Score = 82.4 bits (202), Expect = 8e-16, Method: Composition-based stats.
Identities = 44/89 (49%), Positives = 58/89 (65%), Gaps = 4/89 (4%)
Query: 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDLPNE---FKFTSSILKKENLSKYHPLVDY 57
+ V A +KPFYV+ ES KFVR++PL+ DLP FT E+ + P +DY
Sbjct: 216 VGVLAHNARKPFYVVTESHKFVRMFPLSSDDLPMAGPPLDFTRRTDDLEDALR-GPTIDY 274
Query: 58 TPPQYITLLFTDLGILTPSAVSDELIKLY 86
T +YIT L TDLG+LTPSAVS+ELIK++
Sbjct: 275 TAQEYITALITDLGVLTPSAVSEELIKMW 303
Acts as a non-essential regulatory component of the translation initiation factor 2B (eIF2-B or GCD complex), which catalyzes the exchange of eukaryotic initiation factor 2 (eIF-2)-bound GDP for GTP and is regulated by phosphorylated eIF-2. It activates the synthesis of GCN4 in yeast under amino acid starvation conditions by suppressing the inhibitory effects of multiple AUG codons present in the leader of GCN4 mRNA. It may promote either repression or activation of GCN4 expression depending on amino acid availability. Modulation of GCN3 regulatory function in response to amino acid availability occurs post-translationally.
Score = 87.0 bits (216), Expect = 2e-22
Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDL-----PNEFK-FTSSILKKENLSKYHPL 54
+A+ AK PFYV+AE++KF +PL++ P E T + ENL +P
Sbjct: 201 LALLAKAHNVPFYVVAETYKFDPRFPLDEDIFIEERDPEEVLYRTGVRIAPENLKVRNPA 260
Query: 55 VDYTPPQYITLLFTDLGILTP 75
DYTPP+ ITL+ T++G+L P
Sbjct: 261 FDYTPPELITLIITEVGVLPP 281
This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft. Length = 281
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Score = 52.8 bits (127), Expect = 8e-10
Identities = 25/82 (30%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 1 MAVCAKELKKPFYVLAESFKF------VRLYPLNQRDLPNEFKFTSSI-LKKENLSKYHP 53
+AV AKE + PF+V A F + +RD P E + + + Y+P
Sbjct: 223 LAVLAKEFRIPFFVAAPLSTFDTKTSCGEDIVIEERD-PEEVAQVGGVRIAPLGVKVYNP 281
Query: 54 LVDYTPPQYITLLFTDLGILTP 75
D TP I + T+ GI+TP
Sbjct: 282 AFDITPHDLIDAIITEKGIITP 303
This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins [Unknown function, General]. Length = 303
>gnl|CDD|223260 COG0182, COG0182, Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Score = 46.6 bits (111), Expect = 1e-07
Identities = 28/97 (28%), Positives = 43/97 (44%), Gaps = 16/97 (16%)
Query: 1 MAVCAKELKKPFYVLAESFKFV------RLYPLNQRD----LPNEFKFTSSILKKENLSK 50
+A+ A+E + PF V AE++KF L + +RD L E +K N
Sbjct: 209 LALAAREARVPFMVAAETYKFHPKTITGELVEIEERDPTEVLDEEDLKQLGNVKVRN--- 265
Query: 51 YHPLVDYTPPQYITLLFTDLGILTPSAVSDELIKLYL 87
P D TPP+Y+ + T+ G + P +IK
Sbjct: 266 --PAFDVTPPEYVDAIITERGQIPPEMAYT-IIKELF 299
The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase [Energy metabolism, Other]. Length = 301
The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=99.89 E-value=3e-24 Score=154.44 Aligned_cols=74 Identities=31% Similarity=0.448 Sum_probs=65.7
Q ss_pred CccccccCCCcEEEEcccccCccCccCCCCCCCccccCCcccccC-------CCccccCCeeeecCCCCccEEEeCCCCc
Q psy6494 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDLPNEFKFTSSILKK-------ENLSKYHPLVDYTPPQYITLLFTDLGIL 73 (87)
Q Consensus 1 iA~~Ak~~~vPv~v~a~~~K~~~~~~~~~~~~~~e~~~~~~v~~~-------~~~~~~np~fD~tPp~lI~~~iTe~G~~ 73 (87)
+|++||+++|||||+||+|||+++.+ .++++++|++++.|+... ++++++||+||+|||+|||++|||.|++
T Consensus 223 lA~~Ak~~~vPv~V~a~s~K~~~~~~-~g~~i~~e~~~~~ev~~~~~~~~~~~~~~v~np~fD~TP~~lIt~iiTe~Gv~ 301 (303)
T TIGR00524 223 LAVLAKEFRIPFFVAAPLSTFDTKTS-CGEDIVIEERDPEEVAQVGGVRIAPLGVKVYNPAFDITPHDLIDAIITEKGII 301 (303)
T ss_pred HHHHHHHhCCCEEEecccccccCCCC-CccccccccCCHHHhccccCcccCCCCceeecccccCCCHHHCCEEEcCCCcc
Confidence 58999999999999999999999976 446778899988887532 5789999999999999999999999999
Q ss_pred CC
Q psy6494 74 TP 75 (87)
Q Consensus 74 ~p 75 (87)
+|
T Consensus 302 ~p 303 (303)
T TIGR00524 302 TP 303 (303)
T ss_pred Cc
