RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12281
(456 letters)
>gnl|CDD|191232 pfam05207, zf-CSL, CSL zinc finger. This is a zinc binding motif
which contains four cysteine residues which chelate
zinc. This domain is often found associated with a
pfam00226 domain. This domain is named after the
conserved motif of the final cysteine.
Length = 55
Score = 94.6 bits (236), Expect = 3e-24
Identities = 31/51 (60%), Positives = 42/51 (82%)
Query: 6 DEIEIEDFEYDEDDETYYYPCPCGDRFQITKEQLKAGEDVATCPTCSLIIK 56
DE+E+EDFE+DE++ ++YYPC CGD F+IT+E L+ GE V CP+CSL IK
Sbjct: 1 DEVELEDFEFDEEEGSFYYPCRCGDEFEITEEDLEEGEVVVQCPSCSLWIK 51
>gnl|CDD|222269 pfam13621, Cupin_8, Cupin-like domain. This cupin like domain
shares similarity to the JmjC domain.
Length = 247
Score = 93.9 bits (234), Expect = 6e-22
Identities = 56/256 (21%), Positives = 100/256 (39%), Gaps = 42/256 (16%)
Query: 101 FNNFLSKNKPFILKSCVNEWNSSLHWVQNKQPNFEYLSNHYGDIEVPVA----------- 149
F +++K KP +LK +W + V+ +YL YGD+EV V
Sbjct: 5 FREYVAKRKPVVLKGAAKDWPA----VKKWTDALDYLKEKYGDVEVSVEVTPPGRADRFF 60
Query: 150 -NCNSYYFNAHEKTNMTLKEYTIYWQNKIDGKLSETEPLYYLKDWHFTRDFKTEDIYRVP 208
N + N E+ M K++ G ET P YL+ + +F +
Sbjct: 61 YNDDLSGVNFKEER-MPFKDF---LDLLRAGSDQETPPYLYLQSSNLDSEF-----PGLR 111
Query: 209 NVFSSDWLNEYYSEHLEHKDDYRFVYMGPKETWTPLHADVFHSYSWSVNICGRKQWLLLA 268
E + + + + +++G T T LH D + + + GRK++ L
Sbjct: 112 EDNDLPLAPEAFGKLPQAVN----LWIGNGGTTTSLHYDAYEN--LYCVVSGRKRFTLFP 165
Query: 269 PG-------NEKYFKDSMGNLISDMRSVDWSTLPRDT---VIIVEQEAGDSIFVPSGWHH 318
P + D + D PR ++ E E GD++++P+GW H
Sbjct: 166 PSQVPNLYPGPLDRTGGQPFSLVDPDNPDLEKFPRFKDAKALVAELEPGDALYIPAGWWH 225
Query: 319 QVTNLEH-TISINHNW 333
V +L+ I++N+ +
Sbjct: 226 HVRSLDDFNIAVNYWF 241
>gnl|CDD|227541 COG5216, COG5216, Uncharacterized conserved protein [Function
unknown].
Length = 67
Score = 88.0 bits (218), Expect = 9e-22
Identities = 34/55 (61%), Positives = 44/55 (80%), Gaps = 1/55 (1%)
Query: 1 MSVYHDEIEIEDFEYDEDDETYYYPCPCGDRFQITKEQLKAGEDVATCPTCSLII 55
MS Y DEIEIEDF + +++T+ YPCPCGDRF+I+ E L+ GE VA CP+CSLI+
Sbjct: 1 MSFY-DEIEIEDFTFSREEKTFTYPCPCGDRFEISLEDLRNGEVVARCPSCSLIV 54
>gnl|CDD|202224 pfam02373, JmjC, JmjC domain, hydroxylase. The JmjC domain belongs
to the Cupin superfamily. JmjC-domain proteins may be
protein hydroxylases that catalyze a novel histone
modification. This is confirmed to be a hydroxylase: the
human JmjC protein named Tyw5p unexpectedly acts in the
biosynthesis of a hypermodified nucleoside,
hydroxy-wybutosine, in tRNA-Phe by catalyzing
hydroxylation.
