Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate BWI76_RS12880 BWI76_RS12880 aspartate-semialdehyde dehydrogenase
Query= BRENDA::C5BB06 (367 letters) >FitnessBrowser__Koxy:BWI76_RS12880 Length = 372 Score = 420 bits (1079), Expect = e-122 Identities = 208/369 (56%), Positives = 265/369 (71%), Gaps = 4/369 (1%) Query: 1 MKNVGFIGWRGMVGSVLMQRMSEERDFDAIRPLFFSTSQHGQPAPTFGGHGGTLQDASDI 60 MK VG +GWRGMVGSVL+QRM EE DFD I FFSTS G P G TL+DA+ + Sbjct: 1 MKQVGIVGWRGMVGSVLLQRMIEENDFDNISAHFFSTSSAGAAGPVIDGISYTLKDANSV 60 Query: 61 DALKALDIIITCQGGDYTHAVYPRLRAAGWQGYWIDAASALRMQDDAIIILDPVNRAVID 120 AL +DIIITCQGGDYT A+YP L GW GYWIDAASALRM + A IILDPVNR ID Sbjct: 61 SALAEMDIIITCQGGDYTKAIYPNLLNHGWGGYWIDAASALRMDEKACIILDPVNRNNID 120 Query: 121 RGLENGVKTFVGGNCTVSLMLMSLGGLFAADLVEWVSVATYQAASGGGARHMRELLTQMG 180 R ++ G+K FVGGNC+++L LM L GL ADL+EW+SV TYQ+ASG GA+++REL+ Q Sbjct: 121 RAIKEGIKLFVGGNCSITLSLMGLAGLIKADLIEWMSVMTYQSASGAGAQYVRELIAQSA 180 Query: 181 MLHGQVAPALENPASAILDIERQVTDLMRNGTLPTDNFGVPLAGSLIPWIDKALDNGQSR 240 + ++P + ++L + +V++L+ + +PT NFG PL GS+IPWID L +G SR Sbjct: 181 YISRHLSPDELASSGSVLPLVNKVSELINSADMPTQNFGAPLMGSIIPWIDSDLGDGNSR 240 Query: 241 EEWKGQAETNKILA-SPQTIPIDGLCVRVGALRCHSQAFTVKLKRDIAIPEVEQLLARHN 299 EEWKG+AETNKIL SP TIP++GLC+RVG +RCHS A T+KLKR++ E +L+ + Sbjct: 241 EEWKGEAETNKILGLSPGTIPVNGLCIRVGVIRCHSAAITLKLKREVNEEEFAELVMNSH 300 Query: 300 EWVRVIPNDRELSMRELTPAAVTGTLATPVGRLRK--LNMGPQYLSAFTVGDQLLWGAAE 357 WV +PN++E S+ LTPA ++G+L +GR +K LN P Y S TVGDQLLWGAAE Sbjct: 301 PWVNYVPNNKEESVSTLTPAHISGSLKVGIGRYKKMSLNNEPIY-SVLTVGDQLLWGAAE 359 Query: 358 PLRRMLRLL 366 PLRRML +L Sbjct: 360 PLRRMLNIL 368 Lambda K H 0.321 0.137 0.418 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: 395 Number of extensions: 10 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: 367 Length of database: 372 Length adjustment: 30 Effective length of query: 337 Effective length of database: 342 Effective search space: 115254 Effective search space used: 115254 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate BWI76_RS12880 BWI76_RS12880 (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.23646.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-159 516.5 0.2 2e-159 516.3 0.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS12880 BWI76_RS12880 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS12880 BWI76_RS12880 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.3 0.2 2e-159 2e-159 1 365 [. 2 368 .. 2 369 .. 0.98 Alignments for each domain: == domain 1 score: 516.3 bits; conditional E-value: 2e-159 TIGR01745 1 kkvglvgwrgmvgsvllkrmqeekdfdaikpvffstsqlgqkapslakisailedaydidalkeldiiitc 71 k+vg+vgwrgmvgsvll+rm ee+dfd i++ ffsts +g ++p++++is++l+da+ + al e+diiitc lcl|FitnessBrowser__Koxy:BWI76_RS12880 2 KQVGIVGWRGMVGSVLLQRMIEENDFDNISAHFFSTSSAGAAGPVIDGISYTLKDANSVSALAEMDIIITC 72 68********************************************************************* PP TIGR01745 72 qggdytkeiypklrkagwkgywidaasslrmkddaviildpvnldvikdavnkgirtfvggnctvslllms 142 qggdytk iyp+l + gw gywidaas+lrm++ a iildpvn + i+ a+++gi+ fvggnc+++l lm+ lcl|FitnessBrowser__Koxy:BWI76_RS12880 73 QGGDYTKAIYPNLLNHGWGGYWIDAASALRMDEKACIILDPVNRNNIDRAIKEGIKLFVGGNCSITLSLMG 143 *********************************************************************** PP TIGR01745 143 lgglfrdelvewvsvatyqaasgggarhmrellkqmgvlykeveeelakpssaileierkvtklsrseelp 213 l gl++ +l+ew+sv+tyq+asg+ga+++rel+ q + +++ + +++s ++l + +kv++l+ s ++p lcl|FitnessBrowser__Koxy:BWI76_RS12880 144 LAGLIKADLIEWMSVMTYQSASGAGAQYVRELIAQSAYISRHLSPDELASSGSVLPLVNKVSELINSADMP 214 ********************************************999999********************* PP TIGR01745 214 venfsvplagslipwidkqldngqsreewkgqaetnkilgtk.dtilvdglcvrigalrchsqaltiklkk 283 ++nf++pl gs+ipwid +l +g+sreewkg+aetnkilg + ti+v+glc+r+g +rchs a+t+klk+ lcl|FitnessBrowser__Koxy:BWI76_RS12880 215 TQNFGAPLMGSIIPWIDSDLGDGNSREEWKGEAETNKILGLSpGTIPVNGLCIRVGVIRCHSAAITLKLKR 285 ****************************************87369************************** PP TIGR01745 284 dvsleeieeiirahnkwvkvvpnereitlreltpaavtgtldipvgrlrklnmgke.ylsaftvgdqllwg 353 +v+ ee e++ + +wv++vpn++e ++ ltpa ++g+l++++gr +k+ + +e s +tvgdqllwg lcl|FitnessBrowser__Koxy:BWI76_RS12880 286 EVNEEEFAELVMNSHPWVNYVPNNKEESVSTLTPAHISGSLKVGIGRYKKMSLNNEpIYSVLTVGDQLLWG 356 ***************************************************9998834599********** PP TIGR01745 354 aaeplrrmlril 365 aaeplrrml+il lcl|FitnessBrowser__Koxy:BWI76_RS12880 357 AAEPLRRMLNIL 368 **********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (366 nodes) Target sequences: 1 (372 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.94 // [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