RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17740
(384 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 39.3 bits (92), Expect = 6e-05
Identities = 15/28 (53%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 280 HLKAHMRTHTGERPFLCQWTGCGRRFSR 307
+L+ HMRTHTGE+P+ C CG+ FS
Sbjct: 1 NLRRHMRTHTGEKPYKC--PVCGKSFSS 26
Score = 36.2 bits (84), Expect = 7e-04
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 310 ELSRHKRTHTGEKKFGCSICNRRF 333
L RH RTHTGEK + C +C + F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSF 24
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys. The
C2H2 zinc finger is composed of two short beta strands
followed by an alpha helix. The amino terminal part of
the helix binds the major groove in DNA binding zinc
fingers. The accepted consensus binding sequence for Sp1
is usually defined by the asymmetric hexanucleotide core
GGGCGG but this sequence does not include, among others,
the GAG (=CTC) repeat that constitutes a high-affinity
site for Sp1 binding to the wt1 promoter.
Length = 22
Score = 32.7 bits (75), Expect = 0.014
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 326 CSICNRRFMRSDHLAKHVKRH 346
C C + F R +L +H++ H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 31.9 bits (73), Expect = 0.024
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 265 ECNYENCGKNYFKSSHLKAHMRTH 288
+C CGK++ + S+LK H+RTH
Sbjct: 1 KCPD--CGKSFSRKSNLKRHLRTH 22
Score = 31.9 bits (73), Expect = 0.026
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 299 TGCGRRFSRSDELSRHKRTH 318
CG+ FSR L RH RTH
Sbjct: 3 PDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 32.4 bits (74), Expect = 0.018
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 326 CSICNRRFMRSDHLAKHVKRH 346
C C + F L +H++ H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
Score = 29.4 bits (66), Expect = 0.20
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 2/25 (8%)
Query: 294 FLCQWTGCGRRFSRSDELSRHKRTH 318
+ C CG+ F L H RTH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
Score = 27.8 bits (62), Expect = 0.62
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 264 FECNYENCGKNYFKSSHLKAHMRTH 288
+ C CGK + S L+ HMRTH
Sbjct: 1 YRCPE--CGKVFKSKSALREHMRTH 23
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family contains
a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 32.2 bits (73), Expect = 0.018
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 324 FGCSICNRRFMRSDHLAKHVKRH 346
F C +C + F D L +H+++H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 29.5 bits (66), Expect = 0.20
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 294 FLCQWTGCGRRFSRSDELSRHKRTH 318
F C CG+ FS D L RH R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
Score = 28.0 bits (62), Expect = 0.57
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 264 FECNYENCGKNYFKSSHLKAHMRTH 288
F+C CGK++ LK H+R H
Sbjct: 1 FKCPL--CGKSFSSKDALKRHLRKH 23
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.4 bits (81), Expect = 0.040
Identities = 33/89 (37%), Positives = 46/89 (51%), Gaps = 4/89 (4%)
Query: 243 VTSNKIKKSNKPATNDPRRRIFECNYENCGKNYFKSSHLKAHMRTHTGERPFLCQWTGCG 302
V S+ K + K +N PR + NC ++ + HL H+R+HTGE+P C ++GC
Sbjct: 15 VLSSTPKSTLKSLSNAPR----PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCD 70
Query: 303 RRFSRSDELSRHKRTHTGEKKFGCSICNR 331
+ FSR ELSRH RTH S
Sbjct: 71 KSFSRPLELSRHLRTHHNNPSDLNSKSLP 99
Score = 28.5 bits (63), Expect = 6.9
Identities = 24/123 (19%), Positives = 43/123 (34%), Gaps = 4/123 (3%)
Query: 223 KSNCPSFLFFAQPPRENKEIVTSNKIKKSNKPATNDPR---RRIFECNYENCGKNYFKSS 279
S + + + + + + E +C +N+ + S
Sbjct: 343 ILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDS 402
Query: 280 HLKAHMRTHTGERPFLCQWTGCGRRFSRSDELSRHKRTHTGEKKFGCSICNRRFMRSDHL 339
+L H+ TH RP+ C+ C + F+R L HK+ HT + F R L
Sbjct: 403 NLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIHT-NHAPLLCSILKSFRRDLDL 461
Query: 340 AKH 342
+ H
Sbjct: 462 SNH 464
>gnl|CDD|233280 TIGR01128, holA, DNA polymerase III, delta subunit. DNA polymerase
III delta (holA) and delta prime (holB) subunits are
distinct proteins encoded by separate genes. The delta
prime subunit (holB) exhibits sequence homology to the
tau and gamma subunits (dnaX), but the delta subunit
(holA) does not demonstrate this same homology with
dnaX. The delta, delta prime, gamma, chi and psi
subunits form the gamma complex subassembly of DNA
polymerase III holoenzyme, which couples ATP to assemble
the ring-shaped beta subunit around DNA forming a DNA
sliding clamp [DNA metabolism, DNA replication,
recombination, and repair].
