Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_003543997.1 RL_RS24260 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000009265.1:WP_003543997.1 Length = 344 Score = 333 bits (855), Expect = 3e-96 Identities = 171/332 (51%), Positives = 231/332 (69%), Gaps = 5/332 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 F VA+ GATG VG ML +L ER FP DE+ LAS RS+G + +T++V N+E +D+ Sbjct: 3 FKVAVAGATGNVGREMLNILSERGFPADEVVALASSRSQGTEVSYGDRTLKVSNLENYDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 S I L SAGGE+S K++P + G +VIDN+S +RYD D+PL+VPEVNP+AI++F R Sbjct: 63 SDTDICLMSAGGEVSKKYSPKIGQQGCIVIDNSSAWRYDADVPLIVPEVNPDAISQFTKR 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 NIIANPNCST Q++VALKP++D I+R+ ++TYQSVSGAGK G+DEL QT + P Sbjct: 123 NIIANPNCSTAQLVVALKPLHDFAKIKRVVISTYQSVSGAGKDGMDELFNQTRAVFVADP 182 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 E F+++IAFN IP ID FM++GYTKEE K++ ET+K+ DP I V T VRVPVF G Sbjct: 183 IENKKFTKRIAFNVIPHIDVFMEDGYTKEEWKVLAETKKML-DPKIKVTCTAVRVPVFIG 241 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVRND 301 H+E+V++E I A+Q D+L G I+ + T A G+D + R+R D Sbjct: 242 HSESVNIEFENEITADQARDILRDAPGCLVIDKREDGGYITPYESA-GEDATYISRIRED 300 Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLV 333 + +G+N+WVV+DN+RKGAA NA+QIAELLV Sbjct: 301 ATVENGLNIWVVSDNLRKGAALNAIQIAELLV 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: 332 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_003543997.1 RL_RS24260 (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.3700424.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-143 464.2 0.4 1.4e-143 464.0 0.4 1.0 1 NCBI__GCF_000009265.1:WP_003543997.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000009265.1:WP_003543997.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 464.0 0.4 1.4e-143 1.4e-143 1 338 [. 4 333 .. 4 334 .. 0.99 Alignments for each domain: == domain 1 score: 464.0 bits; conditional E-value: 1.4e-143 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 +va+ GatG+vG+e+l++L er fp+d++v+las+rs+G++v + ++ l+v+++e+ +f++ di l+saGg v NCBI__GCF_000009265.1:WP_003543997.1 4 KVAVAGATGNVGREMLNILSERGFPADEVVALASSRSQGTEVSYGDRTLKVSNLENYDFSDTDICLMSAGGEV 76 69*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk++ pk+ ++g+iviDn+sa+r d dvPL+vpevn + + ++ k++iianPnCst qlvv+Lkpl+d ak+k NCBI__GCF_000009265.1:WP_003543997.1 77 SKKYSPKIGQQGCIVIDNSSAWRYDADVPLIVPEVNPDAISQFTKRNIIANPNCSTAQLVVALKPLHDFAKIK 149 ************************************************************************* PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 rvv+stYq+vsGaGk+g++eL nqt+av++ +e kkf+k+iafn+ip+id ++edGytkee k+ NCBI__GCF_000009265.1:WP_003543997.1 150 RVVISTYQSVSGAGKDGMDELFNQTRAVFVADPIE-------NKKFTKRIAFNVIPHIDVFMEDGYTKEEWKV 215 ****************************9976655.......69***************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 l et+k+l+ +++kv+ t+vrvPvf+ghsesv+iefe+e+++++++++L++apg vid+ ++ y+tP e + NCBI__GCF_000009265.1:WP_003543997.1 216 LAETKKMLD-PKIKVTCTAVRVPVFIGHSESVNIEFENEITADQARDILRDAPGCLVIDKREDGGYITPYESA 287 ********9.*************************************************************** PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 g+d+++++rir+D + e+gl+++vv+DnlrkGaalna+qiaell++ NCBI__GCF_000009265.1:WP_003543997.1 288 GEDATYISRIREDATVENGLNIWVVSDNLRKGAALNAIQIAELLVN 333 *******************************************987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 21.59 // [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