Confidence 87
This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=99.88 E-value=7.9e-24 Score=153.73 Aligned_cols=74 Identities=28% Similarity=0.432 Sum_probs=66.4
Q ss_pred CccccccCCCcEEEEcccccCccCccCCCCCCCccccCCcccccC-------CCccccCCeeeecCCCCccEEEeCCCCc
Q psy6494 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDLPNEFKFTSSILKK-------ENLSKYHPLVDYTPPQYITLLFTDLGIL 73 (87)
Q Consensus 1 iA~~Ak~~~vPv~v~a~~~K~~~~~~~~~~~~~~e~~~~~~v~~~-------~~~~~~np~fD~tPp~lI~~~iTe~G~~ 73 (87)
+|++||+++|||||+||++||++..+ +++++++|+|++.|+... ++++++||+||+|||+|||++|||.|++
T Consensus 251 lA~~Ak~~~vPfyV~a~~~kfd~~~~-~~~~i~iE~r~p~ev~~~~g~~~~~~~~~v~Np~FD~TP~~lIt~iITe~Gv~ 329 (331)
T TIGR00512 251 LAVLAKHHGVPFYVAAPTSTIDLETK-DGAEIPIEERPPEEVTHVGGVRIAPPGIDVWNPAFDVTPAELITGIITEKGVI 329 (331)
T ss_pred HHHHHHHhCCCEEEeccccccccCCC-CccccccccCCHHHhcccCCcccCCCCceeecccccCCCHHHCCEEEccCCcc
Confidence 58999999999999999999999875 556788999999887642 5789999999999999999999999999
Q ss_pred CC
Q psy6494 74 TP 75 (87)
Q Consensus 74 ~p 75 (87)
.|
T Consensus 330 ~p 331 (331)
T TIGR00512 330 TP 331 (331)
T ss_pred CC
Confidence 76
The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA.
>PF01008 IF-2B: Initiation factor 2 subunit family; InterPro: IPR000649 Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit
Probab=99.88 E-value=3.3e-24 Score=151.45 Aligned_cols=74 Identities=51% Similarity=0.878 Sum_probs=58.1
Q ss_pred CccccccCCCcEEEEcccccCccCccCCCCCCCccccCCcccccC-------CCccccCCeeeecCCCCccEEEeCCCCc
Q psy6494 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDLPNEFKFTSSILKK-------ENLSKYHPLVDYTPPQYITLLFTDLGIL 73 (87)
Q Consensus 1 iA~~Ak~~~vPv~v~a~~~K~~~~~~~~~~~~~~e~~~~~~v~~~-------~~~~~~np~fD~tPp~lI~~~iTe~G~~ 73 (87)
+|++||+++|||||+|++|||++.+++++... +|.+++.+++.. +++++.||+||+|||+|||++|||.|++
T Consensus 202 ~a~~Ak~~~vPv~v~~~~~K~~~~~~~~~~~~-~e~~~~~~v~~~~~~~~~~~~v~~~~p~~D~tP~~~It~~iTe~G~~ 280 (282)
T PF01008_consen 202 LALAAKEFNVPVYVLAESYKFSPRYPLDQDSF-NELRDPQEVLPFDGSSIVPENVDVINPLFDYTPPDLITLIITELGIL 280 (282)
T ss_dssp HHHHHHHTT-EEEEE--GGGBETTCSSGGGSS-S-B--THHHHEETTEEESTTTEEEE-BSEEEEEGGG-SEEEETTEEE
T ss_pred HHHHHHhhCCCEEEEcccccccccccccchhh-hhccccceeeccCCcccccceeeccCccEeecCHHHCCEEEcCCCCC
Confidence 58999999999999999999999998887665 788888877543 4889999999999999999999999999
Q ss_pred CC
Q psy6494 74 TP 75 (87)
Q Consensus 74 ~p 75 (87)
+|
T Consensus 281 ~P 282 (282)
T PF01008_consen 281 PP 282 (282)
T ss_dssp -C
T ss_pred Cc
Confidence 98
The eukaryotic translation initiation factor EIF-2B is a complex made up of five different subunits, alpha, beta, gamma, delta and epsilon, and catalyses the exchange of EIF-2-bound GDP for GTP. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes; related proteins from archaebacteria and IF-2 from prokaryotes and also contains a subfamily of proteins in eukaryotes, archaeae (e.g. Pyrococcus furiosus), or eubacteria such as Bacillus subtilis and Thermotoga maritima. Many of these proteins were initially annotated as putative translation initiation factors despite the fact that there is no evidence for the requirement of an IF2 recycling factor in prokaryotic translation initiation. Recently, one of these proteins from B. subtilis has been functionally characterised as a 5-methylthioribose-1-phosphate isomerase (MTNA) []. This enzyme participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthioribulose-1-phosphate []. The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species.; GO: 0044237 cellular metabolic process; PDB: 1VB5_A 1T5O_D 3A11_E 3VM6_C 1W2W_A 1T9K_A 3ECS_B 2YRF_A 2YVK_B 2A0U_A ....
>pdb|3VM6|A Chain A, Crystal Structure Of Ribose-1,5-Bisphosphate Isomerase From Thermococcus Kodakarensis Kod1 In Complex With Alpha-D-Ribose-1,5- Bisphosphate Length = 338
