Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate PP_3446 PP_3446 threonine deaminase
Query= BRENDA::P04968 (514 letters) >FitnessBrowser__Putida:PP_3446 Length = 530 Score = 545 bits (1405), Expect = e-159 Identities = 276/501 (55%), Positives = 361/501 (72%), Gaps = 2/501 (0%) Query: 14 AEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGL 73 +E +R +L APVY+ A TPLQ LS+ L N +L+KRED QP SFK+RGAY ++ L Sbjct: 29 SEQVRRILAAPVYDLAIETPLQAAPALSAALGNQVLLKREDLQPTFSFKIRGAYTRLSRL 88 Query: 74 TEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGA 133 T+ Q+ GVITASAGNHAQGVA +++ LG+KA IVMPT T +KV+ VR GG V+LHG Sbjct: 89 TDVQRERGVITASAGNHAQGVALAASHLGMKATIVMPTTTPSLKVEGVRSRGGHVVLHGE 148 Query: 134 NFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQ-DAHLDRVFVPVGGGGL 192 +F A A++L+ +G T+VPPFD P VIAGQGT+A+E+L+Q LD +FVPVGGGGL Sbjct: 149 SFPHALTHALKLADSEGATFVPPFDDPDVIAGQGTVAMEILRQRPGALDAIFVPVGGGGL 208 Query: 193 AAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETF 252 AG+A +K L P +KVI VE DS CL+AA+ G V LP+VG FA+GVAV +IG F Sbjct: 209 IAGIAAYVKYLRPDVKVIGVEPADSNCLQAAMAVGERVILPQVGTFADGVAVAQIGAHCF 268 Query: 253 RLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAH 312 LC+ ++D+++TV SD +CAA+KD+++D R++ EPSGALA+AG+KKY+A ++G+ L Sbjct: 269 ELCRHFVDEVVTVSSDELCAAIKDIYDDTRSITEPSGALAVAGIKKYVAREGVQGQTLVA 328 Query: 313 ILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFA 372 I SGANVNF LR+V+ER ELGEQREA++AVTIPE+ GSF FC LG R +TEFNYRF Sbjct: 329 IDSGANVNFDRLRHVAERAELGEQREAIIAVTIPEQPGSFRAFCHALGKRQITEFNYRFY 388 Query: 373 DAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQ 432 K A +FVGV+ + R+++L L + GYSV+DL+D+E+AKLHVR+ VGG + Sbjct: 389 PGKEARLFVGVQTHPVHDPREQLLASLREQGYSVLDLTDNELAKLHVRHTVGGHAASGAD 448 Query: 433 ERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFEL-GDHEPDFETR 491 ER+ FEFPE PGALL FL LG WNISLFHYR+HG RV AA E+ D + Sbjct: 449 ERVLRFEFPERPGALLGFLERLGKRWNISLFHYRNHGAAEARVFAALEVPADELAGLPST 508 Query: 492 LNELGYDCHDETNNPAFRFFL 512 L+E+GY DET+NPA++ FL Sbjct: 509 LDEMGYRYWDETDNPAYKLFL 529 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: 736 Number of extensions: 38 Number of successful extensions: 4 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: 530 Length adjustment: 35 Effective length of query: 479 Effective length of database: 495 Effective search space: 237105 Effective search space used: 237105 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 PP_3446 PP_3446 (threonine deaminase)
