Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_004514734.1 GMET_RS03020 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000012925.1:WP_004514734.1 Length = 339 Score = 352 bits (903), Expect = e-102 Identities = 186/339 (54%), Positives = 237/339 (69%), Gaps = 5/339 (1%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 M++ +NVA+ GATGAVG M+E L+ER FPV ++ LAS RS G+ F GK V V+ + Sbjct: 1 MAKLWNVAVVGATGAVGGQMIECLEERNFPVGKIRYLASARSAGEVLEFKGKPVMVEELT 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 + + IALFSAGG+ S + P AA AG V IDN+S +R D D+PLVVPEVNP AIA+ Sbjct: 61 RDSFEGIDIALFSAGGDRSRDFCPAAAAAGAVCIDNSSAWRMDPDVPLVVPEVNPHAIAD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 +R + IIANPNCSTIQM+VALKP++D I RI V+TYQ+VSG GK I+EL Q L Sbjct: 121 YRKKGIIANPNCSTIQMVVALKPLHDHAVIRRIVVSTYQAVSGTGKKAIEELQKQVVTLF 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 G E T+ QIAFNC+PQID F DNGYTKEEMKMV ET+KI + +I V T VRVP Sbjct: 181 QGKSPEVATYPHQIAFNCLPQIDSFGDNGYTKEEMKMVHETRKIL-EANIGVTATAVRVP 239 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGR 297 VFYGH+E+V++ET + ++L + G+EL + +P + DA G+D LVGR Sbjct: 240 VFYGHSESVNIETENKLTVATARELLAKAPGVELVDDPATSSYPMAI-DAAGQDLTLVGR 298 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 +R D S +G+NLWVVADN+RKGAATNAVQIAE+L+ Y Sbjct: 299 IREDESIANGLNLWVVADNIRKGAATNAVQIAEILIEKY 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: 340 Number of extensions: 14 Number of successful extensions: 3 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: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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_004514734.1 GMET_RS03020 (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.18095.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-148 480.9 0.4 1.2e-148 480.7 0.4 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004514734.1 GMET_RS03020 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004514734.1 GMET_RS03020 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 480.7 0.4 1.2e-148 1.2e-148 1 338 [. 6 335 .. 6 336 .. 0.99 Alignments for each domain: == domain 1 score: 480.7 bits; conditional E-value: 1.2e-148 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nva+vGatGavG ++++ Leernfp+ k++ las+rsaG+ ++fkgk + vee+++ sfegidialfsa lcl|NCBI__GCF_000012925.1:WP_004514734.1 6 NVAVVGATGAVGGQMIECLEERNFPVGKIRYLASARSAGEVLEFKGKPVMVEELTRDSFEGIDIALFSA 74 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg s+ f p aa+ag++ iDn+sa+r+d+dvPLvvpevn + +++ +kkgiianPnCstiq+vv+Lkp lcl|NCBI__GCF_000012925.1:WP_004514734.1 75 GGDRSRDFCPAAAAAGAVCIDNSSAWRMDPDVPLVVPEVNPHAIADYRKKGIIANPNCSTIQMVVALKP 143 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d+a ++r+vvstYqavsG+Gkk++eeL++q+ + ++gk e+ ++++qiafn +p+id++ lcl|NCBI__GCF_000012925.1:WP_004514734.1 144 LHDHAVIRRIVVSTYQAVSGTGKKAIEELQKQVVTLFQGKSPEV-------ATYPHQIAFNCLPQIDSF 205 **********************************9999988776.......89**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 ++Gytkee+k+++etrkil+ ++ v+at+vrvPvf+ghsesv+ie+e++l+v ++elL +apgv + lcl|NCBI__GCF_000012925.1:WP_004514734.1 206 GDNGYTKEEMKMVHETRKILE-ANIGVTATAVRVPVFYGHSESVNIETENKLTVATARELLAKAPGVEL 273 *********************.9********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +ddp yp+ ++a+g+d ++vgrir+D s ++gl+l+vvaDn+rkGaa+navqiae li+ lcl|NCBI__GCF_000012925.1:WP_004514734.1 274 VDDPATSSYPMAIDAAGQDLTLVGRIREDESIANGLNLWVVADNIRKGAATNAVQIAEILIE 335 ***********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (339 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: 7.70 // [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