Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate YP_001328841.1 Smed_3182 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000017145.1:YP_001328841.1 Length = 344 Score = 322 bits (824), Expect = 1e-92 Identities = 165/332 (49%), Positives = 228/332 (68%), Gaps = 5/332 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 F +A+ GATG VG ML +L ER FP DE+ LAS RS G + KT+RV N++ +D+ Sbjct: 3 FKIAVAGATGNVGREMLNILSERGFPADEVVALASSRSVGTEVSYGDKTLRVTNLDTYDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 S I L SAGG +S K++P G VVIDN+S +RYD ++PL+VPEVN +AI+ F + Sbjct: 63 SDTDICLMSAGGAVSQKYSPKIGREGCVVIDNSSAWRYDSEVPLIVPEVNADAISMFSKK 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKLLNGYP 184 NIIANPNCST Q++VALKP++D I+R+ V+TYQSVSGAGK G+DEL QT + P Sbjct: 123 NIIANPNCSTAQLVVALKPLHDRAKIKRVVVSTYQSVSGAGKDGMDELFNQTRAVFVADP 182 Query: 185 AETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFYG 244 E+ F+++IAFN IP ID FM++GYTKEE K++ ET+K+ DP I V T VRVPVF G Sbjct: 183 IESKKFTKRIAFNVIPHIDVFMEDGYTKEEWKVLAETKKML-DPKIKVTCTAVRVPVFIG 241 Query: 245 HAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVRND 301 H+E+V++E I A++ ++L + G ++ + T + G+D + R+R D Sbjct: 242 HSESVNIEFENEITADEAREILREAPGCLVVDKHENGGYVTPY-ECAGEDATYISRIRED 300 Query: 302 ISHHSGINLWVVADNVRKGAATNAVQIAELLV 333 + +G+N+W+V+DN+RKGAA NAVQIAELLV Sbjct: 301 ATVENGLNIWIVSDNLRKGAALNAVQIAELLV 332 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: 317 Number of extensions: 10 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: 337 Length of database: 344 Length adjustment: 28 Effective length of query: 309 Effective length of database: 316 Effective search space: 97644 Effective search space used: 97644 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 YP_001328841.1 Smed_3182 (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.25527.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-144 465.6 0.8 5.2e-144 465.4 0.8 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001328841.1 Smed_3182 aspartate-semialdehyde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001328841.1 Smed_3182 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.4 0.8 5.2e-144 5.2e-144 1 338 [. 4 333 .. 4 334 .. 0.99 Alignments for each domain: == domain 1 score: 465.4 bits; conditional E-value: 5.2e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 ++a+ GatG+vG+e+l++L er fp+d++v+las+rs G++v + +k l+v+++++ +f++ di l+sa lcl|NCBI__GCF_000017145.1:YP_001328841.1 4 KIAVAGATGNVGREMLNILSERGFPADEVVALASSRSVGTEVSYGDKTLRVTNLDTYDFSDTDICLMSA 72 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg+vs+++ pk+ ++g++viDn+sa+r d +vPL+vpevna+ + + kk+iianPnCst qlvv+Lkp lcl|NCBI__GCF_000017145.1:YP_001328841.1 73 GGAVSQKYSPKIGREGCVVIDNSSAWRYDSEVPLIVPEVNADAISMFSKKNIIANPNCSTAQLVVALKP 141 ********************************************************************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d+ak+krvvvstYq+vsGaGk+g++eL nqt+av++ +e +kkf+k+iafn+ip+id + lcl|NCBI__GCF_000017145.1:YP_001328841.1 142 LHDRAKIKRVVVSTYQSVSGAGKDGMDELFNQTRAVFVADPIE-------SKKFTKRIAFNVIPHIDVF 203 ************************************9976655.......7****************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edGytkee k+l et+k+l+ +++kv+ t+vrvPvf+ghsesv+iefe+e++++e++e+L+eapg v lcl|NCBI__GCF_000017145.1:YP_001328841.1 204 MEDGYTKEEWKVLAETKKMLD-PKIKVTCTAVRVPVFIGHSESVNIEFENEITADEAREILREAPGCLV 271 ********************9.*********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +d+ ++ y+tP e +g+d+++++rir+D + e+gl++++v+DnlrkGaalnavqiaell++ lcl|NCBI__GCF_000017145.1:YP_001328841.1 272 VDKHENGGYVTPYECAGEDATYISRIREDATVENGLNIWIVSDNLRKGAALNAVQIAELLVN 333 ***********************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (344 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: 8.70 // [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