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.8785.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.4e-239 779.5 0.0 7.4e-239 779.3 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3446 PP_3446 threonine deaminase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3446 PP_3446 threonine deaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 779.3 0.0 7.4e-239 7.4e-239 2 499 .] 31 529 .. 30 529 .. 0.99 Alignments for each domain: == domain 1 score: 779.3 bits; conditional E-value: 7.4e-239 TIGR01124 2 ylrailkarvyeaavetplekaaklserlknrvllkredlqpvfsfklrGaynkmaqlsaeqkakGviaasaGnh 76 +r+il a vy+ a+etpl+ a ls+ l+n+vllkredlqp fsfk+rGay+++++l++ q+ +Gvi+asaGnh lcl|FitnessBrowser__Putida:PP_3446 31 QVRRILAAPVYDLAIETPLQAAPALSAALGNQVLLKREDLQPTFSFKIRGAYTRLSRLTDVQRERGVITASAGNH 105 5799*********************************************************************** PP TIGR01124 77 aqGvalsakklGvkavivmpettpeikvdavkafGgevvlhGenydeakakalelaqekgltfiapfddplviaG 151 aqGval+a++lG+ka+ivmp+ttp++kv+ v+++Gg+vvlhGe++ +a ++al+la+ +g tf++pfddp+viaG lcl|FitnessBrowser__Putida:PP_3446 106 AQGVALAASHLGMKATIVMPTTTPSLKVEGVRSRGGHVVLHGESFPHALTHALKLADSEGATFVPPFDDPDVIAG 180 *************************************************************************** PP TIGR01124 152 qGtvalellrqveedldavfvpvGGGGliaGvaalvkqllpeikvigveaedsaalkqaleaGervkldqvGlfa 226 qGtva+e+lrq lda+fvpvGGGGliaG+aa+vk l+p++kvigve+ ds++l++a++ Gerv l qvG fa lcl|FitnessBrowser__Putida:PP_3446 181 QGTVAMEILRQRPGALDAIFVPVGGGGLIAGIAAYVKYLRPDVKVIGVEPADSNCLQAAMAVGERVILPQVGTFA 255 *************************************************************************** PP TIGR01124 227 dGvavkevGdetfrlckeylddivlvdtdevcaaikdvfedtravlepaGalalaGlkkyvakkgiedktlvail 301 dGvav ++G++ f+lc++++d++v+v +de+caaikd+++dtr+++ep+Gala+aG+kkyva++g++++tlvai lcl|FitnessBrowser__Putida:PP_3446 256 DGVAVAQIGAHCFELCRHFVDEVVTVSSDELCAAIKDIYDDTRSITEPSGALAVAGIKKYVAREGVQGQTLVAID 330 *************************************************************************** PP TIGR01124 302 sGanlnfdrlryvseraelGeqreallavtipeekGsllkfvevlGeraitefnyrladdekahifvGvqlaee. 375 sGan+nfdrlr+v+eraelGeqrea++avtipe++Gs++ f++ lG+r+itefnyr+ + ++a++fvGvq++ lcl|FitnessBrowser__Putida:PP_3446 331 SGANVNFDRLRHVAERAELGEQREAIIAVTIPEQPGSFRAFCHALGKRQITEFNYRFYPGKEARLFVGVQTHPVh 405 ***********************************************************************9873 PP TIGR01124 376 eerkellarleeagykvvdltddelaklhvrylvGGraakvenerlysfefperpGallkfletlqaewnislfh 450 + r++lla+l+e+gy+v+dltd+elaklhvr+ vGG aa+ +er+++fefperpGall fle l ++wnislfh lcl|FitnessBrowser__Putida:PP_3446 406 DPREQLLASLREQGYSVLDLTDNELAKLHVRHTVGGHAASGADERVLRFEFPERPGALLGFLERLGKRWNISLFH 480 56999********************************************************************** PP TIGR01124 451 yrnhGadyGrvlvglevpdeeaeefeqflaelgyryedetenpayrlfl 499 yrnhGa+ rv+++levp +e + + ++l+e+gyry+det+npay+lfl lcl|FitnessBrowser__Putida:PP_3446 481 YRNHGAAEARVFAALEVPADELAGLPSTLDEMGYRYWDETDNPAYKLFL 529 ************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (499 nodes) Target sequences: 1 (530 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 11.84 // [ok]
This GapMind analysis is from Sep 17 2021. 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