Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate NP_347207.1 CA_C0568 aspartate-semialdehyde dehydrogenase
Query= BRENDA::Q4WWR8 (363 letters) >NCBI__GCF_000008765.1:NP_347207.1 Length = 359 Score = 264 bits (674), Expect = 3e-75 Identities = 149/364 (40%), Positives = 223/364 (61%), Gaps = 15/364 (4%) Query: 6 KKKCGVLGATGSVGQRFILLLADHPFLELHAIGASNRSAGKKYKDAV--RWKQTTAMSER 63 K + G+LG TG VGQRF LL +HP+ E+ I AS RSAG+KY DAV RWK M E Sbjct: 4 KLRVGLLGGTGLVGQRFATLLDNHPYFEVTCIAASPRSAGQKYSDAVKGRWKLDIPMPEY 63 Query: 64 LSNLVLRDCR-ADQFS-DCDLVFSGLNSDVAG--EIEMEFIKAEIPVFSNAKNYRKHPLV 119 + + +++D D+ S + D VF +N D + +IE + K EIPV SN +R V Sbjct: 64 IKDFIVKDIYDIDEISKEVDFVFCAVNMDKSEIKKIEENYAKHEIPVVSNNSAHRFTEDV 123 Query: 120 PLVVPTVNPQHLDLIPHQRKEFGLKKGFLVCNSNCAVIGVVIPFAALQAKFGPVEEVEVF 179 P+++P +NP+HLD+IP Q++ G KKGF+V NC++ V +AL +F P ++ V Sbjct: 124 PVIIPEINPEHLDIIPKQKERLGTKKGFIVAKPNCSIQSYVPAISAL-LEFKPT-KILVC 181 Query: 180 TEQAVSGAGYPGVPSMDIMDNVIPYISGEEDKLENEAQKILGSLNADATAFDEQKGLTVG 239 T QA+SG+G +I+DN IPYI GEE K E+E K+ G + + +K + Sbjct: 182 TYQAISGSGKTFEQFPEIVDNTIPYIPGEEQKSEDEPLKVWGHIEGNKIV--SKKDPLIT 239 Query: 240 ATCTRVGVTDGHMAFVSLRFKNRPGPSAEEVKQAMREYQSEAQKLGCPSAPREAIKVFDE 299 + C RV V+DGH+A + F+N+ P+ E++ + ++ Y+ + Q L P+AP + I F++ Sbjct: 240 SQCIRVAVSDGHLAATFVSFENK--PTKEQIVEKLKNYKGKPQLLNLPTAPEQFITYFED 297 Query: 300 PDRPQPRLDRDISKGYTVSVGRVREAAPGSYFDLRFAALSHNTVIGAAGSSILNAEVAVI 359 RPQP+LDR+I KG +S+GR+RE + FD +F LSHN + GAAG ++L AE+ Sbjct: 298 EFRPQPKLDRNIEKGMGISIGRLRE---DTLFDYKFVGLSHNALRGAAGGAVLTAELLYK 354 Query: 360 KGYI 363 +GY+ Sbjct: 355 EGYL 358 Lambda K H 0.318 0.135 0.393 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: 320 Number of extensions: 18 Number of successful extensions: 6 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: 363 Length of database: 359 Length adjustment: 29 Effective length of query: 334 Effective length of database: 330 Effective search space: 110220 Effective search space used: 110220 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate NP_347207.1 CA_C0568 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR00978 (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/TIGR00978.hmm # target sequence database: /tmp/gapView.27997.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00978 [M=342] Accession: TIGR00978 Description: asd_EA: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-108 348.3 0.0 2.6e-108 348.1 0.0 1.0 1 lcl|NCBI__GCF_000008765.1:NP_347207.1 CA_C0568 aspartate-semialdehyde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008765.1:NP_347207.1 CA_C0568 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.1 0.0 2.6e-108 2.6e-108 1 342 [] 5 354 .. 5 354 .. 0.96 Alignments for each domain: == domain 1 score: 348.1 bits; conditional E-value: 2.6e-108 TIGR00978 1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvk..wilsgdipeevrdleiketepaa 70 ++v++LG tGlvGq++ ll++hpyfe++ ++as+r+aG+ky+++vk w+l+ ++pe+++d+ +k++ + lcl|NCBI__GCF_000008765.1:NP_347207.1 5 LRVGLLGGTGLVGQRFATLLDNHPYFEVTCIAASPRSAGQKYSDAVKgrWKLDIPMPEYIKDFIVKDIYDID 76 69********************************************7558*****************99887 PP TIGR00978 71 e.ekdvdlvfsalpseva..eevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker..gw 137 e +k+vd vf a++ +++ +++E+++a++ ++v+sn sa+R+ +dvp+i+pE+n++hl+++ +qker lcl|NCBI__GCF_000008765.1:NP_347207.1 77 EiSKEVDFVFCAVNMDKSeiKKIEENYAKHEIPVVSNNSAHRFTEDVPVIIPEINPEHLDIIPKQKERlgTK 148 7799********9877763369**********************************************9668 PP TIGR00978 138 kGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekEtk 209 kG+iv+ pnCs+ a+ l+ ++ +k+ v t qa+sG G + +i+dn+iPyi gEE+k e E++ lcl|NCBI__GCF_000008765.1:NP_347207.1 149 KGFIVAKPNCSIQSYVPAISALL-EFKPTKILVCTYQAISGSGKTFEQFPEIVDNTIPYIPGEEQKSEDEPL 219 9**********************.9999******************************************** PP TIGR00978 210 kilGkleegkve.paelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsaPekp 280 k+ G++e++k+ + + ++ +++Rv v +GH+ + fv++++k e+i+e+lk++k++pq l+lp+aPe+ lcl|NCBI__GCF_000008765.1:NP_347207.1 220 KVWGHIEGNKIVsKKDPLITSQCIRVAVSDGHLAATFVSFENKPTKEQIVEKLKNYKGKPQLLNLPTAPEQF 291 *********98615677899**************************************************** PP TIGR00978 281 ivlldeedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaEllyk 342 i++ ++e rPqp+ld+++ekgm +++Grlre++ + k+v l+hn +RGAAG a+l+aEllyk lcl|NCBI__GCF_000008765.1:NP_347207.1 292 ITYFEDEFRPQPKLDRNIEKGMGISIGRLREDTLfDYKFVGLSHNALRGAAGGAVLTAELLYK 354 *********************************99*************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (359 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.54 // [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