RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14386
(344 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 33.1 bits (76), Expect = 0.009
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 312 HKRLHTGERPYSCELCNKAFVS 333
H R HTGE+PY C +C K+F S
Sbjct: 5 HMRTHTGEKPYKCPVCGKSFSS 26
Score = 32.4 bits (74), Expect = 0.018
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 210 YLIVHQRVHSTDKPYACKTCPRSFKT 235
L H R H+ +KPY C C +SF +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 29.3 bits (66), Expect = 0.19
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 183 LDEHEAKHTGRYEYECNACGKGF 205
L H HTG Y+C CGK F
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSF 24
Score = 28.9 bits (65), Expect = 0.24
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 239 LLDHENRHMGVKPYSCEICGRGFIT 263
L H H G KPY C +CG+ F +
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.5 bits (64), Expect = 0.38
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 158 HVSNHGVDKPFQCFKCEKRFRS 179
H+ H +KP++C C K F S
Sbjct: 5 HMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.1 bits (63), Expect = 0.54
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 268 KSHQKIHSGNDNRQYPCPVCKKLFVS 293
+ H + H+G + Y CPVC K F S
Sbjct: 3 RRHMRTHTGE--KPYKCPVCGKSFSS 26
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.1 bits (68), Expect = 0.096
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 322 YSCELCNKAFVSRSTLMVHKKKH 344
Y C C K F S+S L H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 29.0 bits (65), Expect = 0.21
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 196 YECNACGKGFQNKSYLIVHQRVH 218
Y C CGK F++KS L H R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 1.5
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 224 YACKTCPRSFKTKQTLLDHENRH 246
Y C C + FK+K L +H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 1.8
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 168 FQCFKCEKRFRSKLGLDEHEAKH 190
++C +C K F+SK L EH H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 1.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 252 YSCEICGRGFITKGLCKSHQKIH 274
Y C CG+ F +K + H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.7 bits (54), Expect = 7.3
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 140 HKCDRCPKKFSSLAKYNFHVSNH 162
++C C K F S + H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.7 bits (54), Expect = 8.3
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 296 CNICGQSFTQFSPMAIHKRLH 316
C CG+ F S + H R H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
>gnl|CDD|220362 pfam09723, CxxC_CxxC_SSSS, Zinc ribbon domain. This entry
represents a region of about 41 amino acids found in a
number of small proteins in a wide range of bacteria.
The region usually begins with the initiator Met and
contains two CxxC motifs separated by 17 amino acids.
One protein in this entry has been noted as a putative
regulatory protein, designated FmdB. Most proteins in
this entry have a C-terminal region containing highly
degenerate sequence.
Length = 42
Score = 30.2 bits (69), Expect = 0.14
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 194 YEYECNACGKGFQNKSYLIVHQRVHSTDKPYACKTC 229
YEY C CG F+ V Q++ C C
Sbjct: 4 YEYRCEDCGHTFE------VLQKISDDPLA-TCPEC 32
>gnl|CDD|197903 smart00834, CxxC_CXXC_SSSS, Putative regulatory protein.
CxxC_CXXC_SSSS represents a region of about 41 amino
acids found in a number of small proteins in a wide
range of bacteria. The region usually begins with the
initiator Met and contains two CxxC motifs separated by
17 amino acids. One protein in this entry has been noted
as a putative regulatory protein, designated FmdB. Most
proteins in this entry have a C-terminal region
containing highly degenerate sequence.
Length = 41
Score = 29.1 bits (66), Expect = 0.32
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 7/36 (19%)
Query: 194 YEYECNACGKGFQNKSYLIVHQRVHSTDKPYACKTC 229
YEY C CG F+ V Q++ C C
Sbjct: 4 YEYRCEDCGHTFE------VLQKISDDPLT-TCPEC 32
>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 = 28.5 bits (64), Expect = 0.38
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 323 SCELCNKAFVSRSTLMVHKKKH 344
C C K+F +S L H + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.1 bits (63), Expect = 0.47
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 197 ECNACGKGFQNKSYLIVHQRVH 218
+C CGK F KS L H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 1.7
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 226 CKTCPRSFKTKQTLLDHENRH 246
C C +SF K L H H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 24.6 bits (54), Expect = 7.7
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 295 SCNICGQSFTQFSPMAIHKRLH 316
C CG+SF++ S + H R H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|224213 COG1294, AppB, Cytochrome bd-type quinol oxidase, subunit 2 [Energy
production and conversion].
