Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_055435891.1 ASC41_RS06840 diaminopimelate decarboxylase
Query= reanno::Cola:Echvi_1295 (410 letters) >NCBI__GCF_001418085.1:WP_055435891.1 Length = 408 Score = 476 bits (1226), Expect = e-139 Identities = 235/397 (59%), Positives = 300/397 (75%), Gaps = 2/397 (0%) Query: 15 LLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVN-LKIKYATKALSNINILKLMKKAGT 73 LL IA ++ +PVYVY+ + I Q L +AF+ V +K+ YA KALSNI+ILKLMK G Sbjct: 6 LLKIAKDFESPVYVYNSEIITQQYKRLTSAFNKVKKVKVNYAVKALSNISILKLMKTLGA 65 Query: 74 GVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINIDNIPMLEHFGTYY 133 G+D VSI+EV+L + GY+ +I+FTPN V+ EEI+ A LG INIDN+ +LE FGT + Sbjct: 66 GLDTVSIQEVQLGIAAGYKAEQIIFTPNGVSLEEIENAAKLGCQINIDNLSILEQFGTKH 125 Query: 134 GNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEVHNLKVAGLHVHTG 193 N +P+CIR+NPH++AGGN ISVGHIDSKFGISI Q+ H+L+IVE N+ + G+H+HTG Sbjct: 126 PN-IPVCIRINPHVMAGGNTNISVGHIDSKFGISIHQIPHILRIVENTNMNINGIHMHTG 184 Query: 194 SDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTDMVEVGRKVSAAFK 253 SDILD +VFL +EILF+ AK FK+L F+DFG GFKV YK GDI T++ E G K+S F Sbjct: 185 SDILDIDVFLYASEILFETAKNFKNLDFIDFGSGFKVPYKPGDIETNIEEFGEKLSVRFN 244 Query: 254 EFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDSGLNHLIRPMMYDA 313 EFCK+YG+EL + FEPGKFLVSE G L NVVK T ++ F +DSG NHLIRPM+Y + Sbjct: 245 EFCKDYGKELILAFEPGKFLVSEAGQFLAKVNVVKQTTSTVFAQIDSGFNHLIRPMLYGS 304 Query: 314 YHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIKNAGAYGFSMASNY 373 H +ENIS G +R Y++VGYICETDT A +R++ E+ EGD+L KNAGAY +SMASNY Sbjct: 305 QHEIENISNPKGRERFYSVVGYICETDTFANNRRISEINEGDILTFKNAGAYCYSMASNY 364 Query: 374 NSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDIGL 410 NSR RPAEVL +G+AHLIR RE+F+DIL +QI I L Sbjct: 365 NSRYRPAEVLWHNGEAHLIRKRETFDDILNNQIQIDL 401 Lambda K H 0.320 0.139 0.403 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: 561 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: 410 Length of database: 408 Length adjustment: 31 Effective length of query: 379 Effective length of database: 377 Effective search space: 142883 Effective search space used: 142883 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: 50 (23.9 bits)
Align candidate WP_055435891.1 ASC41_RS06840 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))
# 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/TIGR01048.hmm # target sequence database: /tmp/gapView.3737147.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01048 [M=417] Accession: TIGR01048 Description: lysA: diaminopimelate decarboxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-118 380.7 0.1 3.8e-118 380.5 0.1 1.0 1 NCBI__GCF_001418085.1:WP_055435891.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055435891.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.5 0.1 3.8e-118 3.8e-118 13 416 .. 3 396 .. 1 397 [. 0.96 Alignments for each domain: == domain 1 score: 380.5 bits; conditional E-value: 3.8e-118 TIGR01048 13 gvdlkelaeefgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 +++l ++a+ f +P+Yvy++e +++++++l++af++ ++ +v YAvKA sn+++l+l++ +G+gld vs E+ NCBI__GCF_001418085.1:WP_055435891.1 3 NTQLLKIAKDFESPVYVYNSEIITQQYKRLTSAFNKVKKvKVNYAVKALSNISILKLMKTLGAGLDTVSIQEV 75 678999*****************************96666********************************* PP TIGR01048 85 eralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157 + aAg+kae+i+f+ ng+s ee+e+a++l+++ in+d+++ le++ + ++ +v++R+np+v a NCBI__GCF_001418085.1:WP_055435891.1 76 QLGIAAGYKAEQIIFTPNGVSLEEIENAAKLGCQ-INIDNLSILEQFGTKHPNI----PVCIRINPHVMAGGN 143 *********************************9.*****99999996655555....*************** PP TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiele 230 is G+ +sKFGi+++ + + + +++++ ++++ Gih+H GS ild++ f a e +++++++ +l NCBI__GCF_001418085.1:WP_055435891.1 144 TNISVGHIDSKFGISIH-QIPHILRIVENTNMNINGIHMHTGSDILDIDVFLYASEILFETAKN----FKNLD 211 *****************.7778888888899*******************************99....5799* PP TIGR01048 231 eldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesr 302 ++d+G G+ ++y++ + + ++ee+ ekl ++++ + ++g++l l +EpG++lv++ag +l++V++vK++ s+ NCBI__GCF_001418085.1:WP_055435891.1 212 FIDFGSGFKVPYKPGDIETNIEEFGEKLSVRFNEFCkDYGKELILAFEPGKFLVSEAGQFLAKVNVVKQTTST 284 ************************************9************************************ PP TIGR01048 303 kfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGA 375 f+ +D+g+n liRp+lY+++hei ++++ + + + ++vvG +CE+ D++a++r+++e++eGd+l ++aGA NCBI__GCF_001418085.1:WP_055435891.1 285 VFAQIDSGFNHLIRPMLYGSQHEIENISNPKGR-ERFYSVVGYICET-DTFANNRRISEINEGDILTFKNAGA 355 ***************************887766.899*********7.************************* PP TIGR01048 376 YgasmssnYnsrprpaevlveegkarlirrretledllale 416 Y++sm+snYnsr rpaevl+++g+a+lir+ret++d+l+++ NCBI__GCF_001418085.1:WP_055435891.1 356 YCYSMASNYNSRYRPAEVLWHNGEAHLIRKRETFDDILNNQ 396 **************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (408 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: 00:00:00.00 # Mc/sec: 17.53 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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