Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_011610425.1 TERY_RS02765 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >NCBI__GCF_000014265.1:WP_011610425.1 Length = 345 Score = 347 bits (890), Expect = e-100 Identities = 179/335 (53%), Positives = 242/335 (72%), Gaps = 8/335 (2%) Query: 41 LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFNG 100 +A++G TGAVG E L +L R+FP +K+LAS+ SAGK + F VE +T DSFN Sbjct: 7 VAILGATGAVGTELLELLETRNFPVGELKLLASEFSAGKTLKFKEQSLQVEAVTNDSFNK 66 Query: 101 VDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGMG 160 VD+ L SAG S+SK + A E G +V+DNSSAFRM VPLV+PEVNPEA + Sbjct: 67 VDLVLASAGASVSKVWAKKAVEAGAVVIDNSSAFRMDSQVPLVVPEVNPEA-----AALH 121 Query: 161 KGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLEG 220 KG ++ANPNC+TI+ +AV PLH V+R+VV+TYQ+ASGAG+ AM E+ Q +E+L+G Sbjct: 122 KG-IVANPNCTTILMSVAVWPLHKIQPVQRLVVATYQSASGAGSRAMAEMKIQAQEILDG 180 Query: 221 KPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPVM 280 K PT +IF AFNLF HN+ + + GY +EEMK++ ETRKI+ E+++TATCIRVPV+ Sbjct: 181 KTPTTDIFPYPLAFNLFPHNSQLNEQGYCQEEMKMLDETRKIFGSKELRITATCIRVPVL 240 Query: 281 RAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIRR 340 RAH+E++NL+F P ARE+L +APGV ++++ N FP P+ S KDDV VGRIR+ Sbjct: 241 RAHSEAINLEFAEPFSVVKAREVLSQAPGVTLVENWQENYFPMPMVASGKDDVLVGRIRQ 300 Query: 341 DVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375 D+SQ GL++++ GDQ+RKGAALNAVQIAE+L+ Sbjct: 301 DISQAE--GLELWLSGDQVRKGAALNAVQIAELLV 333 Lambda K H 0.318 0.133 0.380 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: 321 Number of extensions: 3 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: 375 Length of database: 345 Length adjustment: 29 Effective length of query: 346 Effective length of database: 316 Effective search space: 109336 Effective search space used: 109336 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: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_011610425.1 TERY_RS02765 (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.19706.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-130 418.8 0.1 9.6e-130 418.5 0.1 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011610425.1 TERY_RS02765 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011610425.1 TERY_RS02765 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 418.5 0.1 9.6e-130 9.6e-130 1 338 [. 6 334 .. 6 335 .. 0.98 Alignments for each domain: == domain 1 score: 418.5 bits; conditional E-value: 9.6e-130 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +vai+GatGavG ell++Le rnfp+ +l+llase saGk +kfk++ l+ve++++ sf+++d+ l sa lcl|NCBI__GCF_000014265.1:WP_011610425.1 6 RVAILGATGAVGTELLELLETRNFPVGELKLLASEFSAGKTLKFKEQSLQVEAVTNDSFNKVDLVLASA 74 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 G+svsk++a ka++ag++viDn+safr+d +vPLvvpevn e + +k gi+anPnC+ti + v++ p lcl|NCBI__GCF_000014265.1:WP_011610425.1 75 GASVSKVWAKKAVEAGAVVIDNSSAFRMDSQVPLVVPEVNPEAAALHK--GIVANPNCTTILMSVAVWP 141 ******************************************998877..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l++ ++r+vv+tYq+ sGaG ++++e+k q++ +l+gk + ++ f++++afn++p+ +l lcl|NCBI__GCF_000014265.1:WP_011610425.1 142 LHKIQPVQRLVVATYQSASGAGSRAMAEMKIQAQEILDGKTPT-------TDIFPYPLAFNLFPHNSQL 203 ************************************9998655.......699**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e+Gy +ee+k+l etrki+g ++l+++atc+rvPv+++hse++++ef++++sv +++e+L +apgv++ lcl|NCBI__GCF_000014265.1:WP_011610425.1 204 NEQGYCQEEMKMLDETRKIFGSKELRITATCIRVPVLRAHSEAINLEFAEPFSVVKAREVLSQAPGVTL 272 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +++ +en +p+P+ a+gkd+v+vgrir+D+s+++gl+l++++D++rkGaalnavqiaell++ lcl|NCBI__GCF_000014265.1:WP_011610425.1 273 VENWQENYFPMPMVASGKDDVLVGRIRQDISQAEGLELWLSGDQVRKGAALNAVQIAELLVA 334 ***********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (345 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: 9.60 // [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