Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011840384.1 RSPH17029_RS02435 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000015985.1:WP_011840384.1 Length = 461 Score = 545 bits (1403), Expect = e-159 Identities = 276/461 (59%), Positives = 342/461 (74%), Gaps = 2/461 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRG APVLGF +A+L GLARDGGLY+P+ P + +I AL G SY EVA ++ Sbjct: 1 MQYISTRGTAPVLGFGEAMLTGLARDGGLYVPETVPALSESEIAALAGLSYEEVAFRIMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G +F ++ AY F H A PLVQ N F+LELFHGPTLAFKD AMQL+ Sbjct: 61 PFVGETFGDDEFRGLIAAAYEGFGHAARAPLVQLGPNHFLLELFHGPTLAFKDFAMQLIG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 ++ LA+ G+R TIVGATSGDTG AAIEAF G N D+FILFP+GRVS VQ+RQMT+ Sbjct: 121 QLFQAALAKNGQRITIVGATSGDTGSAAIEAFRGLSNVDVFILFPHGRVSEVQRRQMTTP 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 +NVHAL+++G+FDDCQ +K MFND F DA+ L+GVNSINWAR++ QVVYYFT+A++ Sbjct: 181 SEANVHALAVDGDFDDCQARLKDMFNDFAFRDAVGLAGVNSINWARVLAQVVYYFTSAVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAP R VSFTVPTGNFGDIFAGY+A+RMGLPI +L++ATN NDIL R L +GAYE GV Sbjct: 241 LGAPHREVSFTVPTGNFGDIFAGYIARRMGLPIARLVVATNQNDILHRALSTGAYETEGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 + SPSMDIQ+SSNFER LF+A+GRD AAV LM LKQ GGF ISE L +R+ F++ Sbjct: 301 TPSISPSMDIQVSSNFERALFDAYGRDGAAVAALMAELKQ-GGFRISENALGTLRATFAS 359 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420 GR++ +ET ATI + + G LL PHSA+GVKVA E+A G PM+ LATAHPAKFPDAV+ Sbjct: 360 GRASEEETLATIRATHAATGELLCPHSAVGVKVA-EEALGPEPMITLATAHPAKFPDAVE 418 Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHS 461 AA G+ P LPA + DL R E T + N+L +E +R + Sbjct: 419 AATGLRPPLPARMADLFDRPERVTRVPNDLSALETLIRERT 459 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: 598 Number of extensions: 23 Number of successful extensions: 3 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: 461 Length adjustment: 33 Effective length of query: 430 Effective length of database: 428 Effective search space: 184040 Effective search space used: 184040 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_011840384.1 RSPH17029_RS02435 (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.26185.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-83 265.8 0.0 3.5e-83 265.5 0.0 1.0 1 lcl|NCBI__GCF_000015985.1:WP_011840384.1 RSPH17029_RS02435 threonine synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_011840384.1 RSPH17029_RS02435 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 265.5 0.0 3.5e-83 3.5e-83 34 333 .. 93 422 .. 60 428 .. 0.91 Alignments for each domain: == domain 1 score: 265.5 bits; conditional E-value: 3.5e-83 TIGR00260 34 evgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkv 100 ++g n +++elfhgPtlaFKD+++q +++l+++al + + t+++AtsGdtg+aa+ea++g +nv+v lcl|NCBI__GCF_000015985.1:WP_011840384.1 93 QLG-PNHFLLELFHGPTLAFKDFAMQLIGQLFQAALAKNGQriTIVGATSGDTGSAAIEAFRGLSNVDV 160 344.489*************************99876655557************************** PP TIGR00260 101 vvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinpariea 165 ++L P+g++s v +++t + n++ la++GdFDd+q+ +k++f+d +++l vNsin+ar++a lcl|NCBI__GCF_000015985.1:WP_011840384.1 161 FILFPHGRVSEVqRRQMTTPSEANVHALAVDGDFDDCQARLKDMFNDFAfrdAVGLAGVNSINWARVLA 229 ************99*******************************8544667***************** PP TIGR00260 166 qktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdl 234 q++y+f + +lg +v + vp gnfg+i++G+ + +++ lpi+ l +a++++ di++r l +g lcl|NCBI__GCF_000015985.1:WP_011840384.1 230 QVVYYFTSAVALG-APHREVSFTVPTGNFGDIFAGYIARRMG-LPIARLVVATNQN-DILHRALSTGAY 295 *************.67778****************9999999.***9999999998.**********66 PP TIGR00260 235 epkedkeTlstAmdignpsnverale.larrslgnledlke........................svsd 278 e+ +s++mdi +sn+eral+ + r ++ + +l + ++s+ lcl|NCBI__GCF_000015985.1:WP_011840384.1 296 ETEGVTPSISPSMDIQVSSNFERALFdAYGRDGAAVAALMAelkqggfrisenalgtlratfasgRASE 364 66666699*****************97888888888888779999************************ PP TIGR00260 279 eeileaikklaeeegyllephtavavaalkklvekg...vsatadpaKFeevvealtg 333 ee+l +i+ + g ll ph+av+v++ ++ + + + ata+paKF+++vea tg lcl|NCBI__GCF_000015985.1:WP_011840384.1 365 EETLATIRATHAATGELLCPHSAVGVKVAEEALGPEpmiTLATAHPAKFPDAVEAATG 422 *********************************99986555*************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (461 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: 10.95 // [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