RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5894
(233 letters)
>gnl|CDD|192393 pfam09816, EAF, RNA polymerase II transcription elongation factor.
Members of this family act as transcriptional
transactivators of ELL and ELL2 elongation activities.
Eaf proteins form a stable heterodimer complex with ELL
proteins to facilitate the binding of RNA polymerase II
to activate transcription elongation. The N-terminus of
approx 120 residues is globular and highly conserved.
Length = 108
Score = 95.8 bits (239), Expect = 2e-25
Identities = 42/106 (39%), Positives = 61/106 (57%), Gaps = 8/106 (7%)
Query: 12 RELKLGSSFTNANKGS--SFHTLRYDFKPASMDPNEVAKLDVGESNQVTVTVPHGSRE-- 67
L LG S + S SF T+RY+FKPAS+D + L+ G+ +QVT+T+P+ +
Sbjct: 2 YPLILGDSLLGKSSSSPDSFVTIRYNFKPASVDTTQPGSLEQGKDDQVTLTLPNPNGSKK 61
Query: 68 ---TVFKGSHKPYQ-KECVLIIDNVTGEITLEKLSNNIQLKKTRTA 109
VF+GS +P + KECVLI D T LE+L + + + KTR
Sbjct: 62 PLTYVFEGSVRPAKEKECVLIFDPETKVFVLERLDSTLNVNKTRAP 107
>gnl|CDD|153433 cd08010, yceG_like, proteins similar to Escherichia coli yceG.
The gene product of Escherichia coli yceG has been
erroneously annotated as an aminodeoxychorismate lyase.
Its overexpression has been reported to cause abnormal
biofilm architecture, and it has been reported to be
part of a putative five-gene operon. It might function
as a periplasmic solute-binding protein. The family
also includes Streptomyces caeruleus NovB, an
uncharacterized member of the novobiocin biosynthetic
gene cluster.
Length = 245
Score = 31.4 bits (72), Expect = 0.28
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 33 RYDFKPASMDPNEVAK-LDVGESNQVTVTVPHGSR 66
Y+ P M E+ + L G+S QV VT+P G
Sbjct: 5 EYELSP-GMSLAEILERLTSGKSAQVKVTIPEGYT 38
>gnl|CDD|176510 cd08567, GDPD_SpGDE_like, Glycerophosphodiester phosphodiesterase
domain of putative Silicibacter pomeroyi
glycerophosphodiester phosphodiesterase and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in a group of uncharacterized bacterial
glycerophosphodiester phosphodiesterases (GP-GDE, EC
3.1.4.46) and similar proteins. The prototype of this CD
is a putative GP-GDE from Silicibacter pomeroyi (SpGDE).
It shows high sequence similarity to Escherichia coli
GP-GDE, which catalyzes the degradation of
glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols.
Length = 263
Score = 30.4 bits (69), Expect = 0.73
Identities = 15/70 (21%), Positives = 23/70 (32%), Gaps = 11/70 (15%)
Query: 7 LNPDIRELKLGSSFTNANKGSSFHTLRYDFKPASMDPNEVAKLDVGESNQVTVTVPHGSR 66
LNPDI G+ + + L E+ +LDVGE +
Sbjct: 52 LNPDITRDPDGAWLPYEGP--ALYELTLA---------EIKQLDVGEKRPGSDYAKLFPE 100
Query: 67 ETVFKGSHKP 76
+ G+ P
Sbjct: 101 QIPVPGTRIP 110
>gnl|CDD|217147 pfam02618, YceG, YceG-like family. This family of proteins is
found in bacteria. Proteins in this family are
typically between 332 and 389 amino acids in length.
This family was previously incorrectly annotated and
names as aminodeoxychorismate lyase. The structure of
Escherichia coli yceG was solved by X-ray
crystallography.
Length = 291
Score = 29.8 bits (68), Expect = 1.0
Identities = 19/70 (27%), Positives = 27/70 (38%), Gaps = 7/70 (10%)
Query: 1 MADKL---GLNPDIRELKLGSSFTNANKGSSFHTLRYDFKPASMDPNE-VAKLDVGESNQ 56
+AD L G+ +L + K Y+ KP M E + KL G+ Q
Sbjct: 14 IADILEEAGVIKSALAFRLYARLKG--KDGKLKAGEYELKP-GMSAAEILEKLVSGKVVQ 70
Query: 57 VTVTVPHGSR 66
VT+P G
Sbjct: 71 YKVTIPEGLT 80
>gnl|CDD|220401 pfam09786, CytochromB561_N, Cytochrome B561, N terminal. Members
of this family are found in the N terminal region of
cytochrome B561, as well as in various other putative
uncharacterized proteins.
