNCSTIQM+VA+KPIY+AVGI+RINV TYQ+VSG+GK I+ELAGQT +L Sbjct: 121 YTQRNIIANPNCSTIQMMVAIKPIYEAVGIKRINVATYQAVSGSGKEAIEELAGQTRDIL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 N P +T + +QIAFNCIPQID F DNGYTKEEMKMVWET+KI D +++VNPT VRVP Sbjct: 181 NLQPVKTEVYPKQIAFNCIPQIDVFQDNGYTKEEMKMVWETKKILEDETVLVNPTAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFR---GADFPTQVRDAGGKDHVLVGR 297 VF+GH+EA+H+ET+ I A++ D+ E+T+GI L +PT V DA D V VGR Sbjct: 241 VFFGHSEAIHIETKKKITAQEAKDLFEKTEGIVLMDTHVDGGYPTAVTDAADTDPVYVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 VR DI+ +G+NLWVVADNVRKGAATN VQIAELL++ + Sbjct: 301 VREDITCDNGLNLWVVADNVRKGAATNTVQIAELLIQKH 339 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: 393 Number of extensions: 9 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: 340 Length adjustment: 28 Effective length of query: 309 Effective length of database: 312 Effective search space: 96408 Effective search space used: 96408 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_028485423.1 A377_RS0109010 (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.20943.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-139 449.2 0.8 5.2e-139 449.0 0.8 1.0 1 lcl|NCBI__GCF_000384235.1:WP_028485423.1 A377_RS0109010 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_028485423.1 A377_RS0109010 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 449.0 0.8 5.2e-139 5.2e-139 2 338 .. 7 337 .. 6 338 .. 0.98 Alignments for each domain: == domain 1 score: 449.0 bits; conditional E-value: 5.2e-139 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 +a+vGatGavG+++lkvLeer+fp+ +l++las+rsaGkk++f+g +e++++ +++f++++i lfs G lcl|NCBI__GCF_000384235.1:WP_028485423.1 7 IAVVGATGAVGETILKVLEERDFPVRNLYPLASSRSAGKKIEFNGSWVEIQDLATFDFSKVQIGLFSPG 75 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 gsvs+e+apkaa+ag++v+Dnts fr d+dvPL+vpevn + ++ +++iianPnCstiq++v++kp+ lcl|NCBI__GCF_000384235.1:WP_028485423.1 76 GSVSREYAPKAAAAGCVVVDNTSEFRYDKDVPLIVPEVNPDAVAGYTQRNIIANPNCSTIQMMVAIKPI 144 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 ++++++kr+ v+tYqavsG+Gk+++eeL+ qt+ +l+ + +k++ ++kqiafn ip+id ++ lcl|NCBI__GCF_000384235.1:WP_028485423.1 145 YEAVGIKRINVATYQAVSGSGKEAIEELAGQTRDILNLQP-------VKTEVYPKQIAFNCIPQIDVFQ 206 **********************************998753.......6789****************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 ++Gytkee+k+++et+kil++e + v t+vrvPvf ghse+++ie++k+++++e+k+l+++ +g+v++ lcl|NCBI__GCF_000384235.1:WP_028485423.1 207 DNGYTKEEMKMVWETKKILEDETVLVNPTAVRVPVFFGHSEAIHIETKKKITAQEAKDLFEKTEGIVLM 275 ********************************************************************* PP TIGR01296 278 ddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 d + ypt + +a+++d v+vgr+r+D++ ++gl+l+vvaDn+rkGaa+n+vqiaelli+ lcl|NCBI__GCF_000384235.1:WP_028485423.1 276 DTHVDGGYPTAVtDAADTDPVYVGRVREDITCDNGLNLWVVADNVRKGAATNTVQIAELLIQ 337 *********99746999******************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (340 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: 11.27 // [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