RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14554
(78 letters)
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 29.1 bits (66), Expect = 0.17
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 40 LEEGDTFFFAPRSLRNLVLVDEM 62
L+ GDTF FA R L V + +M
Sbjct: 502 LKPGDTFLFAGRVLE-FVRIRDM 523
>gnl|CDD|220751 pfam10433, MMS1_N, Mono-functional DNA-alkylating methyl
methanesulfonate N-term. MMS1 is a protein that
protects against replication-dependent DNA damage in
Saccharomyces cerevisiae. MMS1 belongs to the DDB1
family of cullin 4 adaptors and the two proteins are
homologous. MMS1 bridges the interaction of MMS22 and
Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein
involved in the regulation of DNA replication subsequent
to DNA damage. The N-terminal region of MMS1 and the
C-terminal of MMS22 are required for the the MMS1-MMS22
interaction. The human HIV-1 virion-associated protein
Vpr assembles with DDB1 through interaction with DCAF1
(chromatin assembly factor) to form an E3 ubiquitin
ligase that targets cellular substrates for
proteasome-mediated degradation and subsequent G2
arrest.
Length = 513
Score = 26.9 bits (60), Expect = 0.86
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 43 GDTFFFAPRSLRNLVLVDEMQSLSPILDCKVADLGS 78
GD F + N V + + +PILD V D G+
Sbjct: 288 GDGGLFKISARDNPRCVQDFPNWAPILDFVVVDSGN 323
>gnl|CDD|216852 pfam02028, BCCT, BCCT family transporter.
Length = 484
Score = 26.7 bits (60), Expect = 1.0
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 25 LGDDDDEPEFS 35
LG DD++PEFS
Sbjct: 66 LGGDDEKPEFS 76
>gnl|CDD|224211 COG1292, BetT, Choline-glycine betaine transporter [Cell envelope
biogenesis, outer membrane].
Length = 537
Score = 26.1 bits (58), Expect = 1.9
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 24 HLGDDDDEPEFS 35
LG DD++PEFS
Sbjct: 78 RLGKDDEKPEFS 89
>gnl|CDD|217433 pfam03223, V-ATPase_C, V-ATPase subunit C.
Length = 371
Score = 25.7 bits (57), Expect = 2.6
Identities = 11/44 (25%), Positives = 20/44 (45%)
Query: 5 EKRIRKTMVSIFSYLYQIAHLGDDDDEPEFSSAMPLEEGDTFFF 48
EK++RK + +F YL A D D + ++ +E +
Sbjct: 328 EKKVRKILNQLFGYLGGNAASYDKDGDIVDDPSLLGDEEYYPYV 371
>gnl|CDD|213565 TIGR00842, bcct, choline/carnitine/betaine transport. The
Betaine/Carnitine/Choline Transporter (BCCT) Family (TC
2.A.15) Proteins of the BCCT family share the common
functional feature of transporting molecules with a
quaternary ammonium group [R-N+(CH3)3]. The BCCT family
includes transporters for carnitine, choline and
glycine betaine. BCCT transporters have 12 putative
TMS, and are energized by pmf-driven proton symport.
Some of these permeases exhibit osmosensory and
osmoregulatory properties inherent to their polypeptide
chains [Transport and binding proteins, Other].
Length = 452
Score = 24.6 bits (54), Expect = 6.1
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 25 LGDDDDEPEFS 35
LG DD++PEFS
Sbjct: 28 LGRDDEKPEFS 38
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional.
Length = 780
Score = 24.7 bits (54), Expect = 6.1
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 8/35 (22%)
Query: 27 DDDDEPEFSSAMP--------LEEGDTFFFAPRSL 53
DD+++P F+S P LEE F PR+L
Sbjct: 618 DDEEKPRFASLRPGQSIDSITLEEALELFKLPRAL 652
>gnl|CDD|220634 pfam10220, DUF2146, Uncharacterized conserved protein (DUF2146).
This is a family of proteins conserved from plants to
humans. In Dictyostelium it is annotated as Mss11p but
this could not be confirmed. Mss11p is required for the
activation of pseudo-hyphal and invasive growth by
Ste12p in yeast.
Length = 890
Score = 24.8 bits (54), Expect = 6.3
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 2 TSWEKRIRKTMVSIFSYLYQIAHLGDDDDEPEFSSAMP 39
T +E I V + L+Q+ + ++DD E
Sbjct: 339 THFELPIYSKWVEVARRLHQLL-IENEDDPNEERGGED 375
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 24.6 bits (54), Expect = 6.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 46 FFFAPRSLRNLVLVDEMQSL 65
+ PR R + ++DE SL
Sbjct: 630 MYLTPRKRRKICIIDEAWSL 649
>gnl|CDD|211327 cd02553, PseudoU_synth_RsuA, Pseudouridine synthase, Escherichia
coli RsuA like. This group is comprised of eukaryotic
and bacterial proteins similar to Escherichia coli RsuA.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required.
E.coli RsuA makes psi516 in 16S RNA. Psi at this
position is not generally conserved in other organisms.
Length = 167
Score = 24.4 bits (54), Expect = 7.1
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 1 MTSWEKRIRKTMVSIFSYLYQIAHLGDDDDEPEFSSAMPLEEGDTF 46
+TS +K + KT Y +A +DD F+ + L +G
Sbjct: 62 LTSPKKHVPKT------YEVTLAGPLTEDDIEAFAEGVLLHDGYPT 101
>gnl|CDD|111859 pfam03015, Sterile, Male sterility protein. This family
represents the C-terminal region of the male sterility
protein in a number of arabidopsis and drosophila. A
sequence-related jojoba acyl CoA reductase is also
included.
Length = 94
Score = 23.8 bits (52), Expect = 7.8
Identities = 8/27 (29%), Positives = 11/27 (40%)
Query: 27 DDDDEPEFSSAMPLEEGDTFFFAPRSL 53
D+ + E M E+ F F SL
Sbjct: 48 DNKNTRELREKMSEEDKKLFNFDMESL 74
>gnl|CDD|235267 PRK04266, PRK04266, fibrillarin; Provisional.
Length = 226
Score = 24.1 bits (53), Expect = 8.6
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 48 FAPRSLRNLVLVDE 61
FAPR +R L+ V E
Sbjct: 104 FAPRPMRELLEVAE 117
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 24.4 bits (53), Expect = 9.1
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 12 MVSIFSYLYQIAHLGDDDD-----EPEFS------SAMPLE 41
MVS F YQIA D+D +PEF+ + PLE
Sbjct: 268 MVSGFDRYYQIARCFRDEDLRADRQPEFTQLDMELAFTPLE 308
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 23.9 bits (52), Expect = 9.7
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 46 FFFAPRSLRNLVLVDEMQSL 65
F APR LR L+++DE L
Sbjct: 225 AFEAPRGLRKLIVIDEAWRL 244
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
0.320 0.136 0.399
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,111,887
Number of extensions: 325752
Number of successful extensions: 280
Number of sequences better than 10.0: 1
Number of HSP's gapped: 280
Number of HSP's successfully gapped: 18
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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: 53 (24.3 bits)