Length = 559
Score = 30.1 bits (68), Expect = 1.2
Identities = 20/82 (24%), Positives = 26/82 (31%), Gaps = 16/82 (19%)
Query: 126 LSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQTSPS-------YFSP---PHTKS 175
+S+ KK + S P +P HS SPS FSP
Sbjct: 113 VSQAKKSPPASKTSTPMNTS------EPLVPGHSSFSDSPSRSASPSRKFSPSSTIQQSP 166
Query: 176 PTAPFKSPSPGQGSSLSPMVNS 197
P P+ S SP +S
Sbjct: 167 QLTPSNKPASPSSSYQSPSYSS 188
>gnl|CDD|221625 pfam12533, Neuro_bHLH, Neuronal helix-loop-helix transcription
factor. This domain family is found in eukaryotes, and
is approximately 80 amino acids in length. The family is
found C-terminal to pfam00010. There is a single
completely conserved residue W that may be functionally
important. Neuronal basic helix-loop-helix (bHLH)
transcription factors such as neuroD and neurogenin have
been shown to play important roles in neuronal
development.
Length = 120
Score = 28.1 bits (63), Expect = 1.8
Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 1/49 (2%)
Query: 153 PSIPRHSPLQTSPSYFSPPH-TKSPTAPFKSPSPGQGSSLSPMVNSLPA 200
+H SP SPPH + S + G S+ P S
Sbjct: 50 SPFSQHPYPYQSPGLPSPPHGSMSSSHSLHLKPHGYCSAYEPFYESHSP 98
>gnl|CDD|218825 pfam05956, APC_basic, APC basic domain. This region of the APC
family of proteins is known as the basic domain. It
contains a high proportion of positively charged amino
acids and interacts with microtubules.
Length = 359
Score = 28.6 bits (63), Expect = 2.8
Identities = 17/37 (45%), Positives = 20/37 (54%)
Query: 156 PRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLS 192
P + T+PS PP P+ P KSPSPGQ S S
Sbjct: 14 PANRSQSTTPSKKGPPLKTQPSDPPKSPSPGQQRSRS 50
>gnl|CDD|217835 pfam03999, MAP65_ASE1, Microtubule associated protein (MAP65/ASE1
family).
Length = 619
Score = 28.3 bits (63), Expect = 3.9
Identities = 21/96 (21%), Positives = 28/96 (29%), Gaps = 6/96 (6%)
Query: 104 KKTRTAPTNKTDTSHVMPSAIPLSRLKKKTSGKANNNHKTKSGNNLSVPPSIPRHSPLQT 163
T T + T+ A S AN N + ++LS P SI SP +
Sbjct: 511 GNTHKHSTPRRLTTLPKLPAASRSSKGNLIRSGANGN----ASSDLSSPGSINSKSPEHS 566
Query: 164 SP--SYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNS 197
P F S T S + S
Sbjct: 567 VPLVRVFDIHLRASTTKGRHSTPSTNEKKKRLLKRS 602
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport
and metabolism].
Length = 342
Score = 28.0 bits (63), Expect = 4.6
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 24 NKGSSFHTLRYDFKPASMDPNE-VAKLDVGESNQVTVTVPHGSR 66
S Y +P M + + L+ G+S Q VT+P G
Sbjct: 83 PAAGSLKAGEYRLRP-GMSAADILKLLESGKSAQFKVTIPEGYT 125
>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421). This
family represents a conserved region approximately 350
residues long within a number of plant proteins of
unknown function.
Length = 357
Score = 28.0 bits (62), Expect = 4.8
Identities = 10/42 (23%), Positives = 13/42 (30%)
Query: 152 PPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSP 193
PP +P+ Q+ P P A G SP
Sbjct: 144 PPQVPQQQQYQSPPQQPQYQQNPPPQAQSAPQVSGLYPEESP 185
>gnl|CDD|132858 cd07219, Pat_PNPLA1, Patatin-like phospholipase domain containing
protein 1. Members of this family share a patatin
domain, initially discovered in potato tubers. Some
members of PNPLA1 subfamily do not have the lipase
consensus sequence Gly-X-Ser-X-Gly which is essential
for hydrolase activity. This family includes PNPLA1
from Homo sapiens and Gallus gallus. Currently, there is
no literature available on the physiological role,
structure, or enzymatic activity of PNPLA1. It is
expressed in various human tissues in low mRNA levels.
