Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_077277799.1 B1C78_RS03695 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_002000365.1:WP_077277799.1 Length = 340 Score = 426 bits (1094), Expect = e-124 Identities = 211/339 (62%), Positives = 259/339 (76%), Gaps = 3/339 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 MS++F+VA+ GATGAVGETML +L ER+ P+ E++ +AS RS G +F + + VQ++ Sbjct: 1 MSKKFDVAVVGATGAVGETMLSILAERDLPLGEVYAVASARSAGSRVKFGDRHLVVQDLA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 EFD+S+V I LFS G +S ++AP AA AG VVIDNTS FRYD DIPLVVPEVNP A+A Sbjct: 61 EFDFSKVQIGLFSPGASVSKEYAPKAAAAGCVVIDNTSQFRYDDDIPLVVPEVNPHAVAG 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 + NR IIANPNCSTIQMLVALKPI DAVGI RINV TYQ+VSG GK ++ELA QTA LL Sbjct: 121 YTNRGIIANPNCSTIQMLVALKPIQDAVGIARINVATYQAVSGTGKEAVEELAAQTANLL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 NG P E + + +QIAFN +P ID F+DNGYTKEEMKMVWET+KI D SI VNPT VR+P Sbjct: 181 NGKPIEKHVYPKQIAFNALPHIDVFLDNGYTKEEMKMVWETRKIMGDDSIQVNPTAVRIP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGR 297 VFYGH+EAVHVETR I AEQ ++L + G+ + + +PT V + D V VGR Sbjct: 241 VFYGHSEAVHVETREKITAEQARELLSKAPGVVVLDERKDGGYPTAVTEGANHDPVYVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 +R DISH G+NLWVVADNVRKGAA N++QIAE+L++DY Sbjct: 301 IREDISHPQGLNLWVVADNVRKGAALNSIQIAEILIKDY 339 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: 343 Number of extensions: 8 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: 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 WP_077277799.1 B1C78_RS03695 (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.15312.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-138 446.3 0.2 3.9e-138 446.1 0.2 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077277799.1 B1C78_RS03695 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077277799.1 B1C78_RS03695 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.1 0.2 3.9e-138 3.9e-138 2 339 .] 7 338 .. 6 338 .. 0.98 Alignments for each domain: == domain 1 score: 446.1 bits; conditional E-value: 3.9e-138 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 va+vGatGavG+++l +L+er+ p+ +++++as+rsaG +vkf +++l v+++ +++f++++i lfs G lcl|NCBI__GCF_002000365.1:WP_077277799.1 7 VAVVGATGAVGETMLSILAERDLPLGEVYAVASARSAGSRVKFGDRHLVVQDLAEFDFSKVQIGLFSPG 75 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 +svske+apkaa+ag++viDnts fr d+d+PLvvpevn + ++ ++giianPnCstiq++v+Lkp+ lcl|NCBI__GCF_002000365.1:WP_077277799.1 76 ASVSKEYAPKAAAAGCVVIDNTSQFRYDDDIPLVVPEVNPHAVAGYTNRGIIANPNCSTIQMLVALKPI 144 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +d++++ r+ v+tYqavsG+Gk++veeL+ qt l+gk +e + ++kqiafna+p+id + lcl|NCBI__GCF_002000365.1:WP_077277799.1 145 QDAVGIARINVATYQAVSGTGKEAVEELAAQTANLLNGKPIE-------KHVYPKQIAFNALPHIDVFL 206 ************************************999877.......489***************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 ++Gytkee+k+++etrki+g++ ++v t+vr+Pvf+ghse+v++e+ +++++e+++elL +apgvvv+ lcl|NCBI__GCF_002000365.1:WP_077277799.1 207 DNGYTKEEMKMVWETRKIMGDDSIQVNPTAVRIPVFYGHSEAVHVETREKITAEQARELLSKAPGVVVL 275 ********************************************************************* PP TIGR01296 278 ddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 d+ ++ ypt + e +++d v+vgrir+D+s+ +gl+l+vvaDn+rkGaaln++qiae lik+ lcl|NCBI__GCF_002000365.1:WP_077277799.1 276 DERKDGGYPTAVtEGANHDPVYVGRIREDISHPQGLNLWVVADNVRKGAALNSIQIAEILIKD 338 **********983568899*****************************************986 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.02 // [ok]
This GapMind analysis is from Apr 10 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