RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2575
(165 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 = 112 bits (283), Expect = 4e-31
Identities = 39/117 (33%), Positives = 65/117 (55%), Gaps = 2/117 (1%)
Query: 44 QACEHIHSNEIILTLGYSKIVELFLKNAAQH-RKFQCIVMENSPENKGHELAVSLAKSKI 102
A E I + ILT S V L+ A + ++F+ IV E+ P +G A L ++ I
Sbjct: 100 IAAELIKDGDTILTHCNSGTVLGVLRAAHKEGKRFRVIVTESRPRLQGRLTAKELVQAGI 159
Query: 103 QTVLIPDSAMFGLISRVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIP-YPCT 158
LI DSA+ ++ V+K+I+G ++ANGG+ + GT+ +AL A+ +++P Y
Sbjct: 160 PVTLITDSAVGYVMQEVDKVIVGADRILANGGIANKIGTYQLALLAKAHNVPFYVVA 216
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B
alpha/beta/delta family [Translation, ribosomal
structure and biogenesis].
Length = 301
Score = 107 bits (269), Expect = 6e-29
Identities = 44/113 (38%), Positives = 65/113 (57%), Gaps = 1/113 (0%)
Query: 43 SQACEHIHSNEIILTLGYSKIVELFLKNAAQHRK-FQCIVMENSPENKGHELAVSLAKSK 101
E IH ++ILT +SK V LK AA K F+ IV E+ P +G +A L +S
Sbjct: 111 EIGAERIHDGDVILTHSFSKTVLEVLKTAADRGKRFKVIVTESRPRGEGRIMAKELRQSG 170
Query: 102 IQTVLIPDSAMFGLISRVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIP 154
I +I DSA+ +SRV+K+++G ++ANG L + GT +ALAA+ +P
Sbjct: 171 IPVTVIVDSAVGAFMSRVDKVLVGADAILANGALVNKIGTSPLALAARELRVP 223
>gnl|CDD|235788 PRK06372, PRK06372, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 253
Score = 56.5 bits (136), Expect = 4e-10
Identities = 29/103 (28%), Positives = 61/103 (59%), Gaps = 2/103 (1%)
Query: 53 EIILTLGYSKIVELFLKNAAQHRKFQCIVMENSPENKGHELAVSLAKSKIQTVLIPDSAM 112
+I T+ S++++ F+ ++ + + ++E+ P +G ++A L KS I VL+ D++M
Sbjct: 88 SVIGTISSSQVLKAFISSSEKIKSV--YILESRPMLEGIDMAKLLVKSGIDVVLLTDASM 145
Query: 113 FGLISRVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIPY 155
+ V+ +I+G+ +V+ +GGL GT +AL A++ P+
Sbjct: 146 CEAVLNVDAVIVGSDSVLYDGGLIHKNGTFPLALCARYLKKPF 188
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 55.3 bits (134), Expect = 1e-09
Identities = 41/137 (29%), Positives = 65/137 (47%), Gaps = 9/137 (6%)
Query: 17 ESLHKLVVSSDDEATDFANPTSDTAPSQACE----HIHSNEIILTLGYSKIVELFLKNA- 71
E + V+ A +F +S+ A + E I ++I+T S +K A
Sbjct: 86 EEARESVIER---AEEFIE-SSENAVEKIGEIGAKRIRDGDVIMTHCNSSAALSVIKTAH 141
Query: 72 AQHRKFQCIVMENSPENKGHELAVSLAKSKIQTVLIPDSAMFGLISRVNKIIIGTHTVMA 131
Q + + I E P N+GH A LA+ I LI DSA+ + V+K+++G + A
Sbjct: 142 EQGKDIEVIATETRPRNQGHITAKELAEYGIPVTLIVDSAVRYFMKDVDKVVVGADAITA 201
Query: 132 NGGLRSVCGTHAVALAA 148
NG + + GT +ALAA
Sbjct: 202 NGAVINKIGTSQIALAA 218
>gnl|CDD|169387 PRK08335, PRK08335, translation initiation factor IF-2B subunit
alpha; Validated.
