Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_028950286.1 Q385_RS0103220 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000619805.1:WP_028950286.1 Length = 337 Score = 370 bits (951), Expect = e-107 Identities = 186/344 (54%), Positives = 250/344 (72%), Gaps = 8/344 (2%) Query: 3 RGLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPE 62 + +VA++GATGAVGQ M+K LE+RNF ++ + L+S+RSAG +V + G + V+ S + Sbjct: 2 KSYNVAILGATGAVGQTMIKVLEERNFPINEIKFLASERSAGKEVEYMGVKYKVEAVSED 61 Query: 63 SFEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHN 122 +F+G++IALFSAGG S+ AP AV +GA+VIDN+SAFRMD + PLVVPEVN D+ H Sbjct: 62 AFKGIDIALFSAGGERSKKWAPIAVSKGAVVIDNSSAFRMDSDVPLVVPEVNPEDVKWHK 121 Query: 123 GIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEE 182 GIIANPNCSTIQMV AL PI K + ++IV+TYQAVSGAG A+ +L ++T+A++ Sbjct: 122 GIIANPNCSTIQMVVALYPIHKVKKIKRIIVATYQAVSGAGATAIADLENETKAVMEGRY 181 Query: 183 IEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCV 242 P+ +P + IAFN IP+ID F+ NGYT EEMKMINET+KIMH PD++V+ TCV Sbjct: 182 YYPQALP-------HHIAFNVIPRIDNFEPNGYTKEEMKMINETRKIMHEPDIKVSPTCV 234 Query: 243 RLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVF 302 R+P+ GHSE+V IE + T E+ + +L +APGV ++DDP +YP+P + GK+DVF Sbjct: 235 RVPVYVGHSEAVTIETEL-PITAEEAREILMKAPGVIVEDDPINNVYPVPIEVAGKDDVF 293 Query: 303 VGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 VGRIRKD NG +W+V DNL KGAA N+VQIAE L K L+ Sbjct: 294 VGRIRKDAGFENGLSMWIVGDNLRKGAATNAVQIAELLIKYELI 337 Lambda K H 0.314 0.131 0.366 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: 346 Number of extensions: 12 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: 346 Length of database: 337 Length adjustment: 29 Effective length of query: 317 Effective length of database: 308 Effective search space: 97636 Effective search space used: 97636 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_028950286.1 Q385_RS0103220 (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.677514.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-154 499.5 1.3 2.5e-154 499.3 1.3 1.0 1 NCBI__GCF_000619805.1:WP_028950286.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000619805.1:WP_028950286.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 499.3 1.3 2.5e-154 2.5e-154 1 338 [. 5 333 .. 5 334 .. 0.99 Alignments for each domain: == domain 1 score: 499.3 bits; conditional E-value: 2.5e-154 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 nvai+GatGavGq+++kvLeernfpi+++++lasersaGk+v++ g +++ve++++ f+gidialfsaGg NCBI__GCF_000619805.1:WP_028950286.1 5 NVAILGATGAVGQTMIKVLEERNFPINEIKFLASERSAGKEVEYMGVKYKVEAVSEDAFKGIDIALFSAGGER 77 79*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk++ap a+++g++viDn+safr+d dvPLvvpevn e++k +k giianPnCstiq+vv+L p+++ k+k NCBI__GCF_000619805.1:WP_028950286.1 78 SKKWAPIAVSKGAVVIDNSSAFRMDSDVPLVVPEVNPEDVKWHK--GIIANPNCSTIQMVVALYPIHKVKKIK 148 *****************************************998..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 r++v+tYqavsGaG+ ++++L+n+tkav+eg+ p ++ ++ iafn+ip id+++ +Gytkee+k+ NCBI__GCF_000619805.1:WP_028950286.1 149 RIIVATYQAVSGAGATAIADLENETKAVMEGRYYYP-------QALPHHIAFNVIPRIDNFEPNGYTKEEMKM 214 *******************************99997.......99**************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 ++etrki++ +d+kvs tcvrvPv++ghse+v+ie+e ++++ee++e+L +apgv+v ddp +n+yp+P+e++ NCBI__GCF_000619805.1:WP_028950286.1 215 INETRKIMHEPDIKVSPTCVRVPVYVGHSEAVTIETELPITAEEAREILMKAPGVIVEDDPINNVYPVPIEVA 287 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 gkd+vfvgrirkD e+gl++++v+DnlrkGaa+navqiaellik NCBI__GCF_000619805.1:WP_028950286.1 288 GKDDVFVGRIRKDAGFENGLSMWIVGDNLRKGAATNAVQIAELLIK 333 ********************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (337 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 14.14 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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