Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_012970812.1 ALVIN_RS07955 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000025485.1:WP_012970812.1 Length = 371 Score = 552 bits (1422), Expect = e-162 Identities = 271/371 (73%), Positives = 310/371 (83%), Gaps = 1/371 (0%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFD-LIEPVFFTTSNVGGQGPEVGKDIAPLKDAYS 59 MKRVG +GWRGMVGSVLM+RM E DF L EPVFFTTS VG GP+VG+ +PL DA S Sbjct: 1 MKRVGFVGWRGMVGSVLMERMRAENDFARLAEPVFFTTSQVGQPGPDVGQGASPLLDAES 60 Query: 60 IDELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVI 119 +D L+ +D I+TCQGGDYT + P+LR +GW GYWIDAASSLRME DA I+LDPVNR VI Sbjct: 61 LDALREMDAIVTCQGGDYTKSIHPRLRASGWNGYWIDAASSLRMEPDATIILDPVNRPVI 120 Query: 120 DQALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQM 179 D ALD+G R++IGGNCTVSLMLMA+GGLF GLVEW+SAMTYQAASGAGA+NMRELL QM Sbjct: 121 DAALDSGKRDFIGGNCTVSLMLMAIGGLFREGLVEWVSAMTYQAASGAGAKNMRELLAQM 180 Query: 180 GAAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQS 239 GA H SV LA+PASAILDIDR+V ETLR FPTE FG PL GSLIPWID +L NGQS Sbjct: 181 GALHGSVESLLADPASAILDIDRRVTETLRDPGFPTESFGVPLAGSLIPWIDTQLDNGQS 240 Query: 240 REEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQH 299 REEWK QAETN+IL R PIPVDG+CVRVGAMRCHSQ LTIKLN+D+ L++IE LI+ Sbjct: 241 REEWKGQAETNRILGRTDQPIPVDGLCVRVGAMRCHSQGLTIKLNRDIALSEIESLIASA 300 Query: 300 NPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEP 359 N WV++VPN R V++R+L+PAAVTG+L VPVGRLR +NMGS+YL AFTVGDQLLWGAAEP Sbjct: 301 NDWVRVVPNDRAVTMRDLSPAAVTGSLHVPVGRLRTMNMGSRYLSAFTVGDQLLWGAAEP 360 Query: 360 LRRMLRILLER 370 LRRML ILL+R Sbjct: 361 LRRMLMILLDR 371 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: 525 Number of extensions: 16 Number of successful extensions: 2 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: 371 Length adjustment: 30 Effective length of query: 340 Effective length of database: 341 Effective search space: 115940 Effective search space used: 115940 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_012970812.1 ALVIN_RS07955 (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.18265.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-191 621.6 0.0 2.4e-191 621.4 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012970812.1 ALVIN_RS07955 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012970812.1 ALVIN_RS07955 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 621.4 0.0 2.4e-191 2.4e-191 1 366 [] 2 369 .. 2 369 .. 0.99 Alignments for each domain: == domain 1 score: 621.4 bits; conditional E-value: 2.4e-191 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdai.kpvffstsqlgqkapslakisailedaydidalkeldii 68 k+vg+vgwrgmvgsvl++rm+ e+df ++ +pvff+tsq+gq +p +++ +++l da +dal+e+d i lcl|NCBI__GCF_000025485.1:WP_012970812.1 2 KRVGFVGWRGMVGSVLMERMRAENDFARLaEPVFFTTSQVGQPGPDVGQGASPLLDAESLDALREMDAI 70 68************************987479************************************* PP TIGR01745 69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137 +tcqggdytk i+p+lr++gw+gywidaasslrm+ da iildpvn vi+ a++ g r+f+ggnctvs lcl|NCBI__GCF_000025485.1:WP_012970812.1 71 VTCQGGDYTKSIHPRLRASGWNGYWIDAASSLRMEPDATIILDPVNRPVIDAALDSGKRDFIGGNCTVS 139 ********************************************************************* PP TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206 l+lm++gglfr++lvewvs++tyqaasg+ga+ mrell qmg l+++ve+ la p+sail+i+r+vt++ lcl|NCBI__GCF_000025485.1:WP_012970812.1 140 LMLMAIGGLFREGLVEWVSAMTYQAASGAGAKNMRELLAQMGALHGSVESLLADPASAILDIDRRVTET 208 ********************************************************************* PP TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilg.tkdtilvdglcvrigalrchs 274 r +p+e f+vplagslipwid+qldngqsreewkgqaetn+ilg t + i+vdglcvr+ga+rchs lcl|NCBI__GCF_000025485.1:WP_012970812.1 209 LRDPGFPTESFGVPLAGSLIPWIDTQLDNGQSREEWKGQAETNRILGrTDQPIPVDGLCVRVGAMRCHS 277 **********************************************856788***************** PP TIGR01745 275 qaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsa 343 q+ltikl++d++l eie++i++ n+wv+vvpn+r +t+r+l+paavtg+l++pvgrlr +nmg +ylsa lcl|NCBI__GCF_000025485.1:WP_012970812.1 278 QGLTIKLNRDIALSEIESLIASANDWVRVVPNDRAVTMRDLSPAAVTGSLHVPVGRLRTMNMGSRYLSA 346 ********************************************************************* PP TIGR01745 344 ftvgdqllwgaaeplrrmlrill 366 ftvgdqllwgaaeplrrml ill lcl|NCBI__GCF_000025485.1:WP_012970812.1 347 FTVGDQLLWGAAEPLRRMLMILL 369 *******************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (371 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.70 // [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