Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate Synpcc7942_1848 Synpcc7942_1848 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >FitnessBrowser__SynE:Synpcc7942_1848 Length = 354 Score = 335 bits (859), Expect = 1e-96 Identities = 166/335 (49%), Positives = 235/335 (70%), Gaps = 8/335 (2%) Query: 41 LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFNG 100 +A++G TGAVG E L +L +R FP + +++LAS RSAG+ + F G T++E T +F G Sbjct: 16 VAILGATGAVGTELLQILEERQFPIAELRLLASPRSAGQTLTFAGETLTIQEATPSAFQG 75 Query: 101 VDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGMG 160 +DI L SAGGS SK G +++DNSSAFRM VPLV+PEVNPEA + Sbjct: 76 LDIVLASAGGSTSKALAEAIVAAGAVMIDNSSAFRMDPTVPLVVPEVNPEAAAQHQ---- 131 Query: 161 KGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLEG 220 +IANPNC+TI+ +A+ PL ++R+VVSTYQ+ASGAGA AM E+ +Q+R +L G Sbjct: 132 --GIIANPNCTTILMAIALWPLQQRHPIRRIVVSTYQSASGAGARAMAEVQEQSRAILAG 189 Query: 221 KPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPVM 280 +P I AFNLF HN+P+ ++GY EEE+K++ E+RKI+ ++K+TATC+RVPV+ Sbjct: 190 QPAIAEILPYPLAFNLFPHNSPLTESGYCEEELKMLNESRKIFGLPDLKLTATCVRVPVL 249 Query: 281 RAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIRR 340 RAH+E++N++F P ARE + APG +++D N FP P++ S +DDV VGRIR+ Sbjct: 250 RAHSEAINVEFTEPFSVAEAREAIAAAPGARLLEDWDRNYFPMPIEASGEDDVLVGRIRQ 309 Query: 341 DVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375 D+S+ L++++CGDQIRKGAALNAVQIAE+L+ Sbjct: 310 DLSEPN--ALELWICGDQIRKGAALNAVQIAELLV 342 Lambda K H 0.318 0.133 0.380 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: 303 Number of extensions: 7 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: 375 Length of database: 354 Length adjustment: 29 Effective length of query: 346 Effective length of database: 325 Effective search space: 112450 Effective search space used: 112450 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: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate Synpcc7942_1848 Synpcc7942_1848 (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.24460.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-129 416.2 0.0 5.5e-129 416.0 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1848 Synpcc7942_1848 aspartate-semial Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1848 Synpcc7942_1848 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.0 0.0 5.5e-129 5.5e-129 1 338 [. 15 343 .. 15 344 .. 0.99 Alignments for each domain: == domain 1 score: 416.0 bits; conditional E-value: 5.5e-129 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +vai+GatGavG ell++Leer+fpi +l+llas rsaG+ ++f g+ l+++ea+ f+g+di l sa lcl|FitnessBrowser__SynE:Synpcc7942_1848 15 RVAILGATGAVGTELLQILEERQFPIAELRLLASPRSAGQTLTFAGETLTIQEATPSAFQGLDIVLASA 83 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggs+sk++a +++ag+++iDn+safr+d+ vPLvvpevn e ++++ giianPnC+ti + +L p lcl|FitnessBrowser__SynE:Synpcc7942_1848 84 GGSTSKALAEAIVAAGAVMIDNSSAFRMDPTVPLVVPEVNPEAAAQHQ--GIIANPNCTTILMAIALWP 150 *******************************************99999..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+++ ++r+vvstYq+ sGaG+++++e+++q +a+l g+ a+ ++++afn++p+ l lcl|FitnessBrowser__SynE:Synpcc7942_1848 151 LQQRHPIRRIVVSTYQSASGAGARAMAEVQEQSRAILAGQPAI-------AEILPYPLAFNLFPHNSPL 212 *************************************997655.......6899*************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e Gy +eelk+l+e+rki+g +dlk++atcvrvPv+++hse++++ef +++sv e++e + apg + lcl|FitnessBrowser__SynE:Synpcc7942_1848 213 TESGYCEEELKMLNESRKIFGLPDLKLTATCVRVPVLRAHSEAINVEFTEPFSVAEAREAIAAAPGARL 281 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 ++d ++n +p+P+ea+g+d+v+vgrir+Dls+ ++l+l++ +D++rkGaalnavqiaell+k lcl|FitnessBrowser__SynE:Synpcc7942_1848 282 LEDWDRNYFPMPIEASGEDDVLVGRIRQDLSEPNALELWICGDQIRKGAALNAVQIAELLVK 343 ************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (354 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: 6.85 // [ok]
This GapMind analysis is from Apr 09 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