Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 6939184 Sama_3278 threonine dehydratase (RefSeq)
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__SB2B:6939184 Length = 531 Score = 604 bits (1557), Expect = e-177 Identities = 308/506 (60%), Positives = 382/506 (75%), Gaps = 10/506 (1%) Query: 16 YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTE 75 YL+ +L + VY+ A+VTPL M KLS+RL I +KRED QPVHSFKLRGAY ++ LT+ Sbjct: 24 YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQ 83 Query: 76 EQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANF 135 + GV+ ASAGNHAQGVA S++ G+ A+IVMPT T DIK+DAVR GG VLLHG +F Sbjct: 84 PECERGVVCASAGNHAQGVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESF 143 Query: 136 DEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAG 195 D+A A A L+Q +G ++ PFD VIAGQGT+A E+LQQ L+ VFVPVGGGGL AG Sbjct: 144 DQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQRDLELVFVPVGGGGLVAG 203 Query: 196 VAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLC 255 +A K + P +K+I VE ED+ACLKAA+ AG PV L +VGLFA+GVAVKRIG E FR+ Sbjct: 204 IAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIA 263 Query: 256 QEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIR-------GE 308 + Y+D+++TV SD ICAA+KD+FED RA+AEP+GAL+LAG+KKY+A Sbjct: 264 KHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTTPALAEAGKPAR 323 Query: 309 RLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFN 368 ++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE GSFLKFC+LLG R++TEFN Sbjct: 324 KVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFN 383 Query: 369 YRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPS 428 YRF+ +A +F G+RLS G E KEI+ L GG+ V DLS DE AKLHVRYMVGG P+ Sbjct: 384 YRFSGRDSAVVFAGIRLSGGQSELKEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGHPT 443 Query: 429 HPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL--GDHEP 486 PL ERL+SFEFPE PGALL+FL TLG+ WNISLFHYR+HG +GRVLA FE+ GD+E Sbjct: 444 EPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGDNEA 503 Query: 487 DFETRLNELGYDCHDETNNPAFRFFL 512 F L ELG+ +ET++PA+R FL Sbjct: 504 -FGRFLTELGFVWQEETHSPAYRLFL 528 Lambda K H 0.321 0.138 0.403 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: 746 Number of extensions: 30 Number of successful extensions: 5 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: 514 Length of database: 531 Length adjustment: 35 Effective length of query: 479 Effective length of database: 496 Effective search space: 237584 Effective search space used: 237584 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: 52 (24.6 bits)
Align candidate 6939184 Sama_3278 (threonine dehydratase (RefSeq))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))
# 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.carbon/TIGR01124.hmm # target sequence database: /tmp/gapView.664940.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01124 [M=499] Accession: TIGR01124 Description: ilvA_2Cterm: threonine ammonia-lyase, biosynthetic 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-235 768.3 0.0 1.9e-235 768.1 0.0 1.0 1 FitnessBrowser__SB2B:6939184 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6939184 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 768.1 0.0 1.9e-235 1.9e-235 2 499 .] 24 528 .. 23 528 .. 0.98 Alignments for each domain: == domain 1 score: 768.1 bits; conditional E-value: 1.9e-235 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnhaqGval 82 yl++il ++vy++a++tpl+++ kls+rl+ +++lkred+qpv+sfklrGayn+++ql++ + +Gv++asaGnhaqGval FitnessBrowser__SB2B:6939184 24 YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQPECERGVVCASAGNHAQGVAL 104 89******************************************************************************* PP TIGR01124 83 sakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaGqGtvalellrqv 163 sa+ G+ avivmp+ttp+ik+dav+ +Gg+v+lhGe++d+a+a+a++laq +g +iapfdd+ viaGqGtva e+l+q+ FitnessBrowser__SB2B:6939184 105 SASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESFDQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQ 185 ********************************************************************************9 PP TIGR01124 164 eedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfadGvavkevGdetfrlcke 244 + dl+ vfvpvGGGGl+aG+aa+ k+++p +k+igve+ed+a+lk+a++aGe+v+l+qvGlfadGvavk++G+e fr++k+ FitnessBrowser__SB2B:6939184 186 R-DLELVFVPVGGGGLVAGIAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIAKH 265 9.9****************************************************************************** PP TIGR01124 245 ylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakk.......giedktlvailsGanlnfdrlryvsera 318 y+d++v+v +de+caa+kd+fedtra++epaGal+laGlkky+a+ g ++++ailsGan+nf++lryvser+ FitnessBrowser__SB2B:6939184 266 YVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTtpalaeaGKPARKVAAILSGANVNFHSLRYVSERC 346 ******************************************98752222111455789********************** PP TIGR01124 319 elGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee.eerkellarleeagykvvdltdd 398 elGeq+ea+lav +pe +Gs+lkf+e+lG+ra+tefnyr++ +++a +f G++l+ +e ke++a+l++ g++v dl+ d FitnessBrowser__SB2B:6939184 347 ELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEFNYRFSGRDSAVVFAGIRLSGGqSELKEIIASLTSGGFEVQDLSSD 427 ******************************************************9864899******************** PP TIGR01124 399 elaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfhyrnhGadyGrvlvglevpdeeaeefeqfl 479 e aklhvry+vGG +++ erl+sfefpe pGallkfl+tl ++wnislfhyrnhGa++Grvl+g+evp+ ++e+f fl FitnessBrowser__SB2B:6939184 428 ETAKLHVRYMVGGHPTEPLSERLFSFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGDNEAFGRFL 508 ********************************************************************************* PP TIGR01124 480 aelgyryedetenpayrlfl 499 elg+ ++et++payrlfl FitnessBrowser__SB2B:6939184 509 TELGFVWQEETHSPAYRLFL 528 *******************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (531 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: 16.57 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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