RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6552
(254 letters)
>gnl|CDD|217934 pfam04157, EAP30, EAP30/Vps36 family. This family includes EAP30
as well as the Vps36 protein. Vps36 is involved in Golgi
to endosome trafficking. EAP30 is a subunit of the ELL
complex. The ELL is an 80-kDa RNA polymerase II
transcription factor. ELL interacts with three other
proteins to form the complex known as ELL complex. The
ELL complex is capable of increasing that catalytic rate
of transcription elongation, but is unable to repress
initiation of transcription by RNA polymerase II as is
the case of ELL. EAP30 is thought to lead to the
derepression of ELL's transcriptional inhibitory
activity.
Length = 219
Score = 228 bits (584), Expect = 9e-76
Identities = 100/225 (44%), Positives = 142/225 (63%), Gaps = 7/225 (3%)
Query: 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFR 64
G+ I++ + EQ KY D G + LE L + F + LESFA ++K+EIK + +FR
Sbjct: 1 VGIAGIERSREEQRKYNDLGLQLAFEDLEALMKQAKDFVELLESFAKKHKSEIKANPEFR 60
Query: 65 RHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRT 124
FQ MCAS+GVDPLAS+KG L G+GDFYYEL+VQIVE+CLAT +NGG+I L +L
Sbjct: 61 AQFQSMCASLGVDPLASKKG-SVLGGVGDFYYELAVQIVEICLATLKENGGIISLQDLYA 119
Query: 125 RLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP-GELSLDHSL 183
++RG + + ++ EDLL A KKL+ G GF ++ IG G +VQS+P ELS D +
Sbjct: 120 LYNRARGGT---ELVSPEDLLKACKKLEKLGLGFKLVKIGSGVLVVQSVPKSELSEDQTK 176
Query: 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228
+L ++A + ++ S L +L WS RA+ L+ +EG W D
Sbjct: 177 IL-ELAEELG-GVTASELAEKLGWSIGRAKEVLEKAEKEGLLWRD 219
>gnl|CDD|133057 cd06435, CESA_NdvC_like, NdvC_like proteins in this family are
putative bacterial beta-(1,6)-glucosyltransferase.
NdvC_like proteins in this family are putative
bacterial beta-(1,6)-glucosyltransferase. Bradyrhizobium
japonicum synthesizes periplasmic cyclic
beta-(1,3),beta-(1,6)-D-glucans during growth under
hypoosmotic conditions. Two genes (ndvB, ndvC) are
involved in the beta-(1, 3), beta-(1,6)-glucan
synthesis. The ndvC mutant strain resulted in synthesis
of altered cyclic beta-glucans composed almost entirely
of beta-(1, 3)-glycosyl linkages. The periplasmic cyclic
beta-(1,3),beta-(1,6)-D-glucans function for
osmoregulation. The ndvC mutation also affects the
ability of the bacteria to establish a successful
symbiotic interaction with host plant. Thus, the
beta-glucans may function as suppressors of a host
defense response.
Length = 236
Score = 30.1 bits (68), Expect = 0.99
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 230 QSPQEHLYWFPSLFTECMNAE 250
Q+PQ++ SLF AE
Sbjct: 118 QAPQDYRDGEESLFKRMCYAE 138
>gnl|CDD|217211 pfam02743, Cache_1, Cache domain.
Length = 81
Score = 28.0 bits (63), Expect = 1.2
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLV 170
D++ EDLL K +K+ G++ I G+ L
Sbjct: 35 DVSLEDLLKITKSIKLGKTGYAFIVDNNGKVLA 67
>gnl|CDD|146727 pfam04240, DUF422, Protein of unknown function (DUF422). Predicted
to be an integral membrane protein.
Length = 215
Score = 29.3 bits (66), Expect = 1.4
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 70 MCASIGVDPLASRKGFWSLLGMGDFY 95
+ +DP A GFW G FY
Sbjct: 115 TLWDVVLDPAAVALGFWVWFDPGPFY 140
>gnl|CDD|144876 pfam01442, Apolipoprotein, Apolipoprotein A1/A4/E domain. These
proteins contain several 22 residue repeats which form a
pair of alpha helices. This family includes:
Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein
E.
Length = 191
Score = 29.1 bits (66), Expect = 1.7
Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 12 KQKLEQ--EKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ-FRRHFQ 68
+QKL + E+ K+ E QLS+ + R+KLE +A + + +++ A+ ++
Sbjct: 128 RQKLAERLEELKESVGPYAEEYKAQLSEQVEELREKLEPYAEDLREKLEPYAEDLKKQLA 187
Query: 69 EM 70
++
Sbjct: 188 QL 189
>gnl|CDD|236886 PRK11249, katE, hydroperoxidase II; Provisional.
