Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_084276090.1 B8779_RS08115 threonine synthase
Query= curated2:O24924 (486 letters) >NCBI__GCF_900176045.1:WP_084276090.1 Length = 488 Score = 419 bits (1076), Expect = e-121 Identities = 232/489 (47%), Positives = 305/489 (62%), Gaps = 8/489 (1%) Query: 1 MPFVPTRS---LKEKKIDFIEAILNPNAPKGGLYTLERFETLQ---WQDCLNLSYNDLVE 54 M F+ TR K KK+ F EAILNP+A GGLY E+ + Q L Y +L Sbjct: 1 MYFIETRGNDGKKPKKVTFSEAILNPSASYGGLYVPEKLPNIDEKFLQRHLTSHYKELAF 60 Query: 55 CVFERLGLEIPKNLLASALKRYENFDNPKNPAPIFALNERLFVQELYHGPSLAFKDMALQ 114 + ++I + L+ AL Y+ FD+P NP P+ + E LF+ ELYHGP+ AFKDMALQ Sbjct: 61 DLLRLFSIDIDEELIKEALNLYDKFDDPANPIPVVKVEENLFIAELYHGPTRAFKDMALQ 120 Query: 115 PLASLFSNLAVGKNEKYLMLVSTSGDTGPATLESLAGMPNVFVVCLYPKDGTSLVQKLQM 174 P + S+LA + E YL+L +TSGDTGPATLE+ NV V C+YP GTS VQ+LQM Sbjct: 121 PFGYILSSLAKARGENYLILAATSGDTGPATLETFKNRENVKVACIYPAGGTSDVQRLQM 180 Query: 175 VTQSASNLKVFGISGDFDDAQNALKNLLKDDDFNEALKACQLKLSVANSVNFGRIAFQIV 234 VT+ NLKV GI GDFDDAQ+ALK+LL + F+ L+ +KLS ANSVNFGRI FQI+ Sbjct: 181 VTEDGENLKVIGIEGDFDDAQSALKSLLASEKFHAILQEKGIKLSAANSVNFGRIIFQII 240 Query: 235 YHIWGFLELYKKGAINSKEKITLAIPSGNFGNALGAFYAKKMGLNIDKIKVVTNSNDVLR 294 YHI +LEL ++ I + I L +PSGNFGNALG +YAKKMGL I KI + +N+N+VL Sbjct: 241 YHIHSYLELVRRKEITFGDTINLIVPSGNFGNALGGYYAKKMGLPIKKILIASNANNVLT 300 Query: 295 EFIETGRYDLTHRSLKQTYSPAMDILKSSNVERALFSLFGFERTLELMQALEEEKFYALK 354 E I GRYDL ++ L +T SPAMDILKSSNVER LF FG +RT ELM +L ++ +Y L Sbjct: 301 ELINEGRYDLRNKHLIKTSSPAMDILKSSNVERVLFDKFGAQRTKELMDSLNDKGYYKLN 360 Query: 355 PKELALLQEHFSCASCSDEACLKTIQEVYAEHQYLIDPHTATALNASLK-THEKTLVSAT 413 ELA LQE F+ +D+ I+E E YL+DPHTAT + + +K + +T Sbjct: 361 EDELAALQEDFAADFSNDDEVKAIIKEYALEKTYLMDPHTATTIKLFKRYAADKNVAYST 420 Query: 414 ASYEKFPRITLLALNEQKKNDNDKAALETLKNSYNTPDSQRLDDLFERGIKHQEVLKLNE 473 A + KF L AL +K +D AL+ + QR+ +LF + I H V+ + Sbjct: 421 AEWTKFAPTVLEALEGGEKK-SDLEALQIISEKLGVAIPQRIAELFHKRIVHTTVVPKEK 479 Query: 474 IKSSILLWL 482 I+ IL +L Sbjct: 480 IEEEILKFL 488 Lambda K H 0.318 0.134 0.381 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: 655 Number of extensions: 25 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: 486 Length of database: 488 Length adjustment: 34 Effective length of query: 452 Effective length of database: 454 Effective search space: 205208 Effective search space used: 205208 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
Align candidate WP_084276090.1 B8779_RS08115 (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.43612.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-88 281.0 0.1 9.3e-88 280.6 0.1 1.1 1 NCBI__GCF_900176045.1:WP_084276090.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900176045.1:WP_084276090.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 280.6 0.1 9.3e-88 9.3e-88 12 338 .. 71 441 .. 62 443 .. 0.91 Alignments for each domain: == domain 1 score: 280.6 bits; conditional E-value: 9.3e-88 TIGR00260 12 ekdlvdlaegstelfrspklaeevga..enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 +++l++ a + f+ p+++ +v + enl++ el+hgPt aFKD++lq+ + +l+ ++++ e ++l At NCBI__GCF_900176045.1:WP_084276090.1 71 DEELIKEALNLYDKFDDPANPIPVVKveENLFIAELYHGPTRAFKDMALQPFGYILSSLAKARGEnyLILAAT 143 56667777788999999999988877789****************************9987665557****** PP TIGR00260 81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke.... 148 sGdtg+a++e ++ ++nvkv ++yP+g++s v ++vt en+kv++i+GdFDdaq ++k+++ ++ NCBI__GCF_900176045.1:WP_084276090.1 144 SGDTGPATLETFKNRENVKVACIYPAGGTSDVqRLQMVTEDGENLKVIGIEGDFDDAQSALKSLLASEKfhai 216 ********************************99******************************994445889 PP TIGR00260 149 ....klklnsvNsinparieaqk.tyafeiveqlgk...espdkvvvpvpsgnfgailkGflekkelglpiek 213 +kl+++Ns+n++ri +q+ +++++ +e + + d + + vpsgnfg++l G+++kk++ lpi+k NCBI__GCF_900176045.1:WP_084276090.1 217 lqekGIKLSAANSVNFGRIIFQIiYHIHSYLELVRRkeiTFGDTINLIVPSGNFGNALGGYYAKKMG-LPIKK 288 99989***************************99984444579***********************9.***** PP TIGR00260 214 laiaaegaadivrrflksg.dlepkedk.eTlstAmdignpsnverale...larrslgnledlke....... 274 + ia++ + +++++ +++g +++ +++ +T s+Amdi+++snver+l+ +a+r+++ +++l+ NCBI__GCF_900176045.1:WP_084276090.1 289 ILIASNAN-NVLTELINEGrYDLRNKHLiKTSSPAMDILKSSNVERVLFdkfGAQRTKELMDSLNDkgyykln 360 ******98.99999988887777777778*******************9999************88******* PP TIGR00260 275 ..............svsdeeileaikklaeeegyllephtavavaalkklvekg..vsatadpaKFeevve.a 330 +d+e+ ik+ a e+ yl++phta++++ k+ +++ ++ta+ KF+ +v+ a NCBI__GCF_900176045.1:WP_084276090.1 361 edelaalqedfaadFSNDDEVKAIIKEYALEKTYLMDPHTATTIKLFKRYAADKnvAYSTAEWTKFAPTVLeA 433 ************9656667777777888889******************999888777***********9999 PP TIGR00260 331 ltgnklkd 338 l g ++k+ NCBI__GCF_900176045.1:WP_084276090.1 434 LEGGEKKS 441 99988875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (488 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: 00:00:00.00 # Mc/sec: 20.90 // [ok]
This GapMind analysis is from Jul 25 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