Length = 114
Score = 67.3 bits (165), Expect = 8e-14
Identities = 26/114 (22%), Positives = 45/114 (39%), Gaps = 12/114 (10%)
Query: 232 FVYMGPKETWTPLHADVFHSYS-WSVNICGRKQWLLLAPGNEKYFKDSMG--NLISDMRS 288
++YMG + TP H + YS ++ G K W ++ + F+ + N
Sbjct: 1 WLYMGMPGSTTPWHIEDQGLYSINYLHFGGPKVWYIIPSEYAEKFEKVLSKHNGGEQPDL 60
Query: 289 VDWST--LPRDT-------VIIVEQEAGDSIFVPSGWHHQVTNLEHTISINHNW 333
+ + V Q+ G+ +F GW+HQV NL I+ N+
Sbjct: 61 LLHLNTIISPKQLLENGIPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
>gnl|CDD|214721 smart00558, JmjC, A domain family that is part of the cupin
metalloenzyme superfamily. Probable enzymes, but of
unknown functions, that regulate chromatin
reorganisation processes (Clissold and Ponting, in
press).
Length = 58
Score = 35.7 bits (83), Expect = 0.003
Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 200 KTEDIYRVPNVFSSDWLNEYYSEHLEHKDDYRFVYMGPKETWTPLHADVFHSYSW 254
+ ++ ++P L E + D ++YMG + TP H D + ++
Sbjct: 1 QLWNLAKLPF---KLNLLSDLPEDIPGPDVGPYLYMGMAGSTTPWHIDDYDLVNY 52
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 38.4 bits (90), Expect = 0.008
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 9/56 (16%)
Query: 10 IEDFEYDE-DDETYYYPCP-CGDRFQITKEQLKAGEDVA------TCPTCSLIIKP 57
IE Y+E D YY PCP CG+ ++ E+LK + A CP C +I+
Sbjct: 187 IEA-LYEESDQRRYYVPCPHCGEEQELRWERLKWDKGEAPETARYVCPHCGCVIEE 241
>gnl|CDD|225051 COG2140, COG2140, Thermophilic glucose-6-phosphate isomerase and
related metalloenzymes [Carbohydrate transport and
metabolism / General function prediction only].
Length = 209
Score = 35.9 bits (83), Expect = 0.022
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 295 PRDTVIIVEQEAGDSIFVPSGWHHQVTN 322
P ++ AGD I+VP G+ H N
Sbjct: 121 PEGEARVIAVRAGDVIYVPPGYGHYTIN 148
>gnl|CDD|182985 PRK11130, moaD, molybdopterin synthase small subunit; Provisional.
Length = 81
Score = 31.9 bits (73), Expect = 0.097
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 414 LSLDH---TMFDLRKASDVLKLCAQHEDWDLKLETNKLIEDLNSSI 456
L L T+ LR+ L + + W L LE KL+ +N ++
Sbjct: 19 LELAADFPTVEALRQH-----LAQKGDRWALALEDGKLLAAVNQTL 59
>gnl|CDD|219088 pfam06560, GPI, Glucose-6-phosphate isomerase (GPI). This family
consists of several bacterial and archaeal
glucose-6-phosphate isomerase (GPI) proteins
(EC:5.3.1.9).
Length = 181
Score = 30.2 bits (68), Expect = 1.6
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 297 DTVIIVEQEAGDSIFVPSGWHHQVTN 322
D V ++E E G ++VP + H+ N
Sbjct: 106 DDVRVIEMEKGTVVYVPPYYGHRTIN 131
>gnl|CDD|205894 pfam13719, zinc_ribbon_5, zinc-ribbon domain. This family
consists of a single zinc ribbon domain, ie half of a
pair as in family DZR, pfam12773.
Length = 37
Score = 27.2 bits (61), Expect = 1.6
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 26 CP-CGDRFQITKEQLKAGEDVATCPTCS 52
CP C +++I E++ C C
Sbjct: 5 CPNCQAKYEIDDEKIPPKGRKVRCSKCG 32
>gnl|CDD|205892 pfam13717, zinc_ribbon_4, zinc-ribbon domain. This family
consists of a single zinc ribbon domain, ie half of a
pair as in family DZR, pfam12773.
