RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15249
(235 letters)
>gnl|CDD|216954 pfam02270, TFIIF_beta, Transcription initiation factor IIF, beta
subunit. Accurate transcription in vivo requires at
least six general transcription initiation factors, in
addition to RNA polymerase II. Transcription initiation
factor IIF (TFIIF) is a tetramer of two beta subunits
associate with two alpha subunits which interacts
directly with RNA polymerase II. The beta subunit of
TFIIF is required for recruitment of RNA polymerase II
onto the promoter.
Length = 259
Score = 175 bits (446), Expect = 1e-54
Identities = 94/262 (35%), Positives = 122/262 (46%), Gaps = 75/262 (28%)
Query: 27 NLDLTQASRGVWLVKVPKYVANKWEKVPGN--IEAGKLKIVRNPGQKPVVSLSLSEATMC 84
+LDL+ A + VWLVKVPKY++ KW K PG+ E GKL+I +N G K VSL L+E
Sbjct: 3 DLDLSNAKQSVWLVKVPKYLSEKWSKAPGDSGGEVGKLRIKKNNGGKAQVSLLLNEE--- 59
Query: 85 VDPNEEKIPKDHRLDVQIVNRQTLGVFSH-----------------YIPPVNPDAIVPES 127
IPK++ LD+Q VN Q VF+ P + +
Sbjct: 60 --LENYDIPKEYDLDMQNVNVQNTYVFTESNLGKYKQKSKEVAGMPEQPQLAYPYVKTIP 117
Query: 128 EKLMLEGKIVQKLECRPYADSCYMKLKLDSIIKASQPLRQVKHLDKIV-QNYKPVSNHKH 186
+K LEG++V + ECRP + YM+LK I+KAS+P R V+ LDKIV Q+YKP SNH +
Sbjct: 118 KKTALEGRVVHECECRPVENEEYMRLKKKRILKASKPKRTVQVLDKIVTQSYKPPSNHSN 177
Query: 187 --------------------------------------------------LTYLKEILKE 196
YLKEIL E
Sbjct: 178 NSEYFIKKKKKSEGKRARMPKNELLDLLFKAFEKHQYWSLKDLKERTRQPEAYLKEILDE 237
Query: 197 VCNYNLKNPHKNMWELKPEYRC 218
+ N K P+ N WELKPEYR
Sbjct: 238 IAVLNKKGPYANTWELKPEYRH 259
Score = 51.6 bits (124), Expect = 5e-08
Identities = 24/51 (47%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 1 MLFAAFEKHQYYNIKDLVKITKQPIVNLDLTQASRGVWLVKVPKYVANKWE 51
+LF AFEKHQY+++KDL + T+QP L V L K Y AN WE
Sbjct: 204 LLFKAFEKHQYWSLKDLKERTRQPEAYLKEILDEIAV-LNKKGPY-ANTWE 252
>gnl|CDD|227421 COG5090, TFG2, Transcription initiation factor IIF, small subunit
(RAP30) [Transcription].
