Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012467024.1 CLIM_RS10710 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000020465.1:WP_012467024.1 Length = 342 Score = 312 bits (800), Expect = 7e-90 Identities = 171/333 (51%), Positives = 222/333 (66%), Gaps = 8/333 (2%) Query: 4 QFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFD 63 ++ VA+ GATG VG TM++VL+ER FPVDEL LAS RS G+ RF G+ Sbjct: 7 RYRVAVLGATGLVGRTMIQVLEERNFPVDELVPLASPRSAGQIVRFKGREFITAVPSGEI 66 Query: 64 WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAI--AEF 121 + V IALFSAG S +WAP+AA AG VVIDN+S FR + IPLVVPEVNPEAI A+ Sbjct: 67 FRNVDIALFSAGASASREWAPVAAAAGAVVIDNSSAFRMEPGIPLVVPEVNPEAIFKADG 126 Query: 122 RNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLN 181 +IIANPNCSTIQM+V LKP++D G++R+ V+TYQSV+G GKAG D L + A Sbjct: 127 TPESIIANPNCSTIQMVVVLKPLHDRYGVKRVVVSTYQSVTGKGKAGRDALESELA---- 182 Query: 182 GYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPV 241 G E T QIAFN +PQID F +NGYTKEEMKMV ET+KI D ++ V+PT VR+PV Sbjct: 183 GEEQEQFTHFHQIAFNAVPQIDTFTENGYTKEEMKMVNETRKIMGDEALAVSPTTVRIPV 242 Query: 242 FYGHAEAVHVETRAPIDAEQVMDMLEQTDGIEL--FRGADFPTQVRDAGGKDHVLVGRVR 299 + GH E++++E D +++ +L + GI L A + +D V GR+R Sbjct: 243 YGGHGESLNIELENEFDIDELRTLLASSPGILLQDDPSARIYPMPLTSYERDEVFAGRIR 302 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELL 332 D + +N+W+VADN+RKGAATNAVQIAE++ Sbjct: 303 RDFWNPKTLNMWIVADNLRKGAATNAVQIAEVI 335 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: 349 Number of extensions: 11 Number of successful extensions: 5 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_012467024.1 CLIM_RS10710 (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.24888.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-136 438.4 0.0 1e-135 438.2 0.0 1.0 1 lcl|NCBI__GCF_000020465.1:WP_012467024.1 CLIM_RS10710 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020465.1:WP_012467024.1 CLIM_RS10710 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.2 0.0 1e-135 1e-135 1 337 [. 9 336 .. 9 338 .. 0.96 Alignments for each domain: == domain 1 score: 438.2 bits; conditional E-value: 1e-135 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +va++GatG vG+++++vLeernfp+d+lv+las rsaG+ v+fkg+e+ + e f+++dialfsa lcl|NCBI__GCF_000020465.1:WP_012467024.1 9 RVAVLGATGLVGRTMIQVLEERNFPVDELVPLASPRSAGQIVRFKGREFITAVPSGEIFRNVDIALFSA 77 69***********************************************9999999************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeak..kkgiianPnCstiqlvvvL 136 G+s s+e+ap aa+ag++viDn+safr+++ +PLvvpevn e +++a + +iianPnCstiq+vvvL lcl|NCBI__GCF_000020465.1:WP_012467024.1 78 GASASREWAPVAAAAGAVVIDNSSAFRMEPGIPLVVPEVNPEAIFKADgtPESIIANPNCSTIQMVVVL 146 *******************************************9876422799**************** PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl+d++++krvvvstYq+v G Gk+g + L+++ l g+e+e ++ +qiafna+p+id lcl|NCBI__GCF_000020465.1:WP_012467024.1 147 KPLHDRYGVKRVVVSTYQSVTGKGKAGRDALESE----LAGEEQEQ-------FTHFHQIAFNAVPQID 204 ***************************9999876....56777774.......56779*********** PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 +++e+Gytkee+k+++etrki+g+e l vs t+vr+Pv+ gh es++ie+e+e++++e++ lL +pg+ lcl|NCBI__GCF_000020465.1:WP_012467024.1 205 TFTENGYTKEEMKMVNETRKIMGDEALAVSPTTVRIPVYGGHGESLNIELENEFDIDELRTLLASSPGI 273 ********************************************************************* PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 ++ddps + yp+Pl+ ++devf grir+D + k+l++++vaDnlrkGaa+navqiae + lcl|NCBI__GCF_000020465.1:WP_012467024.1 274 LLQDDPSARIYPMPLTSYERDEVFAGRIRRDFWNPKTLNMWIVADNLRKGAATNAVQIAEVIA 336 ***********************************************************9875 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: 00:00:00.01 # Mc/sec: 11.42 // [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