Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_010530677.1 ON01_RS08875 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000224785.1:WP_010530677.1 Length = 348 Score = 473 bits (1217), Expect = e-138 Identities = 231/336 (68%), Positives = 285/336 (84%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESF 64 ++VAVVGATGAVG+++++ LE+++ + L LLSSKRSAG KVTF QELTV+EA PESF Sbjct: 7 VNVAVVGATGAVGEKIIEILENKDLPIKELKLLSSKRSAGKKVTFNNQELTVEEALPESF 66 Query: 65 EGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGI 124 ++IALFSAGGSVS+ LAPEAVKRGA+V+DNTSA+RM E+ PLVVPEVNE+D+ HNGI Sbjct: 67 SNIDIALFSAGGSVSKKLAPEAVKRGAVVVDNTSAYRMAEDVPLVVPEVNESDIQSHNGI 126 Query: 125 IANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIE 184 IANPNCSTIQMVAAL+PI++A+GL++VIVSTYQAVSGAGN+A +EL +Q + +N E++ Sbjct: 127 IANPNCSTIQMVAALKPIQEAFGLSRVIVSTYQAVSGAGNKANEELDNQVKQYVNNEDMT 186 Query: 185 PEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRL 244 E++PVKGD+KHY IAFNA+PQID FQ+NGYTFEEMKMINE+KKI+H DL VAATCVRL Sbjct: 187 AELLPVKGDEKHYPIAFNALPQIDVFQENGYTFEEMKMINESKKILHAQDLPVAATCVRL 246 Query: 245 PIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVG 304 P T H+ESVYI+++++ +VEDI N L+ A GVTLQDDP+ Q YP P A K DVFVG Sbjct: 247 PFFTSHAESVYIDVEKEGLSVEDIWNALRGADGVTLQDDPATQTYPTPLSAANKEDVFVG 306 Query: 305 RIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340 R+RKDLD GFHLWVVSDNL+KGAAWN++QIAE L Sbjct: 307 RVRKDLDSNKGFHLWVVSDNLIKGAAWNTIQIAERL 342 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: 414 Number of extensions: 5 Number of successful extensions: 1 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: 348 Length adjustment: 29 Effective length of query: 317 Effective length of database: 319 Effective search space: 101123 Effective search space used: 101123 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_010530677.1 ON01_RS08875 (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.3875959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-156 505.9 2.1 3e-156 505.7 2.1 1.0 1 NCBI__GCF_000224785.1:WP_010530677.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530677.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 505.7 2.1 3e-156 3e-156 1 339 [] 8 345 .. 8 345 .. 0.99 Alignments for each domain: == domain 1 score: 505.7 bits; conditional E-value: 3e-156 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 nva+vGatGavG++++++Le+++ pi++l+ll+s+rsaGkkv+f+++el+veea esf++idialfsaGgsv NCBI__GCF_000224785.1:WP_010530677.1 8 NVAVVGATGAVGEKIIEILENKDLPIKELKLLSSKRSAGKKVTFNNQELTVEEALPESFSNIDIALFSAGGSV 80 79*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk++ap+a+k+g++v+Dntsa+r+ edvPLvvpevn+++++ ++ giianPnCstiq+v++Lkp++++++l NCBI__GCF_000224785.1:WP_010530677.1 81 SKKLAPEAVKRGAVVVDNTSAYRMAEDVPLVVPEVNESDIQSHN--GIIANPNCSTIQMVAALKPIQEAFGLS 151 ********************************************..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelkl 219 rv+vstYqavsGaG+k+ eeL nq+k ++ +++++e ++k+++++++iafna+p+id ++e+Gyt+ee+k+ NCBI__GCF_000224785.1:WP_010530677.1 152 RVIVSTYQAVSGAGNKANEELDNQVKQYVNNEDMTAELLPVKGDEKHYPIAFNALPQIDVFQENGYTFEEMKM 224 ************************************999********************************** PP TIGR01296 220 lfetrkilgiedlkvsatcvrvPvftghsesvsiefek.elsveevkelLkeapgvvviddpsenlyptPlea 291 ++e++kil+ +dl+v+atcvr+P ft+h+esv+i++ek lsve++ + L++a+gv+++ddp ++yptPl+a NCBI__GCF_000224785.1:WP_010530677.1 225 INESKKILHAQDLPVAATCVRLPFFTSHAESVYIDVEKeGLSVEDIWNALRGADGVTLQDDPATQTYPTPLSA 297 *************************************9669******************************** PP TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 ++k++vfvgr+rkDl+++kg++l+vv+Dnl kGaa+n++qiae li++ NCBI__GCF_000224785.1:WP_010530677.1 298 ANKEDVFVGRVRKDLDSNKGFHLWVVSDNLIKGAAWNTIQIAERLIAN 345 *********************************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (348 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.49 // [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