Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 5209855 Shew_2308 aspartate-semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__PV4:5209855 Length = 338 Score = 484 bits (1246), Expect = e-141 Identities = 238/338 (70%), Positives = 274/338 (81%), Gaps = 1/338 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 MSQ+FNV + GA+GAVG+TM+E+L+ER FPV L+ LAS RS G T F+GK V + +VE Sbjct: 1 MSQEFNVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGDTVTFHGKQVEILDVE 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FDWSQ I FSAGG++SAKWAPIAAE G VVIDNTSHFRYD DIPLVVPEVNP+AIA+ Sbjct: 61 TFDWSQAQIGFFSAGGDVSAKWAPIAAEHGCVVIDNTSHFRYDIDIPLVVPEVNPQAIAD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 FRNRNIIANPNCSTIQMLVALKPIYDA GI RINV TYQSVSG+GK I+ELA Q AKLL Sbjct: 121 FRNRNIIANPNCSTIQMLVALKPIYDAYGISRINVATYQSVSGSGKQAIEELANQCAKLL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 G P E + +QIAFN +PQID+FMDNGYTKEEMKMVWETQKIF D I+VNPT VRVP Sbjct: 181 QGLPVEPKAYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDQIVVNPTAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFR-GADFPTQVRDAGGKDHVLVGRVR 299 VFYGH+EAVH+ET P+ AE V +L G+ELF ++PT V +A G D V VGRVR Sbjct: 241 VFYGHSEAVHIETVQPVSAEDVKAVLRDAPGVELFESNEEYPTAVTEAAGTDPVYVGRVR 300 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDYF 337 DISH +GINLWVV+DN+RKGAA N+VQIAE+LVRDY+ Sbjct: 301 EDISHPNGINLWVVSDNIRKGAALNSVQIAEVLVRDYY 338 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: 402 Number of extensions: 6 Number of successful extensions: 2 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: 338 Length adjustment: 28 Effective length of query: 309 Effective length of database: 310 Effective search space: 95790 Effective search space used: 95790 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 5209855 Shew_2308 (aspartate-semialdehyde dehydrogenase (RefSeq))
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.16097.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-138 446.8 0.2 2.7e-138 446.6 0.2 1.0 1 lcl|FitnessBrowser__PV4:5209855 Shew_2308 aspartate-semialdehyde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209855 Shew_2308 aspartate-semialdehyde dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.6 0.2 2.7e-138 2.7e-138 1 338 [. 6 335 .. 6 336 .. 0.98 Alignments for each domain: == domain 1 score: 446.6 bits; conditional E-value: 2.7e-138 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefa 78 nv ++Ga+GavGq+++++Leernfp+ +l++las+rsaG v+f+gk++e+ ++e+++ ++ +i +fsaGg vs ++a lcl|FitnessBrowser__PV4:5209855 6 NVVVLGASGAVGQTMIEILEERNFPVANLYPLASSRSAGDTVTFHGKQVEILDVETFDWSQAQIGFFSAGGDVSAKWA 83 689*************************************************************************** PP TIGR01296 79 pkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqav 156 p aa++g++viDnts fr d d+PLvvpevn + ++++++++iianPnCstiq++v+Lkp++d++++ r+ v+tYq+v lcl|FitnessBrowser__PV4:5209855 84 PIAAEHGCVVIDNTSHFRYDIDIPLVVPEVNPQAIADFRNRNIIANPNCSTIQMLVALKPIYDAYGISRINVATYQSV 161 ****************************************************************************** PP TIGR01296 157 sGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkv 234 sG+Gk+++eeL+nq l+g ep k+++kqiafn++p+idk++++Gytkee+k+++et+ki+g++++ v lcl|FitnessBrowser__PV4:5209855 162 SGSGKQAIEELANQCAKLLQGLPVEP-------KAYPKQIAFNVLPQIDKFMDNGYTKEEMKMVWETQKIFGDDQIVV 232 ***************99999887765.......9******************************************** PP TIGR01296 235 satcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDlskekg 311 t+vrvPvf+ghse+v+ie+ +++s+e+vk +L++apgv + + + ++ypt + ea+g+d v+vgr+r+D+s+ +g lcl|FitnessBrowser__PV4:5209855 233 NPTAVRVPVFYGHSEAVHIETVQPVSAEDVKAVLRDAPGVELFESN--EEYPTAVtEAAGTDPVYVGRVREDISHPNG 308 *******************************************988..89*9987479******************** PP TIGR01296 312 lalfvvaDnlrkGaalnavqiaellik 338 ++l+vv+Dn+rkGaaln+vqiae l++ lcl|FitnessBrowser__PV4:5209855 309 INLWVVSDNIRKGAALNSVQIAEVLVR 335 ************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (338 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.50 // [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