Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_084057661.1 B9A12_RS09570 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_900176285.1:WP_084057661.1 Length = 339 Score = 354 bits (909), Expect = e-102 Identities = 182/343 (53%), Positives = 245/343 (71%), Gaps = 8/343 (2%) Query: 4 GLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPES 63 G VAVVGATGAVG M++ LE+R F + L LL+S RS G +++F+G +++V+E + +S Sbjct: 5 GYRVAVVGATGAVGTTMVRVLEERRFPVRELKLLASSRSVGKQISFRGAQVSVEELTEDS 64 Query: 64 FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNG 123 F+G+++ALFSAG SVS+ AP A + G +V+DN+SAFRMD +TPLVVPEVN + H G Sbjct: 65 FQGLDVALFSAGASVSRRFAPIAARVGCVVVDNSSAFRMDPHTPLVVPEVNPHAVRHHQG 124 Query: 124 IIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEI 183 IIANPNCSTIQMV AL+PI+ A G+ +++V+T+QAVSG G +A++EL Q +A + E + Sbjct: 125 IIANPNCSTIQMVVALKPIQDAVGIQRIVVTTFQAVSGTGMKAIQELRRQVEATVKGEPL 184 Query: 184 EPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243 E+ P +QIAFN +P I F D+GYT EEMKM+NET+KI PD+QV AT VR Sbjct: 185 PQEVYP-------HQIAFNCLPHIGSFLDSGYTEEEMKMVNETRKIFEDPDIQVCATTVR 237 Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303 +P+ GHSESV +E+ R V+D LL +A GV + DDP YPMP DA G+++ FV Sbjct: 238 VPVYYGHSESVAVEM-RKPLEVQDAVALLSKAQGVQVVDDPLAGRYPMPLDAEGRDETFV 296 Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 GRIRKD+ NG WVV+DN+ KGAA N+VQIAE L + L+ Sbjct: 297 GRIRKDISIPNGLVFWVVADNIRKGAATNAVQIAELLVQEGLL 339 Lambda K H 0.314 0.131 0.366 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: 299 Number of extensions: 9 Number of successful extensions: 3 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: 346 Length of database: 339 Length adjustment: 29 Effective length of query: 317 Effective length of database: 310 Effective search space: 98270 Effective search space used: 98270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_084057661.1 B9A12_RS09570 (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.3149.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-144 465.6 0.2 5.3e-144 465.4 0.2 1.0 1 lcl|NCBI__GCF_900176285.1:WP_084057661.1 B9A12_RS09570 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176285.1:WP_084057661.1 B9A12_RS09570 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.4 0.2 5.3e-144 5.3e-144 1 338 [. 7 335 .. 7 336 .. 0.98 Alignments for each domain: == domain 1 score: 465.4 bits; conditional E-value: 5.3e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +va+vGatGavG ++++vLeer fp+ +l+llas+rs Gk++ f+g ++ vee+++ sf+g+d+alfsa lcl|NCBI__GCF_900176285.1:WP_084057661.1 7 RVAVVGATGAVGTTMVRVLEERRFPVRELKLLASSRSVGKQISFRGAQVSVEELTEDSFQGLDVALFSA 75 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 G+svs+ fap aa+ g++v+Dn+safr+d+++PLvvpevn + +++++ giianPnCstiq+vv+Lkp lcl|NCBI__GCF_900176285.1:WP_084057661.1 76 GASVSRRFAPIAARVGCVVVDNSSAFRMDPHTPLVVPEVNPHAVRHHQ--GIIANPNCSTIQMVVALKP 142 ***********************************************9..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 ++d+++++r+vv t+qavsG+G k+++eL+ q+ a+++g+ l+ + +++qiafn +p+i+++ lcl|NCBI__GCF_900176285.1:WP_084057661.1 143 IQDAVGIQRIVVTTFQAVSGTGMKAIQELRRQVEATVKGEP-------LPQEVYPHQIAFNCLPHIGSF 204 **********************************9998754.......45799**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 + Gyt+ee+k+++etrki++++d++v at+vrvPv++ghsesv +e+ k+l+v+++ lL +a+gv+v lcl|NCBI__GCF_900176285.1:WP_084057661.1 205 LDSGYTEEEMKMVNETRKIFEDPDIQVCATTVRVPVYYGHSESVAVEMRKPLEVQDAVALLSKAQGVQV 273 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +ddp yp+Pl+a+g+de+fvgrirkD+s +gl +vvaDn+rkGaa+navqiaell++ lcl|NCBI__GCF_900176285.1:WP_084057661.1 274 VDDPLAGRYPMPLDAEGRDETFVGRIRKDISIPNGLVFWVVADNIRKGAATNAVQIAELLVQ 335 ***********************************************************997 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.04 // [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