Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_013645475.1 METBO_RS09410 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q57658 (354 letters) >NCBI__GCF_000191585.1:WP_013645475.1 Length = 348 Score = 409 bits (1052), Expect = e-119 Identities = 206/343 (60%), Positives = 268/343 (78%), Gaps = 6/343 (1%) Query: 9 IKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIKD 68 + VG+LGATG VGQRF+QLLADHP FE+TAL AS RSAGKKY+DA W + IP+ +KD Sbjct: 2 VNVGILGATGMVGQRFIQLLADHPDFEVTALTASSRSAGKKYEDAVTWHLETKIPDAVKD 61 Query: 69 MVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIP 128 VV+ TDP+ E +DV+IVFSALPS A K EP+FA+ G + SNASA RME DVPLV+P Sbjct: 62 TVVVNTDPR--EVKDVEIVFSALPSQNAAKVEPKFAEAGMKVASNASAMRMEPDVPLVVP 119 Query: 129 EVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSG 188 EVN +HL+LIE Q+++RGWDG I+TNPNCSTI V+TLKP+ D+F ++ V+++TMQAVSG Sbjct: 120 EVNPEHLDLIETQQKRRGWDGFIVTNPNCSTIALVMTLKPLYDQFNIKRVYVSTMQAVSG 179 Query: 189 AGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVID 248 AGYNGVPSMAI+DNL+PFI EEEKM++E+L LLG V ANF +SASC+RVAV+D Sbjct: 180 AGYNGVPSMAIVDNLVPFIGEEEEKMESETLHLLGDFDGETVNNANFGVSASCHRVAVLD 239 Query: 249 GHTESIFVKTKEGAEPEEIKEVMDKFDPL-KDLNLPTYAK-PIVIREEIDRPQPRLDRNE 306 GHTE++F++ + + +E+K + F L + LNL + + P+VIREE +RPQPR+DR Sbjct: 240 GHTEAVFIEMDDDFDLDEVKGSLTNFKGLPQKLNLYSAPEDPVVIREEDNRPQPRMDRMA 299 Query: 307 GNGMSIVVGRIRKDPIF--DVKYTALEHNTIRGAAGASVLNAE 347 GNGM++ VGR+R+D ++ +KY + HNTIRGAAGAS+LNAE Sbjct: 300 GNGMAVSVGRLRRDEVYSNSLKYVLVGHNTIRGAAGASILNAE 342 Lambda K H 0.317 0.136 0.388 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: 405 Number of extensions: 15 Number of successful extensions: 4 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: 354 Length of database: 348 Length adjustment: 29 Effective length of query: 325 Effective length of database: 319 Effective search space: 103675 Effective search space used: 103675 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_013645475.1 METBO_RS09410 (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.3730.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-156 504.5 0.1 7.5e-156 504.4 0.1 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013645475.1 METBO_RS09410 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013645475.1 METBO_RS09410 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 504.4 0.1 7.5e-156 7.5e-156 1 341 [. 2 345 .. 2 346 .. 0.98 Alignments for each domain: == domain 1 score: 504.4 bits; conditional E-value: 7.5e-156 TIGR00978 1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepa 69 v+v++LGatG+vGq++++ll+ hp+fe+++++as+r+aGkky+++v+w+l+++ip+ v+d +++t+p lcl|NCBI__GCF_000191585.1:WP_013645475.1 2 VNVGILGATGMVGQRFIQLLADHPDFEVTALTASSRSAGKKYEDAVTWHLETKIPDAVKDTVVVNTDPR 70 78******************************************************************9 PP TIGR00978 70 aeekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.gw 137 + kdv++vfsalps+ a++vE+k+ae+G++v+snasa+R++pdvpl+vpEvn++hl+l+++q++r gw lcl|NCBI__GCF_000191585.1:WP_013645475.1 71 EV-KDVEIVFSALPSQNAAKVEPKFAEAGMKVASNASAMRMEPDVPLVVPEVNPEHLDLIETQQKRrGW 138 66.79*********************************************************99998** PP TIGR00978 138 kGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiek 206 +G+ivtnpnCst++l ++lkPl+d++ ik+v+v+t+qavsGAGy+Gv+s++i+dn++P+i+ EEek+e+ lcl|NCBI__GCF_000191585.1:WP_013645475.1 139 DGFIVTNPNCSTIALVMTLKPLYDQFNIKRVYVSTMQAVSGAGYNGVPSMAIVDNLVPFIGEEEEKMES 207 ********************************************************************* PP TIGR00978 207 EtkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglps 275 Et+++lG+++++ v++a++ vsa+++Rv vl+GHte+vf+e+d+++d++e++ +l +fk+lpqkl+l s lcl|NCBI__GCF_000191585.1:WP_013645475.1 208 ETLHLLGDFDGETVNNANFGVSASCHRVAVLDGHTEAVFIEMDDDFDLDEVKGSLTNFKGLPQKLNLYS 276 ********************************************************************* PP TIGR00978 276 aPekpivlldeedrPqprldldaekgmavtvGrlreese...slklvvlghnlvRGAAGaallnaElly 341 aPe p+v+++e++rPqpr+d+ a++gmav+vGrlr ++ slk+v++ghn++RGAAGa++lnaEl++ lcl|NCBI__GCF_000191585.1:WP_013645475.1 277 APEDPVVIREEDNRPQPRMDRMAGNGMAVSVGRLRRDEVysnSLKYVLVGHNTIRGAAGASILNAELIN 345 ***********************************9987777************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (348 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: 6.61 // [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