Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 6938019 Sama_2152 aspartate-semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__SB2B:6938019 Length = 338 Score = 488 bits (1256), Expect = e-143 Identities = 239/337 (70%), Positives = 276/337 (81%), Gaps = 1/337 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 MSQ+FNV + GA+GAVG+TM+E+L+ER FPV +LF LAS RS G T F+GK V + +VE Sbjct: 1 MSQEFNVVVLGASGAVGQTMIEILEERNFPVAKLFPLASARSAGDTVSFHGKQVEILDVE 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 FDWSQ I FSAGG++SAKWAPIAAE G VVIDNTSHFRYD DIPLVVPEVNPEAIA+ Sbjct: 61 TFDWSQAQIGFFSAGGDVSAKWAPIAAEHGCVVIDNTSHFRYDLDIPLVVPEVNPEAIAD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 FRNRNIIANPNCSTIQMLVALKPIYDA GI+RINV TYQSVSG GK I+ELAGQ AKLL Sbjct: 121 FRNRNIIANPNCSTIQMLVALKPIYDAYGIDRINVCTYQSVSGTGKKAIEELAGQCAKLL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 G P E + + +QIAFN +P ID+F DNGYTKEEMKMVWET+KIF D SI+VNPT VRVP Sbjct: 181 QGLPIEPSVYPKQIAFNVLPHIDKFQDNGYTKEEMKMVWETRKIFGDDSILVNPTAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELFR-GADFPTQVRDAGGKDHVLVGRVR 299 VFYGH+EAVH+ETR P+DA+ V +L G+ LF D+PT V D G+D V VGRVR Sbjct: 241 VFYGHSEAVHIETRDPVDADTVKALLRDAPGVVLFEDDDDYPTAVTDGAGQDPVFVGRVR 300 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 NDISH +GINLWVV+DN+RKGAA N+VQI E+L+RDY Sbjct: 301 NDISHPNGINLWVVSDNIRKGAALNSVQIGEILIRDY 337 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: 410 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 6938019 Sama_2152 (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.1124.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-135 436.0 0.0 5.2e-135 435.8 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6938019 Sama_2152 aspartate-semialdehyde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938019 Sama_2152 aspartate-semialdehyde dehydrogenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.8 0.0 5.2e-135 5.2e-135 1 338 [. 6 335 .. 6 336 .. 0.98 Alignments for each domain: == domain 1 score: 435.8 bits; conditional E-value: 5.2e-135 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskef 77 nv ++Ga+GavGq+++++Leernfp+ kl +las+rsaG v f+gk++e+ ++e+++ ++ +i +fsaGg vs ++ lcl|FitnessBrowser__SB2B:6938019 6 NVVVLGASGAVGQTMIEILEERNFPVAKLFPLASARSAGDTVSFHGKQVEILDVETFDWSQAQIGFFSAGGDVSAKW 82 689************************************************************************** PP TIGR01296 78 apkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYq 154 ap aa++g++viDnts fr d d+PLvvpevn e ++++++++iianPnCstiq++v+Lkp++d++++ r+ v tYq lcl|FitnessBrowser__SB2B:6938019 83 APIAAEHGCVVIDNTSHFRYDLDIPLVVPEVNPEAIADFRNRNIIANPNCSTIQMLVALKPIYDAYGIDRINVCTYQ 159 ***************************************************************************** PP TIGR01296 155 avsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgied 231 +vsG+Gkk++eeL+ q l+g +ep + ++kqiafn++p+idk++++Gytkee+k+++etrki+g++ lcl|FitnessBrowser__SB2B:6938019 160 SVSGTGKKAIEELAGQCAKLLQGLPIEP-------SVYPKQIAFNVLPHIDKFQDNGYTKEEMKMVWETRKIFGDDS 229 *****************99999998886.......89**************************************** PP TIGR01296 232 lkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDls 307 + v t+vrvPvf+ghse+v+ie+ ++++++ vk lL++apgvv+ +d+ + ypt + + +g+d vfvgr+r+D+s lcl|FitnessBrowser__SB2B:6938019 230 ILVNPTAVRVPVFYGHSEAVHIETRDPVDADTVKALLRDAPGVVLFEDD--DDYPTAVtDGAGQDPVFVGRVRNDIS 304 **********************************************999..78999873689*************** PP TIGR01296 308 kekglalfvvaDnlrkGaalnavqiaellik 338 + +g++l+vv+Dn+rkGaaln+vqi e li+ lcl|FitnessBrowser__SB2B:6938019 305 HPNGINLWVVSDNIRKGAALNSVQIGEILIR 335 ***************************9997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.55 // [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