Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_012283361.1 HM1_RS10580 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >NCBI__GCF_000019165.1:WP_012283361.1 Length = 336 Score = 332 bits (850), Expect = 1e-95 Identities = 176/336 (52%), Positives = 234/336 (69%), Gaps = 9/336 (2%) Query: 40 SLAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFN 99 ++A+VG TGAVGQE L VL++R+FP +++LAS RSAGK +++ G EYT+ +F Sbjct: 5 NVAIVGATGAVGQELLKVLAERNFPVGELRLLASARSAGKVISYQGQEYTIGLTDEKAFA 64 Query: 100 GVDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGM 159 G+DIALF AGGS S EF A E G +V+DNSSAFRM VPLV+PEVNPE V Sbjct: 65 GIDIALF-AGGSASTEFAQAAVEAGAVVIDNSSAFRMHPEVPLVVPEVNPE-----DVDW 118 Query: 160 GKGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLE 219 KG +IANPNCSTII +A+ PLH A ++R+VVSTYQA SGAG + EL +QT +VL Sbjct: 119 HKG-IIANPNCSTIIMAVALKPLHDAAGIERVVVSTYQAVSGAGKEGITELTEQTSQVLR 177 Query: 220 GKPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPV 279 G+P N+F AFNL H D Y +EE K++KETRKI ++ ++++TAT +RVPV Sbjct: 178 GEPVKPNVFAHPIAFNLIPHIDVFQDGDYTKEEWKMIKETRKIMHEADMRITATTVRVPV 237 Query: 280 MRAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIR 339 R+H+ES+N++F+ + A+E+L A GV +IDD + +P PL S+KD+V VGRIR Sbjct: 238 YRSHSESINIEFKRKITAAEAKEVLANASGVIVIDDVQNKQYPMPLYTSDKDEVFVGRIR 297 Query: 340 RDVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375 D+S D GL+++V DQIRKGAA NAVQIAE L+ Sbjct: 298 EDLSIDK--GLNLWVVADQIRKGAATNAVQIAETLI 331 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: 309 Number of extensions: 16 Number of successful extensions: 4 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: 336 Length adjustment: 29 Effective length of query: 346 Effective length of database: 307 Effective search space: 106222 Effective search space used: 106222 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_012283361.1 HM1_RS10580 (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.26271.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-147 475.8 1.6 4.1e-147 475.6 1.6 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012283361.1 HM1_RS10580 aspartate-semialdehy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012283361.1 HM1_RS10580 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.6 1.6 4.1e-147 4.1e-147 1 338 [. 5 332 .. 5 333 .. 0.98 Alignments for each domain: == domain 1 score: 475.6 bits; conditional E-value: 4.1e-147 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nvaivGatGavGqellkvL+ernfp+ +l+llas+rsaGk + ++g+e+++ ++++ f gidialf a lcl|NCBI__GCF_000019165.1:WP_012283361.1 5 NVAIVGATGAVGQELLKVLAERNFPVGELRLLASARSAGKVISYQGQEYTIGLTDEKAFAGIDIALF-A 72 79*****************************************************************.7 PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggs s efa a++ag++viDn+safr+ ++vPLvvpevn e++ +k giianPnCsti + v+Lkp lcl|NCBI__GCF_000019165.1:WP_012283361.1 73 GGSASTEFAQAAVEAGAVVIDNSSAFRMHPEVPLVVPEVNPEDVDWHK--GIIANPNCSTIIMAVALKP 139 8999***************************************99887..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d+a+++rvvvstYqavsGaGk+g+ eL++qt vl g+ +k++ fa++iafn+ip+id + lcl|NCBI__GCF_000019165.1:WP_012283361.1 140 LHDAAGIERVVVSTYQAVSGAGKEGITELTEQTSQVLRGEP-------VKPNVFAHPIAFNLIPHIDVF 201 **********************************9998865.......567****************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 ++ ytkee k++ etrki++ d++++at+vrvPv+++hses++ief++++++ e+ke+L +a+gv+v lcl|NCBI__GCF_000019165.1:WP_012283361.1 202 QDGDYTKEEWKMIKETRKIMHEADMRITATTVRVPVYRSHSESINIEFKRKITAAEAKEVLANASGVIV 270 **99***************************************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 idd ++++yp+Pl +++kdevfvgrir+Dls +kgl+l+vvaD++rkGaa+navqiae+li+ lcl|NCBI__GCF_000019165.1:WP_012283361.1 271 IDDVQNKQYPMPLYTSDKDEVFVGRIREDLSIDKGLNLWVVADQIRKGAATNAVQIAETLIQ 332 ***********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (336 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: 11.95 // [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