Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_013460944.1 SULKU_RS10495 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000183725.1:WP_013460944.1 Length = 342 Score = 325 bits (833), Expect = 1e-93 Identities = 175/339 (51%), Positives = 239/339 (70%), Gaps = 15/339 (4%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF- 64 +VAVVGA+GAVG+++L+ E+ +F + L L+S RSAG VTF QEL ++E +P F Sbjct: 5 NVAVVGASGAVGEEILRIFEEIDFPLAKLVPLASARSAGNTVTFNDQELVIKELTPTVFA 64 Query: 65 -EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHE--H 121 EG+ IALFSAGGSVS AP A + GA+VIDNTS FRM ++ PLVVPEVN D+ + Sbjct: 65 EEGIEIALFSAGGSVSAEFAPYAAEAGAVVIDNTSHFRMFDDVPLVVPEVNPEDIAQWKK 124 Query: 122 NGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILN-- 179 GIIANPNCSTIQMV AL+P+ AY L ++ VSTYQA SGAG A++EL Q QA + Sbjct: 125 TGIIANPNCSTIQMVQALKPLDDAYDLQRIDVSTYQATSGAGKTAMEELVEQMQAFFSFK 184 Query: 180 KEEIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAA 239 +++EP+ P ++IA NAIPQID F NGYT EE+KM+NET+KIMH +++V+A Sbjct: 185 LDDMEPKKFP-------HRIALNAIPQIDSFTANGYTKEELKMVNETQKIMHK-EIEVSA 236 Query: 240 TCVRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKN 299 TCVR+P GH+E++ + D + + LL++AP + + D+PS+ +YPMP+ + +N Sbjct: 237 TCVRIPTLRGHAETLTLTFD-GAVDAAEARELLRKAPNIIVLDEPSESIYPMPSLCMDQN 295 Query: 300 DVFVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAE 338 + FVGRIR D+ R N H+WVV+DNL GAA N+V+IA+ Sbjct: 296 ETFVGRIRNDIYRDNVLHMWVVADNLRVGAATNAVRIAQ 334 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: 309 Number of extensions: 10 Number of successful extensions: 6 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: 342 Length adjustment: 29 Effective length of query: 317 Effective length of database: 313 Effective search space: 99221 Effective search space used: 99221 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_013460944.1 SULKU_RS10495 (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.11333.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-140 452.0 0.2 7.4e-140 451.8 0.2 1.0 1 lcl|NCBI__GCF_000183725.1:WP_013460944.1 SULKU_RS10495 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183725.1:WP_013460944.1 SULKU_RS10495 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.8 0.2 7.4e-140 7.4e-140 1 337 [. 5 337 .. 5 339 .. 0.98 Alignments for each domain: == domain 1 score: 451.8 bits; conditional E-value: 7.4e-140 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg..idialf 67 nva+vGa+GavG+e+l+++ee +fp+ klv+las+rsaG+ v+f+++el ++e++ ++f + i+ialf lcl|NCBI__GCF_000183725.1:WP_013460944.1 5 NVAVVGASGAVGEEILRIFEEIDFPLAKLVPLASARSAGNTVTFNDQELVIKELTPTVFAEegIEIALF 73 79*****************************************************99885555****** PP TIGR01296 68 saGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvL 136 saGgsvs efap aa+ag++viDnts fr+ +dvPLvvpevn e++++ kk giianPnCstiq+v++L lcl|NCBI__GCF_000183725.1:WP_013460944.1 74 SAGGSVSAEFAPYAAEAGAVVIDNTSHFRMFDDVPLVVPEVNPEDIAQWKKTGIIANPNCSTIQMVQAL 142 ********************************************************************* PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl+d++ l+r+ vstYqa sGaGk ++eeL +q++a +++k + +++kkf+++ia naip+id lcl|NCBI__GCF_000183725.1:WP_013460944.1 143 KPLDDAYDLQRIDVSTYQATSGAGKTAMEELVEQMQAFFSFKLDD-----MEPKKFPHRIALNAIPQID 206 ****************************************99888.....599**************** PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 +++ +Gytkeelk+++et+ki++ ++++vsatcvr+P ++gh+e +++ f+ +++ e++elL++ap + lcl|NCBI__GCF_000183725.1:WP_013460944.1 207 SFTANGYTKEELKMVNETQKIMH-KEIEVSATCVRIPTLRGHAETLTLTFDGAVDAAEARELLRKAPNI 274 ***********************.********************************************* PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +v+d+pse yp+P ++++e+fvgrir+D+ +++ l+++vvaDnlr+Gaa+nav+ia++++ lcl|NCBI__GCF_000183725.1:WP_013460944.1 275 IVLDEPSESIYPMPSLCMDQNETFVGRIRNDIYRDNVLHMWVVADNLRVGAATNAVRIAQKWV 337 ***********************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (342 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: 9.60 // [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