Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_004265800.1 C665_RS00835 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000310185.1:WP_004265800.1 Length = 377 Score = 543 bits (1400), Expect = e-159 Identities = 273/377 (72%), Positives = 313/377 (83%), Gaps = 7/377 (1%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVG--KDIAPLKDAY 58 M RVGL+GWRGMVGSVLMQRM+EE DF IEPV+F+TSN GG+ P G + APL+DA Sbjct: 1 MNRVGLVGWRGMVGSVLMQRMVEEGDFAFIEPVYFSTSNAGGKAPSFGGKEAAAPLQDAS 60 Query: 59 SIDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKV 118 +ID LK+ D+++TCQGGDYT EVFPKLR GW G+WIDAAS+LRM DDAVI+LDPVNR V Sbjct: 61 NIDALKSCDIVITCQGGDYTKEVFPKLRATGWNGHWIDAASALRMNDDAVIILDPVNRNV 120 Query: 119 IDQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQ 178 ID AL G RN+IGGNCTVSLMLM LGGLF GLVEW+SAMTYQAASGAGAQNMREL+ Q Sbjct: 121 IDAALAKGGRNWIGGNCTVSLMLMGLGGLFRHGLVEWISAMTYQAASGAGAQNMRELISQ 180 Query: 179 MGAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHF-GAPLGGSLIPWIDKELPNG 237 MG H SV D LA+PASAIL+IDRKVAET+RS+AFP ++F PL GSLIPWID + +G Sbjct: 181 MGTIHDSVKDLLADPASAILEIDRKVAETMRSDAFPKKNFRNTPLAGSLIPWIDVPVEHG 240 Query: 238 QSREEWKAQAETNKILAR--FKNP--IPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIE 293 QS+EEWK AE NKIL F+ P IP+DG+CVR+GAMRCHSQALTIKL KDVPL +I Sbjct: 241 QSKEEWKGGAECNKILGNPAFRTPGSIPIDGLCVRIGAMRCHSQALTIKLKKDVPLDEIT 300 Query: 294 GLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLL 353 +I+ NPWVK+VPN RE++ RELTP AVTGTL+VPVGRL K+ MG +YLGAFTVGDQLL Sbjct: 301 EIIAGANPWVKVVPNDREITERELTPTAVTGTLTVPVGRLHKMAMGPEYLGAFTVGDQLL 360 Query: 354 WGAAEPLRRMLRILLER 370 WGAAEPLRRMLRILLER Sbjct: 361 WGAAEPLRRMLRILLER 377 Lambda K H 0.319 0.136 0.409 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: 565 Number of extensions: 13 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: 370 Length of database: 377 Length adjustment: 30 Effective length of query: 340 Effective length of database: 347 Effective search space: 117980 Effective search space used: 117980 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: 50 (23.9 bits)
Align candidate WP_004265800.1 C665_RS00835 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (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/TIGR01745.hmm # target sequence database: /tmp/gapView.3033.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01745 [M=366] Accession: TIGR01745 Description: asd_gamma: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-195 633.4 0.0 6.3e-195 633.1 0.0 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004265800.1 C665_RS00835 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004265800.1 C665_RS00835 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 633.1 0.0 6.3e-195 6.3e-195 2 366 .] 3 375 .. 2 375 .. 0.97 Alignments for each domain: == domain 1 score: 633.1 bits; conditional E-value: 6.3e-195 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa..iledaydidalkeldii 68 +vglvgwrgmvgsvl++rm+ee df i+pv+fsts++g+kaps+++ +a +l+da +idalk++di+ lcl|NCBI__GCF_000310185.1:WP_004265800.1 3 RVGLVGWRGMVGSVLMQRMVEEGDFAFIEPVYFSTSNAGGKAPSFGGKEAaaPLQDASNIDALKSCDIV 71 79*******************************************98765569**************** PP TIGR01745 69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137 itcqggdytke++pklr++gw+g+widaas+lrm+ddaviildpvn +vi+ a++kg r+++ggnctvs lcl|NCBI__GCF_000310185.1:WP_004265800.1 72 ITCQGGDYTKEVFPKLRATGWNGHWIDAASALRMNDDAVIILDPVNRNVIDAALAKGGRNWIGGNCTVS 140 ********************************************************************* PP TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206 l+lm+lgglfr++lvew+s++tyqaasg+ga+ mrel++qmg+++ +v++ la p+sailei+rkv+++ lcl|NCBI__GCF_000310185.1:WP_004265800.1 141 LMLMGLGGLFRHGLVEWISAMTYQAASGAGAQNMRELISQMGTIHDSVKDLLADPASAILEIDRKVAET 209 ********************************************************************* PP TIGR01745 207 srseelpvenf.svplagslipwidkqldngqsreewkgqaetnkilg.....tkdtilvdglcvriga 269 +rs+ +p +nf ++plagslipwid ++ gqs+eewkg ae nkilg t i++dglcvriga lcl|NCBI__GCF_000310185.1:WP_004265800.1 210 MRSDAFPKKNFrNTPLAGSLIPWIDVPVEHGQSKEEWKGGAECNKILGnpafrTPGSIPIDGLCVRIGA 278 ***********558*********************************8444445678************ PP TIGR01745 270 lrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgk 338 +rchsqaltiklkkdv+l+ei eii+ n+wvkvvpn+reit+reltp+avtgtl++pvgrl k+ mg+ lcl|NCBI__GCF_000310185.1:WP_004265800.1 279 MRCHSQALTIKLKKDVPLDEITEIIAGANPWVKVVPNDREITERELTPTAVTGTLTVPVGRLHKMAMGP 347 ********************************************************************* PP TIGR01745 339 eylsaftvgdqllwgaaeplrrmlrill 366 eyl aftvgdqllwgaaeplrrmlrill lcl|NCBI__GCF_000310185.1:WP_004265800.1 348 EYLGAFTVGDQLLWGAAEPLRRMLRILL 375 **************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (377 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: 00:00:00.01 # Mc/sec: 10.47 // [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