Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_068173968.1 HTA01S_RS17205 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_001592305.1:WP_068173968.1 Length = 376 Score = 502 bits (1293), Expect = e-147 Identities = 247/372 (66%), Positives = 295/372 (79%), Gaps = 5/372 (1%) Query: 2 KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61 K VGL+GWRGMVGSVLM RM+EE+DFDLIEP+FF+TSN GG+ P + K+ L+DA+ I Sbjct: 3 KLVGLVGWRGMVGSVLMDRMVEEKDFDLIEPLFFSTSNAGGKAPAMAKNETTLQDAHDIA 62 Query: 62 ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121 LK D+++T QGGDYTSEVFPKLR AGW G+WIDAAS+LRME DAVI+LDPVN VI Sbjct: 63 ALKRCDIVITAQGGDYTSEVFPKLRAAGWNGHWIDAASTLRMEKDAVIILDPVNMPVIKD 122 Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181 AL G +N++GGNCTVS MLM +G L+ AGLVEWMS TYQAASG GAQ+MRELL Q G Sbjct: 123 ALANGGKNWVGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGT 182 Query: 182 AHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 +A V L +P SAIL+IDRKV R+ + T +FG PLGGSLIPWIDK+L NG S+ Sbjct: 183 LNAEVKSLLDDPKSAILEIDRKVIAKQRALSSSETANFGVPLGGSLIPWIDKDLGNGMSK 242 Query: 241 EEWKAQAETNKILARFKN----PIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLI 296 EEWK AETNKIL + IPVDG CVRVGAMRCHSQALT KL KDVP+ D+E +I Sbjct: 243 EEWKGMAETNKILGMGEGFGSAAIPVDGFCVRVGAMRCHSQALTFKLRKDVPVADLEAMI 302 Query: 297 SQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGA 356 + N WVK+VPN+RE ++++LTP AVTGT+++PVGR+RKL MG +Y+GAFT+GDQLLWGA Sbjct: 303 AADNEWVKVVPNNREATIKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGA 362 Query: 357 AEPLRRMLRILL 368 AEPLRRMLRILL Sbjct: 363 AEPLRRMLRILL 374 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: 535 Number of extensions: 20 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: 370 Length of database: 376 Length adjustment: 30 Effective length of query: 340 Effective length of database: 346 Effective search space: 117640 Effective search space used: 117640 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_068173968.1 HTA01S_RS17205 (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.2707235.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-186 605.4 0.4 2e-186 605.2 0.4 1.0 1 NCBI__GCF_001592305.1:WP_068173968.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001592305.1:WP_068173968.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 605.2 0.4 2e-186 2e-186 2 366 .] 4 374 .. 3 374 .. 0.97 Alignments for each domain: == domain 1 score: 605.2 bits; conditional E-value: 2e-186 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqgg 74 vglvgwrgmvgsvl++rm+eekdfd+i+p+ffsts++g+kap++ak +++l+da+di alk++di+it qgg NCBI__GCF_001592305.1:WP_068173968.1 4 LVGLVGWRGMVGSVLMDRMVEEKDFDLIEPLFFSTSNAGGKAPAMAKNETTLQDAHDIAALKRCDIVITAQGG 76 69*********************************************************************** PP TIGR01745 75 dytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglf 147 dyt+e++pklr+agw+g+widaas+lrm++daviildpvn+ vikda+++g +++vggnctvs +lm++g l+ NCBI__GCF_001592305.1:WP_068173968.1 77 DYTSEVFPKLRAAGWNGHWIDAASTLRMEKDAVIILDPVNMPVIKDALANGGKNWVGGNCTVSCMLMGVGALY 149 ************************************************************************* PP TIGR01745 148 rdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrs.eelpvenfsv 219 + +lvew+s++tyqaasggga+hmrell+q g+l ev++ l p sailei+rkv r+ + + nf+v NCBI__GCF_001592305.1:WP_068173968.1 150 KAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLNAEVKSLLDDPKSAILEIDRKVIAKQRAlSSSETANFGV 222 ********************************************************9999972456799**** PP TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalrchsqaltiklkkdvsl 287 pl gslipwidk+l ng s+eewkg aetnkilg + +i+vdg cvr+ga+rchsqalt+kl+kdv++ NCBI__GCF_001592305.1:WP_068173968.1 223 PLGGSLIPWIDKDLGNGMSKEEWKGMAETNKILGMgegfgSAAIPVDGFCVRVGAMRCHSQALTFKLRKDVPV 295 *********************************9633333679****************************** PP TIGR01745 288 eeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrr 360 ++e +i+a+n+wvkvvpn+re t+++ltp avtgt++ipvgr+rkl mg+ey+ aft+gdqllwgaaeplrr NCBI__GCF_001592305.1:WP_068173968.1 296 ADLEAMIAADNEWVKVVPNNREATIKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGAAEPLRR 368 ************************************************************************* PP TIGR01745 361 mlrill 366 mlrill NCBI__GCF_001592305.1:WP_068173968.1 369 MLRILL 374 ****96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (376 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: 18.87 // [ok]
This GapMind analysis is from Jul 25 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