Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012569048.1 RC1_RS18790 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000016185.1:WP_012569048.1 Length = 338 Score = 334 bits (856), Expect = 2e-96 Identities = 182/337 (54%), Positives = 227/337 (67%), Gaps = 10/337 (2%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFN-GKTVRVQNVEEFD 63 + VA+ GATG VG ML++L ER FP DE+ LASERS G+ F +RVQ++ FD Sbjct: 3 YKVAVVGATGNVGREMLQILAERSFPADEVVALASERSVGQVVSFGEDDELRVQDLSRFD 62 Query: 64 WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123 + + I L S G ++SA +AP AAEAG VVIDNTS FR D D+PLVVPEVNP AIA + Sbjct: 63 FKGIDIVLSSPGAKVSAAFAPRAAEAGAVVIDNTSQFRMDPDVPLVVPEVNPGAIAGWCK 122 Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGY 183 + IIANPNCSTIQM+VALKP++D I R+ V TYQSVSGAGK +DEL QT + Sbjct: 123 KGIIANPNCSTIQMVVALKPLHDLATIRRVVVATYQSVSGAGKDAMDELFTQTRAIYVND 182 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 P E F++QIAFN IP ID FMD+G TKEE KMV ET+KI DP I V TCVRVPVF Sbjct: 183 PVERKKFTKQIAFNVIPHIDSFMDDGATKEEWKMVVETKKIL-DPKIKVTATCVRVPVFI 241 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF-----RGADFPTQVRDAGGKDHVLVGRV 298 GH+E V+VE PI E+ L G+ + G P +V G+D+V V R+ Sbjct: 242 GHSEVVNVEFERPITVEEARRALRAAPGVSVIDHRVDEGYVTPVEV---AGEDNVFVSRL 298 Query: 299 RNDISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335 R DI+ +G+++W+V DN+RKGAA NAVQIAE ++RD Sbjct: 299 REDITVENGLSMWIVGDNLRKGAALNAVQIAETMIRD 335 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: 11 Number of successful extensions: 4 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: 338 Length adjustment: 28 Effective length of query: 309 Effective length of database: 310 Effective search space: 95790 Effective search space used: 95790 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_012569048.1 RC1_RS18790 (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.21883.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-144 467.3 1.8 1.6e-144 467.1 1.8 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012569048.1 RC1_RS18790 aspartate-semialdehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012569048.1 RC1_RS18790 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.1 1.8 1.6e-144 1.6e-144 1 338 [. 4 334 .. 4 335 .. 0.98 Alignments for each domain: == domain 1 score: 467.1 bits; conditional E-value: 1.6e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkg.keleveeaekesfegidialfs 68 +va+vGatG+vG+e+l++L+er+fp+d++v+lasers G+ v f + el+v+++++++f+gidi l s lcl|NCBI__GCF_000016185.1:WP_012569048.1 4 KVAVVGATGNVGREMLQILAERSFPADEVVALASERSVGQVVSFGEdDELRVQDLSRFDFKGIDIVLSS 72 69******************************************86268******************** PP TIGR01296 69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLk 137 G+ vs +fap+aa+ag++viDnts fr+d+dvPLvvpevn ++ kkgiianPnCstiq+vv+Lk lcl|NCBI__GCF_000016185.1:WP_012569048.1 73 PGAKVSAAFAPRAAEAGAVVIDNTSQFRMDPDVPLVVPEVNPGAIAGWCKKGIIANPNCSTIQMVVALK 141 ********************************************************************* PP TIGR01296 138 plkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidk 206 pl+d a ++rvvv+tYq+vsGaGk++++eL qt+a+++ ++ kkf+kqiafn+ip+id+ lcl|NCBI__GCF_000016185.1:WP_012569048.1 142 PLHDLATIRRVVVATYQSVSGAGKDAMDELFTQTRAIYVNDP-------VERKKFTKQIAFNVIPHIDS 203 *************************************98644.......567***************** PP TIGR01296 207 lkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvv 275 +++dG tkee k++ et+kil+ +++kv+atcvrvPvf+ghse v++efe++++vee++ L+ apgv lcl|NCBI__GCF_000016185.1:WP_012569048.1 204 FMDDGATKEEWKMVVETKKILD-PKIKVTATCVRVPVFIGHSEVVNVEFERPITVEEARRALRAAPGVS 271 **********************.********************************************** PP TIGR01296 276 viddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 vid+ ++ y+tP+e++g+d+vfv+r+r+D++ e+gl++++v+DnlrkGaalnavqiae++i+ lcl|NCBI__GCF_000016185.1:WP_012569048.1 272 VIDHRVDEGYVTPVEVAGEDNVFVSRLREDITVENGLSMWIVGDNLRKGAALNAVQIAETMIR 334 ***********************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (338 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: 00:00:00.01 # Mc/sec: 9.26 // [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