Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_012044404.1 BBTA_RS20400 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >NCBI__GCF_000015165.1:WP_012044404.1 Length = 341 Score = 353 bits (907), Expect = e-102 Identities = 180/337 (53%), Positives = 233/337 (69%), Gaps = 7/337 (2%) Query: 39 PSLAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSF 98 P++A+VGVTGAVG EF++ L R+ +K LAS RSAG+ V+F G +EEL SF Sbjct: 5 PTIAIVGVTGAVGAEFIATLDRRNVRVGKLKALASARSAGQTVSFRGQSIVIEELNERSF 64 Query: 99 NGVDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVG 158 GVDIALFSAG ISK+F P+A G +VVDNSSAFRM VPLVIPE+N ++ K Sbjct: 65 EGVDIALFSAGSGISKKFAPIAVRSGAVVVDNSSAFRMDPNVPLVIPEINARRIRDHK-- 122 Query: 159 MGKGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVL 218 +IANPNC+ I L+ + P+H ++KR+++STYQAASGAGAAAM+ELVQ TR L Sbjct: 123 ----GIIANPNCAAITALVPLWPIHQKNRIKRVIISTYQAASGAGAAAMDELVQSTRANL 178 Query: 219 EGKPPTCNIFGQQYAFNLFSHNAPI-LDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRV 277 G+ + +AFNLFSHN I + GYN+EE K++ ETRKI+ D + + TC+RV Sbjct: 179 NGQVYAPKVMPHPFAFNLFSHNTAIDPETGYNDEETKVINETRKIFEDEGIAIGVTCVRV 238 Query: 278 PVMRAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGR 337 PV+RAH ES+ + E P+ E+ R IL APGV I+DDRA+N FP P+D S +DDV VGR Sbjct: 239 PVLRAHCESITFECEKPISEDEVRRILATAPGVRIVDDRANNYFPMPVDASGQDDVLVGR 298 Query: 338 IRRDVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEML 374 IR+D+S + +FV DQ+ KGAALNAVQIAE+L Sbjct: 299 IRKDLSDPSGHSIAMFVAADQLLKGAALNAVQIAELL 335 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: 327 Number of extensions: 9 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: 341 Length adjustment: 29 Effective length of query: 346 Effective length of database: 312 Effective search space: 107952 Effective search space used: 107952 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 WP_012044404.1 BBTA_RS20400 (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.31311.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-126 408.6 0.4 1.2e-126 408.4 0.4 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012044404.1 BBTA_RS20400 aspartate-semialdeh Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012044404.1 BBTA_RS20400 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.4 0.4 1.2e-126 1.2e-126 2 336 .. 7 335 .. 6 338 .. 0.97 Alignments for each domain: == domain 1 score: 408.4 bits; conditional E-value: 1.2e-126 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 +aivG tGavG e++ +L+ rn + kl++las+rsaG+ v f+g+ + +ee+++ sfeg+dialfsaG lcl|NCBI__GCF_000015165.1:WP_012044404.1 7 IAIVGVTGAVGAEFIATLDRRNVRVGKLKALASARSAGQTVSFRGQSIVIEELNERSFEGVDIALFSAG 75 9******************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 + +sk+fap a+++g++v+Dn+safr+d++vPLv+pe+na++++++k giianPnC++i+++v L p+ lcl|NCBI__GCF_000015165.1:WP_012044404.1 76 SGISKKFAPIAVRSGAVVVDNSSAFRMDPNVPLVIPEINARRIRDHK--GIIANPNCAAITALVPLWPI 142 *********************************************99..******************** PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +++ ++krv++stYqa sGaG+++++eL + t+a l+g+ p k ++++ afn++++ + lcl|NCBI__GCF_000015165.1:WP_012044404.1 143 HQKNRIKRVIISTYQAASGAGAAAMDELVQSTRANLNGQVYAP-------KVMPHPFAFNLFSHNTAID 204 *************************************998886.......8899**********99997 PP TIGR01296 209 .edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 e Gy +ee+k+++etrki+++e + + +tcvrvPv+++h es++ e ek++s +ev+ +L apgv + lcl|NCBI__GCF_000015165.1:WP_012044404.1 205 pETGYNDEETKVINETRKIFEDEGIAIGVTCVRVPVLRAHCESITFECEKPISEDEVRRILATAPGVRI 273 4789***************************************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlsk..ekglalfvvaDnlrkGaalnavqiaell 336 +dd +n +p+P++a+g+d+v+vgrirkDls+ ++++a+fv+aD+l+kGaalnavqiaell lcl|NCBI__GCF_000015165.1:WP_012044404.1 274 VDDRANNYFPMPVDASGQDDVLVGRIRKDLSDpsGHSIAMFVAADQLLKGAALNAVQIAELL 335 *****************************987225679**********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (341 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: 7.07 // [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