RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6494
(87 letters)
>gnl|CDD|216240 pfam01008, IF-2B, Initiation factor 2 subunit family. 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
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
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B
alpha/beta/delta family [Translation, ribosomal
structure and biogenesis].
Length = 301
Score = 83.2 bits (206), Expect = 7e-21
Identities = 36/93 (38%), Positives = 49/93 (52%), Gaps = 12/93 (12%)
Query: 2 AVCAKELKKPFYVLAESFKFVRLYPLNQRDL-----PNEFKFTS--SILKKENLSKYHPL 54
A+ A+EL+ PFYV+AES+KFV L+ P E LK N P
Sbjct: 214 ALAARELRVPFYVVAESYKFVPKTLLDTLVEIELRDPLEVAREEPLGNLKVRN-----PA 268
Query: 55 VDYTPPQYITLLFTDLGILTPSAVSDELIKLYL 87
D TPP+YI + T+LGI+ PS++ L +LY
Sbjct: 269 FDVTPPEYIDAIITELGIIPPSSIYRILRELYG 301
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 56.8 bits (138), Expect = 3e-11
Identities = 32/97 (32%), Positives = 46/97 (47%), Gaps = 16/97 (16%)
Query: 1 MAVCAKELKKPFYVLAESFKFV------RLYPLNQRD----LPNEFKFTSSILKKENLSK 50
+A+ A E + PF V AE++KF L + +RD LP E +K N
Sbjct: 214 IALAAHEARVPFMVAAETYKFSPKTLLGELVEIEERDPTEVLPEEILAKLPGVKVRN--- 270
Query: 51 YHPLVDYTPPQYITLLFTDLGILTPSAVSDELIKLYL 87
P D TPP+YI + T++G + P +IK YL
Sbjct: 271 --PAFDVTPPEYIDAIITEIGAIPPEMAYT-IIKEYL 304
>gnl|CDD|168237 PRK05772, PRK05772, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 363
Score = 54.4 bits (131), Expect = 3e-10
Identities = 31/80 (38%), Positives = 46/80 (57%), Gaps = 7/80 (8%)
Query: 2 AVCAKELKKPFYVLAESFKF-----VRLYPLNQRDLPNEFKFTSSI-LKKENLSKYHPLV 55
AV A EL PFY LA + F V + +RD PNE + + + E+++ Y+P+
Sbjct: 273 AVIAHELGIPFYALAPTSTFDLKSDVNDVKIEERD-PNEVRTIRGVPITPEDVNVYNPVF 331
Query: 56 DYTPPQYITLLFTDLGILTP 75
D TPP+YIT + T+ GI+ P
Sbjct: 332 DVTPPKYITGIITEKGIIYP 351
>gnl|CDD|233008 TIGR00524, eIF-2B_rel, eIF-2B alpha/beta/delta-related
uncharacterized proteins. 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
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
>gnl|CDD|223260 COG0182, COG0182, Predicted translation initiation factor 2B
subunit, eIF-2B alpha/beta/delta family [Translation,
ribosomal structure and biogenesis].
Length = 346
Score = 50.4 bits (121), Expect = 6e-09
Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 16/94 (17%)
Query: 2 AVCAKELKKPFYVLA---------ESFKFVRLYPLNQRDLPNEFKFTSSI-LKKENLSKY 51
AV AK PFYV A +S + + P+ +RD P E + + E + Y
Sbjct: 255 AVLAKHHGIPFYVAAPLSTIDFELKSGEDI---PIEERD-PEEVLEVGGVRIAPEGVEAY 310
Query: 52 HPLVDYTPPQYITLLFTDLGILTPSAVSDELIKL 85
+P D TPP+ IT + T+ G+ TP +E +KL
Sbjct: 311 NPAFDVTPPELITGIITEKGVFTPP--FEENLKL 342
>gnl|CDD|188057 TIGR00511, ribulose_e2b2, ribose-1,5-bisphosphate isomerase, e2b2
family. 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
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
>gnl|CDD|235788 PRK06372, PRK06372, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 253
Score = 46.4 bits (110), Expect = 1e-07
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 1 MAVCAKELKKPFYVLAESFKFVRLYPLNQRDLPNEFKFTSSILKKENLSKYHPLVDYTPP 60
+A+CA+ LKKPFY L S K R + + FK ++ + D TPP
Sbjct: 177 LALCARYLKKPFYSLTISMKIERNFLYSTYP---NFKNHPCSEWNIDIPCINRYFDKTPP 233
Query: 61 QYITLLFTDLGILTPSAVS 79
I + G + PS V+
Sbjct: 234 DLIDYYINENGFVKPSDVN 252
>gnl|CDD|180362 PRK06036, PRK06036, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 339
Score = 45.1 bits (107), Expect = 5e-07
Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 7/89 (7%)
Query: 2 AVCAKELKKPFYVLA--ESFKFVRL---YPLNQRDLPNEFKFTSSI-LKKENLSKYHPLV 55
+V AKE + PFYV A +F F + +RD P+E ++ + +++ Y+P
Sbjct: 252 SVLAKEHEIPFYVAAPLSTFDFEGWEGSVKIEERD-PDELRYCGKTQIAPKDVPVYNPAF 310
Query: 56 DYTPPQYITLLFTDLGILTPSAVSDELIK 84
D TP + +T + T+ G+ P + DE++
Sbjct: 311 DATPMENVTAIITEKGVFYPPFLLDEVLV 339
>gnl|CDD|235578 PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
Length = 344
Score = 39.8 bits (94), Expect = 4e-05
Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 9/93 (9%)
Query: 1 MAVCAKELKKPFYVLAESFKF------VRLYPLNQRDLPNE-FKFTSSILKKENLSKYHP 53
+A+ AK PFYV A S + P+ +RD P E + + E + Y+P
Sbjct: 251 LAIAAKYHGVPFYVAAPSSTIDLTLADGKEIPIEERD-PEEVTEVGGVRIAPEGVKVYNP 309
Query: 54 LVDYTPPQYITLLFTDLGILTPSAVSDELIKLY 86
D TP + IT + T+ GI+ P + L L+
Sbjct: 310 AFDVTPAELITGIITEKGIVAPPD-TANLAALF 341
>gnl|CDD|180547 PRK06371, PRK06371, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 329
Score = 39.5 bits (92), Expect = 4e-05
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 14/92 (15%)
Query: 2 AVCAKELKKPFYVLA--ESFKFV----RLYPLNQRDLPNEFKFTSS--ILKKENLSKYHP 53
AV AK PFYV A +F F P+ +RD NE + I +E+ ++ +P
Sbjct: 242 AVLAKVNGIPFYVAAPGSTFDFSIKSGDEIPIEERD-ENEVLEINGCRIGPQESHAR-NP 299
Query: 54 LVDYTPPQYITLLFTDLGILTPSAVSDELIKL 85
D TP +Y+T T+ GI P+ EL KL
Sbjct: 300 AFDVTPNEYVTGFITEYGIFKPN----ELWKL 327
>gnl|CDD|169387 PRK08335, PRK08335, translation initiation factor IF-2B subunit
alpha; Validated.
Length = 275
Score = 39.4 bits (92), Expect = 5e-05
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 6/65 (9%)
Query: 11 PFYVLAESFKFVRLYPLNQRDLPNEFKFTSSILKKENLSKYHPLVDYTPPQYITLLFTDL 70
PFYV AE+FKF + E + ++ + L D TP +Y+ + T+L
Sbjct: 213 PFYVAAETFKF------HPELKSEEVELVERPYARQGHRVRNVLFDVTPWKYVRGIITEL 266
Query: 71 GILTP 75
GIL P
Sbjct: 267 GILVP 271
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 36.5 bits (84), Expect = 6e-04
Identities = 25/81 (30%), Positives = 39/81 (48%), Gaps = 7/81 (8%)
Query: 1 MAVCAKELKKPFYVLAE------SFKFVRLYPLNQRDLPNEFKFTSSILKKENLSKYHPL 54
+AV AKE PF+ +A S K + P+ +R P E ++ Y+P
Sbjct: 264 LAVLAKEHGIPFFTVAPLSTIDMSLKSGKEIPIEERS-PEEVLTCGGCRIAPDVDVYNPA 322
Query: 55 VDYTPPQYITLLFTDLGILTP 75
D TP +Y+T + TD G++ P
Sbjct: 323 FDVTPHKYLTGIITDRGVVWP 343
>gnl|CDD|233003 TIGR00512, salvage_mtnA, S-methyl-5-thioribose-1-phosphate
isomerase. 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 [Amino acid
biosynthesis, Aspartate family].
Length = 331
Score = 31.4 bits (72), Expect = 0.034
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 8/82 (9%)
Query: 1 MAVCAKELKKPFYVLAESFKF-VRL-----YPLNQRDLPNEFKFTSSI-LKKENLSKYHP 53
+AV AK PFYV A + + P+ +R P E + + + ++P
Sbjct: 251 LAVLAKHHGVPFYVAAPTSTIDLETKDGAEIPIEERP-PEEVTHVGGVRIAPPGIDVWNP 309
Query: 54 LVDYTPPQYITLLFTDLGILTP 75
D TP + IT + T+ G++TP
Sbjct: 310 AFDVTPAELITGIITEKGVITP 331
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 25.3 bits (56), Expect = 4.5
Identities = 7/17 (41%), Positives = 7/17 (41%)
Query: 50 KYHPLVDYTPPQYITLL 66
K Y PP Y LL
Sbjct: 322 KKRGFTRYQPPSYWRLL 338
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.140 0.407
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,472,485
Number of extensions: 358937
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 21
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
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 (21.9 bits)
S2: 53 (24.2 bits)