Length = 302
Score = 31.5 bits (72), Expect = 0.69
Identities = 16/96 (16%), Positives = 31/96 (32%), Gaps = 11/96 (11%)
Query: 210 PLFIFDKKPVNSVKSNCPSFLFFAQPPRENKEIVTSNKI---KKSNKPATNDPRRRIFEC 266
P K + +++ + A PP + ++ + K+ KK K I EC
Sbjct: 55 PEGKPGAKGLKALEE------YLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAEIVEC 108
Query: 267 N--YENCGKNYFKSSHLKAHMRTHTGERPFLCQWTG 300
E + ++ K +R L +
Sbjct: 109 KTPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVE 144
>gnl|CDD|181091 PRK07720, fliJ, flagellar biosynthesis chaperone; Validated.
Length = 146
Score = 30.4 bits (69), Expect = 0.82
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 11/87 (12%)
Query: 42 MKPK----QIKDISLKKMLNVQDMRKKCVQMNNEET---SYNILKSLKYKMSDRKEMIFV 94
+K K Q K+ L+ L++Q++R + N E Y +L + +RK+
Sbjct: 43 LKQKEDLEQAKEEKLQSGLSIQEIRHYQQFVTNLERTIDHYQLLVMQAREQMNRKQQDLT 102
Query: 95 ----ESKDTNRDKETSEEAANHETKNA 117
E K + KE +E E K A
Sbjct: 103 EKNIEVKKYEKMKEKKQEMFALEEKAA 129
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 29.1 bits (65), Expect = 1.7
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 5/56 (8%)
Query: 293 PFLCQWTGCGRRFSRSDELSRHKRTHTGEKKFGCSICNRRFMRSDHLAKHV-KRHS 347
P++C C FS S L +H R K C +C + F +D HV K+H+
Sbjct: 73 PYVCPL--CLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHVCKKHN 124
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 27.2 bits (60), Expect = 2.0
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 301 CGRRFSRSDELSRHKRTHTGEKKFGCSICNRRFMRSDHLA 340
C FS SD + R + + + F CS+C+R+ + D
Sbjct: 4 CRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFC 43
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 26.4 bits (59), Expect = 2.1
Identities = 11/19 (57%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 326 CSICNRRFMRSDHLAKHVK 344
C IC R+F D LAKH K
Sbjct: 5 CPICGRKF-APDRLAKHEK 22
>gnl|CDD|240257 PTZ00073, PTZ00073, 60S ribosomal protein L37; Provisional.
Length = 91
Score = 28.2 bits (63), Expect = 2.3
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 15/66 (22%)
Query: 282 KAHMRTHT-----GERPFLCQWTGCG---------RRFSRSDELSRHKRTHTGEKKFGCS 327
K H +THT G+R F Q C RR++ S + R + T TG ++ +
Sbjct: 10 KRHGKTHTLCRRCGKRSFHVQKKRCASCGYPSAKMRRYNWSVKAKRRRTTGTGRCRYLKT 69
Query: 328 ICNRRF 333
+ RR
Sbjct: 70 V-ARRA 74
>gnl|CDD|117355 pfam08785, Ku_PK_bind, Ku C terminal domain like. The
non-homologous end joining (NHEJ) pathway is one method
by which double stranded breaks in chromosomal DNA are
repaired. Ku is a component of a multi-protein complex
that is involved in the NHEJ. Ku has affinity for DNA
ends and recruits the DNA-dependent protein kinase
catalytic subunit (DNA-PKcs). This domain is found at
the C terminal of Ku which binds to DNA-PKcs.
Length = 120
Score = 28.5 bits (64), Expect = 2.4
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 53 KKMLNVQDMRKKCVQMNNEETSYNILKSLKYKMSDRKEMIFVE----------SKDTNRD 102
K + + +R++C++ + E LK LK K+ +R+ F E SKD
Sbjct: 45 KAIECILALREECIKESEPEQFNEFLKHLKEKVQERQLNDFWELLVQKKITLISKDEAEG 104
Query: 103 KETSEEAAN 111
+ ++E A
Sbjct: 105 SDVTDEEAK 113
>gnl|CDD|215361 PLN02673, PLN02673, quinolinate synthetase A.
Length = 724
Score = 30.0 bits (67), Expect = 2.9
Identities = 22/84 (26%), Positives = 34/84 (40%), Gaps = 15/84 (17%)
Query: 169 SISNGFPDMLPNPNPSSPSYGPGPQTVIFTGGSFIPVDKS-------SPLFIFDKKPVNS 221
S S+ F +LPNP+P+ + P + G P+ KS P D P N+
Sbjct: 8 SSSSSFLSLLPNPSPNFRTTHPNFGSQRRIGTIN-PLFKSFKCIQSPPP----DSAPSNA 62
Query: 222 VKSNCPSFLFFAQPPRENKEIVTS 245
+C + F P + E+V
Sbjct: 63 SPFSCSAVAF---SPSQTTELVPC 83
>gnl|CDD|234335 TIGR03732, lanti_perm_MutE, lantibiotic protection ABC transporter
permease subunit, MutE/EpiE family. Model TIGR03731
represents the family of all lantibiotics related to
gallidermin, including epidermin, mutatin, and nisin.