Length = 752
Score = 29.6 bits (67), Expect = 1.8
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 75 GVDPLASRKGFWSLLGMGDF-YYELSVQIVE 104
G DP R+ W + GD+ YEL VQ++
Sbjct: 309 GRDPDFHRRDLWEAIEAGDYPEYELGVQLIP 339
>gnl|CDD|163064 TIGR02894, DNA_bind_RsfA, transcription factor, RsfA family. In a
subset of endospore-forming members of the Firmcutes,
members of this protein family are found, several to a
genome. Two very strongly conserved sequences regions
are separated by a highly variable linker region. Much
of the linker region was excised from the seed alignment
for this model. A characterized member is the
prespore-specific transcription RsfA from Bacillus
subtilis, previously called YwfN, which is controlled by
sigma factor F and seems to fine-tune expression of some
genes in the sigma-F regulon. A paralog in Bacillus
subtilis is designated YlbO [Regulatory functions, DNA
interactions, Cellular processes, Sporulation and
germination].
Length = 161
Score = 28.6 bits (64), Expect = 2.2
Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 4 RAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQF 63
+ + Q + E E+ K++ S+Q+ + E+L + L R +L + +Y+ I +
Sbjct: 93 KTTNPSDQALQKENERLKNQNESLQK-RNEELEKELEKLRQRLSTIEEDYQTLIDIMDRA 151
Query: 64 RR 65
R+
Sbjct: 152 RK 153
>gnl|CDD|225726 COG3185, COG3185, 4-hydroxyphenylpyruvate dioxygenase and related
hemolysins [Amino acid transport and metabolism /
General function prediction only].
Length = 363
Score = 29.2 bits (66), Expect = 2.3
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 126 LVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQY--LVQSIPGE 176
L + RG+ +QH +D+ A L+ G +PI + Y L P
Sbjct: 238 LREYRGEGIQHIAFGTDDIYATVAALR--ERGVKFLPIPETYYDDLDARFPLH 288
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 28.4 bits (64), Expect = 3.3
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 3/66 (4%)
Query: 102 IVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI---FGNGF 158
+ E T Y GLI +EL R+ +++++ AAK LKI +G GF
Sbjct: 17 LEENFEVTYYDGLGLISKEELLERIADYDALITPLSTPVDKEIIDAAKNLKIIANYGAGF 76
Query: 159 SIIPIG 164
I +
Sbjct: 77 DNIDVD 82
>gnl|CDD|233583 TIGR01813, flavo_cyto_c, flavocytochrome c. This model describes a
family of redox proteins related to the succinate
dehydrogenases and fumarate reductases of E. coli,
mitochondria, and other well-characterized systems. A
member of this family from Shewanella frigidimarina
NCIMB400 is characterized as a water-soluble periplasmic
protein with four heme groups, a non-covalently bound
FAD, and essentially unidirectional fumarate reductase
activity. At least seven distinct members of this family
are found in Shewanella oneidensis, a species able to
use a wide variety of pathways for respiraton [Energy
metabolism, Electron transport].
Length = 439
Score = 28.8 bits (65), Expect = 3.3
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 18 EKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEI---KKDAQFRR 65
+ Y G + + + LE+L++ L+ +Y N+ KD F R
Sbjct: 309 DNYYRLGVAYKGDSLEELAKQFGIPAAALKKTVKDY-NDYVASGKDTPFGR 358
>gnl|CDD|204339 pfam09922, DUF2154, Cell wall-active antibiotics response protein
(DUF2154).
Length = 115
Score = 27.6 bits (62), Expect = 3.3
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 103 VEVCL--ATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGN 156
VEV L + Y GG+ DE L R +S++ +E+ A ++LKI +
Sbjct: 60 VEVSLDHSAIY--GGVDFFDEEEYGL---RNESIR---YRSENYDEAERRLKIITS 107
>gnl|CDD|222732 pfam14394, DUF4423, Domain of unknown function (DUF4423). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is approximately
170 amino acids in length.
Length = 171
Score = 27.6 bits (62), Expect = 4.3
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 26 SIQENQLEQLSQHLNTFRDKLESFASEYKN 55
+I E E++ + L+ FR K+ + A+E K
Sbjct: 128 AISEEAYEKIKKELDEFRKKIIAIATEDKE 157
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 27.9 bits (63), Expect = 5.4
Identities = 33/134 (24%), Positives = 53/134 (39%), Gaps = 41/134 (30%)
Query: 44 DKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASR---KGFWSLLGM--GDFYYEL 98
D +E+ S + NE A RR + L + KG +++ GD Y L
Sbjct: 137 DSIEALFSGFSNE----AVVRRELRR---------LFAWLKQKGVTAVITGERGDEYGPL 183
Query: 99 SVQIVEVCLATNYKNGGLILLD-----ELRTR---LVKSRGKSLQHQDITNEDLLAAAKK 150
+ VE ++ +I+L E RTR ++K RG + H NE
Sbjct: 184 TRYGVEEFVSDC-----VIILRNRLEGEKRTRTLRILKYRGTT--HG--KNE------YP 228
Query: 151 LKIFGNGFSIIPIG 164
I +G S++P+
Sbjct: 229 FTITEDGISVLPLT 242
>gnl|CDD|184102 PRK13511, PRK13511, 6-phospho-beta-galactosidase; Provisional.
