Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_092344170.1 BLU87_RS01560 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_900107645.1:WP_092344170.1 Length = 341 Score = 308 bits (789), Expect = 1e-88 Identities = 165/341 (48%), Positives = 232/341 (68%), Gaps = 7/341 (2%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65 +VAVVGA G VG++M+ TLE R F + L G V F G++ TV+ A+ E+F+ Sbjct: 8 NVAVVGAMGVVGREMMATLERRKFPIAEFRPLDIPAHEGKIVEFNGKKCTVKTANVENFK 67 Query: 66 GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125 ++IA+FSAGG S AL P+AVK+GAIVIDN+SA+RMD + PLVVPEVN D+ HNGII Sbjct: 68 DIDIAIFSAGGDASLALTPKAVKQGAIVIDNSSAWRMDPDCPLVVPEVNPEDVDWHNGII 127 Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEP 185 ANPNCSTIQMV AL+P++ + +VIVSTYQAVSG+G A+ L ++ + + +++ Sbjct: 128 ANPNCSTIQMVVALKPLQDCSKIKRVIVSTYQAVSGSGKAALDGLDAEIKEYVKYGKVKT 187 Query: 186 EIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLP 245 K QIA N +P ID FQ+ GYT EE+KM+NETKKIM + V ATCVR+P Sbjct: 188 VHAYGK------QIAMNCLPHIDVFQEGGYTKEELKMVNETKKIMKDDSVNVTATCVRIP 241 Query: 246 IQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGR 305 + GHSES+ +E ++ + + + L K APG+ + D+P++ YP+P D+ ++ VGR Sbjct: 242 VIYGHSESINVETEK-KISADKARELFKAAPGLLVVDNPAEVEYPVPCDSDNEDLTMVGR 300 Query: 306 IRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 IR+D + N ++WVVS+N+ KGAA N+VQIAE+L + +V Sbjct: 301 IREDNTKDNALNMWVVSNNIRKGAALNAVQIAETLLERGIV 341 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: 305 Number of extensions: 14 Number of successful extensions: 3 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: 341 Length adjustment: 29 Effective length of query: 317 Effective length of database: 312 Effective search space: 98904 Effective search space used: 98904 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_092344170.1 BLU87_RS01560 (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.16735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-136 438.8 2.0 7.5e-136 438.6 2.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344170.1 BLU87_RS01560 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344170.1 BLU87_RS01560 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.6 2.0 7.5e-136 7.5e-136 1 337 [. 8 336 .. 8 338 .. 0.98 Alignments for each domain: == domain 1 score: 438.6 bits; conditional E-value: 7.5e-136 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nva+vGa G vG+e++ +Le r+fpi ++++l +Gk v+f+gk+ +v+ a+ e+f++idia+fsa lcl|NCBI__GCF_900107645.1:WP_092344170.1 8 NVAVVGAMGVVGREMMATLERRKFPIAEFRPLDIPAHEGKIVEFNGKKCTVKTANVENFKDIDIAIFSA 76 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg s ++ pka+k+g+iviDn+sa+r+d+d PLvvpevn e++ ++ giianPnCstiq+vv+Lkp lcl|NCBI__GCF_900107645.1:WP_092344170.1 77 GGDASLALTPKAVKQGAIVIDNSSAWRMDPDCPLVVPEVNPEDVDWHN--GIIANPNCSTIQMVVALKP 143 *********************************************999..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d k+krv+vstYqavsG+Gk++++ L ++k ++ + +++ kqia+n +p+id + lcl|NCBI__GCF_900107645.1:WP_092344170.1 144 LQDCSKIKRVIVSTYQAVSGSGKAALDGLDAEIKEYVKYGKVK------TVHAYGKQIAMNCLPHIDVF 206 *********************************9999877766......4789**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e Gytkeelk+++et+ki++++ ++v+atcvr+Pv++ghses+++e+ek++s+++++el+k apg+ v lcl|NCBI__GCF_900107645.1:WP_092344170.1 207 QEGGYTKEELKMVNETKKIMKDDSVNVTATCVRIPVIYGHSESINVETEKKISADKARELFKAAPGLLV 275 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +d+p e +yp+P + ++d ++vgrir+D +k+++l+++vv++n+rkGaalnavqiae+l lcl|NCBI__GCF_900107645.1:WP_092344170.1 276 VDNPAEVEYPVPCDSDNEDLTMVGRIREDNTKDNALNMWVVSNNIRKGAALNAVQIAETLL 336 **********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (341 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.37 // [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