Length = 346
Score = 32.2 bits (74), Expect = 0.41
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 61 PVLSNGVLVGALTNGVPVNSDDGDKGGD 88
P L GV +G L GVP+ + G G
Sbjct: 132 PPLLLGVALGNLLQGVPIELNGGYAGLS 159
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 28.3 bits (64), Expect = 0.46
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 322 YSCELCNKAFVSRSTLMVHKKKH 344
++C +C K F S L HKK H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus, particularly
the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 27.2 bits (61), Expect = 1.0
Identities = 10/26 (38%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 321 PYSCELCNKAFVSRSTLMVHK--KKH 344
+ C C+K F S + L H KKH
Sbjct: 1 QFYCVACDKYFKSENALENHLKSKKH 26
Score = 24.8 bits (55), Expect = 7.3
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 223 PYACKTCPRSFKTKQTLLDHEN 244
+ C C + FK++ L +H
Sbjct: 1 QFYCVACDKYFKSENALENHLK 22
>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 = 27.1 bits (61), Expect = 1.1
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 322 YSCELCNKAFVSRSTLMVHK--KKH 344
+ CELCN F S S L H KKH
Sbjct: 1 FYCELCNVTFTSESQLKSHLRGKKH 25
>gnl|CDD|213729 TIGR02605, CxxC_CxxC_SSSS, putative regulatory protein, FmdB
family. This model represents a region of about 50
amino acids found in a number of small proteins in a
wide range of bacteria. The region begins usually with
the initiator Met and contains two CxxC motifs separated
by 17 amino acids. One member of this family is has been
noted as a putative regulatory protein, designated FmdB
(SP:Q50229, PMID:8841393 ). Most members of this family
have a C-terminal region containing highly degenerate
sequence, such as
SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in
Mycobacterium tuberculosis and
VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces
avermitilis. These low complexity regions, which are not
included in the model, resemble low-complexity
C-terminal regions of some heterocycle-containing
bacteriocin precursors [Regulatory functions, DNA
interactions].
Length = 52
Score = 27.7 bits (62), Expect = 1.1
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 7/36 (19%)
Query: 194 YEYECNACGKGFQNKSYLIVHQRVHSTDKPYACKTC 229
YEY C ACG F+ V Q++ S D C C
Sbjct: 4 YEYRCTACGHRFE------VLQKM-SDDPLATCPEC 32
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 30.4 bits (68), Expect = 1.6
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 295 SCNICGQSFTQFSPMAIHKRLHTGERPYSCEL--CNKAFVSRSTLMVHKKKH 344
SC C SF++ + H R HTGE+P C C+K+F L H + H
Sbjct: 35 SCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTH 86
Score = 28.5 bits (63), Expect = 5.8
Identities = 19/81 (23%), Positives = 29/81 (35%), Gaps = 12/81 (14%)
Query: 250 KPYSCEICGRGFITKGLCKSHQ--KIHSGNDNRQYPCPVCKKLFVSKSCNICGQSFTQFS 307
P + C F H HSG + + CP ++CG+ F++
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPY----------SLCGKLFSRND 337
Query: 308 PMAIHKRLHTGERPYSCELCN 328
+ H LHT P +L N
Sbjct: 338 ALKRHILLHTSISPAKEKLLN 358
>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 = 26.8 bits (59), Expect = 1.6
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 322 YSCELCNKAFVSRSTLMVHKKKH 344
+ C LC K+F S+ L H +KH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 26.1 bits (57), Expect = 2.8
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 224 YACKTCPRSFKTKQTLLDHENRH 246
+ C C +SF +K L H +H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.9 bits (54), Expect = 8.3
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 168 FQCFKCEKRFRSKLGLDEHEAKH 190
F+C C K F SK L H KH
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.5 bits (53), Expect = 8.6
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 140 HKCDRCPKKFSSLAKYNFHVSNH 162
KC C K FSS H+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|239958 cd04585, CBS_pair_ACT_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
in the acetoin utilization proteins in bacteria.