Length = 469
Score = 28.0 bits (63), Expect = 5.4
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 160 IIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQ-HALDF 218
I PIG GQYLV P + D + V Q + AH L + + E HAL
Sbjct: 161 IGPIGDGQYLVGKFPPGIKYDLAKVFQSHHNMMVAHARAVKLFKDKGYKGEIGVVHAL-- 218
Query: 219 MVQEGYAWIDTQSPQEH 235
Y ID +P++
Sbjct: 219 --PTKYP-IDPDNPEDV 232
>gnl|CDD|184780 PRK14645, PRK14645, hypothetical protein; Provisional.
Length = 154
Score = 27.4 bits (61), Expect = 5.7
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 32 LEQLSQHLNTFRDKLESFASEYKNEI-----KKDAQFRRHFQEM 70
LE+ S+ L D+L+ EY+ E+ K+ RHF+
Sbjct: 57 LERASRALEAELDRLDPIEGEYRLEVESPGPKRPLFTARHFERF 100
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 27.8 bits (62), Expect = 6.4
Identities = 15/54 (27%), Positives = 24/54 (44%)
Query: 12 KQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRR 65
QK EQ + + ENQLE+ + L+ +LE + NE+ + A
Sbjct: 87 VQKEEQLDARAEKLDNLENQLEEREKALSARELELEELEKQLDNELYRVAGLTP 140
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 27.7 bits (62), Expect = 6.9
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 13 QKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62
+K EK ++K ++E + + L + KLE + ++ K+ +
Sbjct: 319 KKKFTEKIREKEKRLEELE-QNLIEERKELNSKLEEIQKKLEDLEKRLEK 367
>gnl|CDD|227289 COG4953, PbpC, Membrane carboxypeptidase/penicillin-binding protein
PbpC [Cell envelope biogenesis, outer membrane].
Length = 733
Score = 27.7 bits (62), Expect = 7.2
Identities = 12/33 (36%), Positives = 14/33 (42%), Gaps = 7/33 (21%)
Query: 60 DAQFRRHFQEMCASIGVDPLASRKGFWSLLGMG 92
D +F H GVDPLA + W L G
Sbjct: 79 DKRFYWHP-------GVDPLALLRAAWQTLTSG 104
>gnl|CDD|219965 pfam08676, MutL_C, MutL C terminal dimerisation domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognises mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerisation.
Length = 144
Score = 26.8 bits (60), Expect = 7.3
Identities = 15/79 (18%), Positives = 29/79 (36%), Gaps = 16/79 (20%)
Query: 112 KNGGLILLD-----ELRT--RLVKSRGKSLQHQ--------DITNEDLLAAAKKLKIFG- 155
GL L+D E +L + Q Q +++ E+ + ++
Sbjct: 18 NEDGLYLVDQHAAHERILYEKLKSKLKEGGQSQPLLIPLTLELSPEEAALLEEHKELLAR 77
Query: 156 NGFSIIPIGQGQYLVQSIP 174
GF + G +V+S+P
Sbjct: 78 LGFELEEFGPNSLIVRSVP 96
>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 27.5 bits (62), Expect = 8.9
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 11/54 (20%)
Query: 120 DELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSI 173
+ +LV+ GK L+ ITNE+ A K + Y V I
Sbjct: 206 EPFTAKLVEVNGKKLEKFSITNEEQAKALVKA-----------LEGQAYTVDKI 248
>gnl|CDD|216389 pfam01251, Ribosomal_S7e, Ribosomal protein S7e.
Length = 189
Score = 26.9 bits (60), Expect = 9.9
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 19 KYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFR 64
+Y+ G+ + + L+ S+ KL+SF++ YK KD F
Sbjct: 140 RYRLDGSKLIKVFLD--SKDQTNVEHKLDSFSAVYKKLTGKDVVFE 183
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 0.133 0.383
Gapped
Lambda K H
0.267 0.0779 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,692,821
Number of extensions: 1177973
Number of successful extensions: 1478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1471
Number of HSP's successfully gapped: 52
Length of query: 254
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 159
Effective length of database: 6,723,972
Effective search space: 1069111548
Effective search space used: 1069111548
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: 58 (26.0 bits)