Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_014149943.1 MEALZ_RS17275 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000968535.2:WP_014149943.1 Length = 340 Score = 427 bits (1098), Expect = e-124 Identities = 214/339 (63%), Positives = 265/339 (78%), Gaps = 3/339 (0%) Query: 1 MSQQFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVE 60 M++ +NVA+ GATGAVGE ML +L+ER FPV E++ LAS RS GK F G +++VQ++ Sbjct: 1 MTKLYNVAVVGATGAVGEAMLSILEERNFPVGEVYALASSRSVGKRIPFKGGSLKVQDLA 60 Query: 61 EFDWSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAE 120 EFD+S+V I LFS G +SA++AP AA AG +VIDNTS FRYD +IPLVVPEVNPE IA+ Sbjct: 61 EFDFSKVQIGLFSPGASVSAEYAPKAAAAGCIVIDNTSQFRYDENIPLVVPEVNPEKIAD 120 Query: 121 FRNRNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLL 180 ++NR IIANPNCSTIQMLVALKPIYDAVGI RINV TYQ+VSG GK I+EL+ QTA LL Sbjct: 121 YKNRGIIANPNCSTIQMLVALKPIYDAVGISRINVCTYQAVSGTGKEAIEELSLQTAHLL 180 Query: 181 NGYPAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVP 240 NG P + + + +QIAFN +PQID FM+NGYTKEEMKMVWET+KI D SI VN T VRVP Sbjct: 181 NGKPIKPSVYPKQIAFNVLPQIDVFMENGYTKEEMKMVWETRKIIGDESIQVNATAVRVP 240 Query: 241 VFYGHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGR 297 VF+GH+EAVH+ETR ID++ V +LE+ G+ + R +PT V ++ G D V VGR Sbjct: 241 VFFGHSEAVHIETRHKIDSKSVRALLEKAPGVTVLDEHRDGGYPTAVTESSGHDSVFVGR 300 Query: 298 VRNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 +R DISH GI+LWVV DNVRKGAA N+VQIAE LV+++ Sbjct: 301 IREDISHPQGIDLWVVGDNVRKGAALNSVQIAEELVKNH 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: 348 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: 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_014149943.1 MEALZ_RS17275 (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.19432.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-141 455.7 0.3 5.2e-141 455.6 0.3 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014149943.1 MEALZ_RS17275 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_014149943.1 MEALZ_RS17275 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.6 0.3 5.2e-141 5.2e-141 1 339 [] 6 338 .. 6 338 .. 0.98 Alignments for each domain: == domain 1 score: 455.6 bits; conditional E-value: 5.2e-141 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nva+vGatGavG+ +l +Leernfp+ ++++las+rs Gk++ fkg l+v+++ +++f++++i lfs lcl|NCBI__GCF_000968535.2:WP_014149943.1 6 NVAVVGATGAVGEAMLSILEERNFPVGEVYALASSRSVGKRIPFKGGSLKVQDLAEFDFSKVQIGLFSP 74 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 G+svs e+apkaa+ag+iviDnts fr de++PLvvpevn e++++ k++giianPnCstiq++v+Lkp lcl|NCBI__GCF_000968535.2:WP_014149943.1 75 GASVSAEYAPKAAAAGCIVIDNTSQFRYDENIPLVVPEVNPEKIADYKNRGIIANPNCSTIQMLVALKP 143 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 ++d++++ r+ v tYqavsG+Gk+++eeL qt l+gk ++p + ++kqiafn++p+id + lcl|NCBI__GCF_000968535.2:WP_014149943.1 144 IYDAVGISRINVCTYQAVSGTGKEAIEELSLQTAHLLNGKPIKP-------SVYPKQIAFNVLPQIDVF 205 ***********************************999987765.......99**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e+Gytkee+k+++etrki+g+e ++v at+vrvPvf ghse+v+ie+ ++++ + v+ lL++apgv+v lcl|NCBI__GCF_000968535.2:WP_014149943.1 206 MENGYTKEEMKMVWETRKIIGDESIQVNATAVRVPVFFGHSEAVHIETRHKIDSKSVRALLEKAPGVTV 274 ********************************************************************* PP TIGR01296 277 iddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 +d+ ++ ypt + e +g+d+vfvgrir+D+s+ +g++l+vv+Dn+rkGaaln+vqiae l+k+ lcl|NCBI__GCF_000968535.2:WP_014149943.1 275 LDEHRDGGYPTAVtESSGHDSVFVGRIREDISHPQGIDLWVVGDNVRKGAALNSVQIAEELVKN 338 ***********983689********************************************997 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: 11.90 // [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