Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate WP_069662873.1 BCR25_RS06840 diaminopimelate decarboxylase
Query= metacyc::MONOMER-6601 (439 letters) >NCBI__GCF_001730305.1:WP_069662873.1 Length = 433 Score = 504 bits (1298), Expect = e-147 Identities = 244/428 (57%), Positives = 310/428 (72%) Query: 3 LHGTSRQNQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGLKAQVA 62 L GT+ N+ HL IGG D + LAEKYGTPL++YDVA IRERA+ FKQ S G+K +V Sbjct: 4 LFGTATFNESEHLTIGGCDTVTLAEKYGTPLFIYDVAHIRERARGFKQTLNSLGVKNKVI 63 Query: 63 YASKAFSSVAMIQLAEEEGLSLDVVSGGELYTAVAAGFPAERIHFHGNNKSREELRMALE 122 YASKAF +AM +L EEE L DVVS GE+YTA+ AG E I FHGNNK++EEL A+E Sbjct: 64 YASKAFCCLAMYKLLEEEELGCDVVSAGEIYTAIKAGMSPENIEFHGNNKTKEELLYAVE 123 Query: 123 HRIGCIVVDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLH 182 +G I++DNFYEI LL + KE VL RITPG+ A THDYI TGQ DSKFGFD++ Sbjct: 124 QGVGTIIIDNFYEIELLSAILKEKNQKQHVLFRITPGINAETHDYILTGQVDSKFGFDVN 183 Query: 183 NGQTERAIEQVLQSEHIQLLGVHCHIGSQIFDTAGFVLAAEKIFKKLDEWRDSYSFVSKV 242 +GQ +A+E++L +H+ L GVHCHIGSQIF GF+ A EK+ L+EW+ ++ + V Sbjct: 184 SGQATQALERILADDHLVLKGVHCHIGSQIFSAEGFLAAVEKMLTILNEWKQAFGYSVDV 243 Query: 243 LNLGGGFGIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVGDAGTT 302 LN+GGGFG++YTE D+PL +V+ I+ +VK + + PEIW+EPGRS++ +AGTT Sbjct: 244 LNMGGGFGVQYTEADDPLEPEAFVKAIVNSVKGQCALLDYAFPEIWLEPGRSIIAEAGTT 303 Query: 303 LYTVGSQKEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIAGKCCE 362 +YTVGS+K +P VR YV+VDGGM DNIRPALY AKY+ ANRI +I GK CE Sbjct: 304 IYTVGSEKVIPEVRHYVSVDGGMGDNIRPALYGAKYDGFLANRISNEQQSPKTIVGKYCE 363 Query: 363 SGDMLIWDIDLPEVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLVVKRET 422 SGD+LI DI+LP ++ DL AV TGAYGYSMANNYNR +PAVVFVE+G L ++RET Sbjct: 364 SGDVLIKDIELPTLRPEDLFAVTSTGAYGYSMANNYNRNLKPAVVFVEDGHEKLAIRRET 423 Query: 423 YEDIVKLD 430 YED++ LD Sbjct: 424 YEDLISLD 431 Lambda K H 0.319 0.137 0.401 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: 575 Number of extensions: 23 Number of successful extensions: 1 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: 439 Length of database: 433 Length adjustment: 32 Effective length of query: 407 Effective length of database: 401 Effective search space: 163207 Effective search space used: 163207 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate WP_069662873.1 BCR25_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.3740274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-149 481.5 0.0 9.8e-149 481.3 0.0 1.0 1 NCBI__GCF_001730305.1:WP_069662873.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069662873.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 481.3 0.0 9.8e-149 9.8e-149 4 416 .. 11 431 .. 8 432 .. 0.98 Alignments for each domain: == domain 1 score: 481.3 bits; conditional E-value: 9.8e-149 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrllaeeGl 74 +++ +l+i+g+d +lae++gtPl++yd +++rer++ +k+ ++ +++v+YA+KA+ +la+ +ll+ee l NCBI__GCF_001730305.1:WP_069662873.1 11 NESEHLTIGGCDTVTLAEKYGTPLFIYDVAHIRERARGFKQTLNSlgVKNKVIYASKAFCCLAMYKLLEEEEL 83 67889**************************************9986667*********************** PP TIGR01048 75 gldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllR 147 g dvvs GE+++a +Ag+++e+i f+gn+k++eel a+e ++ +i++d++ e+ell++i ke ++k++vl+R NCBI__GCF_001730305.1:WP_069662873.1 84 GCDVVSAGEIYTAIKAGMSPENIEFHGNNKTKEELLYAVEQGVGTIIIDNFYEIELLSAILKEKNQKQHVLFR 156 ************************************************************************* PP TIGR01048 148 vnpdvdaktheyisTGlkesKFGieve..eaeeayelalkleslelvGihvHIGSqildlepfveaaekvvkl 218 ++p+++a+th+yi TG+ +sKFG++v+ +a++a e++l++++l l G+h+HIGSqi+ +e+f +a+ek++++ NCBI__GCF_001730305.1:WP_069662873.1 157 ITPGINAETHDYILTGQVDSKFGFDVNsgQATQALERILADDHLVLKGVHCHIGSQIFSAEGFLAAVEKMLTI 229 ***************************999******************************************* PP TIGR01048 219 leelkee.gieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klklilEpGRslvanagv 288 l+e+k++ g+++ +l++GGG+g++y+e ++++++e +++++++++++++ l ++++lEpGRs++a+ag+ NCBI__GCF_001730305.1:WP_069662873.1 230 LNEWKQAfGYSVDVLNMGGGFGVQYTEADDPLEPEAFVKAIVNSVKGQCaLLDYaFPEIWLEPGRSIIAEAGT 302 *****999****************************************96555579***************** PP TIGR01048 289 lltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelp 360 ++++V+s+K ++ r++v+vD+gm d+iRpalY+a+++ ++++r+++e+++ ++vG+ CEsgDvl+kd+elp NCBI__GCF_001730305.1:WP_069662873.1 303 TIYTVGSEKVIPEvRHYVSVDGGMGDNIRPALYGAKYDGFLANRISNEQQSPKTIVGKYCESGDVLIKDIELP 375 **********9888*********************************************************** PP TIGR01048 361 eveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 + ++ dl av+s+GAYg+sm++nYn+ +pa+v+ve+g+ +l rret+edl++l+ NCBI__GCF_001730305.1:WP_069662873.1 376 TLRPEDLFAVTSTGAYGYSMANNYNRNLKPAVVFVEDGHEKLAIRRETYEDLISLD 431 *****************************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (433 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.81 // [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