Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_038208404.1 Q392_RS13845 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000745855.1:WP_038208404.1 Length = 377 Score = 498 bits (1282), Expect = e-145 Identities = 249/372 (66%), Positives = 293/372 (78%), Gaps = 5/372 (1%) Query: 2 KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61 K VGL+GWRGMVGSVLM RM E+DFDLIEP+FF+TSN GGQ P + K+ L+DA+ I+ Sbjct: 4 KLVGLVGWRGMVGSVLMDRMAAEKDFDLIEPLFFSTSNAGGQAPAMAKNETKLQDAFDIE 63 Query: 62 ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121 +LK ++++T QGGDYT+EVFPKLR AGW+G+WIDAAS+LRM+DDAVIVLDPVN VI Sbjct: 64 QLKRCEIVITAQGGDYTTEVFPKLRAAGWKGHWIDAASTLRMKDDAVIVLDPVNMPVIKN 123 Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181 AL G N+IGGNCTVS MLM +G L+ AGLVEWMS TYQAASG GAQ+MRELL Q G Sbjct: 124 ALAKGGTNWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGT 183 Query: 182 AHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 + V L +P SAIL+IDRKV R+ +FG PLGGSLIPWIDK+L NG S+ Sbjct: 184 LYGEVKALLDDPKSAILEIDRKVIGKQRALSGHEVANFGVPLGGSLIPWIDKDLGNGVSK 243 Query: 241 EEWKAQAETNKILA---RFKNP-IPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLI 296 EEWK AETNKI+ F P IPVDG CVRVGAMRCHSQALT KL KDVPL DIE +I Sbjct: 244 EEWKGMAETNKIMGLGEGFGTPAIPVDGFCVRVGAMRCHSQALTFKLRKDVPLADIEAMI 303 Query: 297 SQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGA 356 + N WVK+VPN RE ++++LTP AVTGT+++PVGR+RKL MG +Y+GAFTVGDQLLWGA Sbjct: 304 ATDNDWVKVVPNTREATMKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTVGDQLLWGA 363 Query: 357 AEPLRRMLRILL 368 AEPLRRMLRILL Sbjct: 364 AEPLRRMLRILL 375 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: 538 Number of extensions: 18 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: 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_038208404.1 Q392_RS13845 (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.2105369.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-185 600.6 0.2 5.7e-185 600.4 0.2 1.0 1 NCBI__GCF_000745855.1:WP_038208404.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038208404.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 600.4 0.2 5.7e-185 5.7e-185 2 366 .] 5 375 .. 4 375 .. 0.97 Alignments for each domain: == domain 1 score: 600.4 bits; conditional E-value: 5.7e-185 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqgg 74 vglvgwrgmvgsvl++rm ekdfd+i+p+ffsts++g++ap++ak ++ l+da+di+ lk+++i+it qgg NCBI__GCF_000745855.1:WP_038208404.1 5 LVGLVGWRGMVGSVLMDRMAAEKDFDLIEPLFFSTSNAGGQAPAMAKNETKLQDAFDIEQLKRCEIVITAQGG 77 69*********************************************************************** PP TIGR01745 75 dytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglf 147 dyt+e++pklr+agwkg+widaas+lrmkddavi+ldpvn+ vik+a++kg +++ggnctvs +lm++g l+ NCBI__GCF_000745855.1:WP_038208404.1 78 DYTTEVFPKLRAAGWKGHWIDAASTLRMKDDAVIVLDPVNMPVIKNALAKGGTNWIGGNCTVSCMLMGVGALY 150 ************************************************************************* PP TIGR01745 148 rdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrs.eelpvenfsv 219 + +lvew+s++tyqaasggga+hmrell+q g+ly+ev+ l p sailei+rkv r+ + v nf+v NCBI__GCF_000745855.1:WP_038208404.1 151 KAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLYGEVKALLDDPKSAILEIDRKVIGKQRAlSGHEVANFGV 223 ********************************************************99999734689****** PP TIGR01745 220 plagslipwidkqldngqsreewkgqaetnkilgtkd.....tilvdglcvrigalrchsqaltiklkkdvsl 287 pl gslipwidk+l ng s+eewkg aetnki+g + +i+vdg cvr+ga+rchsqalt+kl+kdv+l NCBI__GCF_000745855.1:WP_038208404.1 224 PLGGSLIPWIDKDLGNGVSKEEWKGMAETNKIMGLGEgfgtpAIPVDGFCVRVGAMRCHSQALTFKLRKDVPL 296 ********************************99654233338****************************** PP TIGR01745 288 eeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrr 360 +ie +i+++n+wvkvvpn re t+++ltp avtgt++ipvgr+rkl mg+ey+ aftvgdqllwgaaeplrr NCBI__GCF_000745855.1:WP_038208404.1 297 ADIEAMIATDNDWVKVVPNTREATMKDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTVGDQLLWGAAEPLRR 369 ************************************************************************* PP TIGR01745 361 mlrill 366 mlrill NCBI__GCF_000745855.1:WP_038208404.1 370 MLRILL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.78 // [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