Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate AZOBR_RS13975 AZOBR_RS13975 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__azobra:AZOBR_RS13975 Length = 339 Score = 280 bits (716), Expect = 4e-80 Identities = 149/336 (44%), Positives = 216/336 (64%), Gaps = 6/336 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTV-RVQNVEEFD 63 + VA+ GATG VG ML L +R FP D + LA++ + GK F V +V++V FD Sbjct: 3 YTVAVVGATGNVGREMLTTLADRRFPADAVIALAADSAVGKEVSFGEDAVLKVEDVGRFD 62 Query: 64 WSQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRN 123 + V IALF+A ++SA AP A AG VVID + FR D D+PLV+PEVN +A+A + Sbjct: 63 FKGVDIALFAADAKVSAAHAPRGAAAGAVVIDASPQFRMDPDVPLVIPEVNGDALAGYAK 122 Query: 124 RNIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGY 183 +NI+A+P + I + +ALKP+++ V + R+ V+TYQ+ S AGK G+DEL GQT + Sbjct: 123 KNIVASPGGAAILLAMALKPLHEQVTVSRVVVSTYQAASDAGKEGMDELFGQTRAIYVND 182 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 P + + FS+QIAFN IP I FM++G T++E + ET+K+ DP I V+ TCVRVPVF Sbjct: 183 PVQKSVFSKQIAFNVIPHIGPFMEDGATRDEWALTVETKKVL-DPKIKVSATCVRVPVFI 241 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDGIELF---RGADFPTQVRDAGGKDHVLVGRVRN 300 GH+ A+ +E P+ AE+ +L + G+++ + T V + G D V + R+R Sbjct: 242 GHSAAITIECVEPVTAEEARRILRKAPGMQVIDQQENDGYITPV-EIAGDDPVFISRIRE 300 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 D + +G++ W DN+RKGAA NAVQIAELLV++Y Sbjct: 301 DYTVDNGLSFWASTDNLRKGAALNAVQIAELLVKEY 336 Lambda K H 0.319 0.135 0.395 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: 306 Number of extensions: 17 Number of successful extensions: 4 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: 337 Length of database: 339 Length adjustment: 28 Effective length of query: 309 Effective length of database: 311 Effective search space: 96099 Effective search space used: 96099 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate AZOBR_RS13975 AZOBR_RS13975 (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.7970.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-123 398.1 0.5 1.8e-123 397.9 0.5 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS13975 AZOBR_RS13975 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS13975 AZOBR_RS13975 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.9 0.5 1.8e-123 1.8e-123 2 339 .] 5 335 .. 4 335 .. 0.98 Alignments for each domain: == domain 1 score: 397.9 bits; conditional E-value: 1.8e-123 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgke.leveeaekesfegidialfsa 69 va+vGatG+vG+e+l++L++r fp+d++++la++ + Gk+v f + l+ve++ +++f+g+dialf+a lcl|FitnessBrowser__azobra:AZOBR_RS13975 5 VAVVGATGNVGREMLTTLADRRFPADAVIALAADSAVGKEVSFGEDAvLKVEDVGRFDFKGVDIALFAA 73 9******************************************986538******************** PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 + vs + ap+ a+ag++viD + fr+d+dvPLv+pevn + l+ kk+i+a P ++i l ++Lkp lcl|FitnessBrowser__azobra:AZOBR_RS13975 74 DAKVSAAHAPRGAAAGAVVIDASPQFRMDPDVPLVIPEVNGDALAGYAKKNIVASPGGAAILLAMALKP 142 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l++++ + rvvvstYqa s aGk+g++eL qt+a+++ p ++ + f+kqiafn+ip+i+ + lcl|FitnessBrowser__azobra:AZOBR_RS13975 143 LHEQVTVSRVVVSTYQAASDAGKEGMDELFGQTRAIYVND---P----VQKSVFSKQIAFNVIPHIGPF 204 ************************************9853...3....67899**************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edG t++e l+ et+k+l+ +++kvsatcvrvPvf+ghs +++ie +++++ee++ +L++apg++v lcl|FitnessBrowser__azobra:AZOBR_RS13975 205 MEDGATRDEWALTVETKKVLD-PKIKVSATCVRVPVFIGHSAAITIECVEPVTAEEARRILRKAPGMQV 272 *********************.*********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellike 339 id+++++ y+tP+e++g d vf++rir+D + ++gl+ + ++DnlrkGaalnavqiaell+ke lcl|FitnessBrowser__azobra:AZOBR_RS13975 273 IDQQENDGYITPVEIAGDDPVFISRIREDYTVDNGLSFWASTDNLRKGAALNAVQIAELLVKE 335 ************************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (339 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: 9.77 // [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