RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10998
(514 letters)
>gnl|CDD|214713 smart00543, MIF4G, Middle domain of eukaryotic initiation factor 4G
(eIF4G). Also occurs in NMD2p and CBP80. The domain is
rich in alpha-helices and may contain multiple
alpha-helical repeats. In eIF4G, this domain binds
eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G
domain homologues (in press).
Length = 200
Score = 132 bits (333), Expect = 7e-36
Identities = 75/245 (30%), Positives = 120/245 (48%), Gaps = 53/245 (21%)
Query: 186 KQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYE 245
K+V+G++NKL+P NFES+ + + + +++L+F+KA+ EP+F YA++C
Sbjct: 2 KKVKGLINKLSPSNFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCAL 61
Query: 246 MMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPE 305
+ + +F +LLL + Q+EFEK
Sbjct: 62 LNAKN----------------PDFGSLLLERLQEEFEKGL-------------------- 85
Query: 306 KKKELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKK-TEEEPLER 364
E EE ++R +G RF+GELY +LT+KI+ + ELL T+ +P
Sbjct: 86 ---------ESEEESDKQRRLGLVRFLGELYNFQVLTSKIILELLKELLNDLTKLDPPRS 136
Query: 365 ------ACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVID 418
LL T GKDLE +K P + +++ KK+ +SSR+RFML+ +I+
Sbjct: 137 DFSVECLLSLLPTCGKDLE-REKSPKLLDEILERLQDYLLKKDKTELSSRLRFMLELLIE 195
Query: 419 LRKNK 423
LRKNK
Sbjct: 196 LRKNK 200
>gnl|CDD|217253 pfam02854, MIF4G, MIF4G domain. MIF4G is named after Middle domain
of eukaryotic initiation factor 4G (eIF4G). Also occurs
in NMD2p and CBP80. The domain is rich in alpha-helices
and may contain multiple alpha-helical repeats. In
eIF4G, this domain binds eIF4A, eIF3, RNA and DNA.
Length = 198
Score = 131 bits (332), Expect = 1e-35
Identities = 82/244 (33%), Positives = 124/244 (50%), Gaps = 53/244 (21%)
Query: 186 KQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFYAKMCYE 245
K+V+G+LNKL+P NFE + + + ++ L +++L+F+KA+ EP+F YA++C
Sbjct: 2 KKVKGLLNKLSPSNFEKIIDELLKLNMSDKNLLKYILELIFEKAVEEPNFIPAYARLCAG 61
Query: 246 MMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIEAEQDPE 305
+ + +F LLLN+ Q+EFEK
Sbjct: 62 LNSKN----------------PDFGELLLNRLQEEFEKGV-------------------- 85
Query: 306 KKKELRLMFEEEERLIRKRSVGNCRFIGELYKLNMLTTKIMHHCISELLKK-TEEEP--- 361
EEEER RKR +G RF+GEL+ +LT KI+ C+ ELL+ TEE+P
Sbjct: 86 ---------EEEERGNRKRRLGLVRFLGELFNFKVLTEKIILECLKELLESLTEEDPRDE 136
Query: 362 --LERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVIDL 419
LE LL+T GK L+ +K M +++ +SSR+RFML+D+I+L
Sbjct: 137 FSLEILLLLLTTCGKLLDR-EKLKKLMDEILERIQKYLLSA-DPELSSRLRFMLEDLIEL 194
Query: 420 RKNK 423
RKNK
Sbjct: 195 RKNK 198
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 32.0 bits (73), Expect = 0.92
Identities = 25/171 (14%), Positives = 50/171 (29%), Gaps = 41/171 (23%)
Query: 180 EDEKFYKQVRGVLNKLTPENFESMKMQFKEFPINTTKRLDKVIDLVFQKAIAEPSFSEFY 239
E + G+ + + ++ QF N L +V L + + E SF++F
Sbjct: 536 PFESEPSEAAGLASGKL----DPLRSQF-RLSYNMILNLLRVEGLQTAEDLLERSFAQFQ 590
Query: 240 AKMCYEMMKREVVDETKPVNKDGKRPSVNFKNLLLNKCQKEFEKNEFEERKNDIKLDEIE 299
+ + L + +K E N+ ++
Sbjct: 591 NSRSLPEIVEK-----------------------LERLEK--ELNDIATELFGTDENDAP 625
Query: 300 AEQDPEKKKELRLMFEE-----------EERLIRKRSVGNCRFIGELYKLN 339
+K +L E + R+++ + F G L KL
Sbjct: 626 KLSLDYEKLRKKLNEEMRLQAAGLRALRKGRVVQIKDGLAALFWGRLLKLT 676
>gnl|CDD|150747 pfam10107, Endonuc_Holl, Endonuclease related to archaeal Holliday
junction resolvase. This domain is found in various
predicted bacterial endonucleases which are distantly
related to archaeal Holliday junction resolvases.
