Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_024851459.1 N745_RS0107250 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000526715.1:WP_024851459.1 Length = 340 Score = 431 bits (1108), Expect = e-125 Identities = 216/339 (63%), Positives = 265/339 (78%), Gaps = 3/339 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 M++++++A+ GATGAVGET+L+VL+ER FPV +L+ LAS RS GK F G V ++++ Sbjct: 1 MTKKYDIAVVGATGAVGETILKVLEERNFPVGKLYPLASSRSAGKKLEFRGSWVEIEDLA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FD+S+V I LFS G +S ++AP AA AG VV+DNTS FRYD DIPLVVPEVNP+A+A Sbjct: 61 TFDFSKVQIGLFSPGASISREYAPKAAAAGCVVVDNTSEFRYDDDIPLVVPEVNPQAVAG 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 ++NR IIANPNCSTIQMLVALKPIYDAVGI RINV TYQ+VSG+GK I+ELA QTA +L Sbjct: 121 YKNRGIIANPNCSTIQMLVALKPIYDAVGISRINVCTYQAVSGSGKEAIEELAKQTANIL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 N P ETN + +QIAFNCIPQID F DNGYTKEEMKMVWET+KI D +I+VNPT VRVP Sbjct: 181 NLKPVETNVYPKQIAFNCIPQIDVFQDNGYTKEEMKMVWETKKIMGDDAILVNPTAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFR---GADFPTQVRDAGGKDHVLVGR 297 VF+GH+EAVH+ET+ I A+Q ++ + DGI L +PT V DA + V VGR Sbjct: 241 VFFGHSEAVHIETKEKITAKQAKEIFGKADGIVLVDEHVDGGYPTAVTDAVDTNPVYVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 VR DIS G++LWVVADNVRKGAATN VQIAELL++DY Sbjct: 301 VREDISCEKGLDLWVVADNVRKGAATNTVQIAELLIKDY 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: 390 Number of extensions: 15 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_024851459.1 N745_RS0107250 (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.25847.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-140 452.4 0.6 5.3e-140 452.3 0.6 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024851459.1 N745_RS0107250 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024851459.1 N745_RS0107250 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 452.3 0.6 5.3e-140 5.3e-140 2 339 .] 7 338 .. 6 338 .. 0.98 Alignments for each domain: == domain 1 score: 452.3 bits; conditional E-value: 5.3e-140 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 +a+vGatGavG+++lkvLeernfp+ kl++las+rsaGkk++f+g +e+e++ +++f++++i lfs G lcl|NCBI__GCF_000526715.1:WP_024851459.1 7 IAVVGATGAVGETILKVLEERNFPVGKLYPLASSRSAGKKLEFRGSWVEIEDLATFDFSKVQIGLFSPG 75 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 +s+s+e+apkaa+ag++v+Dnts fr d+d+PLvvpevn + ++ k++giianPnCstiq++v+Lkp+ lcl|NCBI__GCF_000526715.1:WP_024851459.1 76 ASISREYAPKAAAAGCVVVDNTSEFRYDDDIPLVVPEVNPQAVAGYKNRGIIANPNCSTIQMLVALKPI 144 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +d++++ r+ v tYqavsG+Gk+++eeL++qt +l+ k e ++ ++kqiafn ip+id ++ lcl|NCBI__GCF_000526715.1:WP_024851459.1 145 YDAVGISRINVCTYQAVSGSGKEAIEELAKQTANILNLKPVE-------TNVYPKQIAFNCIPQIDVFQ 206 *********************************999987655.......699***************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 ++Gytkee+k+++et+ki+g++ + v t+vrvPvf ghse+v+ie++++++++++ke++ +a+g+v++ lcl|NCBI__GCF_000526715.1:WP_024851459.1 207 DNGYTKEEMKMVWETKKIMGDDAILVNPTAVRVPVFFGHSEAVHIETKEKITAKQAKEIFGKADGIVLV 275 ********************************************************************* PP TIGR01296 278 ddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 d+ + ypt + +av+++ v+vgr+r+D+s ekgl+l+vvaDn+rkGaa+n+vqiaellik+ lcl|NCBI__GCF_000526715.1:WP_024851459.1 276 DEHVDGGYPTAVtDAVDTNPVYVGRVREDISCEKGLDLWVVADNVRKGAATNTVQIAELLIKD 338 *********9974799********************************************996 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: 9.22 // [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