Length = 36
Score = 27.2 bits (61), Expect = 1.8
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 26 CP-CGDRFQITKEQLKAGEDVATCPTCS 52
CP C +++I E++ C C
Sbjct: 5 CPNCKAKYEIDDEKIPPKGRKVRCSKCG 32
>gnl|CDD|221153 pfam11638, DnaA_N, DnaA N-terminal domain. This family of proteins
represents the N-terminal domain of DnaA, a protein
involved in the initiation of bacterial chromosomal
replication. The structure of this domain is known. It
is also found in three copies in some proteins. The
exact function of this domain is uncertain but it has
been suggested to play a role in oligomerisation.
Length = 65
Score = 28.0 bits (63), Expect = 1.9
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 207 VPNVFSSDWLNEYYSEHLEH 226
VPN F DW+ E+Y + +
Sbjct: 42 VPNRFVRDWVEEHYLDRILE 61
>gnl|CDD|112832 pfam04033, DUF365, Domain of unknown function (DUF365). Archaeal
domain of unknown function.
Length = 97
Score = 28.6 bits (64), Expect = 2.0
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 4 YHDEIEIEDFEYDEDD----ETYYYPCPCGDRFQITKEQLKAGED 44
+ E EIE E E+ E Y GD +TKE+LK E
Sbjct: 14 FVGEAEIERVEIFENPMEIFEKY------GDALFLTKEELKKYER 52
>gnl|CDD|172627 PRK14138, PRK14138, NAD-dependent deacetylase; Provisional.
Length = 244
Score = 30.2 bits (68), Expect = 2.1
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 23 YYPCPCGDRFQI--TKEQLKAGEDVATCPTCSLIIKPSVI 60
YY CG R+ + E+L+ DV C CS +I+P+++
Sbjct: 120 YYCVRCGKRYTVEDVIEKLEK-SDVPRCDDCSGLIRPNIV 158
>gnl|CDD|225248 COG2373, COG2373, Large extracellular alpha-helical protein [General
function prediction only].
Length = 1621
Score = 30.1 bits (68), Expect = 3.4
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 208 PNVFSSDWLNEYYSEHLEHKDDYRFVYMGPKET 240
PN WL +EH E +DD RFV E
Sbjct: 1544 PNEALLSWLESADAEHGEIRDD-RFVAALDDEG 1575
>gnl|CDD|235502 PRK05560, PRK05560, DNA gyrase subunit A; Validated.
Length = 805
Score = 30.0 bits (69), Expect = 3.5
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 25/65 (38%)
Query: 374 LQVSFGINFRQFFDMLKFIC--QKRLTSLKNGTTIRLYGNWILSLDH--------TMFDL 423
LQ SFGIN ML + Q +L +LK + + L+H T F+L
Sbjct: 321 LQTSFGIN------MLA-LVDGQPKLLNLKE--ILEAF------LEHRKEVITRRTRFEL 365
Query: 424 RKASD 428
RKA +
Sbjct: 366 RKAEE 370
>gnl|CDD|219618 pfam07883, Cupin_2, Cupin domain. This family represents the
conserved barrel domain of the 'cupin' superfamily
('cupa' is the Latin term for a small barrel).
Length = 70
Score = 27.2 bits (61), Expect = 4.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 305 EAGDSIFVPSGWHHQVTN 322
+AGDS++ P+G H+ N
Sbjct: 41 KAGDSVYFPAGVPHRFRN 58
>gnl|CDD|150281 pfam09553, RE_Eco47II, Eco47II restriction endonuclease. This
family includes the Eco47II (which recognises GGNCC, but
the cleavage site unknown) restriction endonuclease.
Length = 214
Score = 29.0 bits (65), Expect = 4.8
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 4/52 (7%)
Query: 313 PSGWHHQVTNLEHTISI----NHNWINGTNIDHVYHEMVSHLEAVKKEIDDC 360
P+GW N E+ I HN +NG + +Y +M + L ++ D
Sbjct: 91 PNGWDVDFENDENRIYAEMKNKHNTMNGASAAKLYMKMQNLLLQKAEKYKDY 142
>gnl|CDD|222758 pfam14446, Prok-RING_1, Prokaryotic RING finger family 1. RING
finger family found sporadically in bacteria and
archaea, and associated in gene neighborhoods with
other components of the ubiquitin-based signaling and
degradation system, including ubiquitin, the E1 and E2
proteins and the JAB-like metallopeptidase. The
bacterial versions contain transmembrane helices.
