Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate GFF3097 PGA1_c31480 aspartate-semialdehyde dehydrogenase Asd
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Phaeo:GFF3097 Length = 340 Score = 319 bits (818), Expect = 6e-92 Identities = 170/335 (50%), Positives = 231/335 (68%), Gaps = 6/335 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + V I GATG VG ML +L ER+FPVDE+ +LAS +S G F KT+ Q+++ FD+ Sbjct: 3 YRVVIAGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVTFGDKTLTTQDLDTFDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 + +ALF+ G + + K+AP AA AG VVIDN+S +RYD+D+PL+VPEVNP+A+ + + Sbjct: 63 AGWDMALFAVGSDATKKYAPKAAAAGCVVIDNSSLYRYDHDVPLIVPEVNPQAVHGYAKK 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLN-GY 183 NIIANPNCST QM+VALKP++D I+R+ V+TYQSVSG+GK IDEL QT + N Sbjct: 123 NIIANPNCSTAQMVVALKPLHDRAKIKRVVVSTYQSVSGSGKDAIDELWDQTKAVYNPTQ 182 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 + +++QIAFN IP ID F+D+G TKEE KMV ET+KI DPSI V TCVRVPVF Sbjct: 183 DVPPSVYTKQIAFNVIPHIDVFLDDGSTKEEWKMVAETKKII-DPSIKVTATCVRVPVFV 241 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300 GH+EA+++E +D ++ D+L + GI + + T V + G + R+R Sbjct: 242 GHSEAINIEFEDFLDEDEARDILREAPGIMVIDKREDGGYVTPV-ECVGDFATFISRIRQ 300 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335 D + +G+NLW V+DN+RKGAA NAVQIAELL R+ Sbjct: 301 DSTLDNGLNLWCVSDNLRKGAALNAVQIAELLGRE 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: 356 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: 340 Length adjustment: 28 Effective length of query: 309 Effective length of database: 312 Effective search space: 96408 Effective search space used: 96408 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 GFF3097 PGA1_c31480 (aspartate-semialdehyde dehydrogenase Asd)
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.9504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-143 461.8 0.1 7.4e-143 461.6 0.1 1.0 1 lcl|FitnessBrowser__Phaeo:GFF3097 PGA1_c31480 aspartate-semialdehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF3097 PGA1_c31480 aspartate-semialdehyde dehydrogenase Asd # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 461.6 0.1 7.4e-143 7.4e-143 2 337 .. 5 333 .. 4 335 .. 0.98 Alignments for each domain: == domain 1 score: 461.6 bits; conditional E-value: 7.4e-143 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskef 77 v i GatG+vG+e+l++L+er+fp+d++ +las++s G++v+f +k l+ +++++++f g d+alf+ G+ k++ lcl|FitnessBrowser__Phaeo:GFF3097 5 VVIAGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVTFGDKTLTTQDLDTFDFAGWDMALFAVGSDATKKY 80 8899************************************************************************ PP TIGR01296 78 apkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstY 153 apkaa+ag++viDn+s++r d+dvPL+vpevn + ++ kk+iianPnCst q+vv+Lkpl+d+ak+krvvvstY lcl|FitnessBrowser__Phaeo:GFF3097 81 APKAAAAGCVVIDNSSLYRYDHDVPLIVPEVNPQAVHGYAKKNIIANPNCSTAQMVVALKPLHDRAKIKRVVVSTY 156 **************************************************************************** PP TIGR01296 154 qavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgi 229 q+vsG+Gk++++eL +qtkav++ + +++ ++kqiafn+ip+id + +dG tkee k++ et+ki++ lcl|FitnessBrowser__Phaeo:GFF3097 157 QSVSGSGKDAIDELWDQTKAVYNPTQDV------PPSVYTKQIAFNVIPHIDVFLDDGSTKEEWKMVAETKKIID- 225 **********************977655......599**************************************. PP TIGR01296 230 edlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkD 305 + +kv+atcvrvPvf+ghse+++iefe+ l+ +e++++L+eapg++vid+ ++ y+tP+e vg ++f++rir+D lcl|FitnessBrowser__Phaeo:GFF3097 226 PSIKVTATCVRVPVFVGHSEAINIEFEDFLDEDEARDILREAPGIMVIDKREDGGYVTPVECVGDFATFISRIRQD 301 **************************************************************************** PP TIGR01296 306 lskekglalfvvaDnlrkGaalnavqiaelli 337 + ++gl+l++v+DnlrkGaalnavqiaell lcl|FitnessBrowser__Phaeo:GFF3097 302 STLDNGLNLWCVSDNLRKGAALNAVQIAELLG 333 *****************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (340 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: 8.92 // [ok]
This GapMind analysis is from Apr 09 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