Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_073040945.1 BUB04_RS15000 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_900129305.1:WP_073040945.1 Length = 339 Score = 359 bits (922), Expect = e-104 Identities = 189/336 (56%), Positives = 239/336 (71%), Gaps = 10/336 (2%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + VA+ GATGAVG TM+ VL+ER FPV +L LLAS RS GK F G V V+ + E + Sbjct: 6 YRVAVVGATGAVGTTMVRVLEERNFPVSDLKLLASSRSVGKELTFRGDKVAVEELTEKSF 65 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 V +ALFSAG +S ++APIAA +G VV+DN+S FR D PLVVPEVNP A+ ++ Sbjct: 66 EGVDVALFSAGASVSRQFAPIAARSGCVVVDNSSAFRMDPQTPLVVPEVNPHAVRG--HQ 123 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 IIANPNCSTIQM+VALKPI DA GI+RI VTT+Q+VSG G I+EL Q L+ G P Sbjct: 124 GIIANPNCSTIQMVVALKPIQDAAGIKRIVVTTFQAVSGTGMKAIEELRLQVEALVRGEP 183 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 + QIAFNC+P I F+D+GYT+EEMKMV ET+KIF DP I V T VRVPV+YG Sbjct: 184 LPRQVYPHQIAFNCLPHIGSFLDSGYTEEEMKMVNETRKIFEDPDIQVCATTVRVPVYYG 243 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGIELFRGADFPTQVR-----DAGGKDHVLVGRVR 299 H+E+V VETR P+D ++ + +L++ DG+++ D P R DA G+D VGR+R Sbjct: 244 HSESVAVETRKPLDVKEAVALLKRADGVQV---VDEPLAARYPMPLDAAGRDETFVGRIR 300 Query: 300 NDISHHSGINLWVVADNVRKGAATNAVQIAELLVRD 335 DIS +G+ LW+VADN+RKGAATNAVQIAELLVR+ Sbjct: 301 KDISVENGLVLWIVADNIRKGAATNAVQIAELLVRE 336 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: 327 Number of extensions: 15 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: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 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_073040945.1 BUB04_RS15000 (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.3694089.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-147 474.9 0.2 7.6e-147 474.8 0.2 1.0 1 NCBI__GCF_900129305.1:WP_073040945.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900129305.1:WP_073040945.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 474.8 0.2 7.6e-147 7.6e-147 1 338 [. 7 335 .. 7 336 .. 0.98 Alignments for each domain: == domain 1 score: 474.8 bits; conditional E-value: 7.6e-147 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 +va+vGatGavG ++++vLeernfp+++l+llas+rs Gk+++f+g ++ vee++++sfeg+d+alfsaG+sv NCBI__GCF_900129305.1:WP_073040945.1 7 RVAVVGATGAVGTTMVRVLEERNFPVSDLKLLASSRSVGKELTFRGDKVAVEELTEKSFEGVDVALFSAGASV 79 69*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 s++fap aa++g++v+Dn+safr+d+++PLvvpevn + ++ ++ giianPnCstiq+vv+Lkp++d+a++k NCBI__GCF_900129305.1:WP_073040945.1 80 SRQFAPIAARSGCVVVDNSSAFRMDPQTPLVVPEVNPHAVRGHQ--GIIANPNCSTIQMVVALKPIQDAAGIK 150 *****************************************999..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 r+vv t+qavsG+G k++eeL+ q+ a + g+ l+ + +++qiafn +p+i+++ + Gyt+ee+k+ NCBI__GCF_900129305.1:WP_073040945.1 151 RIVVTTFQAVSGTGMKAIEELRLQVEALVRGEP-------LPRQVYPHQIAFNCLPHIGSFLDSGYTEEEMKM 216 **************************9988754.......45799**************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 ++etrki++++d++v at+vrvPv++ghsesv +e+ k+l+v+e+ lLk a+gv+v+d+p yp+Pl+a+ NCBI__GCF_900129305.1:WP_073040945.1 217 VNETRKIFEDPDIQVCATTVRVPVYYGHSESVAVETRKPLDVKEAVALLKRADGVQVVDEPLAARYPMPLDAA 289 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 g+de+fvgrirkD+s e+gl l++vaDn+rkGaa+navqiaell++ NCBI__GCF_900129305.1:WP_073040945.1 290 GRDETFVGRIRKDISVENGLVLWIVADNIRKGAATNAVQIAELLVR 335 *******************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (339 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: 00:00:00.00 # Mc/sec: 17.03 // [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