Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_013841939.1 DESRU_RS09745 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000215085.1:WP_013841939.1 Length = 340 Score = 332 bits (850), Expect = 1e-95 Identities = 175/340 (51%), Positives = 234/340 (68%), Gaps = 9/340 (2%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64 ++V VVGA+GAVGQ++L L +RNF ++ L L ++ RSAGT++ F+G++ V+E +P+SF Sbjct: 4 VNVVVVGASGAVGQEILNILSERNFPIENLKLCATSRSAGTEIDFQGRKYRVEETTPDSF 63 Query: 65 EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124 G++IAL AGG S A RG I+IDN+S FRMD PLVVPEVN D+ H GI Sbjct: 64 TGMDIALV-AGGKASVEFREAAFARGCIIIDNSSNFRMDPEVPLVVPEVNPEDVKGHKGI 122 Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184 IANPNCSTI MV AL+PI A G+ +V+VSTYQAVSGAG E ++EL +QT+A+L E Sbjct: 123 IANPNCSTIIMVVALKPIYDAAGIKRVVVSTYQAVSGAGKEGIEELTAQTKAVLEGSEYP 182 Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244 P +K Y IAFN IP ID FQ+ YT EE KM+ ET+KI+H ++++ AT VR+ Sbjct: 183 P-------NKFAYPIAFNLIPHIDVFQEMDYTKEEWKMVKETQKILHDSEIKITATTVRV 235 Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304 P+ HSES+ IE + TVE +K +L +APG+ +QDD + YPMP G+++VFVG Sbjct: 236 PVYRSHSESINIE-TKQKLTVEKVKEILSQAPGMIVQDDVQNKNYPMPLFTSGRDEVFVG 294 Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLN 344 RIR+D G +LWVV D + KGAA N+VQIAE L + N Sbjct: 295 RIREDNTIEKGLNLWVVGDQIRKGAATNAVQIAELLLQYN 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: 315 Number of extensions: 19 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: 340 Length adjustment: 29 Effective length of query: 317 Effective length of database: 311 Effective search space: 98587 Effective search space used: 98587 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_013841939.1 DESRU_RS09745 (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.68612.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-144 466.6 1.0 2.7e-144 466.4 1.0 1.0 1 NCBI__GCF_000215085.1:WP_013841939.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013841939.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.4 1.0 2.7e-144 2.7e-144 1 337 [. 5 331 .. 5 333 .. 0.99 Alignments for each domain: == domain 1 score: 466.4 bits; conditional E-value: 2.7e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 nv +vGa+GavGqe+l++L ernfpi++l+l a +rsaG+++ f+g++++vee++ sf g+dial aGg NCBI__GCF_000215085.1:WP_013841939.1 5 NVVVVGASGAVGQEILNILSERNFPIENLKLCATSRSAGTEIDFQGRKYRVEETTPDSFTGMDIALV-AGGKA 76 689**************************************************************95.8999* PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 s ef a ++g+i+iDn+s fr+d++vPLvvpevn e++k +k giianPnCsti +vv+Lkp++d+a++k NCBI__GCF_000215085.1:WP_013841939.1 77 SVEFREAAFARGCIIIDNSSNFRMDPEVPLVVPEVNPEDVKGHK--GIIANPNCSTIIMVVALKPIYDAAGIK 147 *****************************************999..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 rvvvstYqavsGaGk+g+eeL+ qtkavleg e p +kfa++iafn+ip+id ++e ytkee k+ NCBI__GCF_000215085.1:WP_013841939.1 148 RVVVSTYQAVSGAGKEGIEELTAQTKAVLEGSEYPP-------NKFAYPIAFNLIPHIDVFQEMDYTKEEWKM 213 *********************************997.......****************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 + et+kil+++++k++at+vrvPv+++hses++ie++++l+ve+vke+L +apg++v+dd ++++yp+Pl ++ NCBI__GCF_000215085.1:WP_013841939.1 214 VKETQKILHDSEIKITATTVRVPVYRSHSESINIETKQKLTVEKVKEILSQAPGMIVQDDVQNKNYPMPLFTS 286 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 g+devfvgrir+D + ekgl+l+vv+D++rkGaa+navqiaell NCBI__GCF_000215085.1:WP_013841939.1 287 GRDEVFVGRIREDNTIEKGLNLWVVGDQIRKGAATNAVQIAELLL 331 ******************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (340 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: 00:00:00.00 # Mc/sec: 15.81 // [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