Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_010876434.1 MTH_RS03755 aspartate-semialdehyde dehydrogenase
Query= SwissProt::Q57658 (354 letters) >NCBI__GCF_000008645.1:WP_010876434.1 Length = 347 Score = 395 bits (1016), Expect = e-115 Identities = 198/343 (57%), Positives = 266/343 (77%), Gaps = 7/343 (2%) Query: 9 IKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENIKD 68 + VGVLGATG VGQRF+Q+L HP FELT LAAS RSAGK Y + W+ D ++PE+++D Sbjct: 2 VNVGVLGATGMVGQRFIQMLDKHPEFELTTLAASSRSAGKPYGEVANWYLDCEMPESVRD 61 Query: 69 MVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLVIP 128 M V+ TDP DVDI+FSALP+D+A+K EP+FA E ++ SNASA RME DVPLVIP Sbjct: 62 MEVVETDPS--AVGDVDILFSALPADVARKVEPKFA-EKYIVASNASAMRMEPDVPLVIP 118 Query: 129 EVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAVSG 188 EVN + L+LIE+Q+ +RGWDG I+TNPNCSTI +TLKPI D + ++ V+++TMQAVSG Sbjct: 119 EVNPEFLDLIEVQQRRRGWDGFIVTNPNCSTIALTLTLKPIYDAYTIKRVYVSTMQAVSG 178 Query: 189 AGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAVID 248 AGYNGVPSMAILDNL+PFI EEEK++TE+L LLG L +G V+ A+F +SASC+RV V+D Sbjct: 179 AGYNGVPSMAILDNLVPFIGGEEEKIETETLHLLGELDEGVVKPASFGVSASCHRVPVVD 238 Query: 249 GHTESIFVKTKEGAEPEEIKEVMDKFDPL-KDLNLPTY-AKPIVIREEIDRPQPRLDRNE 306 GHTE++F++ + + ++++E MDKF L + L L + KP+V+R+E +RPQPR+DR+ Sbjct: 239 GHTEAVFIELDDEFDIDDVREAMDKFRGLPQKLGLHSAPEKPVVVRDEENRPQPRMDRDM 298 Query: 307 GNGMSIVVGRIRKDPIF--DVKYTALEHNTIRGAAGASVLNAE 347 GM++ VGR+R+D F ++Y + HNT+RGAAGAS+LNAE Sbjct: 299 DGGMAVTVGRLREDAAFKNSLRYVLVGHNTVRGAAGASILNAE 341 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: 399 Number of extensions: 19 Number of successful extensions: 5 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: 347 Length adjustment: 29 Effective length of query: 325 Effective length of database: 318 Effective search space: 103350 Effective search space used: 103350 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_010876434.1 MTH_RS03755 (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.676672.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-168 544.4 0.0 5.9e-168 544.2 0.0 1.0 1 NCBI__GCF_000008645.1:WP_010876434.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000008645.1:WP_010876434.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 544.2 0.0 5.9e-168 5.9e-168 1 341 [. 2 344 .. 2 345 .. 0.99 Alignments for each domain: == domain 1 score: 544.2 bits; conditional E-value: 5.9e-168 TIGR00978 1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepaaeek 73 v+v+vLGatG+vGq+++++l+khp+fel++++as+r+aGk ygev++w+l++++pe+vrd+e++et+p+a+ NCBI__GCF_000008645.1:WP_010876434.1 2 VNVGVLGATGMVGQRFIQMLDKHPEFELTTLAASSRSAGKPYGEVANWYLDCEMPESVRDMEVVETDPSAVG- 73 78*******************************************************************996. PP TIGR00978 74 dvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.gwkGvivtnp 145 dvd++fsalp++va++vE+k+ae+ ++v+snasa+R++pdvpl++pEvn+++l+l++vq++r gw+G+ivtnp NCBI__GCF_000008645.1:WP_010876434.1 74 DVDILFSALPADVARKVEPKFAEK-YIVASNASAMRMEPDVPLVIPEVNPEFLDLIEVQQRRrGWDGFIVTNP 145 8***********************.*********************************99999********** PP TIGR00978 146 nCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekiekEtkkilGkleeg 218 nCst++ltl+lkP++da++ik+v+v+t+qavsGAGy+Gv+s++ildn++P+i+gEEekie+Et+++lG+l+eg NCBI__GCF_000008645.1:WP_010876434.1 146 NCSTIALTLTLKPIYDAYTIKRVYVSTMQAVSGAGYNGVPSMAILDNLVPFIGGEEEKIETETLHLLGELDEG 218 ************************************************************************* PP TIGR00978 219 kvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglpsaPekpivlldeedrPq 291 v+pa++ vsa+++RvPv++GHte+vf+eld+++di+++rea+++f++lpqklgl+saPekp+v++dee+rPq NCBI__GCF_000008645.1:WP_010876434.1 219 VVKPASFGVSASCHRVPVVDGHTEAVFIELDDEFDIDDVREAMDKFRGLPQKLGLHSAPEKPVVVRDEENRPQ 291 ************************************************************************* PP TIGR00978 292 prldldaekgmavtvGrlreese...slklvvlghnlvRGAAGaallnaElly 341 pr+d+d+++gmavtvGrlre+++ sl++v++ghn+vRGAAGa++lnaEl++ NCBI__GCF_000008645.1:WP_010876434.1 292 PRMDRDMDGGMAVTVGRLREDAAfknSLRYVLVGHNTVRGAAGASILNAELIN 344 *********************98888************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (347 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: 19.55 // [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