Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_013820592.1 METME_RS20200 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000214665.1:WP_013820592.1 Length = 340 Score = 433 bits (1114), Expect = e-126 Identities = 216/339 (63%), Positives = 264/339 (77%), Gaps = 3/339 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 MS+ ++VA+ GATGAVGETM+ +L+ER FPV ++ LASERS GK F G ++ VQ++ Sbjct: 1 MSKTYDVAVVGATGAVGETMIAILEERNFPVGNVYALASERSAGKRIPFKGGSLVVQDLA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FD+S+V I LFS G +SA++AP AA AG VVIDNTS FRYD DIPLVVPEVNPE +A+ Sbjct: 61 GFDFSKVQIGLFSPGASVSAEFAPKAAAAGCVVIDNTSQFRYDDDIPLVVPEVNPEKVAD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 ++NR IIANPNCSTIQMLVALKPIYDAVGI RINV TYQ+VSG GK I+ELA QTA LL Sbjct: 121 YKNRGIIANPNCSTIQMLVALKPIYDAVGISRINVATYQAVSGTGKEAIEELATQTANLL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 N P +N + +QIAFN +PQID FMDNGYTKEEMKMVWET+KI D I+VNPT VRVP Sbjct: 181 NAKPVVSNVYPKQIAFNVLPQIDVFMDNGYTKEEMKMVWETRKIMGDADILVNPTAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGR 297 VFYGH+EAVH+ET+ I A+QV ++L G+ + +PT V ++ G D V VGR Sbjct: 241 VFYGHSEAVHIETKHKISAQQVRELLSSAPGVTVLDERENGGYPTAVTESSGHDDVYVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 +R DISH +GI+LWVV DNVRKGAA N+VQIAE+LV++Y Sbjct: 301 IREDISHPNGIDLWVVGDNVRKGAALNSVQIAEVLVKNY 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: 356 Number of extensions: 6 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_013820592.1 METME_RS20200 (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.2461.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-142 460.6 0.9 1.7e-142 460.4 0.9 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013820592.1 METME_RS20200 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013820592.1 METME_RS20200 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 460.4 0.9 1.7e-142 1.7e-142 2 339 .] 7 338 .. 6 338 .. 0.98 Alignments for each domain: == domain 1 score: 460.4 bits; conditional E-value: 1.7e-142 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 va+vGatGavG++++ +Leernfp+ ++++lasersaGk++ fkg l v+++ ++f++++i lfs G lcl|NCBI__GCF_000214665.1:WP_013820592.1 7 VAVVGATGAVGETMIAILEERNFPVGNVYALASERSAGKRIPFKGGSLVVQDLAGFDFSKVQIGLFSPG 75 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 +svs efapkaa+ag++viDnts fr d+d+PLvvpevn e++++ k++giianPnCstiq++v+Lkp+ lcl|NCBI__GCF_000214665.1:WP_013820592.1 76 ASVSAEFAPKAAAAGCVVIDNTSQFRYDDDIPLVVPEVNPEKVADYKNRGIIANPNCSTIQMLVALKPI 144 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +d++++ r+ v+tYqavsG+Gk+++eeL+ qt l+ k + ++ ++kqiafn++p+id ++ lcl|NCBI__GCF_000214665.1:WP_013820592.1 145 YDAVGISRINVATYQAVSGTGKEAIEELATQTANLLNAKP-------VVSNVYPKQIAFNVLPQIDVFM 206 ********************************99988764.......4579****************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 ++Gytkee+k+++etrki+g+ d+ v t+vrvPvf+ghse+v+ie+++++s+++v+elL apgv+v+ lcl|NCBI__GCF_000214665.1:WP_013820592.1 207 DNGYTKEEMKMVWETRKIMGDADILVNPTAVRVPVFYGHSEAVHIETKHKISAQQVRELLSSAPGVTVL 275 ********************************************************************* PP TIGR01296 278 ddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 d+ ++ ypt + e +g+d+v+vgrir+D+s+ +g++l+vv+Dn+rkGaaln+vqiae l+k+ lcl|NCBI__GCF_000214665.1:WP_013820592.1 276 DERENGGYPTAVtESSGHDDVYVGRIREDISHPNGIDLWVVGDNVRKGAALNSVQIAEVLVKN 338 **********983689********************************************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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.19 // [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