Align aspartate-semialdehyde dehydrogenase (characterized)
to candidate 17495 b3433 aspartate-semialdehyde dehydrogenase (NCBI)
Query= CharProtDB::CH_024631 (367 letters) >FitnessBrowser__Keio:17495 Length = 367 Score = 736 bits (1900), Expect = 0.0 Identities = 367/367 (100%), Positives = 367/367 (100%) Query: 1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL 60 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL Sbjct: 1 MKNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDL 60 Query: 61 EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT 120 EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT Sbjct: 61 EALKALDIIVTCQGGDYTNEIYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVIT 120 Query: 121 DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG 180 DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG Sbjct: 121 DGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVATYQAASGGGARHMRELLTQMG 180 Query: 181 HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR 240 HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR Sbjct: 181 HLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQSR 240 Query: 241 EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP 300 EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP Sbjct: 241 EEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNP 300 Query: 301 WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR 360 WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR Sbjct: 301 WAKVVPNDREITMRELTPAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLR 360 Query: 361 RMLRQLA 367 RMLRQLA Sbjct: 361 RMLRQLA 367 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: 625 Number of extensions: 13 Number of successful extensions: 1 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: 367 Length adjustment: 30 Effective length of query: 337 Effective length of database: 337 Effective search space: 113569 Effective search space used: 113569 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 17495 b3433 (aspartate-semialdehyde dehydrogenase (NCBI))
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.20333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-231 751.6 0.0 7.3e-231 751.4 0.0 1.0 1 lcl|FitnessBrowser__Keio:17495 b3433 aspartate-semialdehyde deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17495 b3433 aspartate-semialdehyde dehydrogenase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 751.4 0.0 7.3e-231 7.3e-231 1 365 [. 2 366 .. 2 367 .] 1.00 Alignments for each domain: == domain 1 score: 751.4 bits; conditional E-value: 7.3e-231 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggdytke 79 k+vg++gwrgmvgsvl++rm+ee+dfdai+pvffstsqlgq+aps+++++++l+da+d++alk+ldii+tcqggdyt+e lcl|FitnessBrowser__Keio:17495 2 KNVGFIGWRGMVGSVLMQRMVEERDFDAIRPVFFSTSQLGQAAPSFGGTTGTLQDAFDLEALKALDIIVTCQGGDYTNE 80 69***************************************************************************** PP TIGR01745 80 iypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrdelvewvsva 158 iypklr++gw+gywidaasslrmkdda+iildpvn+dvi+d++n+girtfvggnctvsl+lmslgglf+++lv+wvsva lcl|FitnessBrowser__Keio:17495 81 IYPKLRESGWQGYWIDAASSLRMKDDAIIILDPVNQDVITDGLNNGIRTFVGGNCTVSLMLMSLGGLFANDLVDWVSVA 159 ******************************************************************************* PP TIGR01745 159 tyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagslipwidkqldngq 237 tyqaasgggarhmrell+qmg+ly++v++ela+pssail+ierkvt+l+rs+elpv+nf+vplagslipwidkqldngq lcl|FitnessBrowser__Keio:17495 160 TYQAASGGGARHMRELLTQMGHLYGHVADELATPSSAILDIERKVTTLTRSGELPVDNFGVPLAGSLIPWIDKQLDNGQ 238 ******************************************************************************* PP TIGR01745 238 sreewkgqaetnkilgtkdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnkwvkvvpnereitlrelt 316 sreewkgqaetnkil+t+++i+vdglcvr+galrchsqa+tiklkkdvs++++ee+++ahn+w+kvvpn+reit+relt lcl|FitnessBrowser__Keio:17495 239 SREEWKGQAETNKILNTSSVIPVDGLCVRVGALRCHSQAFTIKLKKDVSIPTVEELLAAHNPWAKVVPNDREITMRELT 317 ******************************************************************************* PP TIGR01745 317 paavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlril 365 paavtgtl++pvgrlrklnmg+e+lsaftvgdqllwgaaeplrrmlr+l lcl|FitnessBrowser__Keio:17495 318 PAAVTGTLTTPVGRLRKLNMGPEFLSAFTVGDQLLWGAAEPLRRMLRQL 366 ***********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (367 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: 9.05 // [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