Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 16919 b2838 diaminopimelate decarboxylase, PLP-binding (NCBI)
Query= BRENDA::P00861 (420 letters) >FitnessBrowser__Keio:16919 Length = 420 Score = 845 bits (2182), Expect = 0.0 Identities = 420/420 (100%), Positives = 420/420 (100%) Query: 1 MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60 MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH Sbjct: 1 MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60 Query: 61 ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120 ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN Sbjct: 61 ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120 Query: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR Sbjct: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180 Query: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD Sbjct: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240 Query: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA Sbjct: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300 Query: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA Sbjct: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360 Query: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL Sbjct: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420 Lambda K H 0.320 0.136 0.405 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: 792 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: 420 Length of database: 420 Length adjustment: 32 Effective length of query: 388 Effective length of database: 388 Effective search space: 150544 Effective search space used: 150544 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 16919 b2838 (diaminopimelate decarboxylase, PLP-binding (NCBI))
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.12581.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-150 487.7 0.0 1.3e-150 487.5 0.0 1.0 1 lcl|FitnessBrowser__Keio:16919 b2838 diaminopimelate decarboxyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:16919 b2838 diaminopimelate decarboxylase, PLP-binding (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 487.5 0.0 1.3e-150 1.3e-150 5 416 .. 6 418 .. 2 419 .. 0.98 Alignments for each domain: == domain 1 score: 487.5 bits; conditional E-value: 1.3e-150 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGE 83 ++++++++ +l +l +efg+P++vyd++ +r++++alk+++ +v +A+KA+sn+++lrl++e+G+++d+vs GE lcl|FitnessBrowser__Keio:16919 6 FSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFD-----VVRFAQKACSNIHILRLMREQGVKVDSVSLGE 79 57889999********************************98.....79****************************** PP TIGR01048 84 leralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthe 158 +eralaAg++ +++ivf+++++++++le++ el+i +n++sv++l++l ++++++ rv+lRvnp++++ +++ lcl|FitnessBrowser__Keio:16919 80 IERALAAGYNpqthPDDIVFTADVIDQATLERVSELQIP-VNAGSVDMLDQLGQVSPGH----RVWLRVNPGFGHGHSQ 153 *********9899999**********************9.*******************....**************** PP TIGR01048 159 yisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGG 237 +++TG ++sK+Gi+++ +++a+ ++++++l+lvGih+HIGS++++++ + + ++v +++e g++l+++++GGG lcl|FitnessBrowser__Keio:16919 154 KTNTGGENSKHGIWYT-DLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEF----GQDLQAISAGGG 227 ****************.999*******************************************....9*********** PP TIGR01048 238 lgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndli 315 l+++y++ eea+d+e+y+ ++++ e+ a +lg+ +kl +EpGR+lva++gvl+t+V+svK+++sr+fvlvDag+ndl+ lcl|FitnessBrowser__Keio:16919 228 LSVPYQQGEEAVDTEHYYGLWNAAREQIArHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLM 306 *****************************9************************************************* PP TIGR01048 316 RpalYeayheiaalkr....leeeetetvdvvGplCEsgDvlakd.......relpeveeGdllavasaGAYgasmssn 383 Rpa+Y++yh+i+al++ le+++t+++ v+GplCEsgDv++++ r+lpev++Gd+l+++++GAYgasmssn lcl|FitnessBrowser__Keio:16919 307 RPAMYGSYHHISALAAdgrsLEHAPTVETVVAGPLCESGDVFTQQeggnvetRALPEVKAGDYLVLHDTGAYGASMSSN 385 *************987788899********************************************************* PP TIGR01048 384 Ynsrprpaevlveegkarlirrretledllale 416 Ynsrp + evl+++g+arlirrr+t+e+llale lcl|FitnessBrowser__Keio:16919 386 YNSRPLLPEVLFDNGQARLIRRRQTIEELLALE 418 ******************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (420 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 6.80 // [ok]
This GapMind analysis is from Apr 09 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