Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_012332991.1 M446_RS15255 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000019365.1:WP_012332991.1 Length = 344 Score = 324 bits (831), Expect = 2e-93 Identities = 167/331 (50%), Positives = 224/331 (67%), Gaps = 3/331 (0%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + VA+ GATG VG ML++L ER FP D + LAS RS G+ F +T++VQ ++++D+ Sbjct: 3 YKVAVVGATGNVGREMLDILAERAFPADTVVALASRRSLGQEVSFGDRTLKVQALDQYDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 S I L SAGGE S +W+P G VVIDN+S FRYD D+PL+VPEVN +A+ F + Sbjct: 63 SDTDICLMSAGGETSKEWSPRIGAQGCVVIDNSSAFRYDSDVPLIVPEVNADAVVGFSKK 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 NIIANPNCST Q++VALKP++DA I+R+ V TYQSVSGAGK +DEL QT + Sbjct: 123 NIIANPNCSTAQLVVALKPLHDAATIKRVVVATYQSVSGAGKDAMDELFNQTRAVFTAGE 182 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 + F+++IAFN IP ID FM++G TKEE KMV ET+K+ DP I + TCVRVPVF G Sbjct: 183 VKVQKFTKRIAFNVIPHIDVFMEDGSTKEEWKMVAETKKML-DPKIKLTATCVRVPVFIG 241 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDG--IELFRGADFPTQVRDAGGKDHVLVGRVRNDI 302 H+EAV+VE PI AE+ ++L G ++ R +A G+D V R+R DI Sbjct: 242 HSEAVNVEFERPISAEEAREILRSAPGVLVDDKREPGGYITPHEAAGEDATYVSRIREDI 301 Query: 303 SHHSGINLWVVADNVRKGAATNAVQIAELLV 333 + +G++ W V+DN+RKGAA N VQIAE+L+ Sbjct: 302 TVENGLSFWCVSDNLRKGAALNTVQIAEVLI 332 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: 317 Number of extensions: 8 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: 344 Length adjustment: 28 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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_012332991.1 M446_RS15255 (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.22302.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-145 468.6 0.6 6.6e-145 468.4 0.6 1.0 1 lcl|NCBI__GCF_000019365.1:WP_012332991.1 M446_RS15255 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012332991.1 M446_RS15255 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.4 0.6 6.6e-145 6.6e-145 1 338 [. 4 333 .. 4 334 .. 0.99 Alignments for each domain: == domain 1 score: 468.4 bits; conditional E-value: 6.6e-145 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +va+vGatG+vG+e+l++L+er fp+d++v+las+rs G++v f ++ l+v+++++ +f++ di l+sa lcl|NCBI__GCF_000019365.1:WP_012332991.1 4 KVAVVGATGNVGREMLDILAERAFPADTVVALASRRSLGQEVSFGDRTLKVQALDQYDFSDTDICLMSA 72 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg +ske+ p++ ++g++viDn+safr d dvPL+vpevna+ + + kk+iianPnCst qlvv+Lkp lcl|NCBI__GCF_000019365.1:WP_012332991.1 73 GGETSKEWSPRIGAQGCVVIDNSSAFRYDSDVPLIVPEVNADAVVGFSKKNIIANPNCSTAQLVVALKP 141 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d+a +krvvv+tYq+vsGaGk++++eL nqt+av++ e ++ +kf+k+iafn+ip+id + lcl|NCBI__GCF_000019365.1:WP_012332991.1 142 LHDAATIKRVVVATYQSVSGAGKDAMDELFNQTRAVFTAGEVKV-------QKFTKRIAFNVIPHIDVF 203 **************************************999987.......9***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edG tkee k++ et+k+l+ +++k++atcvrvPvf+ghse+v++efe+++s+ee++e+L+ apgv v lcl|NCBI__GCF_000019365.1:WP_012332991.1 204 MEDGSTKEEWKMVAETKKMLD-PKIKLTATCVRVPVFIGHSEAVNVEFERPISAEEAREILRSAPGVLV 271 ********************9.*********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 d+ + y+tP ea+g+d+++v+rir+D++ e+gl+ ++v+DnlrkGaaln+vqiae li+ lcl|NCBI__GCF_000019365.1:WP_012332991.1 272 DDKREPGGYITPHEAAGEDATYVSRIREDITVENGLSFWCVSDNLRKGAALNTVQIAEVLIN 333 ***********************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (344 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.81 // [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