Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate YP_002825092.1 NGR_c05430 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000018545.1:YP_002825092.1 Length = 465 Score = 658 bits (1698), Expect = 0.0 Identities = 328/462 (70%), Positives = 375/462 (81%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 MKY+STRGEA LGF DALLAGLARDGGLYLP+E+P F+ ++IRALRGKSY E+A VL Sbjct: 1 MKYISTRGEAAPLGFCDALLAGLARDGGLYLPKEWPTFSKKEIRALRGKSYQEIAFTVLQ 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PFT GEIPAA F M+ AY TFRH A+ PLVQT N FV+ELFHG TLAFKDVAMQLLA Sbjct: 61 PFTNGEIPAAKFREMIDGAYATFRHPAIAPLVQTGPNAFVMELFHGSTLAFKDVAMQLLA 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+MD+VLA+RGERATIVGATSGDTGGAAI+AF GRD TDIFILFP+G+VSPVQQRQMT++ Sbjct: 121 RLMDHVLAERGERATIVGATSGDTGGAAIDAFAGRDRTDIFILFPHGKVSPVQQRQMTTA 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 SNVHA+++ GNFDDCQNLVK MFND F D + LSGVNSINWARIM Q+VYYFT A++ Sbjct: 181 NASNVHAIAVNGNFDDCQNLVKAMFNDTAFRDRVKLSGVNSINWARIMAQIVYYFTTAIA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG PDR +SFTVPTGNFGDIFAGYVAKRMGLPI++LIIATN+NDIL+RTL++G YEMR V Sbjct: 241 LGGPDRKISFTVPTGNFGDIFAGYVAKRMGLPIDKLIIATNENDILARTLKTGRYEMREV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 TTSPSMDIQISSNFERLLFEA GR+A+ VR M LKQSG F I E L IR EF A Sbjct: 301 KATTSPSMDIQISSNFERLLFEAFGREASEVRAAMASLKQSGSFAIEEGALKKIRKEFRA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420 GR++ + AATI K GYLLDPH+AIGV VA + +APMVVL TAHPAKFPDAVK Sbjct: 361 GRASEKQVAATIRDTFKKSGYLLDPHTAIGVSVAAKHEKPSAPMVVLGTAHPAKFPDAVK 420 Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 +A G++P LP WL DLM R E F +L ELK VE ++ +R Sbjct: 421 SASGIDPTLPTWLADLMTRAERFDILDAELKNVETFIGERTR 462 Lambda K H 0.320 0.135 0.389 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: 616 Number of extensions: 18 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: 463 Length of database: 465 Length adjustment: 33 Effective length of query: 430 Effective length of database: 432 Effective search space: 185760 Effective search space used: 185760 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: 51 (24.3 bits)
Align candidate YP_002825092.1 NGR_c05430 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# 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/TIGR00260.hmm # target sequence database: /tmp/gapView.11323.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-92 294.3 0.1 7.9e-92 293.9 0.1 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002825092.1 NGR_c05430 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002825092.1 NGR_c05430 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 293.9 0.1 7.9e-92 7.9e-92 13 334 .. 70 425 .. 61 430 .. 0.92 Alignments for each domain: == domain 1 score: 293.9 bits; conditional E-value: 7.9e-92 TIGR00260 13 kdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlc 78 ++ +++ g +++fr p++a v+ n +v elfhg tlaFKD+++q +a l+ ++l + e t+++ lcl|NCBI__GCF_000018545.1:YP_002825092.1 70 AKFREMIDGAYATFRHPAIAPLVQTgPNAFVMELFHGSTLAFKDVAMQLLARLMDHVLAERGEraTIVG 138 566778899***********9999999****************************9876554447**** PP TIGR00260 79 AtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifed 146 AtsGdtg aa+ a+ag+ ++++L P+gk+spv + +++ta a+n++ +a++G+FDd+q+lvk++f+d lcl|NCBI__GCF_000018545.1:YP_002825092.1 139 ATSGDTGGAAIDAFAGRDRTDIFILFPHGKVSPVqQRQMTTANASNVHAIAVNGNFDDCQNLVKAMFND 207 *******************************************************************97 PP TIGR00260 147 ke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpie 212 +kl+ vNsin+ari aq++y+f + +lg+ k+ + vp gnfg+i++G+++k+++ lpi+ lcl|NCBI__GCF_000018545.1:YP_002825092.1 208 TAfrdRVKLSGVNSINWARIMAQIVYYFTTAIALGG-PDRKISFTVPTGNFGDIFAGYVAKRMG-LPID 274 77788******************************5.4568******************99999.**** PP TIGR00260 213 klaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke...... 274 kl ia++++ di+ r lk+g e +e k+T s++mdi ++sn+er+l+ ++ r+ ++ + + lcl|NCBI__GCF_000018545.1:YP_002825092.1 275 KLIIATNEN-DILARTLKTGRYEMREVKATTSPSMDIQISSNFERLLFeAFGREASEVRAAMAslkqsg 342 ********9.**********88888999*******************99777666666555446677** PP TIGR00260 275 ...................svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatad 320 ++s++++ +i+ ++ gyll+phta++v + k + + v +ta+ lcl|NCBI__GCF_000018545.1:YP_002825092.1 343 sfaieegalkkirkefragRASEKQVAATIRDTFKKSGYLLDPHTAIGVSVAAKHEKPSapmvVLGTAH 411 ******************************************************99999876444**** PP TIGR00260 321 paKFeevvealtgn 334 paKF+++v +g lcl|NCBI__GCF_000018545.1:YP_002825092.1 412 PAKFPDAVKSASGI 425 ********987775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (465 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 14.80 // [ok]
This GapMind analysis is from Apr 10 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