Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_101444144.1 BD749_RS09560 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_002846395.1:WP_101444144.1 Length = 329 Score = 291 bits (746), Expect = 1e-83 Identities = 160/343 (46%), Positives = 224/343 (65%), Gaps = 15/343 (4%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64 + VAVVGATG VG ++LK L +R+F + L L++S+RS G ++ FKG+++ V Sbjct: 1 MKVAVVGATGLVGGEILKVLAERDFPVTELLLVASERSVGKQMEFKGKQIKVIGMQDAIA 60 Query: 65 EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124 IA+FSAGGS S AP+ + G +V+DN+SA+RMD + LVVPE+N +L + + I Sbjct: 61 AAPQIAIFSAGGSTSTEWAPKFAEVGTVVVDNSSAWRMDPSKKLVVPEINAKELTKEDKI 120 Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184 IANPNCSTIQMV AL + + +++VSTYQ+V+G G +AV++L ++ + Sbjct: 121 IANPNCSTIQMVVALNKLHEELKAKRIVVSTYQSVTGTGVKAVEQLMNEREG-------- 172 Query: 185 PEIMPVKGDKKH-YQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243 +G+K + Y I N +P ID FQDNGYT EEMKMI ETKKIM ++V AT VR Sbjct: 173 -----KEGEKAYPYTIDLNVLPHIDVFQDNGYTKEEMKMILETKKIMGDDSIRVTATAVR 227 Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303 +P+ GHSESV +E ++ D T++++ +L E GV + DD YPMP DA GK++V V Sbjct: 228 IPVIGGHSESVNVEFEK-DFTLDEVYRILNETEGVKVVDDVKNLQYPMPKDAHGKDEVLV 286 Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 GR+R D + +LW+V+DNL KGAA N+VQIAE L K LV Sbjct: 287 GRVRLDETQPRTLNLWIVADNLRKGAATNAVQIAEYLVKQGLV 329 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: 285 Number of extensions: 10 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: 329 Length adjustment: 28 Effective length of query: 318 Effective length of database: 301 Effective search space: 95718 Effective search space used: 95718 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_101444144.1 BD749_RS09560 (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.668489.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-132 427.8 2.7 1.9e-132 427.4 2.7 1.1 1 NCBI__GCF_002846395.1:WP_101444144.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101444144.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.4 2.7 1.9e-132 1.9e-132 1 338 [. 2 325 .. 2 326 .. 0.98 Alignments for each domain: == domain 1 score: 427.4 bits; conditional E-value: 1.9e-132 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 +va+vGatG vG e+lkvL+er+fp+ +l l+asers Gk+++fkgk+++v ++ + +ia+fsaGgs+ NCBI__GCF_002846395.1:WP_101444144.1 2 KVAVVGATGLVGGEILKVLAERDFPVTELLLVASERSVGKQMEFKGKQIKVIGMQDAIAAAPQIAIFSAGGST 74 69*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 s e+apk+a+ g++v+Dn+sa+r+d+ Lvvpe+na+el++ iianPnCstiq+vv+L+ l++e+k k NCBI__GCF_002846395.1:WP_101444144.1 75 STEWAPKFAEVGTVVVDNSSAWRMDPSKKLVVPEINAKELTKED--KIIANPNCSTIQMVVALNKLHEELKAK 145 ****************************************9988..8************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 r+vvstYq+v G+G k+ve+L n+ egke e k++++ i n++p+id ++++Gytkee+k+ NCBI__GCF_002846395.1:WP_101444144.1 146 RIVVSTYQSVTGTGVKAVEQLMNER----EGKEGE--------KAYPYTIDLNVLPHIDVFQDNGYTKEEMKM 206 **********************986....566766........79**************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPleav 292 + et+ki+g++ ++v+at+vr+Pv+ ghsesv++efek+++++ev+ +L+e +gv+v+dd ++ +yp+P +a NCBI__GCF_002846395.1:WP_101444144.1 207 ILETKKIMGDDSIRVTATAVRIPVIGGHSESVNVEFEKDFTLDEVYRILNETEGVKVVDDVKNLQYPMPKDAH 279 ************************************************************************* PP TIGR01296 293 gkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 gkdev+vgr+r D ++ ++l+l++vaDnlrkGaa+navqiae l+k NCBI__GCF_002846395.1:WP_101444144.1 280 GKDEVLVGRVRLDETQPRTLNLWIVADNLRKGAATNAVQIAEYLVK 325 ********************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (329 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: 00:00:00.00 # Mc/sec: 15.13 // [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