Length = 275
Score = 52.9 bits (127), Expect = 7e-09
Identities = 32/111 (28%), Positives = 59/111 (53%), Gaps = 3/111 (2%)
Query: 47 EHIHSNEIILTLGYSKIVELFLKNAAQHRK-FQCIVMENSPENKGHELAVSLAKSKIQTV 105
E I ++I+T +S V LK A + K F+ I+ E++P+ +G LA L I+
Sbjct: 105 ELIDDGDVIITHSFSSAVLEILKTAKRKGKRFKVILTESAPDYEGLALANELEFLGIEFE 164
Query: 106 LIPDSAMFGLISRVNKI-IIGTHTVMANGGLRSVCGTHAVALAAQHYSIPY 155
+I D+ + GL ++ + ++G V +G + + GT+ +ALA +P+
Sbjct: 165 VITDAQL-GLFAKEATLALVGADNVTRDGYVVNKAGTYLLALACHDNGVPF 214
>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 = 50.5 bits (121), Expect = 5e-08
Identities = 34/111 (30%), Positives = 54/111 (48%), Gaps = 1/111 (0%)
Query: 48 HIHSNEIILTLGYSKIVELFLKNAAQHRK-FQCIVMENSPENKGHELAVSLAKSKIQTVL 106
I ++I+T S+ +K A + K + IV E P N+GH A L I L
Sbjct: 112 RIRDGDVIMTHCNSEAALSVIKTAFEQGKDIEVIVTETRPRNQGHITAKELRDYGIPVTL 171
Query: 107 IPDSAMFGLISRVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIPYPC 157
I DSA + V+ +++G + ANG + + GT +ALAA+ +P+
Sbjct: 172 IVDSAARYYMKEVDHVVVGADAITANGAVINKIGTSQLALAAREARVPFMV 222
>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 = 46.7 bits (111), Expect = 1e-06
Identities = 24/104 (23%), Positives = 46/104 (44%), Gaps = 3/104 (2%)
Query: 55 ILTLGYSKIVELFLKNAAQHRKFQCIVMENSPENKGHELAV-SLAKSKIQTVLIPDSAMF 113
+ T Y + + ++ + I E P N+G L L + I LI DS
Sbjct: 131 LATSDYGTALGVIRSAWEDGKRIRVIACETRPRNQGSRLTAWELMQDGIDVTLITDSMAA 190
Query: 114 GLI--SRVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIPY 155
+ ++ +I+G + NG + + GT+ +A+ A+ + IP+
Sbjct: 191 YFMQKGEIDAVIVGADRIARNGDVANKIGTYQLAVLAKEFRIPF 234
>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 = 44.6 bits (106), Expect = 6e-06
Identities = 23/79 (29%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 80 IVMENSPENKGHELAVS-LAKSKIQTVLIPDSAMFGLISR--VNKIIIGTHTVMANGGLR 136
E P +G L L + I LI D+A L+ + ++ +I+G + ANG +
Sbjct: 187 FADETRPYLQGARLTAWELVQDGIPVTLITDNAAGHLMQQGMIDAVIVGADRIAANGDVA 246
Query: 137 SVCGTHAVALAAQHYSIPY 155
+ GT+ +A+ A+H+ IP+
Sbjct: 247 NKIGTYQLAVLAKHHGIPF 265
>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 = 44.5 bits (106), Expect = 7e-06
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 83 ENSPENKGHEL-AVSLAKSKIQTVLIPDSAMFGLISR--VNKIIIGTHTVMANGGLRSVC 139
E P +G L A L + I LI DS L+ V+ +I+G + ANG +
Sbjct: 187 ETRPRLQGARLTAWELVQEGIPATLITDSMAAHLMKHGEVDAVIVGADRIAANGDTANKI 246
Query: 140 GTHAVALAAQHYSIPY 155
