Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_086508772.1 BZY95_RS04435 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_002151265.1:WP_086508772.1 Length = 370 Score = 532 bits (1371), Expect = e-156 Identities = 253/370 (68%), Positives = 305/370 (82%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 M +VG +GWRGMVGSVLMQRM E+ DFD IEP+FFTTS VG GP++G D+ PLKDA I Sbjct: 1 MLKVGFVGWRGMVGSVLMQRMQEDGDFDGIEPIFFTTSQVGKPGPDIGVDVPPLKDATDI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 DELK LDV++TCQGGDYT +V+ LR +GW+GYWIDAAS+LRMED+A IVLDPVNR+VID Sbjct: 61 DELKALDVVITCQGGDYTKQVYGDLRGSGWKGYWIDAASTLRMEDEATIVLDPVNRRVID 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 L G + ++GGNCTVSLMLM LGGLF+A L+EWM++MTYQAASG+GA++MRELL QMG Sbjct: 121 DQLARGAKTFVGGNCTVSLMLMGLGGLFEADLIEWMTSMTYQAASGSGAKHMRELLLQMG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRSEAFPTEHFGAPLGGSLIPWIDKELPNGQSR 240 A VAD+L +PASAIL+IDRKV + +R FP ++F APL GSL+PWID +L NGQSR Sbjct: 181 ALRDCVADELNDPASAILEIDRKVTQAMRGGDFPIDNFTAPLAGSLLPWIDTKLDNGQSR 240 Query: 241 EEWKAQAETNKILARFKNPIPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGLISQHN 300 EEWK ETNKIL NP+P+DGICVR+GAMR HSQA TIKL KDVP+ +IE I++HN Sbjct: 241 EEWKGSVETNKILGIQDNPVPIDGICVRIGAMRSHSQAFTIKLKKDVPIDEIEERIAKHN 300 Query: 301 PWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWGAAEPL 360 WVK++PN +E ++ LTP+ VTGTLSVPVGRLRKLNMG +YL AFT GDQLLWGAAEPL Sbjct: 301 EWVKVIPNDKEATIAGLTPSVVTGTLSVPVGRLRKLNMGGEYLTAFTAGDQLLWGAAEPL 360 Query: 361 RRMLRILLER 370 +RML+IL E+ Sbjct: 361 KRMLKILREQ 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: 522 Number of extensions: 11 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 WP_086508772.1 BZY95_RS04435 (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.18215.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-192 624.1 0.1 4e-192 623.9 0.1 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508772.1 BZY95_RS04435 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508772.1 BZY95_RS04435 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 623.9 0.1 4e-192 4e-192 2 365 .. 3 367 .. 2 368 .. 0.99 Alignments for each domain: == domain 1 score: 623.9 bits; conditional E-value: 4e-192 TIGR01745 2 kvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiit 70 kvg+vgwrgmvgsvl++rmqe+ dfd i+p+ff+tsq+g+ +p ++ +l+da did lk+ld++it lcl|NCBI__GCF_002151265.1:WP_086508772.1 3 KVGFVGWRGMVGSVLMQRMQEDGDFDGIEPIFFTTSQVGKPGPDIGVDVPPLKDATDIDELKALDVVIT 71 79*******************************************99999******************* PP TIGR01745 71 cqggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvsll 139 cqggdytk++y lr +gwkgywidaas+lrm+d+a i+ldpvn vi+d +++g +tfvggnctvsl+ lcl|NCBI__GCF_002151265.1:WP_086508772.1 72 CQGGDYTKQVYGDLRGSGWKGYWIDAASTLRMEDEATIVLDPVNRRVIDDQLARGAKTFVGGNCTVSLM 140 ********************************************************************* PP TIGR01745 140 lmslgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsr 208 lm+lgglf+ +l+ew++++tyqaasg+ga+hmrell qmg l v++el p+sailei+rkvt+ +r lcl|NCBI__GCF_002151265.1:WP_086508772.1 141 LMGLGGLFEADLIEWMTSMTYQAASGSGAKHMRELLLQMGALRDCVADELNDPASAILEIDRKVTQAMR 209 ********************************************************************* PP TIGR01745 209 seelpvenfsvplagslipwidkqldngqsreewkgqaetnkilgtkdt.ilvdglcvrigalrchsqa 276 +++p++nf++plagsl+pwid++ldngqsreewkg etnkilg +d +++dg+cvriga+r hsqa lcl|NCBI__GCF_002151265.1:WP_086508772.1 210 GGDFPIDNFTAPLAGSLLPWIDTKLDNGQSREEWKGSVETNKILGIQDNpVPIDGICVRIGAMRSHSQA 278 *********************************************986449****************** PP TIGR01745 277 ltiklkkdvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaft 345 +tiklkkdv+++eiee i++hn+wvkv+pn++e t+ ltp+ vtgtl++pvgrlrklnmg eyl+aft lcl|NCBI__GCF_002151265.1:WP_086508772.1 279 FTIKLKKDVPIDEIEERIAKHNEWVKVIPNDKEATIAGLTPSVVTGTLSVPVGRLRKLNMGGEYLTAFT 347 ********************************************************************* PP TIGR01745 346 vgdqllwgaaeplrrmlril 365 gdqllwgaaepl+rml+il lcl|NCBI__GCF_002151265.1:WP_086508772.1 348 AGDQLLWGAAEPLKRMLKIL 367 ******************98 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: 8.19 // [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