Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012506494.1 PAES_RS09725 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000020625.1:WP_012506494.1 Length = 339 Score = 320 bits (821), Expect = 2e-92 Identities = 176/333 (52%), Positives = 226/333 (67%), Gaps = 8/333 (2%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + VAI GATG VG TML+VL+ER+FPV E+ LAS RS GK F+G+T + + + Sbjct: 8 YRVAILGATGLVGRTMLDVLEERKFPVSEIVPLASSRSRGKEIVFDGRTFVTREPSKEVF 67 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAI--AEFR 122 ++V IALFSAG S +WA IAAEAG VVIDN+S FR D D+PLVVPEVNPEAI + R Sbjct: 68 AEVDIALFSAGAGASHEWARIAAEAGAVVIDNSSAFRMDPDVPLVVPEVNPEAIFDEDGR 127 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 IIANPNCSTIQM+V LKP++D + R+ V+TYQSV+G GKAG D L + A G Sbjct: 128 PEMIIANPNCSTIQMVVVLKPLHDRYRLRRVVVSTYQSVTGKGKAGRDALEAELA----G 183 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 E+ T QIAFN IP ID F +NGYTKEE+KMV ET+KI D S+ V+PT VR+PV+ Sbjct: 184 TVPESFTHVHQIAFNAIPHIDVFQENGYTKEELKMVNETRKIMGDDSLSVSPTTVRIPVY 243 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDG--IELFRGADFPTQVRDAGGKDHVLVGRVRN 300 GH E++++E + V ++L + G ++ A+ + KD V VGR+R Sbjct: 244 GGHGESLNIEFEEDFSVDDVRELLSKAPGVIVQDNPSANLYPMPLSSYEKDEVFVGRIRR 303 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLV 333 D+ H +N+WVVADN+RKGAATNAVQIAE L+ Sbjct: 304 DLWHPKTLNMWVVADNLRKGAATNAVQIAEQLI 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: 348 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_012506494.1 PAES_RS09725 (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.5883.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-142 460.2 0.0 3.2e-142 459.5 0.0 1.3 1 lcl|NCBI__GCF_000020625.1:WP_012506494.1 PAES_RS09725 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012506494.1 PAES_RS09725 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.5 0.0 3.2e-142 3.2e-142 1 337 [. 9 336 .. 9 338 .. 0.96 Alignments for each domain: == domain 1 score: 459.5 bits; conditional E-value: 3.2e-142 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +vai+GatG vG+++l+vLeer+fp++++v+las+rs+Gk++ f g+ + +e +ke+f ++dialfsa lcl|NCBI__GCF_000020625.1:WP_012506494.1 9 RVAILGATGLVGRTMLDVLEERKFPVSEIVPLASSRSRGKEIVFDGRTFVTREPSKEVFAEVDIALFSA 77 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkea..kkkgiianPnCstiqlvvvL 136 G+ s+e+a aa+ag++viDn+safr+d+dvPLvvpevn e +++ ++ iianPnCstiq+vvvL lcl|NCBI__GCF_000020625.1:WP_012506494.1 78 GAGASHEWARIAAEAGAVVIDNSSAFRMDPDVPLVVPEVNPEAIFDEdgRPEMIIANPNCSTIQMVVVL 146 *******************************************9876226789**************** PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl+d+++l+rvvvstYq+v G Gk+g + L+ ++ ++ ++ ++++qiafnaip+id lcl|NCBI__GCF_000020625.1:WP_012506494.1 147 KPLHDRYRLRRVVVSTYQSVTGKGKAGRDALEAELAGTVP-----------ESFTHVHQIAFNAIPHID 204 ****************************999887765543...........455789************ PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 ++e+Gytkeelk+++etrki+g++ l vs t+vr+Pv+ gh es++iefe+++sv++v+elL +apgv lcl|NCBI__GCF_000020625.1:WP_012506494.1 205 VFQENGYTKEELKMVNETRKIMGDDSLSVSPTTVRIPVYGGHGESLNIEFEEDFSVDDVRELLSKAPGV 273 ********************************************************************* PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +v+d+ps nlyp+Pl+ +kdevfvgrir+Dl + k+l+++vvaDnlrkGaa+navqiae+li lcl|NCBI__GCF_000020625.1:WP_012506494.1 274 IVQDNPSANLYPMPLSSYEKDEVFVGRIRRDLWHPKTLNMWVVADNLRKGAATNAVQIAEQLI 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 3.68 // [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