GT+ +A+ A+H+ +P+
Sbjct: 247 GTYQLAVLAKHHGVPF 262
>gnl|CDD|235578 PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
Length = 344
Score = 39.4 bits (93), Expect = 4e-04
Identities = 21/90 (23%), Positives = 41/90 (45%), Gaps = 9/90 (10%)
Query: 72 AQHRKFQCIVMENSPENKGHELAVS-LAKSKIQTVLIPDSAMFGLISR--VNKIIIGTHT 128
+ E P +G L L ++ I +I D+ L+ ++ +I+G
Sbjct: 176 EKGIDIHVYADETRPRLQGARLTAWELYQAGIDVTVITDNMAAHLMQTGKIDAVIVGADR 235
Query: 129 VMANGGLRSVC---GTHAVALAAQHYSIPY 155
+ ANG V GT+ +A+AA+++ +P+
Sbjct: 236 IAANG---DVANKIGTYQLAIAAKYHGVPF 262
>gnl|CDD|180362 PRK06036, PRK06036, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 339
Score = 34.7 bits (80), Expect = 0.012
Identities = 25/88 (28%), Positives = 44/88 (50%), Gaps = 6/88 (6%)
Query: 72 AQHRKFQCIVMENSPENKGHEL-AVSLAKSKIQTVLIPDSAMFGLISR---VNKIIIGTH 127
Q ++ + I E P N+G L L + I LI DS M G++ R V+K+I+G
Sbjct: 177 EQGKEIKVIACETRPLNQGSRLTTWELMQDNIPVTLITDS-MAGIVMRQGMVDKVIVGAD 235
Query: 128 TVMANGGLRSVCGTHAVALAAQHYSIPY 155
+ + + GT+ ++ A+ + IP+
Sbjct: 236 RITRDAVFNKI-GTYTHSVLAKEHEIPF 262
>gnl|CDD|168237 PRK05772, PRK05772, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 363
Score = 33.2 bits (76), Expect = 0.043
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 80 IVMENSPENKGHELAV-SLAKSKIQTVLIPDSAMFGLI---SRVNKIIIGTHTVMANGGL 135
I E P +G L V L + I+ LI D+A+ GL+ VN +++G ++ +G +
Sbjct: 205 IAPETRPWLQGSRLTVYELMEEGIKVTLITDTAV-GLVMYKDMVNNVMVGADRILRDGHV 263
Query: 136 RSVCGTHAVALAAQHYSIPY 155
+ GT A+ A IP+
Sbjct: 264 FNKIGTFKEAVIAHELGIPF 283
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 33.4 bits (76), Expect = 0.045
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 118 RVNKIIIGTHTVMANGGLRSVCGTHAVALAAQHYSIPY 155
+V+ II+G ++ANG + GT+ +A+ A+ + IP+
Sbjct: 238 KVDAIIVGADRIVANGDFANKIGTYTLAVLAKEHGIPF 275
>gnl|CDD|180547 PRK06371, PRK06371, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 329
Score = 32.9 bits (75), Expect = 0.055
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 81 VMENSPENKGHEL-AVSLAKSKIQTVLIPDSAMFGLISR--VNKIIIGTHTVMANGGLRS 137
V E P +G L A LA+ I +I D+A + + ++ +I+G + +NG +
Sbjct: 175 VDETRPRLQGARLTAWELAQEGIDHAIIADNAAGYFMRKKEIDLVIVGADRIASNGDFAN 234
Query: 138 VCGTHAVALAAQHYSIPY 155
GT+ A+ A+ IP+
Sbjct: 235 KIGTYEKAVLAKVNGIPF 252
>gnl|CDD|223981 COG1053, SdhA, Succinate dehydrogenase/fumarate reductase,
flavoprotein subunit [Energy production and conversion].
