Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate Ac3H11_1530 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11)
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1530 Length = 385 Score = 485 bits (1249), Expect = e-142 Identities = 246/382 (64%), Positives = 295/382 (77%), Gaps = 14/382 (3%) Query: 2 KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSID 61 K VGL+GWRGMVGSVLM RM +E+DFDLIEP+FF+TSN GG+ P K+ L+DA++I+ Sbjct: 3 KLVGLVGWRGMVGSVLMDRMEQEKDFDLIEPMFFSTSNAGGKAPAQAKNETALQDAFNIE 62 Query: 62 ELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQ 121 LK ++I+T QGGDYTSEV+PKLR AGW G+WIDAASSLRME +AVIVLDPVN VI Sbjct: 63 ALKRCEIIITAQGGDYTSEVYPKLRAAGWNGHWIDAASSLRMEKNAVIVLDPVNMPVIKN 122 Query: 122 ALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGA 181 AL G +++IGGNCTVS MLM +G L+ AGLVEWMS TYQAASG GAQ+MRELL Q G Sbjct: 123 ALANGGKDWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGT 182 Query: 182 AHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKEL------ 234 +A V L +P SAIL+IDRKV R+ T +FG PLGGSLIPWIDK+L Sbjct: 183 LNAEVRSLLDDPKSAILEIDRKVIAKQRALTGAETANFGVPLGGSLIPWIDKDLGIGKSQ 242 Query: 235 --PN-GQSREEWKAQAETNKILARFKN----PIPVDGICVRVGAMRCHSQALTIKLNKDV 287 P G S+EEWK AETNKIL + + IPVDG CVRVGAMRCHSQALT KL KDV Sbjct: 243 DEPGWGMSKEEWKGMAETNKILGQGEGFSTAAIPVDGFCVRVGAMRCHSQALTFKLKKDV 302 Query: 288 PLTDIEGLISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFT 347 P+ DIE +++ N WVK+VPN RE ++++LTP AVTGT+++PVGR+RKL MG +Y+GAFT Sbjct: 303 PVADIEAMVAADNEWVKVVPNTREATIQDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFT 362 Query: 348 VGDQLLWGAAEPLRRMLRILLE 369 +GDQLLWGAAEPLRRMLRILL+ Sbjct: 363 IGDQLLWGAAEPLRRMLRILLD 384 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: 528 Number of extensions: 18 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: 385 Length adjustment: 30 Effective length of query: 340 Effective length of database: 355 Effective search space: 120700 Effective search space used: 120700 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 Ac3H11_1530 (Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
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.31140.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-179 581.9 0.3 4e-179 581.2 0.3 1.3 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 Aspartate-semialdehyde dehydroge Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 Aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 581.2 0.3 4e-179 4e-179 2 366 .] 4 383 .. 3 383 .. 0.95 Alignments for each domain: == domain 1 score: 581.2 bits; conditional E-value: 4e-179 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalk 63 vglvgwrgmvgsvl++rm++ekdfd+i+p+ffsts++g+kap+ ak +++l+da++i+alk lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 4 LVGLVGWRGMVGSVLMDRMEQEKDFDLIEPMFFSTSNAGGKAPAQAKNETALQDAFNIEALK 65 69************************************************************ PP TIGR01745 64 eldiiitcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkg 125 +++iiit qggdyt+e+ypklr+agw+g+widaasslrm+++avi+ldpvn+ vik+a+++g lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 66 RCEIIITAQGGDYTSEVYPKLRAAGWNGHWIDAASSLRMEKNAVIVLDPVNMPVIKNALANG 127 ************************************************************** PP TIGR01745 126 irtfvggnctvslllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykevee 187 ++++ggnctvs +lm++g l++ +lvew+s++tyqaasggga+hmrell+q g+l ev + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 128 GKDWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQYGTLNAEVRS 189 ************************************************************** PP TIGR01745 188 elakpssaileierkvtklsrs.eelpvenfsvplagslipwidkqldngq.........sr 239 l p sailei+rkv r+ + + nf+vpl gslipwidk+l g+ s+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 190 LLDDPKSAILEIDRKVIAKQRAlTGAETANFGVPLGGSLIPWIDKDLGIGKsqdepgwgmSK 251 ****************999997356889******************9765422222222279 PP TIGR01745 240 eewkgqaetnkilg.....tkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiira 296 eewkg aetnkilg ++ +i+vdg cvr+ga+rchsqalt+klkkdv++ +ie +++a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 252 EEWKGMAETNKILGqgegfSTAAIPVDGFCVRVGAMRCHSQALTFKLKKDVPVADIEAMVAA 313 9************9333333568*************************************** PP TIGR01745 297 hnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaepl 358 +n+wvkvvpn re t+++ltp avtgt++ipvgr+rkl mg+ey+ aft+gdqllwgaaepl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 314 DNEWVKVVPNTREATIQDLTPVAVTGTMTIPVGRIRKLAMGPEYVGAFTIGDQLLWGAAEPL 375 ************************************************************** PP TIGR01745 359 rrmlrill 366 rrmlrill lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1530 376 RRMLRILL 383 ******96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (385 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04 # Mc/sec: 2.89 // [ok]
This GapMind analysis is from Apr 09 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