Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_015818862.1 TERTU_RS11080 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000023025.1:WP_015818862.1 Length = 368 Score = 536 bits (1381), Expect = e-157 Identities = 268/367 (73%), Positives = 299/367 (81%), Gaps = 1/367 (0%) Query: 3 RVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSIDE 62 +VG +GWRGMVGSVLM RMLEE DF IEPVFFTTSNVGG P+VG + LKDAYSIDE Sbjct: 2 KVGFVGWRGMVGSVLMGRMLEENDFAGIEPVFFTTSNVGGTAPDVGVEAPALKDAYSIDE 61 Query: 63 LKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVIDQA 122 LK LD I++CQGGDYT EVF KLR AGWQGYWIDAASSLRM+ DA+IVLDPVN VI Sbjct: 62 LKQLDAIISCQGGDYTGEVFGKLRAAGWQGYWIDAASSLRMDKDALIVLDPVNDNVIRDG 121 Query: 123 LDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMGAA 182 L G +NYIGGNCTVSLMLM LGGLF LVEW SAMTYQAASGAGAQNMREL+ QMG Sbjct: 122 LAKGIKNYIGGNCTVSLMLMGLGGLFRENLVEWTSAMTYQAASGAGAQNMRELITQMGQI 181 Query: 183 HASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSREE 242 SVA +LA+PASAILDIDRKV E +RS+ + FGAPL GSL+P+IDK+L N QS+EE Sbjct: 182 RDSVATELADPASAILDIDRKVVEAMRSD-LTVDRFGAPLAGSLLPYIDKQLENFQSKEE 240 Query: 243 WKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHNPW 302 WK ETNKIL +PIP+DGICVR+GAMRCHSQALTIKL KDVPL D+E LI+ N W Sbjct: 241 WKGGVETNKILGTSDSPIPIDGICVRIGAMRCHSQALTIKLKKDVPLADVESLIANANSW 300 Query: 303 VKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPLRR 362 VK++PN R+ ++ ELTP VTGTLSVPVGRLRK+ MG +YL AFTVGDQLLWGAAEPLRR Sbjct: 301 VKVIPNDRDATLEELTPTKVTGTLSVPVGRLRKMAMGPEYLSAFTVGDQLLWGAAEPLRR 360 Query: 363 MLRILLE 369 MLRIL E Sbjct: 361 MLRILRE 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: 483 Number of extensions: 8 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: 370 Length of database: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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_015818862.1 TERTU_RS11080 (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.1028.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-193 628.2 0.1 2.3e-193 628.0 0.1 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015818862.1 TERTU_RS11080 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015818862.1 TERTU_RS11080 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 628.0 0.1 2.3e-193 2.3e-193 1 365 [. 1 365 [. 1 366 [. 0.99 Alignments for each domain: == domain 1 score: 628.0 bits; conditional E-value: 2.3e-193 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiii 69 +kvg+vgwrgmvgsvl+ rm ee+df i+pvff+ts++g+ ap ++ + +l+day id lk+ld ii lcl|NCBI__GCF_000023025.1:WP_015818862.1 1 MKVGFVGWRGMVGSVLMGRMLEENDFAGIEPVFFTTSNVGGTAPDVGVEAPALKDAYSIDELKQLDAII 69 69*********************************************9999****************** PP TIGR01745 70 tcqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsl 138 +cqggdyt e++ klr+agw+gywidaasslrm++da+i+ldpvn +vi+d+++kgi++++ggnctvsl lcl|NCBI__GCF_000023025.1:WP_015818862.1 70 SCQGGDYTGEVFGKLRAAGWQGYWIDAASSLRMDKDALIVLDPVNDNVIRDGLAKGIKNYIGGNCTVSL 138 ********************************************************************* PP TIGR01745 139 llmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtkls 207 +lm+lgglfr++lvew s++tyqaasg+ga+ mrel++qmg + +v++ela p+sail+i+rkv + + lcl|NCBI__GCF_000023025.1:WP_015818862.1 139 MLMGLGGLFRENLVEWTSAMTYQAASGAGAQNMRELITQMGQIRDSVATELADPASAILDIDRKVVEAM 207 ********************************************************************* PP TIGR01745 208 rseelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdt.ilvdglcvrigalrchsq 275 r ++l v+ f++plagsl+p+idkql+n qs+eewkg etnkilgt+d i++dg+cvriga+rchsq lcl|NCBI__GCF_000023025.1:WP_015818862.1 208 R-SDLTVDRFGAPLAGSLLPYIDKQLENFQSKEEWKGGVETNKILGTSDSpIPIDGICVRIGAMRCHSQ 275 *.79*******************************************9755****************** PP TIGR01745 276 altiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaf 344 altiklkkdv+l ++e++i++ n wvkv+pn+r+ tl+eltp+ vtgtl++pvgrlrk+ mg+eylsaf lcl|NCBI__GCF_000023025.1:WP_015818862.1 276 ALTIKLKKDVPLADVESLIANANSWVKVIPNDRDATLEELTPTKVTGTLSVPVGRLRKMAMGPEYLSAF 344 ********************************************************************* PP TIGR01745 345 tvgdqllwgaaeplrrmlril 365 tvgdqllwgaaeplrrmlril lcl|NCBI__GCF_000023025.1:WP_015818862.1 345 TVGDQLLWGAAEPLRRMLRIL 365 *******************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.56 // [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