Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate BWI76_RS23360 BWI76_RS23360 diaminopimelate decarboxylase
Query= BRENDA::P00861 (420 letters) >FitnessBrowser__Koxy:BWI76_RS23360 Length = 420 Score = 756 bits (1951), Expect = 0.0 Identities = 366/420 (87%), Positives = 396/420 (94%) Query: 1 MPHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIH 60 MPHSL++TDTDL+AENLLRLPAEFGCPVWVYDAQIIRRQIA L +FDVVRFAQKACSNIH Sbjct: 1 MPHSLYATDTDLSAENLLRLPAEFGCPVWVYDAQIIRRQIAQLSKFDVVRFAQKACSNIH 60 Query: 61 ILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVN 120 ILRLMREQGVKVDSVSLGEIERALAAGY+P HPDD+VFTAD+ID ATL RV ELQIPVN Sbjct: 61 ILRLMREQGVKVDSVSLGEIERALAAGYDPHQHPDDVVFTADLIDDATLARVKELQIPVN 120 Query: 121 AGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQR 180 AGS+DML QLG+VSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIW++ L AAL+V++R Sbjct: 121 AGSIDMLSQLGEVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWHSHLTAALEVMRR 180 Query: 181 HHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVD 240 + LQLVGIHMHIGSGVDY HLEQVCGAMVRQV+EFGQDLQAISAGGGLS+PY + EEA+D Sbjct: 181 YQLQLVGIHMHIGSGVDYGHLEQVCGAMVRQVVEFGQDLQAISAGGGLSIPYHEDEEAID 240 Query: 241 TEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDA 300 T+HY+GLWNAAREQIA+HLGHPVKLEIEPGRFLVA+SGVL++QVRSVK+MGSRHFVL+DA Sbjct: 241 TDHYFGLWNAAREQIAKHLGHPVKLEIEPGRFLVAESGVLVSQVRSVKEMGSRHFVLIDA 300 Query: 301 GFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRA 360 GFNDLMRPAMYGSYHHI+ALAADGR L A +ETVVAGPLCESGDVFTQQEGG VETR Sbjct: 301 GFNDLMRPAMYGSYHHITALAADGRDLRAAAQIETVVAGPLCESGDVFTQQEGGKVETRL 360 Query: 361 LPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL 420 LP V GDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNG+ARLIRRRQTIEELLALELL Sbjct: 361 LPAVAPGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGKARLIRRRQTIEELLALELL 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: 731 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 BWI76_RS23360 BWI76_RS23360 (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.14966.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-142 458.5 0.0 9.7e-142 458.2 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS23360 BWI76_RS23360 diaminopimelate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS23360 BWI76_RS23360 diaminopimelate decarboxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.2 0.0 9.7e-142 9.7e-142 7 416 .. 8 418 .. 3 419 .. 0.97 Alignments for each domain: == domain 1 score: 458.2 bits; conditional E-value: 9.7e-142 TIGR01048 7 geleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgld 77 +++++++ +l +l +efg+P++vyd++ +r+++++l++++ +v +A+KA+sn+++lrl++e+G+++d lcl|FitnessBrowser__Koxy:BWI76_RS23360 8 TDTDLSAENLLRLPAEFGCPVWVYDAQIIRRQIAQLSKFD-----VVRFAQKACSNIHILRLMREQGVKVD 73 67788999*****************************998.....79************************ PP TIGR01048 78 vvsgGEleralaAgvk....aekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarv 144 +vs GE+eralaAg++ ++++vf+++ +++++l+++ el+i +n++s+++l++l e+++++ rv lcl|FitnessBrowser__Koxy:BWI76_RS23360 74 SVSLGEIERALAAGYDphqhPDDVVFTADLIDDATLARVKELQIP-VNAGSIDMLSQLGEVSPGH----RV 139 ***************9888899**********************9.*******************....** PP TIGR01048 145 llRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekv 215 +lRvnp++++ ++++++TG ++sK+Gi+++ ++ a+ ++++ +l+lvGih+HIGS++++ + + + ++v lcl|FitnessBrowser__Koxy:BWI76_RS23360 140 WLRVNPGFGHGHSQKTNTGGENSKHGIWHS-HLTAALEVMRRYQLQLVGIHMHIGSGVDYGHLEQVCGAMV 209 *****************************9.7788888899999*************************** PP TIGR01048 216 vklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvan 285 +++e g++l+++++GGGl+i+y+e+eea+d+++y ++++ e+ a +lg+ +kl +EpGR+lva+ lcl|FitnessBrowser__Koxy:BWI76_RS23360 210 RQVVEF----GQDLQAISAGGGLSIPYHEDEEAIDTDHYFGLWNAAREQIAkHLGHPVKLEIEPGRFLVAE 276 ******....9***************************************99******************* PP TIGR01048 286 agvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr....leeeetetvdvvGplCEsgDv 352 +gvl+ +V+svKe++sr+fvl+Dag+ndl+Rpa+Y++yh+i+al++ l+++++ ++ v+GplCEsgDv lcl|FitnessBrowser__Koxy:BWI76_RS23360 277 SGVLVSQVRSVKEMGSRHFVLIDAGFNDLMRPAMYGSYHHITALAAdgrdLRAAAQIETVVAGPLCESGDV 347 *******************************************98777778899999************** PP TIGR01048 353 lakd.......relpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416 ++++ r lp+v +Gd+l+++++GAYgasmssnYnsrp + evl+++gkarlirrr+t+e+llale lcl|FitnessBrowser__Koxy:BWI76_RS23360 348 FTQQeggkvetRLLPAVAPGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGKARLIRRRQTIEELLALE 418 **********999*******************************************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.02 // [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