Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_101445271.1 BD749_RS13800 diaminopimelate decarboxylase
Query= reanno::Btheta:350902 (386 letters) >NCBI__GCF_002846395.1:WP_101445271.1 Length = 391 Score = 434 bits (1117), Expect = e-126 Identities = 213/361 (59%), Positives = 273/361 (75%), Gaps = 1/361 (0%) Query: 15 TPFYYYDTKVLRDTLSAINQEVAKYPSYSVHYAVKANANPKVLTIIRESGMGADCVSGGE 74 TPFY Y+ +LR TL +QE A+Y ++ VHYA+KAN N +L +R G GADCVSG E Sbjct: 24 TPFYVYNLNLLRQTLQRASQEAARY-NFQVHYALKANTNSPILQEMRAVGFGADCVSGNE 82 Query: 75 IRAAVRAGFPANKIVFAGVGKADWEINLGLEYGIFCFNVESIPELEVINELAAAQNKIAN 134 ++ A+ GFPA+ +VFAGVGK+D EIN L+ IFCFN ES EL V+NELA A+ K A Sbjct: 83 VKCAIENGFPAHHVVFAGVGKSDAEINYALDKDIFCFNCESSHELIVLNELAEAKGKTAR 142 Query: 135 VAFRINPDVGAHTHANITTGLAENKFGISMQDMDRVIDVALEMKNVKFIGLHFHIGSQIL 194 +A RINP+V A+TH ITTGL ENKFGI+ ++ V+ + + N+ IGLHFHIGSQI Sbjct: 143 IALRINPNVNANTHKYITTGLEENKFGINAWELPDVLALLKTLPNLSLIGLHFHIGSQIT 202 Query: 195 DMGDFIALCNRVNELQDKLEARRILVEHINVGGGLGIDYGHPNRQSVPDFKSYFATYAGQ 254 D+ F LC RVNE QD E++++ +EHINVGGGLG+DY +P+ Q +PDF++YF+ + Sbjct: 203 DLSAFKNLCTRVNEFQDWFESQQVHLEHINVGGGLGVDYYNPDEQPIPDFEAYFSLFNQF 262 Query: 255 LKLRPYQTLHFELGRAVVGQCGSLISKVLYVKQGTKKKFAILDAGMTDLIRPALYQAYHK 314 LK+RP Q +HFELGRA+V Q G+LIS+VLY+K+G FAILDAGMT+LIRPALYQ+YHK Sbjct: 263 LKVRPNQQVHFELGRALVAQSGTLISRVLYIKKGVSTNFAILDAGMTELIRPALYQSYHK 322 Query: 315 MENITSEEPVEAYDVVGPICESSDVFGKAIDLNKVKRGDLIALRSAGAYGEIMASGYNCR 374 +ENI+S+ E YDVVGPICESSD FGKA+ L + RGDLIA+R+AGAYGE+MAS YN R Sbjct: 323 IENISSKGAEERYDVVGPICESSDCFGKAVVLPETNRGDLIAIRTAGAYGEVMASAYNLR 382 Query: 375 E 375 + Sbjct: 383 D 383 Lambda K H 0.321 0.138 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: 427 Number of extensions: 16 Number of successful extensions: 2 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: 386 Length of database: 391 Length adjustment: 30 Effective length of query: 356 Effective length of database: 361 Effective search space: 128516 Effective search space used: 128516 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_101445271.1 BD749_RS13800 (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.528631.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-127 410.0 0.0 4.8e-127 409.8 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101445271.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101445271.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 409.8 0.0 4.8e-127 4.8e-127 5 394 .. 5 389 .. 1 391 [] 0.94 Alignments for each domain: == domain 1 score: 409.8 bits; conditional E-value: 4.8e-127 TIGR01048 5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgld 77 ++g++++ + +++el +++ tP+Yvy+ + lr+ l++ ++ ++++ +v+YA+KAn+n +l+ +++ G+g+d NCBI__GCF_002846395.1:WP_101445271.1 5 SKGTTTMLNLSVQEL-QQHATPFYVYNLNLLRQTLQRASQEAARYNFQVHYALKANTNSPILQEMRAVGFGAD 76 677778888888888.6799******************999999989************************** PP TIGR01048 78 vvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnp 150 +vsg E++ a + g++a+++vf+g+gks++e++ al+ +i ++n +s +el l+e+a+ gk+ar++lR+np NCBI__GCF_002846395.1:WP_101445271.1 77 CVSGNEVKCAIENGFPAHHVVFAGVGKSDAEINYALDKDIFCFNCESSHELIVLNELAEAKGKTARIALRINP 149 ************************************************************************* PP TIGR01048 151 dvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelk 223 +v+a+th+yi+TGl+e+KFGi+ e ++ l ++l++l+l+G+h+HIGSqi+dl+ f++ + +v ++ + ++ NCBI__GCF_002846395.1:WP_101445271.1 150 NVNANTHKYITTGLEENKFGINAWELPDVLALLKTLPNLSLIGLHFHIGSQITDLSAFKNLCTRVNEFQDWFE 222 ************************************************************************* PP TIGR01048 224 eegieleeldlGGGlgisyeeeeea..pdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVe 294 +++++le++++GGGlg++y + +e+ pd e y + +++ l+ ++++ +E GR+lva++g+l+ rV NCBI__GCF_002846395.1:WP_101445271.1 223 SQQVHLEHINVGGGLGVDYYNPDEQpiPDFEAYFSLFNQFLKV----RPNQQVHFELGRALVAQSGTLISRVL 291 ******************9876643125667777776665555....5799********************** PP TIGR01048 295 svKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdl 367 ++K+ s++f++ Dagm++liRpalY++yh+i ++++ + ++e++dvvGp+CEs+D ++k + lpe+++Gdl NCBI__GCF_002846395.1:WP_101445271.1 292 YIKKGVSTNFAILDAGMTELIRPALYQSYHKIENISS--KGAEERYDVVGPICESSDCFGKAVVLPETNRGDL 362 ***********************************66..6667****************************** PP TIGR01048 368 lavasaGAYgasmssnYnsrprpaevl 394 +a++ aGAYg m+s Yn r ++a+v NCBI__GCF_002846395.1:WP_101445271.1 363 IAIRTAGAYGEVMASAYNLRDKAAAVY 389 ************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (391 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: 13.76 // [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