Acetoin is a product of fermentative metabolism in many
prokaryotic and eukaryotic microorganisms. They
produce acetoin as an external carbon storage compound
and then later reuse it as a carbon and energy source
during their stationary phase and sporulation. In
addition these CBS domains are associated with a
downstream ACT domain, which is linked to a wide range
of metabolic enzymes that are regulated by amino acid
concentration. Pairs of ACT domains bind specifically
to a particular amino acid leading to regulation of the
linked enzyme. CBS is a small domain originally
identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The
interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains.
It has been proposed that the CBS domain may play a
regulatory role, although its exact function is
unknown.
Length = 122
Score = 28.8 bits (65), Expect = 1.9
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 44 SHMETYRQMPQQTIPVTPVLSNGVLVGALTNG 75
S ME + M + +I PV+ G LVG +T+
Sbjct: 11 SLMEALKLMKENSIRRLPVVDRGKLVGIVTDR 42
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 26.9 bits (59), Expect = 2.8
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 322 YSCELCNKAFVSRSTLMVHKKKH 344
Y C +C + ++ R +++ H +KH
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
Score = 26.5 bits (58), Expect = 4.0
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 196 YECNACGKGFQNKSYLIVHQRVHSTD 221
YEC CG+ + + +I H R H+T+
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTN 31
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 29.3 bits (65), Expect = 2.9
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 11/79 (13%)
Query: 166 KPFQC--FKCEKRFRSKLGLDEHEAKHTGRYEYECNACGKGFQNKSYLIVHQRVHSTDKP 223
KP++C C K+++++ GL H N K +N S + DKP
Sbjct: 348 KPYKCPVEGCNKKYKNQNGLKYH------MLHGHQNQ--KLHENPSP-EKMNIFSAKDKP 398
Query: 224 YACKTCPRSFKTKQTLLDH 242
Y C+ C + +K L H
Sbjct: 399 YRCEVCDKRYKNLNGLKYH 417
>gnl|CDD|180890 PRK07218, PRK07218, replication factor A; Provisional.
Length = 423
Score = 29.2 bits (66), Expect = 3.8
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 252 YSCEICGRGFITKGLCKSHQKIHSGNDNR 280
C CGR I KG C+SH + +D R
Sbjct: 298 ERCPECGR-VIQKGQCRSHGAVEGEDDLR 325
>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 = 29.0 bits (65), Expect = 5.5
Identities = 12/37 (32%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 186 HEAKHTGRYEYECNACGKGFQNKSYLIVHQRV-HSTD 221
+A Y CN C F + L HQR HS
Sbjct: 64 KKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSIG 100
Score = 28.6 bits (64), Expect = 6.0
Identities = 10/34 (29%), Positives = 11/34 (32%)
Query: 307 SPMAIHKRLHTGERPYSCELCNKAFVSRSTLMVH 340
SP K Y C +C F S L H
Sbjct: 59 SPPQSKKATPINPSSYVCNVCMAEFSSMDQLAEH 92
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 27.1 bits (60), Expect = 6.4
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 6/50 (12%)
Query: 167 PFQCFKCEKRFRSKLGLDEH--EAKHTGRYEYECNACGKGFQNKSYLIVH 214
P+ C C F S + L +H +H+ C CGK F+N + H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSKV----CPVCGKEFRNTDSTLDH 118
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 28.4 bits (63), Expect = 7.2
Identities = 9/45 (20%), Positives = 13/45 (28%)
Query: 95 VVKSDLIKDPIASDDNMEDGYMDEPETDINPKEVIDTGKPESKSL 139
V+K + D G + E I + D S L
Sbjct: 341 VLKLETEDKKTIITDTGSTGLLSAQEKTIFDIYINDFLDGRSLDL 385
>gnl|CDD|222478 pfam13966, zf-RVT, zinc-binding in reverse transcriptase. This
domain would appear to be a zinc-binding region of a
putative reverse transcriptase.
Length = 86
Score = 26.4 bits (59), Expect = 8.2
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 8/30 (26%)
Query: 309 MAIHKRLHTGER--------PYSCELCNKA 330
+A RL T +R P C LC +
Sbjct: 39 LAAWNRLLTKDRLQKRGWQLPNRCVLCGQE 68
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 0.411
Gapped
Lambda K H
0.267 0.0804 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,287,662
Number of extensions: 1447154
Number of successful extensions: 1325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1312
Number of HSP's successfully gapped: 75
Length of query: 344
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 246
Effective length of database: 6,590,910
Effective search space: 1621363860
Effective search space used: 1621363860
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: 59 (26.4 bits)