Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate 3609858 Dshi_3240 aspartate-semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Dino:3609858 Length = 340 Score = 309 bits (791), Expect = 8e-89 Identities = 167/332 (50%), Positives = 226/332 (68%), Gaps = 6/332 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + V + GATG VG ML +L ER+FPVDE+ +LAS +S G F KT++ ++++ FD+ Sbjct: 3 YKVVVVGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVSFGDKTLKTKDLDTFDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 + IA F+ G + ++AP AA A VVIDN+S +RYD IPLVVPEVNPEA+ +++N+ Sbjct: 63 TGWDIAFFAVGSTATKEYAPRAAAAKCVVIDNSSLYRYDPQIPLVVPEVNPEAVEDYKNK 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKL-LNGY 183 IIANPNCST QM+VALKP++D I+R+ V+TYQSVSG GK IDEL QT + + G Sbjct: 123 YIIANPNCSTAQMVVALKPLHDRARIKRVVVSTYQSVSGTGKEAIDELWDQTKGMYVPGQ 182 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 + + +QIAFN IP ID F+++G TKEE KMV ET+KI DP+I V TCVRVPVF Sbjct: 183 EKAPSVYPKQIAFNVIPHIDVFLEDGSTKEEWKMVAETKKIV-DPAIKVTATCVRVPVFV 241 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300 GH+EA+++E ID ++V D+L + GI + + T V + G + R+R Sbjct: 242 GHSEAINIEFEEFIDEDEVRDILREAPGIMVVDKREDGGYVTPV-ECVGDFATFISRIRQ 300 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELL 332 D + +GINLW V+DN+RKGAA NAVQIAE L Sbjct: 301 DSTIDNGINLWCVSDNLRKGAALNAVQIAETL 332 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: 340 Number of extensions: 11 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 3609858 Dshi_3240 (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.36484.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-142 459.4 0.2 4.2e-142 459.2 0.2 1.0 1 FitnessBrowser__Dino:3609858 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Dino:3609858 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.2 0.2 4.2e-142 4.2e-142 2 337 .. 5 333 .. 4 335 .. 0.98 Alignments for each domain: == domain 1 score: 459.2 bits; conditional E-value: 4.2e-142 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsvskefapkaa 82 v +vGatG+vG+e+l++L+er+fp+d++ +las++s G++v f +k l+ +++++++f g dia+f+ G++ ke+ap+aa FitnessBrowser__Dino:3609858 5 VVVVGATGNVGREMLNILAERQFPVDEIAVLASRKSLGTEVSFGDKTLKTKDLDTFDFTGWDIAFFAVGSTATKEYAPRAA 85 89******************************************************************************* PP TIGR01296 83 kagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklkrvvvstYqavsGaGkkg 163 +a ++viDn+s++r d+++PLvvpevn e +++ k+k iianPnCst q+vv+Lkpl+d+a++krvvvstYq+vsG+Gk++ FitnessBrowser__Dino:3609858 86 AAKCVVIDNSSLYRYDPQIPLVVPEVNPEAVEDYKNKYIIANPNCSTAQMVVALKPLHDRARIKRVVVSTYQSVSGTGKEA 166 ********************************************************************************* PP TIGR01296 164 veeLknqtkavle.gkekepeidalkakkfakqiafnaiplidklkedGytkeelkllfetrkilgiedlkvsatcvrvPv 243 ++eL +qtk +++ g+ek ++ ++kqiafn+ip+id + edG tkee k++ et+ki++ + +kv+atcvrvPv FitnessBrowser__Dino:3609858 167 IDELWDQTKGMYVpGQEKA-------PSVYPKQIAFNVIPHIDVFLEDGSTKEEWKMVAETKKIVD-PAIKVTATCVRVPV 239 *********9987255665.......599************************************9.************** PP TIGR01296 244 ftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkG 324 f+ghse+++iefe+ ++ +ev+++L+eapg++v+d+ ++ y+tP+e vg ++f++rir+D + ++g++l++v+DnlrkG FitnessBrowser__Dino:3609858 240 FVGHSEAINIEFEEFIDEDEVRDILREAPGIMVVDKREDGGYVTPVECVGDFATFISRIRQDSTIDNGINLWCVSDNLRKG 320 ********************************************************************************* PP TIGR01296 325 aalnavqiaelli 337 aalnavqiae+l FitnessBrowser__Dino:3609858 321 AALNAVQIAETLG 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 14.69 // [ok]
This GapMind analysis is from Jul 25 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