Length = 297
Score = 51.1 bits (122), Expect = 1e-07
Identities = 50/264 (18%), Positives = 85/264 (32%), Gaps = 68/264 (25%)
Query: 26 VNLDLTQASRGVWLVKVPKYVANKWEKVPGNIEAGKLKIVRNPGQKPVVSLSLSEATMCV 85
+LDL VWLVKVP ++A KW L R V+SL LS
Sbjct: 20 ADLDLNNRHTKVWLVKVPLFLAEKWLSRE-AEIGELLGTKRTSTDPAVISLLLSN----- 73
Query: 86 DPNEEKIPKDHRLDVQIVNRQTLGVFSHYIPPVNPDAIVPESEKLMLEGKIVQKLECRPY 145
+ P D++I + V ++Y+ + + ++ + G + + P
Sbjct: 74 EFCNGGFP--SSYDLKIKPKD---VNNYYVFRESETSTHEKNTA--VVGTVNHECYVTPE 126
Query: 146 ADSCYMKLKLDSIIKASQPLRQVKHLDKIVQ---------------NYKPVSNHKHLTYL 190
+ Y++ K D K+ V+ +D + + K L
Sbjct: 127 VNDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGKRGEKFGSLRSSTLEFLARKRKKMLMDK 186
Query: 191 KEI------------------------------------LKE----VCNYNLKNPHKNMW 210
K LKE + N K P+ N +
Sbjct: 187 KRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKY 246
Query: 211 ELKPEYRCYKEEEKKEEATADDDD 234
EL+PEY+ +E ++ + D
Sbjct: 247 ELRPEYKQTMDELRQASQSESSSD 270
Score = 32.6 bits (74), Expect = 0.13
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 1 MLFAAFEKHQYYNIKDLVKITKQPIVNL 28
MLF AFEK+ Y+ +K L + QP L
Sbjct: 199 MLFKAFEKYPYWTLKGLAEFCGQPEAFL 226
>gnl|CDD|119426 cd05166, PI3Kc_II, Phosphoinositide 3-kinase (PI3K), class II,
catalytic domain; The PI3K catalytic domain family is
part of a larger superfamily that includes the catalytic
domains of other kinases such as the typical
serine/threonine/tyrosine protein kinases (PKs),
aminoglycoside phosphotransferase, choline kinase, and
RIO kinases. PI3Ks catalyze the transfer of the
gamma-phosphoryl group from ATP to the 3-hydroxyl of the
inositol ring of D-myo-phosphatidylinositol (PtdIns) or
its derivatives. PI3Ks play an important role in a
variety of fundamental cellular processes, including
cell motility, the Ras pathway, vesicle trafficking and
secretion, immune cell activation and apoptosis. They
can be divided into three main classes (I, II, and III),
defined by their substrate specificity, regulation, and
domain structure. Class II PI3Ks preferentially use
PtdIns as a substrate to produce PtdIns(3)P, but can
also phosphorylate PtdIns(4)P. They function as monomers
and do not associate with any regulatory subunits. Class
II enzymes contain an N-terminal Ras binding domain, a
lipid binding C2 domain, a PI3K homology domain of
unknown function, an ATP-binding cataytic domain, a Phox
homology (PX) domain, and a second C2 domain at the
C-terminus. They are activated by a variety of stimuli
including chemokines, cytokines, lysophosphatidic acid
(LPA), insulin, and tyrosine kinase receptors.
Length = 353
Score = 30.9 bits (70), Expect = 0.50
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 166 RQVKHLDKIVQNYKPVSNHKHLTYLKEILKEVCNYNLKNPHKNMWELKPEYRC 218
+ V L I ++ K S L+ L V ++ L+N + L P
Sbjct: 9 KLVNKLGSIAEDVKSASESARQHVLRTGLGRVDSFLLQNKCR--LPLNPALDV 59
>gnl|CDD|234934 PRK01286, PRK01286, deoxyguanosinetriphosphate
triphosphohydrolase-like protein; Provisional.
Length = 336
Score = 29.8 bits (68), Expect = 1.4
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 191 KEILKEVCNYNLKNPHKNMWELKPEYRCYKEEEKKEEATAD 231
K I++++ Y +++P L PEY+ EEE E A AD
Sbjct: 275 KRIVQDLFEYYMEDPE----LLPPEYQNIAEEEGLERAVAD 311
>gnl|CDD|109186 pfam00119, ATP-synt_A, ATP synthase A chain.
Length = 217
Score = 29.1 bits (66), Expect = 1.5
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 103 VNRQTLGVFSHYIPPVNPDAIVP 125
+ + FSH +PP P ++P
Sbjct: 111 IKNKGFSGFSHLVPPGTPLFLIP 133
>gnl|CDD|216629 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation
domain. DNA ligases catalyze the crucial step of
joining the breaks in duplex DNA during DNA replication,
repair and recombination, utilising either ATP or NAD(+)
as a cofactor. This domain is the catalytic adenylation
domain. The NAD+ group is covalently attached to this
domain at the lysine in the KXDG motif of this domain.
This enzyme- adenylate intermediate is an important
feature of the proposed catalytic mechanism.