Length = 382
Score = 27.9 bits (62), Expect = 5.5
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 6/66 (9%)
Query: 142 KTKSGNNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSP--SPGQGSSLSPM----V 195
G L PP P + +++ + SP +P +S PG + LSP V
Sbjct: 312 PKGDGRGLHDPPLSPPLAAPESTAEWVVESPVSSPASPLESSPSLPGSLTDLSPASLPAV 371
Query: 196 NSLPAL 201
+SLP+
Sbjct: 372 HSLPSS 377
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 27.9 bits (62), Expect = 5.7
Identities = 9/57 (15%), Positives = 16/57 (28%), Gaps = 1/57 (1%)
Query: 146 GNNLSVPPSIPRHSP-LQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNSLPAL 201
G++ PS S P P+ + + P+ P+L
Sbjct: 25 GDSNPYYPSSFGSSWDRPGPPVPEDYDAPSHRPPPYGGSNGDRHGGYQPLGQQDPSL 81
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.0 bits (62), Expect = 5.7
Identities = 14/53 (26%), Positives = 18/53 (33%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNSLPALGLDD 205
P R P +P PP T +P P SPSP ++P
Sbjct: 2601 PVDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR 2653
>gnl|CDD|237782 PRK14666, uvrC, excinuclease ABC subunit C; Provisional.
Length = 694
Score = 27.5 bits (61), Expect = 6.2
Identities = 11/51 (21%), Positives = 19/51 (37%), Gaps = 3/51 (5%)
Query: 153 PSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNSLPALGL 203
P P S P + P S +P +SL+ + ++ PA+
Sbjct: 346 PDAPEGSSDPVVPVAAATPVDASLPDVRTGTAP---TSLANVSHADPAVAQ 393
>gnl|CDD|240420 PTZ00441, PTZ00441, sporozoite surface protein 2 (SSP2);
Provisional.
Length = 576
Score = 27.6 bits (61), Expect = 6.3
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 147 NNLSVPPSIPRHSPLQTSPSYFSPPHTKSPTAPFKSPSP 185
N PP++P S + S +PP+ +P P + P+
Sbjct: 359 NVPPNPPNVPGGSNSEFSSDVENPPNPPNPDIPEQEPNI 397
>gnl|CDD|217600 pfam03529, TF_Otx, Otx1 transcription factor.
Length = 86
Score = 25.9 bits (57), Expect = 6.4
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 162 QTSPSYFSPPHTKSPTAPFKSPSPGQGSSLSPMVNS 197
S SYF S +P S G++LSPM S
Sbjct: 41 PGSSSYFGGLDCGSYLSPMHSQLHAPGAALSPMAAS 76
>gnl|CDD|239181 cd02780, MopB_CT_Tetrathionate_Arsenate-R, This CD contains the
molybdopterin_binding C-terminal (MopB_CT) region of
tetrathionate reductase, subunit A, (TtrA); respiratory
arsenate As(V) reductase, catalytic subunit (ArrA); and
other related proteins.
Length = 143
Score = 26.9 bits (60), Expect = 6.5
Identities = 16/70 (22%), Positives = 22/70 (31%), Gaps = 15/70 (21%)
Query: 38 PASMDPNEVAKLDVGESNQVTVTVPHGS-------RETVFKGS--------HKPYQKECV 82
P ++P + AKL + ++V V P GS E V G H Y
Sbjct: 31 PVWINPEDAAKLGIKTGDRVRVVTPGGSVVGKAKVTEGVRPGVVAIEHGYGHWAYGAVAS 90
Query: 83 LIIDNVTGEI 92
I
Sbjct: 91 TIDGKDLPGD 100
>gnl|CDD|226946 COG4580, LamB, Maltoporin (phage lambda and maltose receptor)
[Carbohydrate transport and metabolism].
