Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_043460171.1 H537_RS0126795 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q51344 (370 letters) >NCBI__GCF_000430725.1:WP_043460171.1 Length = 376 Score = 510 bits (1313), Expect = e-149 Identities = 256/374 (68%), Positives = 298/374 (79%), Gaps = 5/374 (1%) Query: 1 MKRVGLIGWRGMVGSVLMQRMLEERDFDLIEPVFFTTSNVGGQGPEVGKDIAPLKDAYSI 60 M VGL+GWRGMVGSVLM+RM E DF+LIEP+FF+TSN GG P + K+ L++A+ I Sbjct: 1 MALVGLVGWRGMVGSVLMERMRAEGDFELIEPLFFSTSNAGGNAPAMAKNETKLQNAFDI 60 Query: 61 DELKTLDVILTCQGGDYTSEVFPKLREAGWQGYWIDAASSLRMEDDAVIVLDPVNRKVID 120 D LK D+ILT QGGDYTSEV+PKLR AGW G+WIDAAS+LRM+DDAVIVLDPVN VI Sbjct: 61 DALKRCDIILTAQGGDYTSEVYPKLRAAGWNGHWIDAASTLRMKDDAVIVLDPVNLPVIK 120 Query: 121 QALDAGTRNYIGGNCTVSLMLMALGGLFDAGLVEWMSAMTYQAASGAGAQNMRELLKQMG 180 AL G RN+IGGNCTVS MLM +G L+ AGLVEWMS TYQAASG GAQ+MRELL Q G Sbjct: 121 DALAKGGRNWIGGNCTVSCMLMGVGALYKAGLVEWMSTQTYQAASGGGAQHMRELLTQFG 180 Query: 181 AAHASVADDLANPASAILDIDRKVAETLRS-EAFPTEHFGAPLGGSLIPWIDKELPNGQS 239 + V D LA+P SAIL+IDR+V E R+ E +FG PLGGSLIPWIDK+L NG S Sbjct: 181 TLNHEVRDLLADPTSAILEIDRRVIEKQRTLEDAEKANFGVPLGGSLIPWIDKDLGNGMS 240 Query: 240 REEWKAQAETNKILAR---FKNP-IPVDGICVRVGAMRCHSQALTIKLNKDVPLTDIEGL 295 REEWK AETNKIL + F +P +PVDG CVR+GAMRCHSQALT KL KDVPL DIE + Sbjct: 241 REEWKGMAETNKILGQGEGFSSPAVPVDGFCVRIGAMRCHSQALTFKLKKDVPLADIEAM 300 Query: 296 ISQHNPWVKLVPNHREVSVRELTPAAVTGTLSVPVGRLRKLNMGSQYLGAFTVGDQLLWG 355 I+ N WVK+V N+RE +VR+LTP AVTGTL++PVGRLRKL MG +YLGAFT+GDQLLWG Sbjct: 301 IAADNQWVKVVANNREATVRDLTPVAVTGTLTIPVGRLRKLAMGPEYLGAFTIGDQLLWG 360 Query: 356 AAEPLRRMLRILLE 369 AAEPLRRMLR+L+E Sbjct: 361 AAEPLRRMLRLLIE 374 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: 545 Number of extensions: 18 Number of successful extensions: 3 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: 376 Length adjustment: 30 Effective length of query: 340 Effective length of database: 346 Effective search space: 117640 Effective search space used: 117640 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: 50 (23.9 bits)
Align candidate WP_043460171.1 H537_RS0126795 (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.2399797.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-187 608.0 0.1 3.1e-187 607.8 0.1 1.0 1 NCBI__GCF_000430725.1:WP_043460171.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_043460171.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 607.8 0.1 3.1e-187 3.1e-187 3 366 .] 4 373 .. 2 373 .. 0.97 Alignments for each domain: == domain 1 score: 607.8 bits; conditional E-value: 3.1e-187 TIGR01745 3 vglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitcqggd 75 vglvgwrgmvgsvl++rm+ e df++i+p+ffsts++g++ap++ak ++ l++a+didalk++dii+t qggd NCBI__GCF_000430725.1:WP_043460171.1 4 VGLVGWRGMVGSVLMERMRAEGDFELIEPLFFSTSNAGGNAPAMAKNETKLQNAFDIDALKRCDIILTAQGGD 76 9************************************************************************ PP TIGR01745 76 ytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllmslgglfr 148 yt+e+ypklr+agw+g+widaas+lrmkddavi+ldpvnl vikda++kg r+++ggnctvs +lm++g l++ NCBI__GCF_000430725.1:WP_043460171.1 77 YTSEVYPKLRAAGWNGHWIDAASTLRMKDDAVIVLDPVNLPVIKDALAKGGRNWIGGNCTVSCMLMGVGALYK 149 ************************************************************************* PP TIGR01745 149 delvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrs.eelpvenfsvp 220 +lvew+s++tyqaasggga+hmrell+q+g+l +ev + la p+sailei+r+v + r+ e+ nf+vp NCBI__GCF_000430725.1:WP_043460171.1 150 AGLVEWMSTQTYQAASGGGAQHMRELLTQFGTLNHEVRDLLADPTSAILEIDRRVIEKQRTlEDAEKANFGVP 222 *******************************************************9999974678889***** PP TIGR01745 221 lagslipwidkqldngqsreewkgqaetnkilgt.....kdtilvdglcvrigalrchsqaltiklkkdvsle 288 l gslipwidk+l ng sreewkg aetnkilg + +++vdg cvriga+rchsqalt+klkkdv+l NCBI__GCF_000430725.1:WP_043460171.1 223 LGGSLIPWIDKDLGNGMSREEWKGMAETNKILGQgegfsSPAVPVDGFCVRIGAMRCHSQALTFKLKKDVPLA 295 ********************************96222225689****************************** PP TIGR01745 289 eieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgkeylsaftvgdqllwgaaeplrrm 361 +ie +i+a+n+wvkvv n+re t+r+ltp avtgtl+ipvgrlrkl mg+eyl aft+gdqllwgaaeplrrm NCBI__GCF_000430725.1:WP_043460171.1 296 DIEAMIAADNQWVKVVANNREATVRDLTPVAVTGTLTIPVGRLRKLAMGPEYLGAFTIGDQLLWGAAEPLRRM 368 ************************************************************************* PP TIGR01745 362 lrill 366 lr+l+ NCBI__GCF_000430725.1:WP_043460171.1 369 LRLLI 373 **996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (376 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: 25.52 // [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