Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_085218993.1 B9N75_RS11920 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_900177405.1:WP_085218993.1 Length = 342 Score = 321 bits (822), Expect = 2e-92 Identities = 177/335 (52%), Positives = 230/335 (68%), Gaps = 7/335 (2%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRF--NGKTVRVQNVEEF 62 + V + GATG VG ML +L ER+FPVDE+ +AS RS G F +G+ ++V+N+E F Sbjct: 3 YRVVVVGATGNVGREMLNILAERQFPVDEIAAVASPRSTGDVIDFGDSGQELKVRNIEHF 62 Query: 63 DWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFR 122 D++ IALF+AG S +AP AA AG VIDN+S FR D D+PL+VPEVN AI +R Sbjct: 63 DFAGWDIALFAAGSAASKAYAPGAAAAGCTVIDNSSLFRMDPDVPLIVPEVNAHAIDGYR 122 Query: 123 NRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNG 182 +NIIANPNCST QM+VALKP++D I+R+ V TYQSVSGAGK+G+DEL Q+ + G Sbjct: 123 AKNIIANPNCSTAQMVVALKPLHDFARIKRVVVATYQSVSGAGKSGMDELFEQSRNIFVG 182 Query: 183 YPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVF 242 AE+ TF++QIAFN IP ID F+D+G TKEE KMV ET+KI DP I V TCVRVPVF Sbjct: 183 DSAESKTFTKQIAFNVIPHIDAFLDDGSTKEEWKMVVETKKIL-DPKIKVTATCVRVPVF 241 Query: 243 YGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVR 299 GH+EA+++E I A+ +L + G+ L + T V +A G+ V RVR Sbjct: 242 VGHSEAINIEFENEISAKDAQRILREAPGVMLVDKREDGGYVTPV-EAVGEYATYVSRVR 300 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVR 334 D + +G++LW V+DN+RKGAA NAVQIAELL R Sbjct: 301 EDPTVDNGLSLWCVSDNLRKGAALNAVQIAELLGR 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: 341 Number of extensions: 15 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: 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_085218993.1 B9N75_RS11920 (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.673819.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-144 466.4 0.3 3e-144 466.2 0.3 1.0 1 NCBI__GCF_900177405.1:WP_085218993.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085218993.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.2 0.3 3e-144 3e-144 2 336 .. 5 333 .. 4 336 .. 0.98 Alignments for each domain: == domain 1 score: 466.2 bits; conditional E-value: 3e-144 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfk..gkeleveeaekesfegidialfsaGgs 72 v +vGatG+vG+e+l++L+er+fp+d++ ++as rs+G + f g+el+v+++e+++f g dialf+aG++ NCBI__GCF_900177405.1:WP_085218993.1 5 VVVVGATGNVGREMLNILAERQFPVDEIAAVASPRSTGDVIDFGdsGQELKVRNIEHFDFAGWDIALFAAGSA 77 89*****************************************63379************************* PP TIGR01296 73 vskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeakl 145 sk++ap aa+ag++viDn+s+fr+d+dvPL+vpevna+ + + k+iianPnCst q+vv+Lkpl+d a++ NCBI__GCF_900177405.1:WP_085218993.1 78 ASKAYAPGAAAAGCTVIDNSSLFRMDPDVPLIVPEVNAHAIDGYRAKNIIANPNCSTAQMVVALKPLHDFARI 150 ************************************************************************* PP TIGR01296 146 krvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelk 218 krvvv+tYq+vsGaGk g++eL +q + +++g e +k+f+kqiafn+ip+id + +dG tkee k NCBI__GCF_900177405.1:WP_085218993.1 151 KRVVVATYQSVSGAGKSGMDELFEQSRNIFVGDSAE-------SKTFTKQIAFNVIPHIDAFLDDGSTKEEWK 216 ******************************999888.......59**************************** PP TIGR01296 219 llfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPlea 291 ++ et+kil+ +++kv+atcvrvPvf+ghse+++iefe+e+s+++++ +L+eapgv+++d+ ++ y+tP+ea NCBI__GCF_900177405.1:WP_085218993.1 217 MVVETKKILD-PKIKVTATCVRVPVFVGHSEAINIEFENEISAKDAQRILREAPGVMLVDKREDGGYVTPVEA 288 **********.************************************************************** PP TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336 vg+ +++v+r+r+D + ++gl+l++v+DnlrkGaalnavqiaell NCBI__GCF_900177405.1:WP_085218993.1 289 VGEYATYVSRVREDPTVDNGLSLWCVSDNLRKGAALNAVQIAELL 333 *******************************************98 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 22.89 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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