Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate N515DRAFT_0109 N515DRAFT_0109 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >FitnessBrowser__Dyella79:N515DRAFT_0109 Length = 342 Score = 407 bits (1047), Expect = e-118 Identities = 210/335 (62%), Positives = 251/335 (74%), Gaps = 3/335 (0%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + VA+ GATGAVGET+L +L ER+FPV EL LASERS G F GK+V V+N+ ++D+ Sbjct: 7 YKVAMVGATGAVGETLLAILAERKFPVGELVPLASERSAGGKVDFAGKSVTVRNLADYDF 66 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 + V IA FSAGG +S + AP AA AG VVIDNTS FRY DIPLVV EVNP AIA + R Sbjct: 67 TGVDIAFFSAGGSVSREHAPRAAAAGAVVIDNTSEFRYQDDIPLVVSEVNPHAIARYTVR 126 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 IIANPNCST+QMLVAL PI+ GIERINV TYQSVSGAG++G++EL QTA LLN Sbjct: 127 GIIANPNCSTMQMLVALAPIHRQAGIERINVATYQSVSGAGRSGMEELGKQTAALLNFQD 186 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 E + F +QIAFN IP ID F DNGYTKEEMKMVWET+KI D +I VNPT VRVPVFYG Sbjct: 187 VERSKFPKQIAFNVIPHIDDFQDNGYTKEEMKMVWETRKILEDETIQVNPTAVRVPVFYG 246 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDGI---ELFRGADFPTQVRDAGGKDHVLVGRVRND 301 H+EAVH+ETR I A Q +LE+ +G+ + + +PT V DA GKD V VGR+R D Sbjct: 247 HSEAVHIETRDKITAGQARALLEKAEGVVVQDERKAGGYPTPVGDAAGKDPVFVGRIRED 306 Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLVRDY 336 ISH G++LW+V+DN+RKGAA NAVQIAE L+ DY Sbjct: 307 ISHERGLDLWIVSDNIRKGAALNAVQIAERLIEDY 341 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: 372 Number of extensions: 12 Number of successful extensions: 2 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: 342 Length adjustment: 28 Effective length of query: 309 Effective length of database: 314 Effective search space: 97026 Effective search space used: 97026 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 N515DRAFT_0109 N515DRAFT_0109 (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.698.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-142 458.0 0.1 1.1e-141 457.8 0.1 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 N515DRAFT_0109 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 N515DRAFT_0109 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 457.8 0.1 1.1e-141 1.1e-141 1 338 [. 8 339 .. 8 340 .. 0.99 Alignments for each domain: == domain 1 score: 457.8 bits; conditional E-value: 1.1e-141 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidial 66 +va+vGatGavG++ll +L+er+fp+ +lv+lasersaG kv f gk ++v+++ +f g+dia+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 8 KVAMVGATGAVGETLLAILAERKFPVGELVPLASERSAGGKVDFAGKSVTVRNLADYDFTGVDIAF 73 69**************************************************************** PP TIGR01296 67 fsaGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiql 132 fsaGgsvs+e ap+aa+ag++viDnts fr ++d+PLvv+evn + ++ +giianPnCst+q+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 74 FSAGGSVSREHAPRAAAAGAVVIDNTSEFRYQDDIPLVVSEVNPHAIARYTVRGIIANPNCSTMQM 139 ****************************************************************** PP TIGR01296 133 vvvLkplkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiaf 198 +v+L p++++a+++r+ v+tYq+vsGaG+ g+eeL +qt a l++++ e +kf+kqiaf lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 140 LVALAPIHRQAGIERINVATYQSVSGAGRSGMEELGKQTAALLNFQDVER-------SKFPKQIAF 198 *********************************************99885.......9******** PP TIGR01296 199 naiplidklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveev 264 n+ip+id+++++Gytkee+k+++etrkil++e ++v t+vrvPvf+ghse+v+ie+ +++++ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 199 NVIPHIDDFQDNGYTKEEMKMVWETRKILEDETIQVNPTAVRVPVFYGHSEAVHIETRDKITAGQA 264 ****************************************************************** PP TIGR01296 265 kelLkeapgvvviddpsenlyptPl.eavgkdevfvgrirkDlskekglalfvvaDnlrkGaalna 329 + lL++a+gvvv+d+ + yptP+ +a+gkd vfvgrir+D+s+e+gl+l++v+Dn+rkGaalna lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 265 RALLEKAEGVVVQDERKAGGYPTPVgDAAGKDPVFVGRIREDISHERGLDLWIVSDNIRKGAALNA 330 ************************9779************************************** PP TIGR01296 330 vqiaellik 338 vqiae li+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0109 331 VQIAERLIE 339 ******997 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: 7.47 // [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