Length = 314
Score = 28.8 bits (65), Expect = 2.3
Identities = 7/37 (18%), Positives = 18/37 (48%)
Query: 97 RLDVQIVNRQTLGVFSHYIPPVNPDAIVPESEKLMLE 133
+LD +I ++ L F + + + P+++ L+
Sbjct: 205 QLDPEITAKRKLRFFVYGLGLPEGLELGPQTQSEALK 241
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more internally
with limited reactivity in the C-terminal domains, while
P2 proteins seem to be more externally located and are
more likely to interact with other cellular components.
In lower eukaryotes, P1 and P2 are further subdivided
into P1A, P1B, P2A, and P2B, which form P1A/P2B and
P1B/P2A heterodimers. Some plant species have a third
P-protein, called P3, which is not homologous to P1 and
P2. In humans, P1 and P2 are strongly autoimmunogenic.
They play a significant role in the etiology and
pathogenesis of systemic lupus erythema (SLE). In
addition, the ribosome-inactivating protein
trichosanthin (TCS) interacts with human P0, P1, and P2,
with its primary binding site located in the C-terminal
region of P2. TCS inactivates the ribosome by
depurinating a specific adenine in the sarcin-ricin loop
of 28S rRNA.
Length = 103
Score = 27.7 bits (62), Expect = 2.3
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 220 KEEEKKEEATADDDDD 235
K+EEKKEE + DDD
Sbjct: 82 KKEEKKEEEEEESDDD 97
>gnl|CDD|217445 pfam03237, Terminase_6, Terminase-like family. This family
represents a group of terminase proteins.
Length = 380
Score = 28.5 bits (64), Expect = 3.5
Identities = 23/102 (22%), Positives = 31/102 (30%), Gaps = 17/102 (16%)
Query: 13 NIKDLVKITKQPIVNLDLTQASRGVW-------------LVKVPKYVANKWEKVPGNIEA 59
IK L + + +D T V + PK + KV IE+
Sbjct: 272 IIKKLAERYNVIYIYIDDTGGGESVAQLLRRELPGAAFTVRPAPKGKNARVLKVSDLIES 331
Query: 60 GKLKIVRNPGQKPVVSLSLSEATMCVDPNEEKIPK--DHRLD 99
G+LK+ R S EA NE D D
Sbjct: 332 GRLKVPRGAWCP--ASFEELEAYHTDGGNERSDVDGHDDAAD 371
>gnl|CDD|217055 pfam02470, MCE, mce related protein. This family of proteins
contains the mce (mammalian cell entry) proteins from
Mycobacterium tuberculosis. The archetype (Rv0169), was
isolated as being necessary for colonisation of, and
survival within, the macrophage. This family contains
proteins of unknown function from other bacteria.
Length = 80
Score = 26.4 bits (59), Expect = 4.1
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 8/43 (18%)
Query: 73 VVSLSLS------EATMCVDPNEEKIPKDHRLDVQIVNRQTLG 109
V S+ L T+ +DP+ IPKD I + LG
Sbjct: 31 VTSIDLDPDGGGVRVTLRIDPDVVVIPKD--SRAGIRSLGLLG 71
>gnl|CDD|221118 pfam11461, RILP, Rab interacting lysosomal protein. RILP contains
a domain which contains two coiled-coil regions and is
found mainly in the cytosol. RILP is recruited onto late
endosomal and lysosomal membranes by Rab7 and acts as a
downstream effector of Rab7. This recruitment process is
important for phagosome maturation and fusion with late
endosomes and lysosomes.
Length = 60
Score = 25.4 bits (56), Expect = 7.3
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 190 LKEILKEVCNYNLKNPHK-NMWELKPEYRCYKEEEKKEEATADDDDD 235
L+E+L+E +N K ++ L+ E YK E EE
Sbjct: 5 LREVLQE------RNELKAKVFLLQEELAYYKSELLPEERRPGLPLP 45
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
0.315 0.134 0.398
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,960,129
Number of extensions: 1107082
Number of successful extensions: 1064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1056
Number of HSP's successfully gapped: 30
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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 (21.6 bits)
S2: 57 (25.8 bits)