Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_085772432.1 B1812_RS15710 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_002117405.1:WP_085772432.1 Length = 344 Score = 322 bits (824), Expect = 1e-92 Identities = 173/333 (51%), Positives = 225/333 (67%), Gaps = 5/333 (1%) Query: 4 QFNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFD 63 +F VAI GATG VG ML+VL ER FPV E+ LAS RS G+ F K ++ +N+E +D Sbjct: 2 KFKVAIAGATGNVGREMLDVLAERRFPVSEVVALASPRSVGREVSFGDKVLKCRNLENYD 61 Query: 64 WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123 ++ I L SAGG++S ++P G VVIDN+S FR D D+PL+VPEVN EA+A F N Sbjct: 62 FADTDICLMSAGGDVSRAFSPKIGAKGCVVIDNSSAFRMDPDVPLIVPEVNAEAVAGFVN 121 Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGY 183 + I+ANPNCST Q++VALKP++D I R+ V+TYQSVSGAGK +DEL QT + Sbjct: 122 KYIVANPNCSTAQLVVALKPLHDKAKILRVVVSTYQSVSGAGKEAMDELFAQTRAIYVSD 181 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 P E F ++IAFN IPQID FM++G+TKEE KM ET+KI DP I + TCVRVPVF Sbjct: 182 PIEAKKFPKRIAFNVIPQIDVFMEDGFTKEEWKMTAETKKIL-DPKIKLVATCVRVPVFI 240 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVRN 300 GH+E+V++E PI E+ D+L + G I+ + T +A G+D V R+R Sbjct: 241 GHSESVNIEFEHPISPEEARDILREAPGVLVIDKHEPGGYITP-HEAAGEDATYVSRIRC 299 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLV 333 D S +G+ LWVVADN+RKGAA NAVQIAE L+ Sbjct: 300 DPSVENGLALWVVADNLRKGAALNAVQIAETLI 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: 306 Number of extensions: 13 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_085772432.1 B1812_RS15710 (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.8124.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-144 466.3 0.1 3.2e-144 466.1 0.1 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085772432.1 B1812_RS15710 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085772432.1 B1812_RS15710 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.1 0.1 3.2e-144 3.2e-144 1 338 [. 4 333 .. 4 334 .. 0.99 Alignments for each domain: == domain 1 score: 466.1 bits; conditional E-value: 3.2e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +vai GatG+vG+e+l+vL+er fp++++v+las rs G++v f +k l+ +++e+ +f + di l+sa lcl|NCBI__GCF_002117405.1:WP_085772432.1 4 KVAIAGATGNVGREMLDVLAERRFPVSEVVALASPRSVGREVSFGDKVLKCRNLENYDFADTDICLMSA 72 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg vs++f pk+ ++g++viDn+safr+d+dvPL+vpevnae ++ + +k i+anPnCst qlvv+Lkp lcl|NCBI__GCF_002117405.1:WP_085772432.1 73 GGDVSRAFSPKIGAKGCVVIDNSSAFRMDPDVPLIVPEVNAEAVAGFVNKYIVANPNCSTAQLVVALKP 141 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d+ak+ rvvvstYq+vsGaGk++++eL qt+a+++ + +akkf+k+iafn+ip+id + lcl|NCBI__GCF_002117405.1:WP_085772432.1 142 LHDKAKILRVVVSTYQSVSGAGKEAMDELFAQTRAIYVSDPI-------EAKKFPKRIAFNVIPQIDVF 203 ************************************997655.......58****************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edG+tkee k++ et+kil+ +++k+ atcvrvPvf+ghsesv+iefe+++s+ee++++L+eapgv v lcl|NCBI__GCF_002117405.1:WP_085772432.1 204 MEDGFTKEEWKMTAETKKILD-PKIKLVATCVRVPVFIGHSESVNIEFEHPISPEEARDILREAPGVLV 271 *********************.*********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 id+ + y+tP ea+g+d+++v+rir D s e+glal+vvaDnlrkGaalnavqiae+li+ lcl|NCBI__GCF_002117405.1:WP_085772432.1 272 IDKHEPGGYITPHEAAGEDATYVSRIRCDPSVENGLALWVVADNLRKGAALNAVQIAETLIN 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.17 // [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