Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_028989191.1 G579_RS0104295 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000423825.1:WP_028989191.1 Length = 340 Score = 419 bits (1077), Expect = e-122 Identities = 206/335 (61%), Positives = 252/335 (75%), Gaps = 4/335 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 +NVA+ GATGAVGETML +L+ R+FPV EL+ L SERS G +F GK V N +FDW Sbjct: 6 YNVAVLGATGAVGETMLSILESRDFPVGELYPLGSERSAGSKIQFKGKHYTVGNAADFDW 65 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 SQ I LFSAGG +SA++AP AA AG VVIDNT+HFRY+ DIPLVVPEVN A+A + NR Sbjct: 66 SQADIGLFSAGGSVSAEYAPKAAAAGCVVIDNTAHFRYEPDIPLVVPEVNAHAVARYTNR 125 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 IIANPNCSTIQML+ALKPI+DA IER+ V TYQ+VSG GKA I+ELA QT + N P Sbjct: 126 GIIANPNCSTIQMLLALKPIHDAARIERVVVATYQAVSGTGKAAIEELASQTVAIFNQKP 185 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 E + ++IAFNC+PQID F DNGYTKEEMKM WETQKI DP I + TCVRVPVFYG Sbjct: 186 VEAKVYPKRIAFNCLPQIDVFQDNGYTKEEMKMTWETQKIMEDPGIHLTATCVRVPVFYG 245 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRND 301 H+EAV++ T+ + AEQV ++L G+++ + +PT + +A D V VGR+R D Sbjct: 246 HSEAVNIVTQKKLTAEQVRELLAAAPGVQVMDERKPGGYPTAI-EAANADPVYVGRIRED 304 Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 +SH GINLWVVADNVRKGAA N++QIAE+L+RDY Sbjct: 305 VSHERGINLWVVADNVRKGAALNSIQIAEILIRDY 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: 330 Number of extensions: 7 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_028989191.1 G579_RS0104295 (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.20319.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-144 466.6 0.1 2.6e-144 466.4 0.1 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028989191.1 G579_RS0104295 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028989191.1 G579_RS0104295 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.4 0.1 2.6e-144 2.6e-144 1 338 [. 7 337 .. 7 338 .. 0.99 Alignments for each domain: == domain 1 score: 466.4 bits; conditional E-value: 2.6e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nva++GatGavG+++l +Le r+fp+ +l++l sersaG k++fkgk+++v +a ++ ++ di lfsa lcl|NCBI__GCF_000423825.1:WP_028989191.1 7 NVAVLGATGAVGETMLSILESRDFPVGELYPLGSERSAGSKIQFKGKHYTVGNAADFDWSQADIGLFSA 75 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggsvs e+apkaa+ag++viDnt+ fr ++d+PLvvpevna+ ++ ++giianPnCstiq++ +Lkp lcl|NCBI__GCF_000423825.1:WP_028989191.1 76 GGSVSAEYAPKAAAAGCVVIDNTAHFRYEPDIPLVVPEVNAHAVARYTNRGIIANPNCSTIQMLLALKP 144 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 ++d+a+++rvvv+tYqavsG+Gk+++eeL++qt a++++k ++ak ++k+iafn +p+id + lcl|NCBI__GCF_000423825.1:WP_028989191.1 145 IHDAARIERVVVATYQAVSGTGKAAIEELASQTVAIFNQKP-------VEAKVYPKRIAFNCLPQIDVF 206 ***********************************998664.......5689***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +++Gytkee+k+++et+ki++++ ++++atcvrvPvf+ghse+v+i ++k+l++e+v+elL apgv+v lcl|NCBI__GCF_000423825.1:WP_028989191.1 207 QDNGYTKEEMKMTWETQKIMEDPGIHLTATCVRVPVFYGHSEAVNIVTQKKLTAEQVRELLAAAPGVQV 275 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +d+ + ypt +ea++ d v+vgrir+D+s+e+g++l+vvaDn+rkGaaln++qiae li+ lcl|NCBI__GCF_000423825.1:WP_028989191.1 276 MDERKPGGYPTAIEAANADPVYVGRIREDVSHERGINLWVVADNVRKGAALNSIQIAEILIR 337 ***********************************************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.59 // [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