Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_015927025.1 MNOD_RS01315 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000022085.1:WP_015927025.1 Length = 471 Score = 546 bits (1408), Expect = e-160 Identities = 282/464 (60%), Positives = 334/464 (71%), Gaps = 2/464 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M +VSTRG A L F+DALLAGLARDGGLYLP+ +P I L G+ Y A VL+ Sbjct: 1 MLHVSTRGAAAKLTFTDALLAGLARDGGLYLPERWPALDPAAIAGLAGRPYAAAAKTVLS 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 P GEIP D +RM+ AY TFRH AVCPLVQ N F+LEL HGPTLAFKDVAMQLL Sbjct: 61 PLVDGEIPQGDLDRMIEGAYATFRHPAVCPLVQLGDNLFLLELHHGPTLAFKDVAMQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+MD+VL RG RATIVGATSGDTG AA+EAF G D D+FILFP+GRVS VQ+RQMT+ Sbjct: 121 RLMDHVLKARGSRATIVGATSGDTGSAAVEAFRGLDQVDVFILFPHGRVSEVQRRQMTTV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 +NVHA+++EG FDDCQ +VK +F F + + LSGVNSINWAR+ Q VYYFT+A++ Sbjct: 181 DSANVHAVAVEGTFDDCQAIVKALFQHPRFAEEVRLSGVNSINWARVAAQAVYYFTSAVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG+P R VSF+VPTGNFGDI AG+VAKRMGLP+ +L+IATN NDIL+RTL SGAYE+RGV Sbjct: 241 LGSPHRPVSFSVPTGNFGDILAGWVAKRMGLPVGRLMIATNANDILARTLASGAYEVRGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 A TTSPSMDIQ+SSNFERLLFEA R+ + LM LKQSG F++ L +R+EF A Sbjct: 301 APTTSPSMDIQVSSNFERLLFEALDREPEGLNRLMASLKQSGAFSLPPAVLERVRAEFDA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE--KASGTAPMVVLATAHPAKFPDA 418 E AA I GY+LDPHSAIGV+ R A P+V LATAH AKFPDA Sbjct: 361 AAVQEPEVAAEIRETYRSTGYVLDPHSAIGVRAGRRLLDADPATPVVALATAHAAKFPDA 420 Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 V+AA G P LP L DLM R+E F VL N+ VE ++R +R Sbjct: 421 VEAATGQRPALPPHLADLMTRRERFAVLPNDEGAVERFIRERAR 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: 580 Number of extensions: 27 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_015927025.1 MNOD_RS01315 (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.11988.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-89 286.4 0.0 2.1e-89 286.0 0.0 1.0 1 lcl|NCBI__GCF_000022085.1:WP_015927025.1 MNOD_RS01315 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000022085.1:WP_015927025.1 MNOD_RS01315 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 286.0 0.0 2.1e-89 2.1e-89 11 335 .. 68 428 .. 63 432 .. 0.92 Alignments for each domain: == domain 1 score: 286.0 bits; conditional E-value: 2.1e-89 TIGR00260 11 tekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tv 76 ++ dl ++eg +++fr p++ v++ nl+++el hgPtlaFKD+++q ++ l+ ++l++ t+ lcl|NCBI__GCF_000022085.1:WP_015927025.1 68 PQGDLDRMIEGAYATFRHPAVCPLVQLgDNLFLLELHHGPTLAFKDVAMQLLGRLMDHVLKARGSraTI 136 467888999*************8888888*****************************987654446** PP TIGR00260 77 lcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeif 144 ++AtsGdtg+aa+ea++g v+v++L P+g++s v +++t+ n++ +a++G+FDd+q++vk++f lcl|NCBI__GCF_000022085.1:WP_015927025.1 137 VGATSGDTGSAAVEAFRGLDQVDVFILFPHGRVSEVqRRQMTTVDSANVHAVAVEGTFDDCQAIVKALF 205 ************************************99******************************* PP TIGR00260 145 edke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglp 210 ++ + ++ l+ vNsin+ar++aq +y+f + +lg v ++vp gnfg+il+G+++k+++ lp lcl|NCBI__GCF_000022085.1:WP_015927025.1 206 QHPRfaeEVRLSGVNSINWARVAAQAVYYFTSAVALG-SPHRPVSFSVPTGNFGDILAGWVAKRMG-LP 272 95555669*****************************.66778*****************999999.** PP TIGR00260 211 ieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.... 274 + l ia++ + di+ r l sg e + T s++mdi +sn+er+l+ + r+ + l+ l + lcl|NCBI__GCF_000022085.1:WP_015927025.1 273 VGRLMIATNAN-DILARTLASGAYEVRGVAPTTSPSMDIQVSSNFERLLFeALDREPEGLNRLMAslkq 340 ******99998.**********666666669******************99888888877777667888 PP TIGR00260 275 .....................svsdeeileaikklaeeegyllephtavavaalkklvekg....vs.. 316 +v++ e+ +i++ +++ gy+l+ph+a++v+a ++l++++ v lcl|NCBI__GCF_000022085.1:WP_015927025.1 341 sgafslppavlervraefdaaAVQEPEVAAEIRETYRSTGYVLDPHSAIGVRAGRRLLDADpatpVVal 409 ********************99***************************************97652268 PP TIGR00260 317 atadpaKFeevvealtgnk 335 ata+ aKF+++vea tg+ lcl|NCBI__GCF_000022085.1:WP_015927025.1 410 ATAHAAKFPDAVEAATGQR 428 ****************986 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.31 // [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