Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate CCNA_00253 CCNA_00253 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Caulo:CCNA_00253 Length = 342 Score = 310 bits (793), Expect = 4e-89 Identities = 161/330 (48%), Positives = 226/330 (68%), Gaps = 4/330 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + VA+ GATG VG M +L+E +FPVD++ +AS +S G F + ++ +++E+FD+ Sbjct: 3 YRVAVVGATGNVGREMFNILEEVKFPVDKMHAIASRKSIGVEVSFGNEILKCEDLEQFDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 S+V + L SAGG +S W AG +VIDN+SHFR D D+PLVVPEVNPEA+ + Sbjct: 63 SKVDLVLMSAGGSISKAWGEKIGAAGPIVIDNSSHFRMDPDVPLVVPEVNPEAVNSI-PK 121 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 NIIANPNCST Q++VALKP++D I+R+ V+TYQSVSGAGK G+DEL QT + Sbjct: 122 NIIANPNCSTAQLVVALKPLHDEAKIKRVVVSTYQSVSGAGKEGMDELWDQTKGVYVLGA 181 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 F++QIAFN IP ID FMD+G+TKEE KM ETQKI DP+I + TCVRVPV G Sbjct: 182 PPPKKFTKQIAFNVIPHIDVFMDDGFTKEEWKMAVETQKIL-DPAIKLTATCVRVPVMVG 240 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQV--RDAGGKDHVLVGRVRNDI 302 H+E+V+VE +P+D ++ ++L + DGI + + + +++ G+ V + R+R D Sbjct: 241 HSESVNVEFESPLDEDEAREILREADGIVVVDKREDGGYITPKESQGEFPVYISRIRKDP 300 Query: 303 SHHSGINLWVVADNVRKGAATNAVQIAELL 332 + +G+ W V+DN+RKGAA NAVQIA+LL Sbjct: 301 TVENGLAFWCVSDNLRKGAALNAVQIAQLL 330 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: 316 Number of extensions: 10 Number of successful extensions: 5 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 CCNA_00253 CCNA_00253 (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.30053.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-140 453.7 0.1 2.2e-140 453.5 0.1 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00253 CCNA_00253 aspartate-semialdehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00253 CCNA_00253 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.5 0.1 2.2e-140 2.2e-140 1 337 [. 4 331 .. 4 333 .. 0.98 Alignments for each domain: == domain 1 score: 453.5 bits; conditional E-value: 2.2e-140 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 +va+vGatG+vG+e+ ++Lee +fp+dk+ ++as++s G +v f +++l+ e++e+++f+++d+ l+saGgs+ lcl|FitnessBrowser__Caulo:CCNA_00253 4 RVAVVGATGNVGREMFNILEEVKFPVDKMHAIASRKSIGVEVSFGNEILKCEDLEQFDFSKVDLVLMSAGGSI 76 69*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk++ k+ +ag iviDn+s fr+d+dvPLvvpevn e ++ + k+iianPnCst qlvv+Lkpl+deak+k lcl|FitnessBrowser__Caulo:CCNA_00253 77 SKAWGEKIGAAGPIVIDNSSHFRMDPDVPLVVPEVNPEAVNSIP-KNIIANPNCSTAQLVVALKPLHDEAKIK 148 ****************************************9998.**************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 rvvvstYq+vsGaGk+g++eL +qtk v++ ++kkf+kqiafn+ip+id +++dG+tkee k+ lcl|FitnessBrowser__Caulo:CCNA_00253 149 RVVVSTYQSVSGAGKEGMDELWDQTKGVYVLGAP-------PPKKFTKQIAFNVIPHIDVFMDDGFTKEEWKM 214 ****************************987544.......57****************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 + et+kil+ + +k++atcvrvPv++ghsesv++efe +l+ +e++e+L+ea+g+vv+d+ ++ y+tP e + lcl|FitnessBrowser__Caulo:CCNA_00253 215 AVETQKILD-PAIKLTATCVRVPVMVGHSESVNVEFESPLDEDEAREILREADGIVVVDKREDGGYITPKESQ 286 *********.*************************************************************** PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 g+ v+++rirkD + e+gla ++v+DnlrkGaalnavqia+ll lcl|FitnessBrowser__Caulo:CCNA_00253 287 GEFPVYISRIRKDPTVENGLAFWCVSDNLRKGAALNAVQIAQLLH 331 *****************************************9986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.69 // [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