Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_011372269.1 SUDEN_RS03330 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000012965.1:WP_011372269.1 Length = 344 Score = 308 bits (790), Expect = 1e-88 Identities = 170/337 (50%), Positives = 232/337 (68%), Gaps = 11/337 (3%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65 +VAVVGA GAVG+++L L++ F ++ L L+S RS G V + G+E+ ++E + FE Sbjct: 6 NVAVVGANGAVGEEILTILQEVKFPINKLIPLASSRSIGKTVMYAGREVAIKELTDTVFE 65 Query: 66 --GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADL--HEH 121 + IALFSAGGSVS A AV+ GA+VIDNTS FRMDEN PLVVPEVN D+ + Sbjct: 66 EEDIEIALFSAGGSVSAQFAASAVRAGAVVIDNTSHFRMDENVPLVVPEVNPQDIAKWKK 125 Query: 122 NGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKE 181 GIIANPNCSTIQMV AL+P+ +AY + +V VSTYQA SGAG A++EL +Q Q+ + Sbjct: 126 TGIIANPNCSTIQMVQALKPLDEAYNIQRVDVSTYQATSGAGKSAMEELVTQMQSFFAFK 185 Query: 182 EIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATC 241 E E+ ++IA N IPQIDKF DNGYT EEMKM+NET KIMH ++ ++ATC Sbjct: 186 LDEAEVKAFA-----HRIALNVIPQIDKFLDNGYTKEEMKMVNETTKIMHR-EIPLSATC 239 Query: 242 VRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDV 301 VR+P GH+E+V I+ + + ++ LL++AP + + D+P + +YPMP+ A+ KN+ Sbjct: 240 VRVPTLRGHAEAVSIKF-ACEVNADKVRELLEKAPNIIVLDNPEKSIYPMPSIALEKNET 298 Query: 302 FVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAE 338 FVGRIR D HL++V+DNL GAA N+V+IA+ Sbjct: 299 FVGRIRVDNFDKTVLHLFIVADNLRVGAATNAVRIAQ 335 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: 304 Number of extensions: 13 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: 344 Length adjustment: 29 Effective length of query: 317 Effective length of database: 315 Effective search space: 99855 Effective search space used: 99855 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_011372269.1 SUDEN_RS03330 (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.22026.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-138 445.6 5.8 6.6e-138 445.4 5.8 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011372269.1 SUDEN_RS03330 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011372269.1 SUDEN_RS03330 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 445.4 5.8 6.6e-138 6.6e-138 1 337 [. 6 338 .. 6 340 .. 0.98 Alignments for each domain: == domain 1 score: 445.4 bits; conditional E-value: 6.6e-138 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg..idialf 67 nva+vGa GavG+e+l++L+e +fpi+kl++las+rs Gk v + g+e+ ++e++ ++fe+ i+ialf lcl|NCBI__GCF_000012965.1:WP_011372269.1 6 NVAVVGANGAVGEEILTILQEVKFPINKLIPLASSRSIGKTVMYAGREVAIKELTDTVFEEedIEIALF 74 79******************************************************9997666****** PP TIGR01296 68 saGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvL 136 saGgsvs +fa++a++ag++viDnts fr+de+vPLvvpevn +++++ kk giianPnCstiq+v++L lcl|NCBI__GCF_000012965.1:WP_011372269.1 75 SAGGSVSAQFAASAVRAGAVVIDNTSHFRMDENVPLVVPEVNPQDIAKWKKTGIIANPNCSTIQMVQAL 143 ********************************************************************* PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl+++++++rv vstYqa sGaGk ++eeL q+++ + +k e+ + k+fa++ia n+ip+id lcl|NCBI__GCF_000012965.1:WP_011372269.1 144 KPLDEAYNIQRVDVSTYQATSGAGKSAMEELVTQMQSFFAFKLDEA-----EVKAFAHRIALNVIPQID 207 ***************************************9998885.....6799************** PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 k+ ++Gytkee+k+++et ki++ ++++satcvrvP ++gh+e+vsi+f+ e+++++v+elL++ap + lcl|NCBI__GCF_000012965.1:WP_011372269.1 208 KFLDNGYTKEEMKMVNETTKIMH-REIPLSATCVRVPTLRGHAEAVSIKFACEVNADKVRELLEKAPNI 275 ***********************.9******************************************** PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +v+d+p++ yp+P a +k+e+fvgrir D +++ l+lf+vaDnlr+Gaa+nav+ia+++i lcl|NCBI__GCF_000012965.1:WP_011372269.1 276 IVLDNPEKSIYPMPSIALEKNETFVGRIRVDNFDKTVLHLFIVADNLRVGAATNAVRIAQKWI 338 ***********************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (344 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: 00:00:00.01 # Mc/sec: 7.24 // [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