Align diaminopimelate decarboxylase subunit (EC 4.1.1.20) (characterized)
to candidate WP_010530863.1 ON01_RS09805 diaminopimelate decarboxylase
Query= metacyc::MONOMER-6601 (439 letters) >NCBI__GCF_000224785.1:WP_010530863.1 Length = 435 Score = 558 bits (1439), Expect = e-164 Identities = 264/425 (62%), Positives = 338/425 (79%) Query: 10 NQHGHLEIGGVDALYLAEKYGTPLYVYDVALIRERAKSFKQAFISAGLKAQVAYASKAFS 69 N+ GHL IGG+D++ LAEKYGTPLYVYDV+LIRE ++F + F G+ AQVAYASKAFS Sbjct: 11 NEAGHLAIGGIDSVALAEKYGTPLYVYDVSLIRENCRAFVETFRELGVPAQVAYASKAFS 70 Query: 70 SVAMIQLAEEEGLSLDVVSGGELYTAVAAGFPAERIHFHGNNKSREELRMALEHRIGCIV 129 SVAM+Q+ ++EGLSLDVVS GELYTA+ AGFPA++IH HGNNKS +EL MA+E+ IGCIV Sbjct: 71 SVAMLQVIKQEGLSLDVVSQGELYTALEAGFPADKIHMHGNNKSIDELEMAIEYDIGCIV 130 Query: 130 VDNFYEIALLEDLCKETGHSIDVLLRITPGVEAHTHDYITTGQEDSKFGFDLHNGQTERA 189 DNFYEI L+ + + +++VL+R+TPG+E +THDYI TG EDSKFGF+L NGQ + A Sbjct: 131 ADNFYEIELINSILQRKNKAMNVLMRVTPGIEPNTHDYIVTGNEDSKFGFNLANGQADEA 190 Query: 190 IEQVLQSEHIQLLGVHCHIGSQIFDTAGFVLAAEKIFKKLDEWRDSYSFVSKVLNLGGGF 249 Q+ +SEHIQ G+H HIGSQ+F+T +LAA+ +F+KL EW + Y + +VLNLGGGF Sbjct: 191 FLQLQRSEHIQFKGLHSHIGSQLFETEEILLAAKVLFQKLAEWHEKYDYTPEVLNLGGGF 250 Query: 250 GIRYTEDDEPLHATEYVEKIIEAVKENASRYGFDIPEIWIEPGRSLVGDAGTTLYTVGSQ 309 GIRYT++D+PL + +V+++ V+E A+ + +PEIWIEPGR++ G+AG TLYTVGS Sbjct: 251 GIRYTQEDKPLDYSVHVKELSVVVQEQAAYFNLPLPEIWIEPGRAIAGNAGITLYTVGSI 310 Query: 310 KEVPGVRQYVAVDGGMNDNIRPALYQAKYEAAAANRIGEAHDKTVSIAGKCCESGDMLIW 369 KE+PGVR YVAVDGGM DNIRPALY AKYE AN+ + TVSIAGKCCESGDML+W Sbjct: 311 KEIPGVRHYVAVDGGMTDNIRPALYNAKYEGVLANKAAQPVTDTVSIAGKCCESGDMLMW 370 Query: 370 DIDLPEVKEGDLLAVFCTGAYGYSMANNYNRIPRPAVVFVENGEAHLVVKRETYEDIVKL 429 D+ +P V+ D+LAVF TGAYGYSMAN+YNR + AVVFVENG HLVV+RE+Y+D+VK Sbjct: 371 DLPVPAVESNDILAVFSTGAYGYSMANHYNRFAKAAVVFVENGRDHLVVQRESYQDVVKN 430 Query: 430 DLPFK 434 DL ++ Sbjct: 431 DLSYE 435 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: 593 Number of extensions: 22 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: 435 Length adjustment: 32 Effective length of query: 407 Effective length of database: 403 Effective search space: 164021 Effective search space used: 164021 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_010530863.1 ON01_RS09805 (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.1909909.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-147 476.6 0.1 3e-147 476.4 0.1 1.0 1 NCBI__GCF_000224785.1:WP_010530863.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010530863.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 476.4 0.1 3e-147 3e-147 4 416 .. 11 431 .. 8 432 .. 0.97 Alignments for each domain: == domain 1 score: 476.4 bits; conditional E-value: 3e-147 TIGR01048 4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka..eeslvlYAvKAnsnlavlrllaeeGl 74 ++ g+l i+g+d +lae++gtPlYvyd + +re+++a+ e f++ ++v+YA+KA+s++a+l+++++eGl NCBI__GCF_000224785.1:WP_010530863.1 11 NEAGHLAIGGIDSVALAEKYGTPLYVYDVSLIRENCRAFVETFRElgVPAQVAYASKAFSSVAMLQVIKQEGL 83 789****************************************9975556*********************** PP TIGR01048 75 gldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllR 147 +ldvvs+GEl++al+Ag++a+ki+ +gn+ks +ele+a+e++i +i++d++ e+el+++i ++ +k ++vl+R NCBI__GCF_000224785.1:WP_010530863.1 84 SLDVVSQGELYTALEAGFPADKIHMHGNNKSIDELEMAIEYDIGCIVADNFYEIELINSILQRKNKAMNVLMR 156 ************************************************************************* PP TIGR01048 148 vnpdvdaktheyisTGlkesKFGieve..eaeeayelalkleslelvGihvHIGSqildlepfveaaekvvkl 218 v+p+++++th+yi TG ++sKFG++++ +a ea+ + ++e+++ G+h HIGSq++++e++ aa+ +++ NCBI__GCF_000224785.1:WP_010530863.1 157 VTPGIEPNTHDYIVTGNEDSKFGFNLAngQADEAFLQLQRSEHIQFKGLHSHIGSQLFETEEILLAAKVLFQK 229 *************************99899******************************************* PP TIGR01048 219 leelkee.gieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elgl.klklilEpGRslvanagv 288 l+e++e+ ++ e+l+lGGG+gi+y++e++++d + ++ l ++++a +l +++++EpGR++++nag+ NCBI__GCF_000224785.1:WP_010530863.1 230 LAEWHEKyDYTPEVLNLGGGFGIRYTQEDKPLDYSVHVKELSVVVQEQAaYFNLpLPEIWIEPGRAIAGNAGI 302 ****99999*******************************9999999996777789***************** PP TIGR01048 289 lltrVesvKeves.rkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelp 360 +l++V+s+Ke + r++v+vD+gm+d+iRpalY+a++e +++++ + t tv+++G++CEsgD+l++d +p NCBI__GCF_000224785.1:WP_010530863.1 303 TLYTVGSIKEIPGvRHYVAVDGGMTDNIRPALYNAKYEGVLANKAAQPVTDTVSIAGKCCESGDMLMWDLPVP 375 **********9877*********************************************************** PP TIGR01048 361 eveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 +ve+ d+lav+s+GAYg+sm+++Yn+ +++a+v+ve+g+ +l+++re+++d+++++ NCBI__GCF_000224785.1:WP_010530863.1 376 AVESNDILAVFSTGAYGYSMANHYNRFAKAAVVFVENGRDHLVVQRESYQDVVKND 431 ****************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (435 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.11 // [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