Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_057687228.1 ABB28_RS15230 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_001431535.1:WP_057687228.1 Length = 342 Score = 380 bits (975), Expect = e-110 Identities = 195/336 (58%), Positives = 244/336 (72%), Gaps = 4/336 (1%) Query: 3 QQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEF 62 + F+VA+ GATGAVGETML +L ER+FPV L LLAS RS G FNG ++++ +F Sbjct: 6 RSFHVAVVGATGAVGETMLSILAERDFPVGTLTLLASSRSAGGEVEFNGHKHIIKDLADF 65 Query: 63 DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122 D + V IALFSAGG +S +AP A AG VVIDN+S FRYD D+PLVV EVNP+ +A R Sbjct: 66 DPTGVDIALFSAGGSVSKDYAPKFAAAGAVVIDNSSAFRYDDDVPLVVSEVNPDQVAN-R 124 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 R IIANPNCST+QMLVAL P++ GIERINV TYQSVSG G++ ++EL QT +LL+ Sbjct: 125 PRGIIANPNCSTMQMLVALAPLHRRYGIERINVATYQSVSGGGRSALEELGKQTGQLLSF 184 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 + F QIAFN IP ID F+DNG+TKEEMK+VWETQKI D SI+VNPT VRVPVF Sbjct: 185 QEIDPQRFPVQIAFNLIPHIDDFLDNGFTKEEMKLVWETQKILGDSSILVNPTAVRVPVF 244 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIEL---FRGADFPTQVRDAGGKDHVLVGRVR 299 YGH+EAV +ETR + A Q ++L Q+ G+E+ +PT V A G D V VGR+R Sbjct: 245 YGHSEAVAIETRDKVTAAQARELLSQSPGVEVVDRHEAGGYPTPVTHASGTDAVYVGRIR 304 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335 D+SH G+NLW+V+DN+RKGAA NAVQ+AEL+ + Sbjct: 305 EDLSHPRGLNLWIVSDNIRKGAALNAVQLAELVAAE 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: 359 Number of extensions: 15 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: 337 Length of database: 342 Length adjustment: 28 Effective length of query: 309 Effective length of database: 314 Effective search space: 97026 Effective search space used: 97026 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_057687228.1 ABB28_RS15230 (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.12345.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-138 447.2 0.0 2.1e-138 447.0 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057687228.1 ABB28_RS15230 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057687228.1 ABB28_RS15230 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 447.0 0.0 2.1e-138 2.1e-138 1 337 [. 9 338 .. 9 340 .. 0.99 Alignments for each domain: == domain 1 score: 447.0 bits; conditional E-value: 2.1e-138 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +va+vGatGavG+++l +L+er+fp+ +l+llas+rsaG +v+f+g++ ++++ +++ g+dialfsa lcl|NCBI__GCF_001431535.1:WP_057687228.1 9 HVAVVGATGAVGETMLSILAERDFPVGTLTLLASSRSAGGEVEFNGHKHIIKDLADFDPTGVDIALFSA 77 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggsvsk +apk+a+ag++viDn+safr d+dvPLvv+evn +++++++ +giianPnCst+q++v+L p lcl|NCBI__GCF_001431535.1:WP_057687228.1 78 GGSVSKDYAPKFAAAGAVVIDNSSAFRYDDDVPLVVSEVNPDQVANRP-RGIIANPNCSTMQMLVALAP 145 **********************************************99.******************** PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+++++++r+ v+tYq+vsG G+ ++eeL +qt l+++e++p ++f+ qiafn+ip+id++ lcl|NCBI__GCF_001431535.1:WP_057687228.1 146 LHRRYGIERINVATYQSVSGGGRSALEELGKQTGQLLSFQEIDP-------QRFPVQIAFNLIPHIDDF 207 *******************************************7.......9***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 ++G+tkee+kl++et+kilg++ + v t+vrvPvf+ghse+v ie+ +++++ +++elL ++pgv v lcl|NCBI__GCF_001431535.1:WP_057687228.1 208 LDNGFTKEEMKLVWETQKILGDSSILVNPTAVRVPVFYGHSEAVAIETRDKVTAAQARELLSQSPGVEV 276 ********************************************************************* PP TIGR01296 277 iddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +d + yptP+ +a+g+d+v+vgrir+Dls+ +gl+l++v+Dn+rkGaalnavq+ael+ lcl|NCBI__GCF_001431535.1:WP_057687228.1 277 VDRHEAGGYPTPVtHASGTDAVYVGRIREDLSHPRGLNLWIVSDNIRKGAALNAVQLAELVA 338 ************94599******************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (342 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.03 # Mc/sec: 3.17 // [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