Length = 153
Score = 28.9 bits (65), Expect = 3.7
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 283 KNEFEERKNDI----KLDEIEAEQDPEKKKELRLMFEEEERLIRKRSV 326
+ + E+R ++ + E EA+ E + + ++EE+ IRK +V
Sbjct: 17 QGKVEKRARELFEQWRNAEREAQAMREAEAKFEEWQKKEEKEIRKDAV 64
>gnl|CDD|147569 pfam05456, eIF_4EBP, Eukaryotic translation initiation factor 4E
binding protein (EIF4EBP). This family consists of
several eukaryotic translation initiation factor 4E
binding proteins (EIF4EBP1,2 and 3). Translation
initiation in eukaryotes is mediated by the cap
structure (m7GpppN, where N is any nucleotide) present
at the 5' end of all cellular mRNAs, except organellar.
The cap is recognised by eukaryotic initiation factor
4F (eIF4F), which consists of three polypeptides,
including eIF4E, the cap-binding protein subunit. The
interaction of the cap with eIF4E facilitates the
binding of the ribosome to the mRNA. eIF4E activity is
regulated in part by translational repressors, 4E-BP1,
4E-BP2 and 4E-BP3 which bind to it and prevent its
assembly into eIF4F.
Length = 113
Score = 27.7 bits (62), Expect = 6.9
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 53 YSRDFLLELQFEAMSKPKPANLPDLEIVL 81
Y R FLLEL+ +++ P LP++ V
Sbjct: 50 YDRKFLLELRNSPLARTPPCCLPNIPGVT 78
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 29.3 bits (65), Expect = 6.9
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 284 NEFEERKNDIKLDEIEAEQDPEKKKELRLMFEEEER 319
E EE +++ E E E++ KK+ELR FE EER
Sbjct: 628 AENEESADEVDY-ETEREENARKKEELRGNFELEER 662
>gnl|CDD|227603 COG5278, COG5278, Predicted periplasmic ligand-binding sensor
domain [Signal transduction mechanisms].
Length = 207
Score = 28.5 bits (64), Expect = 7.3
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 9/63 (14%)
Query: 360 EPLERACKLLSTIGKDLESHDKDPTQMKGYFTTMEELASKKNSHAISSRVRFMLQDVIDL 419
EP E A + L ++L + D ++ +E L K + I L
Sbjct: 80 EPYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQWK---------LAEADETIPL 130
Query: 420 RKN 422
R++
Sbjct: 131 RRD 133
>gnl|CDD|225940 COG3405, CelA, Endoglucanase Y [Carbohydrate transport and
metabolism].
Length = 360
Score = 28.3 bits (63), Expect = 9.3
Identities = 27/153 (17%), Positives = 38/153 (24%), Gaps = 24/153 (15%)
Query: 351 SELLKKTEEEPLERACKLLSTIGK----DLESHDKDPTQMKGYFTTMEELASKKNSHAIS 406
K+ E + LL T D ++ P Q+KG IS
Sbjct: 196 EPDWKEALRETNQI--LLLETAPTGLSPDWVRYEGKPGQLKGE------------KTFIS 241
Query: 407 SR-VRFML---QDVIDLRKNKWIPRRNENKPKTIQQIQYEAESEKFGNVNKKPLLDKPYS 462
S +R L + N K + K V + P
Sbjct: 242 SDAIRVYLYAGMMADGDPQLLR--MLNRFKGMATFTAKKGYPPLKVDVVTGEAKSKAPVG 299
Query: 463 LEKPMLDNDRKSAFQQQQKDWNKPNNPIYKASY 495
+ + Q Q N P P A Y
Sbjct: 300 FIAALAPFLQNRDAQAVQLFRNAPVFPGSDAYY 332
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
0.314 0.131 0.377
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,813,903
Number of extensions: 2521913
Number of successful extensions: 2016
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1991
Number of HSP's successfully gapped: 72
Length of query: 514
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 413
Effective length of database: 6,457,848
Effective search space: 2667091224
Effective search space used: 2667091224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (27.4 bits)