Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_012855185.1 TCUR_RS23940 aspartate-semialdehyde dehydrogenase
Query= BRENDA::Q8KQ27 (354 letters) >NCBI__GCF_000024385.1:WP_012855185.1 Length = 351 Score = 437 bits (1124), Expect = e-127 Identities = 229/352 (65%), Positives = 274/352 (77%), Gaps = 7/352 (1%) Query: 3 PVLALVGATGAVGTVMIDIINNRETVPWGEIRLIASARSAGKKLTVRGEELTVIELTAEA 62 P LA+VGATGAVG+VM+++++ RE V +GEIRL+AS RSAGKKLTVRGE+L V+ L E Sbjct: 4 PTLAVVGATGAVGSVMLELLSTREDV-YGEIRLVASPRSAGKKLTVRGEQLEVLALAPEV 62 Query: 63 FDGVDVAMFDVPDEISAEWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADKVGERPR 122 F+GVD+AMFD PDE+S +WAP+AA GAVAVDNSGAFRMD DVPLVVPEVNA+ RP+ Sbjct: 63 FEGVDIAMFDTPDEVSKQWAPIAAEHGAVAVDNSGAFRMDPDVPLVVPEVNAEAARNRPK 122 Query: 123 GIIANPNCTTLSMMAALGALHREFELKELVVASYQAVSGAGKEGVDRLYAELEAVAG-KP 181 GII+NPNCTTLSM+ A+GALHR + L+ELVVASYQA SGAG+ G+D LY +LE V G + Sbjct: 123 GIISNPNCTTLSMIVAMGALHRRYGLRELVVASYQAASGAGQAGIDTLYDQLEKVGGNRE 182 Query: 182 VGVSAGDVRKTLEAAGLSISDSPFPAPLAFNVVPSAGSYKGDGWYSEELKVRNESRKILG 241 +GV AGDVR+ A G + PFPAPLA NVVP AGS K DGW SEE+KVRNESRKILG Sbjct: 183 LGVRAGDVRR---AIGDDL--GPFPAPLAMNVVPWAGSLKEDGWTSEEMKVRNESRKILG 237 Query: 242 IPDLKVSATCVRVPVVTTHSLAVHATFAREVTVEEAHKVFEAQPTIVLVDDPENGVFPTP 301 +P+L+VSATCVRVPVVTTHSLAVHA F + V EA +V A P +VLVDDP G FPTP Sbjct: 238 LPNLRVSATCVRVPVVTTHSLAVHAVFDQPVDQREAQEVLAAAPGVVLVDDPAAGEFPTP 297 Query: 302 AEVVGEDPTYVGRVRQALDFPNTLDFLRVRGQPAQGAAAEHLRDAETLAPQL 353 A+VVG DPT+VGRVR++LD PN LD +GAA + AE +A +L Sbjct: 298 ADVVGTDPTWVGRVRRSLDDPNALDLFLCGDNLRKGAALNTAQIAELVAAEL 349 Lambda K H 0.316 0.133 0.381 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: 446 Number of extensions: 10 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: 351 Length adjustment: 29 Effective length of query: 325 Effective length of database: 322 Effective search space: 104650 Effective search space used: 104650 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_012855185.1 TCUR_RS23940 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (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/TIGR01296.hmm # target sequence database: /tmp/gapView.10685.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01296 [M=339] Accession: TIGR01296 Description: asd_B: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-121 389.2 0.0 9.1e-121 389.0 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012855185.1 TCUR_RS23940 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012855185.1 TCUR_RS23940 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.0 0.0 9.1e-121 9.1e-121 2 337 .. 6 346 .. 5 348 .. 0.97 Alignments for each domain: == domain 1 score: 389.0 bits; conditional E-value: 9.1e-121 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 +a+vGatGavG ++l++L r+ +++l+as rsaGkk++++g++lev ++ e+feg+dia+f lcl|NCBI__GCF_000024385.1:WP_012855185.1 6 LAVVGATGAVGSVMLELLSTREDVYGEIRLVASPRSAGKKLTVRGEQLEVLALAPEVFEGVDIAMFDTP 74 79******************************************************************* PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 vsk++ap aa++g++ +Dn+ afr+d+dvPLvvpevnae ++++ kgii+nPnC+t++++v++ +l lcl|NCBI__GCF_000024385.1:WP_012855185.1 75 DEVSKQWAPIAAEHGAVAVDNSGAFRMDPDVPLVVPEVNAEAARNRP-KGIISNPNCTTLSMIVAMGAL 142 *****************************************999988.********************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeida......lkakkfakqiafnaip 202 +++++l+++vv++Yqa sGaG++g++ L++q+ v + +e + + + f++++a+n++p lcl|NCBI__GCF_000024385.1:WP_012855185.1 143 HRRYGLRELVVASYQAASGAGQAGIDTLYDQLEKVGGNRELGVRAGDvrraigDDLGPFPAPLAMNVVP 211 ****************************************999877545554445578*********** PP TIGR01296 203 lidklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkea 271 +++lkedG t+ee+k+++e+rkilg ++l+vsatcvrvPv+t+hs++v++ f+++++ +e++e+L a lcl|NCBI__GCF_000024385.1:WP_012855185.1 212 WAGSLKEDGWTSEEMKVRNESRKILGLPNLRVSATCVRVPVVTTHSLAVHAVFDQPVDQREAQEVLAAA 280 ********************************************************************* PP TIGR01296 272 pgvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 pgvv++ddp ++ptP+++vg+d ++vgr+r+ l++ ++l+lf+ +DnlrkGaaln+ qiael+ lcl|NCBI__GCF_000024385.1:WP_012855185.1 281 PGVVLVDDPAAGEFPTPADVVGTDPTWVGRVRRSLDDPNALDLFLCGDNLRKGAALNTAQIAELVA 346 ***************************************************************876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (351 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: 8.31 // [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