Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_017549001.1 C792_RS0108270 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000330705.1:WP_017549001.1 Length = 326 Score = 277 bits (709), Expect = 2e-79 Identities = 150/337 (44%), Positives = 217/337 (64%), Gaps = 17/337 (5%) Query: 5 LHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPES- 63 + VA+VGATG VG +M++ E + D +TLLSS RSAG + G+ELTVQE + E+ Sbjct: 2 VRVAIVGATGVVGTKMIEMFEQYGIKADEITLLSSARSAGKSLQVMGEELTVQELTEETP 61 Query: 64 FEGVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNG 123 +G + + SAGGS S+ AP + G+IVIDN+S +RM E+ L+VPE+N L Sbjct: 62 KQGFDYVVMSAGGSTSRQFAPLFEENGSIVIDNSSQWRMHEDIDLIVPEINAPKLDRK-- 119 Query: 124 IIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEI 183 IIANPNCSTIQ V AL+P+++ +GL +V +TYQAVSG+G+ +++L EE Sbjct: 120 IIANPNCSTIQSVVALQPLKEKFGLKRVNYTTYQAVSGSGSGGLRDL----------EEG 169 Query: 184 EPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVR 243 P + Y N +P ID F +NGYT EE KMI+ET+KI+ +PDL V+ATCVR Sbjct: 170 ARGEAPTTYPRPIYD---NVLPHIDVFLENGYTKEEQKMIDETRKILGLPDLAVSATCVR 226 Query: 244 LPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFV 303 +P+ HS + + ++ ++AT E++++ + P + L D+P YP P ++ G+ +VFV Sbjct: 227 VPVSNSHSVHMNVTLE-NEATEEEVRDAFRNIPHIMLLDNPESNEYPTPLESTGRPEVFV 285 Query: 304 GRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESL 340 GRIR+D N FH+W +DN+LKGAA NSVQI + + Sbjct: 286 GRIRRDDSLGNTFHVWCTADNILKGAAQNSVQILKQI 322 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: 297 Number of extensions: 14 Number of successful extensions: 5 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: 326 Length adjustment: 28 Effective length of query: 318 Effective length of database: 298 Effective search space: 94764 Effective search space used: 94764 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_017549001.1 C792_RS0108270 (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.59271.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-115 369.8 0.0 1.5e-114 368.6 0.0 1.5 1 NCBI__GCF_000330705.1:WP_017549001.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549001.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 368.6 0.0 1.5e-114 1.5e-114 1 336 [. 3 322 .. 3 325 .. 0.97 Alignments for each domain: == domain 1 score: 368.6 bits; conditional E-value: 1.5e-114 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg.idialfsaGgs 72 +vaivGatG vG ++++++e+ ++d+++ll+s+rsaGk +++ g+el+v+e+++e++++ d ++saGgs NCBI__GCF_000330705.1:WP_017549001.1 3 RVAIVGATGVVGTKMIEMFEQYGIKADEITLLSSARSAGKSLQVMGEELTVQELTEETPKQgFDYVVMSAGGS 75 69*******************************************************88766*********** PP TIGR01296 73 vskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeakl 145 +s++fap + ++g iviDn+s +r+ ed+ L+vpe+na +l + iianPnCstiq vv+L+plk++++l NCBI__GCF_000330705.1:WP_017549001.1 76 TSRQFAPLFEENGSIVIDNSSQWRMHEDIDLIVPEINAPKLD-R---KIIANPNCSTIQSVVALQPLKEKFGL 144 *************************************99874.4...59************************ PP TIGR01296 146 krvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklkedGytkeelk 218 krv tYqavsG+G g+ +L++ ++ e + +++++i n++p+id + e+Gytkee+k NCBI__GCF_000330705.1:WP_017549001.1 145 KRVNYTTYQAVSGSGSGGLRDLEEGARG-----EA--------PTTYPRPIYDNVLPHIDVFLENGYTKEEQK 204 ***********************99875.....33........479*************************** PP TIGR01296 219 llfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvviddpsenlyptPlea 291 ++ etrkilg +dl vsatcvrvPv +hs+ +++ +e+e++ eev++ +++ p ++++d+p++n+yptPle NCBI__GCF_000330705.1:WP_017549001.1 205 MIDETRKILGLPDLAVSATCVRVPVSNSHSVHMNVTLENEATEEEVRDAFRNIPHIMLLDNPESNEYPTPLES 277 ************************************************************************* PP TIGR01296 292 vgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaell 336 +g+ evfvgrir+D s +++++++++aDn++kGaa n+vqi +++ NCBI__GCF_000330705.1:WP_017549001.1 278 TGRPEVFVGRIRRDDSLGNTFHVWCTADNILKGAAQNSVQILKQI 322 *****************************************8776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (326 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 5.60 // [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