Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_106716046.1 CU100_RS06650 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_003010935.1:WP_106716046.1 Length = 468 Score = 723 bits (1866), Expect = 0.0 Identities = 359/463 (77%), Positives = 405/463 (87%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 MKYVSTRGEAPVLGFSDALL+GLARDGGLYLP+++PQF+ +IR++RGKSY EVA+ VLT Sbjct: 1 MKYVSTRGEAPVLGFSDALLSGLARDGGLYLPEQFPQFSPAEIRSMRGKSYAEVAIEVLT 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G++ ADFE MV EAYGTFRH+AVCPLVQT NEFVLELFHGPTLAFKDVAMQLLA Sbjct: 61 PFVTGDLDQADFEEMVHEAYGTFRHEAVCPLVQTGHNEFVLELFHGPTLAFKDVAMQLLA 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+MD +L++R ERATIVGATSGDTGGAAIEAF RD TDIFILFP+ RVS VQQRQMT+S Sbjct: 121 RLMDRILSERNERATIVGATSGDTGGAAIEAFANRDRTDIFILFPHNRVSQVQQRQMTTS 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 +NVHAL+I+GNFDDCQ+LVKGMFNDL F D+LSLSGVNSINWARIMPQ+VYYFTAA+S Sbjct: 181 AAANVHALAIDGNFDDCQSLVKGMFNDLVFRDSLSLSGVNSINWARIMPQIVYYFTAAVS 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG+P+R +SFTVPTGNFGDIFAGYVAKRMGLPI++L+IATNDNDILSRT+E+G YE RGV Sbjct: 241 LGSPERPISFTVPTGNFGDIFAGYVAKRMGLPIDRLVIATNDNDILSRTIETGIYETRGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 TTSPSMDIQ+SSNFERLLFEAHGRDAAAVR LM GL QSG FTI++ L+AIR+EF A Sbjct: 301 LHTTSPSMDIQVSSNFERLLFEAHGRDAAAVRRLMSGLNQSGSFTIADTVLAAIRAEFDA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420 G ST ET I +VL + GYLLDPHSAIG+K+AREKA P VVLATAHPAKFPDAV+ Sbjct: 361 GSSTTAETDQAIANVLKQSGYLLDPHSAIGLKIAREKAGKETPSVVLATAHPAKFPDAVE 420 Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSRA 463 AA G+ P LP WL DLMQRKE +TVL N+LK VEEYVR HSRA Sbjct: 421 AASGIRPALPLWLGDLMQRKEQYTVLPNDLKSVEEYVRRHSRA 463 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: 713 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: 463 Length of database: 468 Length adjustment: 33 Effective length of query: 430 Effective length of database: 435 Effective search space: 187050 Effective search space used: 187050 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 WP_106716046.1 CU100_RS06650 (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.1267418.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-85 273.9 0.0 1.3e-85 273.5 0.0 1.0 1 NCBI__GCF_003010935.1:WP_106716046.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106716046.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 273.5 0.0 1.3e-85 1.3e-85 12 334 .. 69 425 .. 59 430 .. 0.91 Alignments for each domain: == domain 1 score: 273.5 bits; conditional E-value: 1.3e-85 TIGR00260 12 ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAts 81 ++d +++ + + +fr +++ v+ +n +v+elfhgPtlaFKD+++q +a l+ ++l + ne t+++Ats NCBI__GCF_003010935.1:WP_106716046.1 69 QADFEEMVHEAYGTFRHEAVCPLVQTgHNEFVLELFHGPTLAFKDVAMQLLARLMDRILSERNEraTIVGATS 141 4566666677788999999999998899*********************************99999******* PP TIGR00260 82 GdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...kl 150 Gdtg aa+ea+a + ++++L P+ ++s v + +++t a n++ lai+G+FDd+q lvk +f+d l NCBI__GCF_003010935.1:WP_106716046.1 142 GDTGGAAIEAFANRDRTDIFILFPHNRVSQVqQRQMTTSAAANVHALAIDGNFDDCQSLVKGMFNDLVfrdSL 214 ****************************************************************9655677** PP TIGR00260 151 klnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaad 223 l+ vNsin+ari q++y+f ++ lg + + + vp gnfg+i++G+++k+++ lpi+ l ia++++ d NCBI__GCF_003010935.1:WP_106716046.1 215 SLSGVNSINWARIMPQIVYYFTAAVSLG-SPERPISFTVPTGNFGDIFAGYVAKRMG-LPIDRLVIATNDN-D 284 ****************************.55567******************99999.************9.* PP TIGR00260 224 ivrrflksgdlepkedk.eTlstAmdignpsnverale.larrslgnledlke.................... 274 i+ r +++g +++ + + +T s++mdi +sn+er+l+ + r + + l + NCBI__GCF_003010935.1:WP_106716046.1 285 ILSRTIETG-IYETRGVlHTTSPSMDIQVSSNFERLLFeAHGRDAAAVRRLMSglnqsgsftiadtvlaaira 356 *********.66666656******************987777777778888669999**************** PP TIGR00260 275 .....svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevvealtgn 334 s + +e+ +ai +++++ gyll+ph+a++++ ++ + k+ v ata+paKF+++vea +g NCBI__GCF_003010935.1:WP_106716046.1 357 efdagSSTTAETDQAIANVLKQSGYLLDPHSAIGLKIAREKAGKEtpsvVLATAHPAKFPDAVEAASGI 425 *****99****************************9887777766575444*************99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (468 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: 00:00:00.00 # Mc/sec: 28.44 // [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