Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012332209.1 M446_RS11150 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000019365.1:WP_012332209.1 Length = 471 Score = 560 bits (1444), Expect = e-164 Identities = 289/464 (62%), Positives = 338/464 (72%), Gaps = 2/464 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M +VSTRG AP L F+DALLAGLARDGGLYLP+ +P E I L GK Y E A AVL Sbjct: 1 MLHVSTRGAAPPLTFTDALLAGLARDGGLYLPESWPSLAPETIAGLAGKPYAEAAKAVLA 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 P GEIP A +RM+ AY FRH AVCPLVQ DAN F+LEL HGPTLAFKDVAMQLL Sbjct: 61 PLVDGEIPRAALDRMIEAAYAGFRHPAVCPLVQLDANLFLLELHHGPTLAFKDVAMQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+MD+VL RG RATIVGATSGDTG AA+EAF G D D+FILFP+GRVS VQ+RQMTS Sbjct: 121 RLMDHVLKARGSRATIVGATSGDTGSAAVEAFRGLDQVDVFILFPHGRVSEVQRRQMTSV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 NVHAL++EG FDDCQ +VK +F F + + LSGVNSINWAR+ Q YYFT+A++ Sbjct: 181 DSPNVHALAVEGTFDDCQAIVKALFQHPRFAEEVRLSGVNSINWARVAAQATYYFTSAVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAP R VSF VPTGNFGDI AG+VAKRMGLP+ +L+I TN NDIL+RTL +G YE+RGV Sbjct: 241 LGAPHRPVSFAVPTGNFGDILAGWVAKRMGLPVGRLMIGTNANDILARTLATGTYEVRGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 A TTSPSMDIQ+SSNFERLLFEA GR+ + LM GLKQSG FT+ + L +RSEF A Sbjct: 301 APTTSPSMDIQVSSNFERLLFEALGREPEGLTRLMAGLKQSGRFTLPPEVLKRVRSEFDA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE--KASGTAPMVVLATAHPAKFPDA 418 E AA I ++ G +LDPHSAIGV+ R +A P+V LATAH AKFPDA Sbjct: 361 AAVPEPEVAAEIRDTYARTGQILDPHSAIGVRAGRRLLEADPATPVVALATAHAAKFPDA 420 Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 V+AA G+ P LP L DLM R E F+V+ N+ VE +R +R Sbjct: 421 VEAATGIRPALPPHLADLMTRPERFSVVANDEGAVERVIRERAR 464 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: 579 Number of extensions: 26 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: 463 Length of database: 471 Length adjustment: 33 Effective length of query: 430 Effective length of database: 438 Effective search space: 188340 Effective search space used: 188340 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_012332209.1 M446_RS11150 (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.13732.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-84 268.1 0.0 7.6e-84 267.7 0.0 1.1 1 lcl|NCBI__GCF_000019365.1:WP_012332209.1 M446_RS11150 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019365.1:WP_012332209.1 M446_RS11150 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.7 0.0 7.6e-84 7.6e-84 15 334 .. 72 427 .. 64 432 .. 0.92 Alignments for each domain: == domain 1 score: 267.7 bits; conditional E-value: 7.6e-84 TIGR00260 15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 l ++e ++ fr p++ v++ nl+++el hgPtlaFKD+++q ++ l+ ++l++ t+++At lcl|NCBI__GCF_000019365.1:WP_012332209.1 72 LDRMIEAAYAGFRHPAVCPLVQLdANLFLLELHHGPTLAFKDVAMQLLGRLMDHVLKARGSraTIVGAT 140 55678889999******98888888*****************************987654446****** PP TIGR00260 81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke 148 sGdtg+aa+ea++g v+v++L P+g++s v +++ + n++ la++G+FDd+q++vk++f++ + lcl|NCBI__GCF_000019365.1:WP_012332209.1 141 SGDTGSAAVEAFRGLDQVDVFILFPHGRVSEVqRRQMTSVDSPNVHALAVEGTFDDCQAIVKALFQHPR 209 ********************************999******************************9555 PP TIGR00260 149 ...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekl 214 ++ l+ vNsin+ar++aq ty+f + +lg v ++vp gnfg+il+G+++k+++ lp+ l lcl|NCBI__GCF_000019365.1:WP_012332209.1 210 faeEVRLSGVNSINWARVAAQATYYFTSAVALG-APHRPVSFAVPTGNFGDILAGWVAKRMG-LPVGRL 276 5669*****************************.66778*****************999999.****** PP TIGR00260 215 aiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke........ 274 i ++ + di+ r l +g e + T s++mdi +sn+er+l+ + r+ + l+ l + lcl|NCBI__GCF_000019365.1:WP_012332209.1 277 MIGTNAN-DILARTLATGTYEVRGVAPTTSPSMDIQVSSNFERLLFeALGREPEGLTRLMAglkqsgrf 344 ****998.**********666666669******************99888888888888779999**** PP TIGR00260 275 .................svsdeeileaikklaeeegyllephtavavaalkklvekg....vs..atad 320 +v + e+ +i+ +++ g +l+ph+a++v+a ++l+e++ v ata+ lcl|NCBI__GCF_000019365.1:WP_012332209.1 345 tlppevlkrvrsefdaaAVPEPEVAAEIRDTYARTGQILDPHSAIGVRAGRRLLEADpatpVValATAH 413 ****************999**************************************97652268**** PP TIGR00260 321 paKFeevvealtgn 334 aKF+++vea tg lcl|NCBI__GCF_000019365.1:WP_012332209.1 414 AAKFPDAVEAATGI 427 **********9996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (471 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: 00:00:00.01 # Mc/sec: 8.50 // [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