Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate HSERO_RS16495 HSERO_RS16495 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__HerbieS:HSERO_RS16495 Length = 370 Score = 521 bits (1343), Expect = e-153 Identities = 257/368 (69%), Positives = 299/368 (81%), Gaps = 2/368 (0%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 MK VGL+GWRGMVGSVLMQRM +E DFD IEPVFF+TSN GG+ P K LKDA SI Sbjct: 1 MKLVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKKETTLKDANSI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 DELK D+I+T QGGDYT+E+FPKLR AGW GYWIDAASSLRM+DDAVIVLDPVN VI Sbjct: 61 DELKKCDIIITAQGGDYTNEIFPKLRAAGWDGYWIDAASSLRMKDDAVIVLDPVNNNVIK 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 AL G +NYIGGNCT S++LM +GGLF GLVEW+S+MTYQAASG GA +MRELLK MG Sbjct: 121 DALAKGVKNYIGGNCTNSILLMGVGGLFKEGLVEWVSSMTYQAASGGGANHMRELLKGMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 +A+VAD+LA P+SAILDIDRKVA+T+R E PTE FGAPL G LIPWID +L NGQS+ Sbjct: 181 VINAAVADELATPSSAILDIDRKVAKTIR-EDVPTEFFGAPLAGGLIPWIDAQLENGQSK 239 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWK QAE NKIL + IPVDG+CVR+GAMRCHS ALTIKL +D+PL +IE +I N Sbjct: 240 EEWKGQAEVNKILGN-EQIIPVDGLCVRIGAMRCHSLALTIKLKRDLPLAEIESIIRAGN 298 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 WVK VPN R ++V+ELTPA++TG L + VGR+RKLN G +Y+ AF +GDQLLWGAAEPL Sbjct: 299 QWVKWVPNDRAITVKELTPASITGGLEIGVGRVRKLNQGPEYISAFVIGDQLLWGAAEPL 358 Query: 361 RRMLRILL 368 RRMLRI+L Sbjct: 359 RRMLRIIL 366 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: 513 Number of extensions: 14 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: 370 Length adjustment: 30 Effective length of query: 340 Effective length of database: 340 Effective search space: 115600 Effective search space used: 115600 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 HSERO_RS16495 HSERO_RS16495 (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.14100.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-212 689.7 0.5 4.6e-212 689.5 0.5 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS16495 HSERO_RS16495 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS16495 HSERO_RS16495 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.5 0.5 4.6e-212 4.6e-212 2 365 .. 3 365 .. 2 366 .. 0.99 Alignments for each domain: == domain 1 score: 689.5 bits; conditional E-value: 4.6e-212 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 vglvgwrgmvgsvl++rmq+e dfd+i+pvffsts++g+kaps+ak +++l+da+ id lk++diii lcl|FitnessBrowser__HerbieS:HSERO_RS16495 3 LVGLVGWRGMVGSVLMQRMQDEGDFDHIEPVFFSTSNAGGKAPSFAKKETTLKDANSIDELKKCDIII 70 69****************************************************************** PP TIGR01745 70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvs 137 t qggdyt+ei+pklr+agw+gywidaasslrmkddavi+ldpvn +vikda++kg+++++ggnct+s lcl|FitnessBrowser__HerbieS:HSERO_RS16495 71 TAQGGDYTNEIFPKLRAAGWDGYWIDAASSLRMKDDAVIVLDPVNNNVIKDALAKGVKNYIGGNCTNS 138 ******************************************************************** PP TIGR01745 138 lllmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtk 205 +llm++gglf+++lvewvs++tyqaasggga+hmrellk+mgv+ v++ela+pssail+i+rkv+k lcl|FitnessBrowser__HerbieS:HSERO_RS16495 139 ILLMGVGGLFKEGLVEWVSSMTYQAASGGGANHMRELLKGMGVINAAVADELATPSSAILDIDRKVAK 206 ******************************************************************** PP TIGR01745 206 lsrseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrch 273 ++r e++p+e+f++plag+lipwid ql+ngqs+eewkgqae+nkilg +++i+vdglcvriga+rch lcl|FitnessBrowser__HerbieS:HSERO_RS16495 207 TIR-EDVPTEFFGAPLAGGLIPWIDAQLENGQSKEEWKGQAEVNKILGNEQIIPVDGLCVRIGAMRCH 273 ***.**************************************************************** PP TIGR01745 274 sqaltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeyl 341 s+altiklk+d++l eie+iira+n+wvk+vpn+r it++eltpa++tg+l+i+vgr+rkln g+ey+ lcl|FitnessBrowser__HerbieS:HSERO_RS16495 274 SLALTIKLKRDLPLAEIESIIRAGNQWVKWVPNDRAITVKELTPASITGGLEIGVGRVRKLNQGPEYI 341 ******************************************************************** PP TIGR01745 342 saftvgdqllwgaaeplrrmlril 365 saf++gdqllwgaaeplrrmlri+ lcl|FitnessBrowser__HerbieS:HSERO_RS16495 342 SAFVIGDQLLWGAAEPLRRMLRII 365 **********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (370 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.42 // [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