Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_072909625.1 BUB13_RS15225 aspartate-semialdehyde dehydrogenase
Query= BRENDA::P44801 (371 letters) >NCBI__GCF_900142125.1:WP_072909625.1 Length = 369 Score = 499 bits (1284), Expect = e-146 Identities = 240/366 (65%), Positives = 297/366 (81%), Gaps = 2/366 (0%) Query: 4 VGFIGWRGMVGSVLMDRMSQENDFENLNPVFFTTSQAGQKAPVFGGKDAGDLKSAFDIEE 63 VG +GWRGMVGSVLM RM +END ++ FF+TSQAGQ AP FG L+ A DI + Sbjct: 3 VGLVGWRGMVGSVLMQRMVEENDLVGVDATFFSTSQAGQTAPDFGQTGGTTLEDASDITK 62 Query: 64 LKKLDIIVTCQGGDYTNEVYPKLKATGWDGYWVDAASALRMKDDAIIVLDPVNQHVISEG 123 L + D+I+TCQGGDYT EV+PKL++ GW+GYW+DAAS+LRM+D+A+I+LDP N VI E Sbjct: 63 LAEQDVIITCQGGDYTKEVHPKLRSGGWNGYWIDAASSLRMEDNAVIILDPTNLDVIEEA 122 Query: 124 LKKGIKTFVGGNCTVSLMLMAIGGLFEKDLVEWISVATYQAASGAGAKNMRELLSQMGLL 183 LK G+K F+GGNCTVSLMLMAIGGLF+ LVEW+S TYQAASGAGA NMRELLSQMG L Sbjct: 123 LKNGVKDFIGGNCTVSLMLMAIGGLFKAGLVEWVSSMTYQAASGAGAPNMRELLSQMGYL 182 Query: 184 EQAVSSELKDPASSILDIERKVTAKMRADNFPTDNFGAALGGSLIPWIDKLLPETGQTKE 243 ++V+ ELK P S+IL+I++KVTA +R+D PT FG L GS++PWID+ + E GQ++E Sbjct: 183 NESVAEELKTPGSAILEIDQKVTAALRSDGIPTAEFGFPLAGSVLPWIDREV-EDGQSRE 241 Query: 244 EWKGYAETNKILGLSDNPIPVDGLCVRIGALRCHSQAFTIKLKKDLPLEEIEQIIASHNE 303 EWKG+ ETNKILG + PIPVDG+CVRIGA+RCHSQA TIKL KDLP++EIEQII N+ Sbjct: 242 EWKGFVETNKILG-NKTPIPVDGVCVRIGAMRCHSQALTIKLNKDLPIKEIEQIIDGDNQ 300 Query: 304 WVKVIPNDKEITLRELTPAKVTGTLSVPVGRLRKLAMGPEYLAAFTVGDQLLWGAAEPVR 363 WVK++PN K TL +LTP V+GTLSVPVGR+RK+ MGP+YL+AFT GDQLLWGAAEP+R Sbjct: 301 WVKLVPNKKAETLEQLTPTAVSGTLSVPVGRVRKMKMGPQYLSAFTCGDQLLWGAAEPLR 360 Query: 364 RILKQL 369 R+L+ L Sbjct: 361 RMLRIL 366 Lambda K H 0.317 0.136 0.402 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: 482 Number of extensions: 10 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: 371 Length of database: 369 Length adjustment: 30 Effective length of query: 341 Effective length of database: 339 Effective search space: 115599 Effective search space used: 115599 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_072909625.1 BUB13_RS15225 (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.2467.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-190 618.0 0.2 2.8e-190 617.9 0.2 1.0 1 lcl|NCBI__GCF_900142125.1:WP_072909625.1 BUB13_RS15225 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900142125.1:WP_072909625.1 BUB13_RS15225 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 617.9 0.2 2.8e-190 2.8e-190 1 365 [. 1 366 [. 1 367 [. 0.99 Alignments for each domain: == domain 1 score: 617.9 bits; conditional E-value: 2.8e-190 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa.iledaydidalkeldii 68 +kvglvgwrgmvgsvl++rm+ee+d+ +++ ffstsq+gq ap ++++ + +leda di l e d+i lcl|NCBI__GCF_900142125.1:WP_072909625.1 1 MKVGLVGWRGMVGSVLMQRMVEENDLVGVDATFFSTSQAGQTAPDFGQTGGtTLEDASDITKLAEQDVI 69 69***********************************************9879**************** PP TIGR01745 69 itcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137 itcqggdytke++pklr gw+gywidaasslrm+d+aviildp nldvi++a+++g+++f+ggnctvs lcl|NCBI__GCF_900142125.1:WP_072909625.1 70 ITCQGGDYTKEVHPKLRSGGWNGYWIDAASSLRMEDNAVIILDPTNLDVIEEALKNGVKDFIGGNCTVS 138 ********************************************************************* PP TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkl 206 l+lm++gglf+ +lvewvs++tyqaasg+ga mrell+qmg l ++v+eel +p sailei++kvt lcl|NCBI__GCF_900142125.1:WP_072909625.1 139 LMLMAIGGLFKAGLVEWVSSMTYQAASGAGAPNMRELLSQMGYLNESVAEELKTPGSAILEIDQKVTAA 207 ********************************************************************* PP TIGR01745 207 srseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsq 275 rs+ +p+ +f+ plags++pwid+++++gqsreewkg etnkilg k+ i+vdg+cvriga+rchsq lcl|NCBI__GCF_900142125.1:WP_072909625.1 208 LRSDGIPTAEFGFPLAGSVLPWIDREVEDGQSREEWKGFVETNKILGNKTPIPVDGVCVRIGAMRCHSQ 276 ********************************************************************* PP TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344 altikl+kd++++eie+ii +n+wvk+vpn++ tl++ltp+av+gtl++pvgr+rk++mg++ylsaf lcl|NCBI__GCF_900142125.1:WP_072909625.1 277 ALTIKLNKDLPIKEIEQIIDGDNQWVKLVPNKKAETLEQLTPTAVSGTLSVPVGRVRKMKMGPQYLSAF 345 ********************************************************************* PP TIGR01745 345 tvgdqllwgaaeplrrmlril 365 t gdqllwgaaeplrrmlril lcl|NCBI__GCF_900142125.1:WP_072909625.1 346 TCGDQLLWGAAEPLRRMLRIL 366 *******************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (369 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: 11.49 // [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