This protein family is largely restricted to
gallidermin-family lantibiotic cassettes, but also
include orphan transporter cassettes in species that
lack candidate lantibiotic precursor and synthetase
genes. In most species, this subunit is paralogous to an
adjacent gene, modeled separately.
Length = 241
Score = 29.2 bits (66), Expect = 3.6
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 2 NSTPPRTPSPLLSTTSIPVSVIMKV 26
N P SPLL+ + IP+ +I+ +
Sbjct: 197 NGLPLEAGSPLLNYSVIPIGIILSI 221
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a zinc-finger
domain with the CxxCx(12)Hx(6)H motif, found in multiple
copies in a wide range of proteins from plants to
metazoans. Some member proteins, particularly those from
plants, are annotated as being RNA-binding.
Length = 25
Score = 25.9 bits (58), Expect = 3.7
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 324 FGCSICNRRFMRSDHLAKHV--KRH 346
F C +CN F L H+ K+H
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 29.4 bits (66), Expect = 3.8
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 314 HKRTHTGEKKFGCSICNRRFMRSDHLAKHVKRHSKDGAIT 353
K T + C++C F D LA+H + GA +
Sbjct: 64 KKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSIGASS 103
>gnl|CDD|226618 COG4134, COG4134, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 384
Score = 28.7 bits (64), Expect = 5.2
Identities = 15/71 (21%), Positives = 25/71 (35%), Gaps = 7/71 (9%)
Query: 167 AQSISNGFPDMLPNPNPSSPSYGPGPQTVIF---TGGSFIPVDKSSPLFIFDKKPVNSVK 223
A + + + LPN F T G P + +FI+D+ V V
Sbjct: 110 AGLLYTPWAEDLPN----WRYVDHQLPRTDFSVPTEGLESPWGGNQLVFIYDRDKVPQVP 165
Query: 224 SNCPSFLFFAQ 234
+ L +A+
Sbjct: 166 QSFEELLVWAK 176
>gnl|CDD|180330 PRK05965, PRK05965, hypothetical protein; Provisional.
Length = 459
Score = 28.9 bits (65), Expect = 5.8
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 241 EIVTSNKIKKSNKPATNDPRRRIFECNYEN 270
E+V ++K K+ A DP RIF+ Y N
Sbjct: 381 ELV-ADKATKTPFDAALDPADRIFDRAYAN 409
>gnl|CDD|241468 cd13314, PH_Rpn13, Regulatory Particle Non-ATPase 13 Pleckstrin
homology-like domain. Targeted protein degradation is
performed to a great extent by the ubiquitin-proteasome
pathway, in which substrate proteins are marked by
covalently attached ubiquitin chains that mediate
recognition by the proteasome. Rpn13(also called
ADRM1/ARM1) is one of the two major ubiquitin receptors
of the proteasome, the other being S5a/Rpn10 which is
not essential for ubiquitin-mediated protein degradation
in budding yeast2. S5a has two ubiquitin interacting
motifs (UIMs) that bind simultaneously to ubiquitin
moieties to increase affinity while Rpn13 binds
ubiquitin with a single, high affinity surface within
its N-terminal PH domain. Rpn13 also binds and activates
deubiquitinating enzyme Uch37, one of the proteasome's
three deubiquitinating enzymes. Recently it was
discovered that the ubiquitin-binding domain (BD) and
Uch37 BD of human (h) Rpn13 pack against each other when
it is not incorporated into the proteasome reducing
hRpn13's affinity for ubiquitin. However when hRpn13
binds to hRpn2/S1 this abrogates its interdomain
interactions, thus activating hRpn13 for ubiquitin
binding. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 105
Score = 27.2 bits (61), Expect = 6.1
Identities = 9/32 (28%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 81 LKYKMSDRKEMIFVESKDTNRDKETSEEAANH 112
LK+K S +K +++ T++D+E + N
Sbjct: 73 LKFKSSSQKHFFWMQEPSTDKDEEI-CKKVNE 103
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 25.3 bits (56), Expect = 6.2
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 301 CGRRFSRSDELSRHKRTH 318
CG+ FS L HK++H
Sbjct: 7 CGKTFSSLQALGGHKKSH 24
>gnl|CDD|221994 pfam13230, GATase_4, Glutamine amidotransferases class-II. This
family captures members that are not found in pfam00310.
Length = 272
Score = 27.6 bits (62), Expect = 9.4
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 9/41 (21%)
Query: 250 KSNKPATNDPRRRIFECNYENCGKNY-FKSSHLKAHMRTHT 289
K +PA P + K Y KS ++ AH+R T
Sbjct: 50 KDPQPAATSPLAELV--------KRYPIKSKNVIAHIRKAT 82
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 0.129 0.387
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,541,385
Number of extensions: 1682238
Number of successful extensions: 1348
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1341
Number of HSP's successfully gapped: 40
Length of query: 384
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 285
Effective length of database: 6,546,556
Effective search space: 1865768460
Effective search space used: 1865768460
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: 60 (27.0 bits)