Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate GFF2538 Psest_2588 aspartate-semialdehyde dehydrogenase, gamma-proteobacterial
Query= SwissProt::Q51344 (370 letters) >FitnessBrowser__psRCH2:GFF2538 Length = 370 Score = 683 bits (1763), Expect = 0.0 Identities = 336/370 (90%), Positives = 356/370 (96%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGP++GK+ A LKDAYSI Sbjct: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPDIGKETAALKDAYSI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 DELK LDVILTCQGGDYT+EVFPKLREAGWQGYWIDAASSLRM+DDAVIVLDPVNR+VID Sbjct: 61 DELKGLDVILTCQGGDYTNEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRRVID 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 Q LDAGT+NYIGGNCTVSL LM LGGLF+AGLVEWMSAMTYQAASGAGAQNMREL+KQMG Sbjct: 121 QQLDAGTKNYIGGNCTVSLALMGLGGLFEAGLVEWMSAMTYQAASGAGAQNMRELIKQMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 A +A+VADDLANPASAILDIDRKVAET RSEAFP ++FG PL GSLIP+IDKELPNGQSR Sbjct: 181 AINAAVADDLANPASAILDIDRKVAETQRSEAFPVDNFGVPLAGSLIPYIDKELPNGQSR 240 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWKAQAETNKIL RFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVP++DIEGLISQHN Sbjct: 241 EEWKAQAETNKILGRFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPISDIEGLISQHN 300 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 PWVKLVPNHR+ S++EL+PAAVTGTLSVPVGRLRKLNMGS YLGAFTVGDQLLWGAAEPL Sbjct: 301 PWVKLVPNHRDASMQELSPAAVTGTLSVPVGRLRKLNMGSHYLGAFTVGDQLLWGAAEPL 360 Query: 361 RRMLRILLER 370 RRMLRILLER Sbjct: 361 RRMLRILLER 370 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: 634 Number of extensions: 14 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: 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 GFF2538 Psest_2588 (aspartate-semialdehyde dehydrogenase, gamma-proteobacterial)
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.6487.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-200 649.1 0.0 1e-199 648.9 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF2538 Psest_2588 aspartate-semialdehyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF2538 Psest_2588 aspartate-semialdehyde dehydrogenase, gamma-proteobacterial # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 648.9 0.0 1e-199 1e-199 1 366 [] 2 368 .. 2 368 .. 0.99 Alignments for each domain: == domain 1 score: 648.9 bits; conditional E-value: 1e-199 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggd 75 k+vgl+gwrgmvgsvl++rm ee+dfd+i+pvff+ts++g+++p ++k +a+l+day id lk ld+i+tcqggd lcl|FitnessBrowser__psRCH2:GFF2538 2 KRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPDIGKETAALKDAYSIDELKGLDVILTCQGGD 76 68************************************************************************* PP TIGR01745 76 ytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfrde 150 yt+e++pklr+agw+gywidaasslrm+ddavi+ldpvn vi++ ++ g+++++ggnctvsl lm+lgglf+ + lcl|FitnessBrowser__psRCH2:GFF2538 77 YTNEVFPKLREAGWQGYWIDAASSLRMQDDAVIVLDPVNRRVIDQQLDAGTKNYIGGNCTVSLALMGLGGLFEAG 151 *************************************************************************** PP TIGR01745 151 lvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelpvenfsvplagsl 225 lvew+s++tyqaasg+ga+ mrel+kqmg + v+++la+p+sail+i+rkv+++ rse +pv+nf+vplagsl lcl|FitnessBrowser__psRCH2:GFF2538 152 LVEWMSAMTYQAASGAGAQNMRELIKQMGAINAAVADDLANPASAILDIDRKVAETQRSEAFPVDNFGVPLAGSL 226 *************************************************************************** PP TIGR01745 226 ipwidkqldngqsreewkgqaetnkilgt.kdtilvdglcvrigalrchsqaltiklkkdvsleeieeiirahnk 299 ip+idk+l ngqsreewk qaetnkilg k+ i+vdg+cvr+ga+rchsqaltikl+kdv++ +ie +i +hn+ lcl|FitnessBrowser__psRCH2:GFF2538 227 IPYIDKELPNGQSREEWKAQAETNKILGRfKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPISDIEGLISQHNP 301 ***************************964789****************************************** PP TIGR01745 300 wvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrmlrill 366 wvk+vpn+r+ +++el+paavtgtl++pvgrlrklnmg +yl aftvgdqllwgaaeplrrmlrill lcl|FitnessBrowser__psRCH2:GFF2538 302 WVKLVPNHRDASMQELSPAAVTGTLSVPVGRLRKLNMGSHYLGAFTVGDQLLWGAAEPLRRMLRILL 368 *****************************************************************96 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.01 // [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