Length = 55
Score = 26.6 bits (59), Expect = 5.0
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 24 YPCP-CGDRFQITKEQLKAGEDVATCPTCSLI 54
CP CG +F K G+D+ CP C
Sbjct: 6 TRCPVCGKKF-------KPGDDIVVCPECGAP 30
>gnl|CDD|132998 cd00897, UGPase_euk, Eukaryotic UGPase catalyses the synthesis of
UDP-Glucose. UGPase (UDP-Glucose Pyrophosphorylase)
catalyzes the reversible production of UDP-Glucose and
pyrophosphate (PPi) from Glucose-1-phosphate and UTP.
UDP-glucose plays pivotal roles in galactose
utilization, in glycogen synthesis, and in the synthesis
of the carbohydrate moieties of glycolipids,
glycoproteins, and proteoglycans. UGPase is found in
both prokaryotes and eukaryotes. Interestingly, while
the prokaryotic and eukaryotic forms of UGPase catalyze
the same reaction, they share low sequence similarity.
This family consists of mainly eukaryotic
UTP-glucose-1-phosphate uridylyltransferases.
Length = 300
Score = 28.8 bits (65), Expect = 5.6
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 135 EYLSNHYGDIEVPVANCNSYYFNAHEKTNMTLKEYT 170
E+L+ YG ++VP+ NS FN E T LK+Y
Sbjct: 43 EHLNKTYG-VDVPLVLMNS--FNTDEDTKKILKKYA 75
>gnl|CDD|235891 PRK06933, PRK06933, type III secretion system protein; Validated.
Length = 308
Score = 28.9 bits (65), Expect = 5.6
Identities = 28/107 (26%), Positives = 38/107 (35%), Gaps = 20/107 (18%)
Query: 305 EAGDSIFVPSGW--HHQV-TNLEHTISINHNWINGTNIDHVYHEMVSHLEAVKKEIDDCK 361
E GD + P G + V +E W L + E +D
Sbjct: 177 ELGDVLLAPEGSGPNSPVLAYVE-----GRPWAYCQ-----LQSNKLELIGMHTESNDLN 226
Query: 362 DMDDWTSHCQLMLQVSFGINFRQFFDMLKFICQKRLTSLKNGTTIRL 408
T QL +QVSF + RQ D+ LTSL+ G+ I L
Sbjct: 227 PEPLLTDLNQLPVQVSFEVG-RQTLDL------HTLTSLQPGSLIDL 266
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 28.7 bits (65), Expect = 6.0
Identities = 23/125 (18%), Positives = 37/125 (29%), Gaps = 45/125 (36%)
Query: 2 SVYHDEI-------------EIEDFEYDEDDETYYYPCPCGDRFQITKEQLKAGEDVATC 48
SV HDE ++++F Y D C C + C
Sbjct: 51 SVLHDEFIAHRLGLIPLTSDDVDEFLYYSRD------CDCDEF----------------C 88
Query: 49 PTCSLIIKPSVIKSVMLMLSDSCNSNEQINVTTTALPQVDYNIDPSHIYPYCFNNFLSKN 108
CS V L L C ++ VT+ L ++ P ++ +
Sbjct: 89 DKCS----------VELTLDVKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSEDNGE 138
Query: 109 KPFIL 113
+ IL
Sbjct: 139 EDGIL 143
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 28.6 bits (65), Expect = 7.3
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 207 VPNVFSSDWLNEYYSEHLEH----KDDYRF 232
VPN F DW+ + Y + +E Y F
Sbjct: 43 VPNRFVKDWIEKNYLDLIEEALQLNPKYTF 72
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
0.319 0.135 0.435
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,307,933
Number of extensions: 2203828
Number of successful extensions: 1903
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1895
Number of HSP's successfully gapped: 35
Length of query: 456
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 356
Effective length of database: 6,502,202
Effective search space: 2314783912
Effective search space used: 2314783912
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 (21.8 bits)
S2: 61 (27.2 bits)