Length = 562
Score = 28.1 bits (63), Expect = 2.7
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 115 LISRVNKIIIGTHTVMANGGLRSVCGTH 142
L+S+ HTV A GG+ + G
Sbjct: 34 LLSKAP--PKRGHTVAAQGGINAALGNT 59
>gnl|CDD|240058 cd04703, Asparaginase_2_like, A subfamily of the L-Asparaginase
type 2-like enzymes. The wider family, a member of the
Ntn-hydrolase superfamily, includes
Glycosylasparaginase, Taspase 1 and L-Asparaginase type
2 enzymes. The proenzymes undergo autoproteolytic
cleavage before a threonine to generate alpha and beta
subunits. The threonine becomes the N-terminal residue
of the beta subunit and is the catalytic residue.
Length = 246
Score = 26.6 bits (59), Expect = 5.4
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 10/84 (11%)
Query: 80 IVMENSPE-NKGHELAVSLAKSKIQT---VLIPDSAMFGL---ISRVNKIIIGTHTVMAN 132
+E+ P N G A+ + I+T V+ D FG + V ++ VM
Sbjct: 44 RALESDPAFNAGTGAALQSDGA-IRTDAGVMTSDGD-FGAVAAMQGVEHPVLVARAVMEE 101
Query: 133 GGLRSVCGTHAVALAAQHYSIPYP 156
+ G AV AA + P
Sbjct: 102 TPHVLLAGDGAVKFAAL-TGVEDP 124
>gnl|CDD|226471 COG3962, COG3962, Acetolactate synthase [Amino acid transport and
metabolism].
Length = 617
Score = 27.0 bits (60), Expect = 5.7
Identities = 24/84 (28%), Positives = 34/84 (40%), Gaps = 21/84 (25%)
Query: 57 TLGYSKIVELFLKNAAQHRKFQCIV------MENSPENKGHELAVSLAKSKIQTVLIPDS 110
+GY L K A R+ +V M NS ELA S+ K V++ D+
Sbjct: 445 CMGYEIAGGLGAKAAEPDREVYVMVGDGSYMMLNS------ELATSVMLGKKIIVVLLDN 498
Query: 111 AMFGLISRVNKIIIGTHTVMANGG 134
+G I+R+ MA GG
Sbjct: 499 RGYGCINRLQ---------MATGG 513
>gnl|CDD|182371 PRK10309, PRK10309, galactitol-1-phosphate dehydrogenase;
Provisional.
Length = 347
Score = 26.7 bits (59), Expect = 6.1
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 8/59 (13%)
Query: 76 KFQCIVMENSPENKGHELAVSLAKSKIQTVLIP--------DSAMFGLISRVNKIIIGT 126
+F +++E + + ELA+ +A + Q L+ SA FG I R +IG+
Sbjct: 228 RFDQLILETAGVPQTVELAIEIAGPRAQLALVGTLHHDLHLTSATFGKILRKELTVIGS 286
>gnl|CDD|212114 cd10803, YdjC_EF3048_like, Enterococcus faecalis EF3048 and similar
proteins. This subfamily is represented by a putative
cellobiose-phosphate cleavage protein EF3048 from
Enterococcus faecalis v583. It is similar to Escherichia
coli YdjC, a hypothetical protein encoded by the celG
gene. EF3048 might function as a homodimer. Each of the
monomers consists of a (beta/alpha)-barrel fold that
forms an active homodimer. The molecular function of the
EF3048 is unclear.
Length = 228
Score = 26.0 bits (58), Expect = 9.9
Identities = 19/62 (30%), Positives = 24/62 (38%), Gaps = 22/62 (35%)
Query: 113 FGLISRVNKIIIGTH--------TVMANGGLRSVCGT-HAVALAAQHYSIPYPCTFLLNI 163
FGL VN II H T+M N G HAV LA ++ L +
Sbjct: 9 FGLTKGVNYGIIEAHRNGVVTSTTLMVNMP-----GFEHAVELAKEN--------PGLGV 55
Query: 164 GI 165
G+
Sbjct: 56 GV 57
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
0.317 0.131 0.373
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,915,826
Number of extensions: 688680
Number of successful extensions: 547
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 24
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
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: 55 (24.9 bits)