Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_028320904.1 H567_RS0107345 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000422285.1:WP_028320904.1 Length = 372 Score = 499 bits (1285), Expect = e-146 Identities = 237/370 (64%), Positives = 300/370 (81%), Gaps = 1/370 (0%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 M R+G GWRGMVGSVLM RM+EE+DF EPVFFTTSNVGGQGP+VG DI PL+DAY + Sbjct: 1 MLRIGFAGWRGMVGSVLMGRMIEEKDFSGFEPVFFTTSNVGGQGPDVGLDIPPLQDAYDV 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 + LK LD+I+TCQGGDYT +V+P++R AG++GYWIDAAS+LR+E D++IVLDPVNR VID Sbjct: 61 ERLKNLDIIVTCQGGDYTKKVYPQVRAAGFKGYWIDAASALRLEKDSIIVLDPVNRAVID 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 + LD G + Y+GGNCTVSLMLMALGGLF G VEW+S+MTYQAASGAGA++M+EL+ QM Sbjct: 121 KGLDQGIKTYVGGNCTVSLMLMALGGLFAQGEVEWISSMTYQAASGAGAKHMQELIAQMV 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 + L + A+ +D+DR V + LR AFPTE+FGAPL SLIPWID + +GQ+R Sbjct: 181 DLVDAGRPYLKDTAATAIDLDRAVTKKLRDTAFPTENFGAPLAASLIPWIDSPMESGQTR 240 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWK ETNKIL PIP+DG+CVRVGAMRCHSQ LTIKL +++PL +I G+I+ N Sbjct: 241 EEWKGYVETNKILGA-SPPIPIDGLCVRVGAMRCHSQGLTIKLKREIPLDEISGMIATAN 299 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 WV++VPN + S+ +LTPAAV+GTL VPVGR+RK+ +G ++L AFTVGDQLLWGAAEP+ Sbjct: 300 AWVEVVPNEKPASLAKLTPAAVSGTLKVPVGRIRKMLLGPRFLAAFTVGDQLLWGAAEPI 359 Query: 361 RRMLRILLER 370 RR+L+I+++R Sbjct: 360 RRILKIIIDR 369 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: 480 Number of extensions: 12 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: 372 Length adjustment: 30 Effective length of query: 340 Effective length of database: 342 Effective search space: 116280 Effective search space used: 116280 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_028320904.1 H567_RS0107345 (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.30394.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-174 566.0 0.0 1.8e-174 565.9 0.0 1.0 1 lcl|NCBI__GCF_000422285.1:WP_028320904.1 H567_RS0107345 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000422285.1:WP_028320904.1 H567_RS0107345 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 565.9 0.0 1.8e-174 1.8e-174 2 366 .] 3 367 .. 2 367 .. 0.99 Alignments for each domain: == domain 1 score: 565.9 bits; conditional E-value: 1.8e-174 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 ++g+ gwrgmvgsvl+ rm eekdf+ +pvff+ts++g+++p ++ +l+dayd++ lk+ldii+t lcl|NCBI__GCF_000422285.1:WP_028320904.1 3 RIGFAGWRGMVGSVLMGRMIEEKDFSGFEPVFFTTSNVGGQGPDVGLDIPPLQDAYDVERLKNLDIIVT 71 58*******************************************99999******************* PP TIGR01745 71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139 cqggdytk++yp++r+ag+kgywidaas+lr+++d++i+ldpvn vi+ ++++gi+t+vggnctvsl+ lcl|NCBI__GCF_000422285.1:WP_028320904.1 72 CQGGDYTKKVYPQVRAAGFKGYWIDAASALRLEKDSIIVLDPVNRAVIDKGLDQGIKTYVGGNCTVSLM 140 ********************************************************************* PP TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208 lm+lgglf+++ vew+s++tyqaasg+ga+hm+el+ qm l l ++ + ++++r vtk r lcl|NCBI__GCF_000422285.1:WP_028320904.1 141 LMALGGLFAQGEVEWISSMTYQAASGAGAKHMQELIAQMVDLVDAGRPYLKDTAATAIDLDRAVTKKLR 209 ********************************************************************* PP TIGR01745 209 seelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqal 277 + +p+enf++pla+slipwid ++ gq+reewkg etnkilg++ i++dglcvr+ga+rchsq+l lcl|NCBI__GCF_000422285.1:WP_028320904.1 210 DTAFPTENFGAPLAASLIPWIDSPMESGQTREEWKGYVETNKILGASPPIPIDGLCVRVGAMRCHSQGL 278 ********************************************************************* PP TIGR01745 278 tiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftv 346 tiklk++++l+ei +i++ n wv+vvpne+ +l +ltpaav+gtl++pvgr+rk+ +g+++l+aftv lcl|NCBI__GCF_000422285.1:WP_028320904.1 279 TIKLKREIPLDEISGMIATANAWVEVVPNEKPASLAKLTPAAVSGTLKVPVGRIRKMLLGPRFLAAFTV 347 ********************************************************************* PP TIGR01745 347 gdqllwgaaeplrrmlrill 366 gdqllwgaaep+rr+l+i++ lcl|NCBI__GCF_000422285.1:WP_028320904.1 348 GDQLLWGAAEPIRRILKIII 367 *****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (372 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: 00:00:00.01 # Mc/sec: 7.25 // [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