Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_050462303.1 AKL27_RS07655 threonine synthase
Query= BRENDA::Q2SWH9 (483 letters) >NCBI__GCF_001189915.1:WP_050462303.1 Length = 486 Score = 694 bits (1790), Expect = 0.0 Identities = 349/487 (71%), Positives = 402/487 (82%), Gaps = 7/487 (1%) Query: 1 MNYISTRGAGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFEI 60 M Y+STRG +FS+ILLGGLA DGGLYLP+EYPQVS EL +WR+L YADLA+E+ Sbjct: 1 MQYVSTRGHAATP--SFSEILLGGLAPDGGLYLPAEYPQVSRAELDQWRSLSYADLAYEV 58 Query: 61 LSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTLGTENGAPVSLLELSNG 120 L KF DI ADL+A+T +TY ADVY + R G NAADITPL L ++G + L LSNG Sbjct: 59 LRKFATDIPDADLKALTHKTYRADVYCNVRAGENAADITPLRVLEQQDGKKLVLQGLSNG 118 Query: 121 PTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFMLSPH 180 PTLAFKDMAMQLLGNLFEY LA++ LNILGATSGDTGSAAEYAMRGK+G+RVFMLSPH Sbjct: 119 PTLAFKDMAMQLLGNLFEYALARNQAQLNILGATSGDTGSAAEYAMRGKQGIRVFMLSPH 178 Query: 181 KKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSINWAR 240 KKMSAFQTAQM+SLQDPNIFN+AV GVFDDCQDIVKAVSND +KA QKIGTVNSINWAR Sbjct: 179 KKMSAFQTAQMFSLQDPNIFNIAVEGVFDDCQDIVKAVSNDLGYKAAQKIGTVNSINWAR 238 Query: 241 VVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNENDV 300 VVAQVVYYF+GY +AT ++DE+VSFTVPSGNFGN+CAGHIARMMGLPI KLVVATNENDV Sbjct: 239 VVAQVVYYFRGYLSATTASDEQVSFTVPSGNFGNICAGHIARMMGLPIAKLVVATNENDV 298 Query: 301 LDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVEQKG 360 LDEFFRTG YRVR + +TYHTSSPSMDISKASNFERFV+DLLGRD ARV LF V+ G Sbjct: 299 LDEFFRTGIYRVRKSAETYHTSSPSMDISKASNFERFVYDLLGRDSARVKALFHQVDTAG 358 Query: 361 GFDLAAS-----GDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAR 415 GFDL+ + +F V +GF SG+STHADR+ TIR +Y +DTHTADG+KVAR Sbjct: 359 GFDLSGAAGSDGNEFESVIRYGFASGKSTHADRLETIRFAERQYGITVDTHTADGIKVAR 418 Query: 416 EHLRPGVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVKD 475 EHL+PGV M+VLETA P KF E+IREALG++ RPA F+ +EALPQRFEV+ A+A ++K Sbjct: 419 EHLQPGVTMIVLETALPAKFNETIREALGRDAERPAGFENIEALPQRFEVMAADAARIKQ 478 Query: 476 FIAAHTG 482 F+AAHTG Sbjct: 479 FVAAHTG 485 Lambda K H 0.320 0.135 0.392 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: 719 Number of extensions: 23 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: 483 Length of database: 486 Length adjustment: 34 Effective length of query: 449 Effective length of database: 452 Effective search space: 202948 Effective search space used: 202948 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: 52 (24.6 bits)
Align candidate WP_050462303.1 AKL27_RS07655 (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.16684.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-73 232.8 0.1 4.1e-73 232.4 0.1 1.1 1 lcl|NCBI__GCF_001189915.1:WP_050462303.1 AKL27_RS07655 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050462303.1 AKL27_RS07655 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 232.4 0.1 4.1e-73 4.1e-73 37 332 .. 104 446 .. 60 453 .. 0.88 Alignments for each domain: == domain 1 score: 232.4 bits; conditional E-value: 4.1e-73 TIGR00260 37 a...enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkv 100 + ++l ++ l+ gPtlaFKD+++q +++l+++al + ++ +l+AtsGdtg+aa +a++gk++++v lcl|NCBI__GCF_001189915.1:WP_050462303.1 104 QqdgKKLVLQGLSNGPTLAFKDMAMQLLGNLFEYALARNQAqlNILGATSGDTGSAAEYAMRGKQGIRV 172 23448999****************************99999889************************* PP TIGR00260 101 vvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife...dkeklklnsvNsinpariea 165 ++L P+ k+s +++ + n+ +a++G FDd+qd+vk++ + k + k++ vNsin+ar+ a lcl|NCBI__GCF_001189915.1:WP_050462303.1 173 FMLSPHKKMSAFqTAQMFSLQDPNIFNIAVEGVFDDCQDIVKAVSNdlgYKAAQKIGTVNSINWARVVA 241 ************99*******************************96655669**************** PP TIGR00260 166 qktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksg.d 233 q++y+f s ++v + vpsgnfg+i +G ++++glpi+kl +a++++ d++++f ++g + lcl|NCBI__GCF_001189915.1:WP_050462303.1 242 QVVYYFRGYLSATTASDEQVSFTVPSGNFGNICAG-HIARMMGLPIAKLVVATNEN-DVLDEFFRTGiY 308 **8888766666669********************.6667777************9.**********65 PP TIGR00260 234 lepkedk..eTlstAmdignpsnverale.larrslgnledlke......................... 274 + k+ +T s++mdi++ sn+er + l r + +++l + lcl|NCBI__GCF_001189915.1:WP_050462303.1 309 RVRKSAEtyHTSSPSMDISKASNFERFVYdLLGRDSARVKALFHqvdtaggfdlsgaagsdgnefesvi 377 444444357899**************8877999999999999668999********************* PP TIGR00260 275 .......svsdeeileaikklaeeegyllephtavavaalkklvekg.vs...atadpaKFeevvealt 332 + + ++ le+i+ + ++ g+++++hta ++++ ++ ++ g + ta paKF+e++ + lcl|NCBI__GCF_001189915.1:WP_050462303.1 378 rygfasgKSTHADRLETIRFAERQYGITVDTHTADGIKVAREHLQPGvTMivlETALPAKFNETIREAL 446 ******9999*************************************6225679********9998544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (486 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 15.06 // [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