Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_066324151.1 BLR17_RS08045 diaminopimelate decarboxylase
Query= reanno::Cola:Echvi_1295 (410 letters) >NCBI__GCF_900100165.1:WP_066324151.1 Length = 405 Score = 488 bits (1257), Expect = e-142 Identities = 236/400 (59%), Positives = 309/400 (77%), Gaps = 2/400 (0%) Query: 10 VQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVN-LKIKYATKALSNINILKLM 68 +Q LL +A ++G+P+YVYD +KI Q L AFS V L+I YA KALSN+ IL+L+ Sbjct: 1 MQSKDLLQLAEQFGSPLYVYDAEKIKSQYNRLTKAFSKVEKLRINYAMKALSNVAILQLL 60 Query: 69 KKAGTGVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINIDNIPMLEH 128 ++ G+ +DAVSI+EV+L LH GY P +I FTPN V+ EEI+E LGV INIDN+ +LE Sbjct: 61 RELGSCLDAVSIQEVQLGLHAGYSPDQIFFTPNGVSLEEIEEVHSLGVQINIDNLSILEQ 120 Query: 129 FGTYYGNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEVHNLKVAGL 188 FG + + VP+CIR+NPH++AGGN ISVGHIDSKFGIS+ QL H+++IVE N+ +AG+ Sbjct: 121 FGAKHPH-VPVCIRINPHVMAGGNENISVGHIDSKFGISVHQLPHLVRIVENTNMNIAGI 179 Query: 189 HVHTGSDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTDMVEVGRKV 248 H+HTGSDILD EVFL AEILFDAAK FK+L+FLDFG GFKV YK+ DI TD+ E+G+K+ Sbjct: 180 HMHTGSDILDIEVFLYAAEILFDAAKNFKNLEFLDFGSGFKVPYKKDDIETDIEELGKKL 239 Query: 249 SAAFKEFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDSGLNHLIRP 308 S F FC YG+EL + FEPGKFLVSE G+ L NVVK T ++ F G+DSG NHLIRP Sbjct: 240 SKRFNAFCDEYGKELTLIFEPGKFLVSEAGFFLAKVNVVKQTTSTVFAGIDSGFNHLIRP 299 Query: 309 MMYDAYHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIKNAGAYGFS 368 M Y + H +ENIS G +R Y++VGYICETDT A++R+++E+ EGD+L +NAGAY +S Sbjct: 300 MFYGSQHHIENISNPKGKERFYSVVGYICETDTFASNRRIQEIAEGDILCFRNAGAYCYS 359 Query: 369 MASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDI 408 M+SNYNSR +PAEVL ++G+ HLIRA E+FED+L++QI + Sbjct: 360 MSSNYNSRYKPAEVLWINGEGHLIRAHETFEDLLKNQIPL 399 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: 559 Number of extensions: 23 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: 405 Length adjustment: 31 Effective length of query: 379 Effective length of database: 374 Effective search space: 141746 Effective search space used: 141746 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_066324151.1 BLR17_RS08045 (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.4036780.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-121 389.4 0.0 8.8e-121 389.2 0.0 1.0 1 NCBI__GCF_900100165.1:WP_066324151.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066324151.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.2 0.0 8.8e-121 8.8e-121 13 416 .. 3 396 .. 1 397 [. 0.95 Alignments for each domain: == domain 1 score: 389.2 bits; conditional E-value: 8.8e-121 TIGR01048 13 gvdlkelaeefgtPlYvydeetlrerlealkeafkaees.lvlYAvKAnsnlavlrllaeeGlgldvvsgGEl 84 dl +lae+fg+PlYvyd+e++++++++l++af++ e+ ++ YA+KA sn+a+l+ll+e+G++ld+vs E+ NCBI__GCF_900100165.1:WP_066324151.1 3 SKDLLQLAEQFGSPLYVYDAEKIKSQYNRLTKAFSKVEKlRINYAMKALSNVAILQLLRELGSCLDAVSIQEV 75 56899*******************************6666********************************* PP TIGR01048 85 eralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157 + l+Ag+++++i f+ ng+s ee+e++ +l+++ in+d+++ le++ + + +++v++R+np+v a NCBI__GCF_900100165.1:WP_066324151.1 76 QLGLHAGYSPDQIFFTPNGVSLEEIEEVHSLGVQ-INIDNLSILEQFGAKHP----HVPVCIRINPHVMAGGN 143 *********************************9.****9999998854444....56*************** PP TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiele 230 e is G+ +sKFGi+v++ + ++ ++++ ++++ Gih+H GS ild+e f aae +++++++ +le NCBI__GCF_900100165.1:WP_066324151.1 144 ENISVGHIDSKFGISVHQLPHLVR-IVENTNMNIAGIHMHTGSDILDIEVFLYAAEILFDAAKN----FKNLE 211 *****************6655555.556677*******************************99....589** PP TIGR01048 231 eldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesr 302 +ld+G G+ ++y++++ + d+ee+ +kl ++++ + e+g++l+li+EpG++lv++ag +l++V++vK++ s+ NCBI__GCF_900100165.1:WP_066324151.1 212 FLDFGSGFKVPYKKDDIETDIEELGKKLSKRFNAFCdEYGKELTLIFEPGKFLVSEAGFFLAKVNVVKQTTST 284 ************************************9************************************ PP TIGR01048 303 kfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGA 375 f+ +D+g+n liRp+ Y+++h+i ++++ + + + ++vvG +CE+ D++a +r+++e+ eGd+l ++aGA NCBI__GCF_900100165.1:WP_066324151.1 285 VFAGIDSGFNHLIRPMFYGSQHHIENISNPKGK-ERFYSVVGYICET-DTFASNRRIQEIAEGDILCFRNAGA 355 ***************************886665.899*********7.************************* PP TIGR01048 376 YgasmssnYnsrprpaevlveegkarlirrretledllale 416 Y++smssnYnsr +paevl+ +g+ +lir et+edll+++ NCBI__GCF_900100165.1:WP_066324151.1 356 YCYSMSSNYNSRYKPAEVLWINGEGHLIRAHETFEDLLKNQ 396 **************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (405 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.44 // [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