Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_037568868.1 BS73_RS02665 aspartate-semialdehyde dehydrogenase
Query= BRENDA::P9WNX5 (345 letters) >NCBI__GCF_000744815.1:WP_037568868.1 Length = 342 Score = 421 bits (1083), Expect = e-122 Identities = 227/343 (66%), Positives = 258/343 (75%), Gaps = 3/343 (0%) Query: 3 LSIGIVGATGQVGQVMRTLLDERDFPASAVRFFASARSQGRKLAFRGQEIEVEDAETADP 62 + +GIVGATGQVG VMR +L+ERDFP +R FASARS GR L ++G EI VEDA AD Sbjct: 1 MKVGIVGATGQVGGVMRRVLEERDFPVEQLRLFASARSAGRTLPWKGSEITVEDAAAADY 60 Query: 63 SGLDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHRRPK 122 SGLDI LFSAG A SK A + A G VIDNSSAWR DP VPLVV+EVN RPK Sbjct: 61 SGLDIVLFSAGGATSKALAEKVARDGAVVIDNSSAWRMDPQVPLVVAEVN-PHAVVDRPK 119 Query: 123 GIIANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARAVIGGAE 182 GIIANPNCTTMAAMPVLK LH EA L LV ++YQAVSGSGLAGVAEL Q + A Sbjct: 120 GIIANPNCTTMAAMPVLKPLHQEAGLKALVATTYQAVSGSGLAGVAELEAQIQKGADRAA 179 Query: 183 QLVYDGGALEFPPPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGIPDLL 242 L +DG A++ P P+ Y PIAFNV+PLAG +VDDG ETDE++KLR ESRKIL IP+L Sbjct: 180 ALTHDGSAIDLPAPSVYARPIAFNVLPLAGKIVDDGLNETDEEKKLRNESRKILEIPELK 239 Query: 243 VSGTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVDVPTPLAAAGVDESLV 302 VSGTCVRVPVFTGHSL +NA F +P++P+RA ELL GA GV L ++PTPL AAG D S V Sbjct: 240 VSGTCVRVPVFTGHSLQVNARFERPITPDRAAELLAGAPGVALSEIPTPLQAAGQDPSYV 299 Query: 303 GRIRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELLTADL 345 GRIR D V + GLALF+S DNLRKGAALN IQIAEL+ ADL Sbjct: 300 GRIRVDETVDN--GLALFLSNDNLRKGAALNAIQIAELVAADL 340 Lambda K H 0.317 0.135 0.382 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: 412 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: 345 Length of database: 342 Length adjustment: 29 Effective length of query: 316 Effective length of database: 313 Effective search space: 98908 Effective search space used: 98908 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_037568868.1 BS73_RS02665 (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.1918983.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-132 428.1 0.0 1.4e-132 427.9 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037568868.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037568868.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.9 0.0 1.4e-132 1.4e-132 1 337 [. 2 337 .. 2 339 .. 0.96 Alignments for each domain: == domain 1 score: 427.9 bits; conditional E-value: 1.4e-132 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 +v+ivGatG+vG ++++vLeer+fp+++l+l+as+rsaG+ + kg e++ve+a ++++g+di lfsaGg++ NCBI__GCF_000744815.1:WP_037568868.1 2 KVGIVGATGQVGGVMRRVLEERDFPVEQLRLFASARSAGRTLPWKGSEITVEDAAAADYSGLDIVLFSAGGAT 74 599********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk++a k+a++g++viDn+sa+r+d++vPLvv+evn + + +++ kgiianPnC+t+++++vLkpl++ea+lk NCBI__GCF_000744815.1:WP_037568868.1 75 SKALAEKVARDGAVVIDNSSAWRMDPQVPLVVAEVNPHAVVDRP-KGIIANPNCTTMAAMPVLKPLHQEAGLK 146 ******************************************99.**************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeida....lkakkfakqiafnaiplidklkedG..yt 213 +v tYqavsG+G +gv+eL+ q++ + + +++++ + ++ +a++iafn++pl++k+++dG +t NCBI__GCF_000744815.1:WP_037568868.1 147 ALVATTYQAVSGSGLAGVAELEAQIQKGADRAAALTHDGSaidlPAPSVYARPIAFNVLPLAGKIVDDGlnET 219 ************************99887777666655533454999***********************99* PP TIGR01296 214 keelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyp 286 +ee+kl++e+rkil+i++lkvs+tcvrvPvftghs+ v++ fe++++++++ elL +apgv++ + p NCBI__GCF_000744815.1:WP_037568868.1 220 DEEKKLRNESRKILEIPELKVSGTCVRVPVFTGHSLQVNARFERPITPDRAAELLAGAPGVALSEIP------ 286 ***************************************************************9988...... PP TIGR01296 287 tPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 tPl+a+g+d ++vgrir D + ++glalf++ DnlrkGaalna+qiael+ NCBI__GCF_000744815.1:WP_037568868.1 287 TPLQAAGQDPSYVGRIRVDETVDNGLALFLSNDNLRKGAALNAIQIAELVA 337 ************************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (342 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 24.48 // [ok]
This GapMind analysis is from Jul 26 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