Length = 429
Score = 27.5 bits (61), Expect = 7.0
Identities = 8/42 (19%), Positives = 22/42 (52%)
Query: 11 IRELKLGSSFTNANKGSSFHTLRYDFKPASMDPNEVAKLDVG 52
+R + G S + +++ + +D + A+++ A L++G
Sbjct: 174 VRSSEAGGSSSRSSQNIDTNNNVFDVRLANIELWPGATLELG 215
>gnl|CDD|219383 pfam07348, Syd, Syd protein (SUKH-2). This family contains a
number of bacterial Syd proteins approximately 180
residues long. It has been suggested that Syd is loosely
associated with the cytoplasmic surface of the
cytoplasmic membrane, and that interaction with SecY may
be involved in this membrane association. Operon
analysis showed that Syd protein may function as
immunity protein in bacterial toxin systems.
Length = 176
Score = 26.8 bits (60), Expect = 7.4
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 81 CVLIIDNVTGEITLEKL 97
++ +DN++GE+ LE
Sbjct: 139 LLISVDNLSGEVILEDF 155
>gnl|CDD|233588 TIGR01823, PabB-fungal, aminodeoxychorismate synthase, fungal
clade. This model represents the fungal clade of a
para-aminobenzoate synthesis enzyme,
aminodeoxychorismate synthase, which acts on chorismate
in a pathway that yields PABA, a precursor of folate.
Length = 742
Score = 27.6 bits (61), Expect = 7.5
Identities = 23/133 (17%), Positives = 43/133 (32%), Gaps = 4/133 (3%)
Query: 4 KLGLNPDIRELKLGSS-FTNANKGSSFHTLRYDFKPASMDPNEVAKLDVGESNQVTVTVP 62
KL +++ + + S R D + E + V
Sbjct: 202 KLAFINNVKTGRWEKKKLNGSFSDISSRLDRTDDRDPIYKVKEKYP---SGTTYVKQFEV 258
Query: 63 HGSRETVFKGSHKPYQKECVLIIDNVTGEITLEKLSNNIQLKKTRTAPTNKTDTSHVMPS 122
+ F+ + + + V+ +TG ++ L N+ T KT + +
Sbjct: 259 SEDPKLTFEICNIIREPKFVMSSSVITGRYSIIALPNSASQVFTHYGAMLKTTVHYWQDT 318
Query: 123 AIPLSRLKKKTSG 135
I +RLKK SG
Sbjct: 319 EISYTRLKKCLSG 331
>gnl|CDD|111090 pfam02158, Neuregulin, Neuregulin family.
Length = 406
Score = 27.1 bits (59), Expect = 8.6
Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 4/92 (4%)
Query: 115 DTSHVMPSAIPLSRLKKKTSGKANNN---HKTKSGNNLSVPPSIPRHSPLQTSPSYFSPP 171
++ H P+ P RL + + H + ++ P R+ T+P+ SP
Sbjct: 148 NSRHSSPAGGPRGRLHGIGGPPDDCSFLRHARDTPDSYRDSPHSERYVSAMTTPARMSPV 207
Query: 172 HTKSPTAPFKSPSPGQGSSLSPMVNSLPALGL 203
+P +P KSP S + S+P++ +
Sbjct: 208 DFHTPISP-KSPCLEMSPPESSLAVSMPSVAV 238
>gnl|CDD|217461 pfam03261, CDK5_activator, Cyclin-dependent kinase 5 activator
protein.
Length = 314
Score = 27.2 bits (60), Expect = 9.0
Identities = 19/78 (24%), Positives = 27/78 (34%), Gaps = 11/78 (14%)
Query: 130 KKKTSGKANNNHKTKSGNNLS-------VPPSIPRHSPLQTSP----SYFSPPHTKSPTA 178
KKKTS K+ N + S + + S+PR S S S P + P
Sbjct: 67 KKKTSKKSTANLASSSYQKIVIQLNRENLKKSVPRPSDTTLSCANLSSLREPSPGQPPAP 126
Query: 179 PFKSPSPGQGSSLSPMVN 196
P S + + N
Sbjct: 127 PPSVLSGKNANCIPSQKN 144
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
0.308 0.126 0.356
Gapped
Lambda K H
0.267 0.0621 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,273,044
Number of extensions: 990858
Number of successful extensions: 766
Number of sequences better than 10.0: 1
Number of HSP's gapped: 746
Number of HSP's successfully gapped: 62
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 57 (26.0 bits)