Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate AZOBR_RS14735 AZOBR_RS14735 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >FitnessBrowser__azobra:AZOBR_RS14735 Length = 337 Score = 290 bits (741), Expect = 5e-83 Identities = 157/345 (45%), Positives = 215/345 (62%), Gaps = 11/345 (3%) Query: 34 LQESAPS---LAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTV 90 + S+PS +A+VG TGAVG+E + VL R FP + + + AS+RSAG+ V E T+ Sbjct: 1 MSTSSPSPRRVAIVGATGAVGREMVDVLHRRSFPVAELGLFASERSAGRTVETPFGEKTL 60 Query: 91 EELTADSFNGVDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPE 150 + G DI L + G +KE P A G +V+DNSSAFR D VPL++PE+N Sbjct: 61 VAFDVEKVKGYDIVLLAVSGDFAKEHAPAIAAGGALVIDNSSAFRYDDNVPLIVPEINAH 120 Query: 151 AMKGIKVGMGKGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEEL 210 AM G LIANPNC+T I ++A+ PLH +KR++VSTYQA SGAGA M EL Sbjct: 121 AM-------GDAKLIANPNCTTAIAVVALGPLHKAFGLKRVIVSTYQATSGAGAEGMAEL 173 Query: 211 VQQTREVLEGKPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKV 270 +QTR L+GKP ++F FNL +NGY +EEMK+ ETRKI ++ V Sbjct: 174 EEQTRNQLDGKPVVNSVFRHPIPFNLIPQIDAFQENGYTKEEMKVTWETRKILEIPDLPV 233 Query: 271 TATCIRVPVMRAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNK 330 + T +R+P RAH+E++ ++ +P+ + AR +L APGV + D A +P PL+ + + Sbjct: 234 SCTAVRIPTYRAHSEAITVETLSPVTPDAARAVLADAPGVVVKDVPADGVYPMPLNATGQ 293 Query: 331 DDVAVGRIRRDVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375 DV VGRIR + G+ GLD+FVCGDQ+ KGAALNAVQIAE+ L Sbjct: 294 FDVEVGRIRTSLI-FGDHGLDLFVCGDQLLKGAALNAVQIAELSL 337 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: 336 Number of extensions: 14 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: 337 Length adjustment: 29 Effective length of query: 346 Effective length of database: 308 Effective search space: 106568 Effective search space used: 106568 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 AZOBR_RS14735 AZOBR_RS14735 (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.23735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-118 379.2 0.0 1e-117 379.0 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS14735 AZOBR_RS14735 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS14735 AZOBR_RS14735 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.0 0.0 1e-117 1e-117 1 335 [. 10 335 .. 10 337 .] 0.97 Alignments for each domain: == domain 1 score: 379.0 bits; conditional E-value: 1e-117 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +vaivGatGavG+e+++vL+ r+fp+ +l l+asersaG+ v+ e ++ + + e+ +g di l + lcl|FitnessBrowser__azobra:AZOBR_RS14735 10 RVAIVGATGAVGREMVDVLHRRSFPVAELGLFASERSAGRTVETPFGEKTLVAFDVEKVKGYDIVLLAV 78 69****************************************998888899999999************ PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 g +ke ap +a+ g++viDn+safr d++vPL+vpe+na+ + +ak +ianPnC+t +vv+L p lcl|FitnessBrowser__azobra:AZOBR_RS14735 79 SGDFAKEHAPAIAAGGALVIDNSSAFRYDDNVPLIVPEINAHAMGDAK---LIANPNCTTAIAVVALGP 144 **********************************************99...****************** PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+++++lkrv+vstYqa sGaG++g++eL++qt+ l+gk + f ++i fn+ip+id + lcl|FitnessBrowser__azobra:AZOBR_RS14735 145 LHKAFGLKRVIVSTYQATSGAGAEGMAELEEQTRNQLDGKPVV-------NSVFRHPIPFNLIPQIDAF 206 **********************************999887544.......689**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e+Gytkee+k+++etrkil+i+dl+vs t+vr+P +++hse++++e+ +++++ ++ +L +apgvvv lcl|FitnessBrowser__azobra:AZOBR_RS14735 207 QENGYTKEEMKVTWETRKILEIPDLPVSCTAVRIPTYRAHSEAITVETLSPVTPDAARAVLADAPGVVV 275 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkD.lskekglalfvvaDnlrkGaalnavqiael 335 d+p + +yp+Pl+a+g+ +v vgrir ++ ++gl+lfv +D+l+kGaalnavqiael lcl|FitnessBrowser__azobra:AZOBR_RS14735 276 KDVPADGVYPMPLNATGQFDVEVGRIRTSlIFGDHGLDLFVCGDQLLKGAALNAVQIAEL 335 *****************************567799***********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (337 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: 9.32 // [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