Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_041741958.1 CALKRO_RS07895 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000166775.1:WP_041741958.1 Length = 327 Score = 323 bits (828), Expect = 4e-93 Identities = 170/335 (50%), Positives = 228/335 (68%), Gaps = 15/335 (4%) Query: 7 VAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE- 65 +A+VGATG VG+ LK LE++N ++ L +S RSAGTKV F G+E TV+E +SF+ Sbjct: 1 MAIVGATGMVGRTFLKVLEEKNLPVEEYFLFASSRSAGTKVEFMGKEYTVEELKEDSFDR 60 Query: 66 GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125 G++IALFSAG S S AP A +G IVIDN+SA+RM+++ PLVVPEVN D+ H GII Sbjct: 61 GIDIALFSAGASTSLHFAPIAASKGCIVIDNSSAWRMEKDVPLVVPEVNPEDIKWHKGII 120 Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEP 185 ANPNCSTIQ V L+P+ Y + +++ STYQAVSGAG + +L E Sbjct: 121 ANPNCSTIQAVVVLKPLHDRYKIKRIVYSTYQAVSGAGYQGYLDL-------------EE 167 Query: 186 EIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLP 245 + K Y IA N IP ID F +NGYT EEMKMINET+KI+H +++ AT VR+P Sbjct: 168 GLKGAPPKKFPYPIAGNVIPHIDVFLENGYTKEEMKMINETRKILHDDSIKITATTVRVP 227 Query: 246 IQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGR 305 + GHSES+ +E ++ +E++K +LK A GV +QDDP+ LYPMP GK++V+VGR Sbjct: 228 VFNGHSESINVEFEK-QFDLEELKEILKNAKGVVVQDDPANLLYPMPIYVSGKDEVYVGR 286 Query: 306 IRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340 IR+D +G +LWVV+DN+ KGAA N+VQIAE + Sbjct: 287 IRRDESVESGVNLWVVADNIRKGAATNAVQIAEKV 321 Lambda K H 0.314 0.131 0.366 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: 315 Number of extensions: 14 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: 346 Length of database: 327 Length adjustment: 28 Effective length of query: 318 Effective length of database: 299 Effective search space: 95082 Effective search space used: 95082 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: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_041741958.1 CALKRO_RS07895 (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.632969.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-147 477.1 0.1 3.9e-147 475.7 0.1 1.6 1 NCBI__GCF_000166775.1:WP_041741958.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_041741958.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 475.7 0.1 3.9e-147 3.9e-147 2 337 .. 1 322 [. 1 324 [. 0.98 Alignments for each domain: == domain 1 score: 475.7 bits; conditional E-value: 3.9e-147 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg.idialfsaGgsv 73 +aivGatG vG+++lkvLee+n p+++ l+as+rsaG+kv+f gke++vee+++ sf++ idialfsaG+s+ NCBI__GCF_000166775.1:WP_041741958.1 1 MAIVGATGMVGRTFLKVLEEKNLPVEEYFLFASSRSAGTKVEFMGKEYTVEELKEDSFDRgIDIALFSAGAST 73 59********************************************************977************ PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 s fap aa++g+iviDn+sa+r+++dvPLvvpevn e++k +k giianPnCstiq+vvvLkpl+d++k+k NCBI__GCF_000166775.1:WP_041741958.1 74 SLHFAPIAASKGCIVIDNSSAWRMEKDVPLVVPEVNPEDIKWHK--GIIANPNCSTIQAVVVLKPLHDRYKIK 144 *****************************************998..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 r+v stYqavsGaG +g +L++ +k + ++kkf+++ia n+ip+id + e+Gytkee+k+ NCBI__GCF_000166775.1:WP_041741958.1 145 RIVYSTYQAVSGAGYQGYLDLEEGLKGA-------------PPKKFPYPIAGNVIPHIDVFLENGYTKEEMKM 204 *********************9988764.............479***************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 ++etrkil+++ +k++at+vrvPvf ghses+++efek++++ee+ke+Lk+a+gvvv+ddp + lyp+P+ ++ NCBI__GCF_000166775.1:WP_041741958.1 205 INETRKILHDDSIKITATTVRVPVFNGHSESINVEFEKQFDLEELKEILKNAKGVVVQDDPANLLYPMPIYVS 277 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 gkdev+vgrir+D s e g++l+vvaDn+rkGaa+navqiae++i NCBI__GCF_000166775.1:WP_041741958.1 278 GKDEVYVGRIRRDESVESGVNLWVVADNIRKGAATNAVQIAEKVI 322 ******************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (327 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: 7.97 // [ok]
This GapMind analysis is from Jul 26 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