Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_084275376.1 B8779_RS04605 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_900176045.1:WP_084275376.1 Length = 342 Score = 331 bits (848), Expect = 2e-95 Identities = 181/339 (53%), Positives = 236/339 (69%), Gaps = 11/339 (3%) Query: 3 RGLHVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPE 62 R +VAVVG TGAVG++ML+ +E+ +F + L L+SKRSAG+ V +KG+E TVQE + + Sbjct: 2 RKFNVAVVGVTGAVGEEMLRVMEEVDFPVAKLVPLASKRSAGSSVEYKGKEYTVQELTED 61 Query: 63 SFE--GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLH- 119 FE + IALFSAGGSVS AP A + GA+VIDNTS FRMD PLVVPEVN D+ Sbjct: 62 IFEKEDIEIALFSAGGSVSAHYAPYAAEAGAVVIDNTSHFRMDPEVPLVVPEVNPEDIAA 121 Query: 120 -EHNGIIANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAIL 178 + GIIANPNCSTIQMV AL+P+ + +G+ +V V+TYQA SGAG A+ E+ +Q + Sbjct: 122 WKTKGIIANPNCSTIQMVQALKPLDEKFGITRVDVATYQATSGAGKSAMDEMVNQMKDFF 181 Query: 179 NKEEIEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVA 238 N + E E K +QIA N IPQIDKF DNGYT EEMKM+NETKKIMH +++V+ Sbjct: 182 NFKLDESE-----KKKFPHQIALNVIPQIDKFLDNGYTKEEMKMVNETKKIMHK-NIEVS 235 Query: 239 ATCVRLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGK 298 ATCVR+P+ GHSE+V + ++D T E K L + + D+P + +YPMP V K Sbjct: 236 ATCVRVPVLRGHSEAVTVWCEKD-ITPEAAKEALYNGKNIVVMDEPQKSIYPMPITVVDK 294 Query: 299 NDVFVGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIA 337 N+ +VGRIRKD+ R N H+WVV+DNL GAA N+V+IA Sbjct: 295 NETYVGRIRKDVYRDNVLHMWVVADNLRVGAATNAVRIA 333 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: 342 Number of extensions: 9 Number of successful extensions: 6 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: 342 Length adjustment: 29 Effective length of query: 317 Effective length of database: 313 Effective search space: 99221 Effective search space used: 99221 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_084275376.1 B8779_RS04605 (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.19976.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-145 469.8 2.6 2.8e-145 469.6 2.6 1.0 1 lcl|NCBI__GCF_900176045.1:WP_084275376.1 B8779_RS04605 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084275376.1 B8779_RS04605 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 469.6 2.6 2.8e-145 2.8e-145 1 337 [. 5 337 .. 5 339 .. 0.98 Alignments for each domain: == domain 1 score: 469.6 bits; conditional E-value: 2.8e-145 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfeg..idialf 67 nva+vG tGavG+e+l+v+ee +fp+ klv+las+rsaG v++kgke++v+e+++ fe+ i+ialf lcl|NCBI__GCF_900176045.1:WP_084275376.1 5 NVAVVGVTGAVGEEMLRVMEEVDFPVAKLVPLASKRSAGSSVEYKGKEYTVQELTEDIFEKedIEIALF 73 79****************************************************999776555****** PP TIGR01296 68 saGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvL 136 saGgsvs +ap aa+ag++viDnts fr+d++vPLvvpevn e+++ k+kgiianPnCstiq+v++L lcl|NCBI__GCF_900176045.1:WP_084275376.1 74 SAGGSVSAHYAPYAAEAGAVVIDNTSHFRMDPEVPLVVPEVNPEDIAAWKTKGIIANPNCSTIQMVQAL 142 ********************************************************************* PP TIGR01296 137 kplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplid 205 kpl++++++ rv v+tYqa sGaGk +++e+ nq+k +++k e + kkf++qia n+ip+id lcl|NCBI__GCF_900176045.1:WP_084275376.1 143 KPLDEKFGITRVDVATYQATSGAGKSAMDEMVNQMKDFFNFKLDES-----EKKKFPHQIALNVIPQID 206 ****************************************998885.....789*************** PP TIGR01296 206 klkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgv 274 k+ ++Gytkee+k+++et+ki++ ++++vsatcvrvPv++ghse+v++ ek++++e +ke L + + + lcl|NCBI__GCF_900176045.1:WP_084275376.1 207 KFLDNGYTKEEMKMVNETKKIMH-KNIEVSATCVRVPVLRGHSEAVTVWCEKDITPEAAKEALYNGKNI 274 ***********************.********************************************* PP TIGR01296 275 vviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 vv+d+p++ yp+P+++v+k+e++vgrirkD+ +++ l+++vvaDnlr+Gaa+nav+ia ++i lcl|NCBI__GCF_900176045.1:WP_084275376.1 275 VVMDEPQKSIYPMPITVVDKNETYVGRIRKDVYRDNVLHMWVVADNLRVGAATNAVRIALKWI 337 ***********************************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (342 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.51 // [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