Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_041471663.1 CPHAMN1_RS10845 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000020545.1:WP_041471663.1 Length = 339 Score = 317 bits (812), Expect = 3e-91 Identities = 175/336 (52%), Positives = 224/336 (66%), Gaps = 14/336 (4%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 +++AI GATG VG TML+VL ER+FPV E+ LASERS G+ F GK+ R + Sbjct: 8 YSIAILGATGLVGRTMLQVLDERDFPVREILPLASERSRGREIVFRGKSFRTDVPSAEVF 67 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN- 123 S+ IALFSAG S WA +AAEAG VVIDN+S FR + D+PLVVPEVNPEAI + + Sbjct: 68 SRADIALFSAGATASRTWASVAAEAGAVVIDNSSAFRMEPDVPLVVPEVNPEAIFDVQGK 127 Query: 124 -RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 + +IANPNCSTIQM+V LKP++D + R+ V+TYQSV+G GK G D L + A G Sbjct: 128 PKGVIANPNCSTIQMVVVLKPLHDRYRVRRVVVSTYQSVTGKGKQGRDALEDELA----G 183 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 E+ QIAFN +P ID F+DNGYTKEEMKMV ET+KI D S+ V+PT VR+PV+ Sbjct: 184 KMPESFVHGHQIAFNAVPHIDVFLDNGYTKEEMKMVNETRKIMCDESLSVSPTTVRIPVY 243 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPT-----QVRDAGGKDHVLVGR 297 GH E++++E D +++ +ML T GI + D P+ + KD V VGR Sbjct: 244 GGHGESMNIEFEDDFDVDELREMLAGTPGIIV---QDDPSSGLYPMPLTSYEKDEVFVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLV 333 +R D +NLW+VADN+RKGAATNAVQIAE LV Sbjct: 301 IRRDFWQPKTVNLWIVADNLRKGAATNAVQIAEKLV 336 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: 357 Number of extensions: 9 Number of successful extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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_041471663.1 CPHAMN1_RS10845 (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.19052.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-137 443.5 0.0 4.1e-137 442.8 0.0 1.3 1 lcl|NCBI__GCF_000020545.1:WP_041471663.1 CPHAMN1_RS10845 aspartate-semial Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020545.1:WP_041471663.1 CPHAMN1_RS10845 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 442.8 0.0 4.1e-137 4.1e-137 1 337 [. 9 336 .. 9 338 .. 0.97 Alignments for each domain: == domain 1 score: 442.8 bits; conditional E-value: 4.1e-137 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 ++ai+GatG vG+++l+vL+er+fp+ ++ +lasers+G+++ f+gk ++ + + e+f++ dialfsa lcl|NCBI__GCF_000020545.1:WP_041471663.1 9 SIAILGATGLVGRTMLQVLDERDFPVREILPLASERSRGREIVFRGKSFRTDVPSAEVFSRADIALFSA 77 59******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkea..kkkgiianPnCstiqlvvvL 136 G++ s+++a+ aa+ag++viDn+safr+++dvPLvvpevn e +++ k+kg+ianPnCstiq+vvvL lcl|NCBI__GCF_000020545.1:WP_041471663.1 78 GATASRTWASVAAEAGAVVIDNSSAFRMEPDVPLVVPEVNPEAIFDVqgKPKGVIANPNCSTIQMVVVL 146 *******************************************998733589***************** PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl+d+++++rvvvstYq+v G Gk+g + L++++ ++ e+ + +qiafna+p+id lcl|NCBI__GCF_000020545.1:WP_041471663.1 147 KPLHDRYRVRRVVVSTYQSVTGKGKQGRDALEDELAGKMP--ES---------FVHGHQIAFNAVPHID 204 ********************************99876553..33.........34679*********** PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 + ++Gytkee+k+++etrki+ +e l vs t+vr+Pv+ gh es++iefe++++v+e++e+L + pg+ lcl|NCBI__GCF_000020545.1:WP_041471663.1 205 VFLDNGYTKEEMKMVNETRKIMCDESLSVSPTTVRIPVYGGHGESMNIEFEDDFDVDELREMLAGTPGI 273 ********************************************************************* PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +v+ddps+ lyp+Pl+ +kdevfvgrir+D + k+++l++vaDnlrkGaa+navqiae+l+ lcl|NCBI__GCF_000020545.1:WP_041471663.1 274 IVQDDPSSGLYPMPLTSYEKDEVFVGRIRRDFWQPKTVNLWIVADNLRKGAATNAVQIAEKLV 336 ************************************************************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: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.04 # Mc/sec: 2.30 // [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