Align aspartate-semialdehyde dehydrogenase (characterized)
to candidate BWI76_RS26220 BWI76_RS26220 aspartate-semialdehyde dehydrogenase
Query= CharProtDB::CH_024631 (367 letters) >FitnessBrowser__Koxy:BWI76_RS26220 Length = 368 Score = 687 bits (1772), Expect = 0.0 Identities = 343/368 (93%), Positives = 357/368 (97%), Gaps = 1/368 (0%) Query: 1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTG-TLQDAFD 59 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQ APSFGG+TG TLQDAFD Sbjct: 1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQPAPSFGGSTGGTLQDAFD 60 Query: 60 LEALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI 119 LEALKALDIIVTCQGGDYTN+IYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI Sbjct: 61 LEALKALDIIVTCQGGDYTNDIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVI 120 Query: 120 TDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQM 179 T GLNNG++TFVGGNCTVSLMLMSLGGLFA DLV+WVSVATYQAASGGGARHMRELLTQM Sbjct: 121 TAGLNNGVKTFVGGNCTVSLMLMSLGGLFAQDLVEWVSVATYQAASGGGARHMRELLTQM 180 Query: 180 GHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQS 239 G L+ HVA ELA P+SAIL+IERKVT+LTRSGEL VDNFGVPLAGSLIPWIDKQLDNGQS Sbjct: 181 GQLHSHVAAELADPASAILEIERKVTSLTRSGELAVDNFGVPLAGSLIPWIDKQLDNGQS 240 Query: 240 REEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHN 299 REEWKGQAETNKIL T+S IPVDGLCVRVGALRCHSQAFTIKLKK+VSIPTVEELLAAHN Sbjct: 241 REEWKGQAETNKILATASPIPVDGLCVRVGALRCHSQAFTIKLKKEVSIPTVEELLAAHN 300 Query: 300 PWAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPL 359 PWAKVVPNDR+ITMRELTPAAVTGTLTTPVGRLRKLNMGPE+LSAFTVGDQLLWGAAEPL Sbjct: 301 PWAKVVPNDRDITMRELTPAAVTGTLTTPVGRLRKLNMGPEYLSAFTVGDQLLWGAAEPL 360 Query: 360 RRMLRQLA 367 RRML+QLA Sbjct: 361 RRMLKQLA 368 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: 582 Number of extensions: 14 Number of successful extensions: 2 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: 367 Length of database: 368 Length adjustment: 30 Effective length of query: 337 Effective length of database: 338 Effective search space: 113906 Effective search space used: 113906 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 BWI76_RS26220 BWI76_RS26220 (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.3512839.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-222 722.4 0.0 5.5e-222 722.2 0.0 1.0 1 FitnessBrowser__Koxy:BWI76_RS26220 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Koxy:BWI76_RS26220 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 722.2 0.0 5.5e-222 5.5e-222 1 365 [. 2 367 .. 2 368 .] 0.99 Alignments for each domain: == domain 1 score: 722.2 bits; conditional E-value: 5.5e-222 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisa.iledaydidalkeldiiitcqgg 74 k+vg++gwrgmvgsvl++rm+ee+dfdai+pvffstsqlgq aps+++ ++ +l+da+d++alk+ldii+tcqgg FitnessBrowser__Koxy:BWI76_RS26220 2 KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQPAPSFGGSTGgTLQDAFDLEALKALDIIVTCQGG 76 69********************************************998877*********************** PP TIGR01745 75 dytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrd 149 dyt++iypklr++gw+gywidaasslrmkdda+iildpvn+dvi+ ++n+g++tfvggnctvsl+lmslgglf++ FitnessBrowser__Koxy:BWI76_RS26220 77 DYTNDIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITAGLNNGVKTFVGGNCTVSLMLMSLGGLFAQ 151 *************************************************************************** PP TIGR01745 150 elvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplags 224 +lvewvsvatyqaasgggarhmrell+qmg l+ +v+ ela p+saileierkvt l+rs+el v+nf+vplags FitnessBrowser__Koxy:BWI76_RS26220 152 DLVEWVSVATYQAASGGGARHMRELLTQMGQLHSHVAAELADPASAILEIERKVTSLTRSGELAVDNFGVPLAGS 226 *************************************************************************** PP TIGR01745 225 lipwidkqldngqsreewkgqaetnkilgtkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnk 299 lipwidkqldngqsreewkgqaetnkil+t++ i+vdglcvr+galrchsqa+tiklkk+vs++++ee+++ahn+ FitnessBrowser__Koxy:BWI76_RS26220 227 LIPWIDKQLDNGQSREEWKGQAETNKILATASPIPVDGLCVRVGALRCHSQAFTIKLKKEVSIPTVEELLAAHNP 301 *************************************************************************** PP TIGR01745 300 wvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365 w+kvvpn+r+it+reltpaavtgtl++pvgrlrklnmg+eylsaftvgdqllwgaaeplrrml++l FitnessBrowser__Koxy:BWI76_RS26220 302 WAKVVPNDRDITMRELTPAAVTGTLTTPVGRLRKLNMGPEYLSAFTVGDQLLWGAAEPLRRMLKQL 367 ****************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (368 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: 27.03 // [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