RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16923
(159 letters)
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 30.6 bits (69), Expect = 0.15
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 21 TPYGCPHCPMKLNTRRTLRMHLVVHRDTKAYQCVTCGKSFRRSKDLKNH----HNL 72
+PY CP C M ++ +L+ H+ +K C CGK FR + +H HN+
Sbjct: 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKV--CPVCGKEFRNTDSTLDHVCKKHNI 125
>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 = 28.1 bits (63), Expect = 0.23
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 52 QCVTCGKSFRRSKDLKNHHNLH 73
+C CGKSF R +LK H H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.1 bits (71), Expect = 0.24
Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 25/61 (40%)
Query: 24 GCPHCPMKLNTRRTLRMHLVVHRDTKAYQCVTCGKSFRRSKDLKNHHNLHTGKRPYTCPW 83
CP+C L +H+ T +C H+ + P +CP
Sbjct: 446 ECPNCDSPL----------TLHKATGQLRC---------------HYCGYQEPIPQSCPE 480
Query: 84 C 84
C
Sbjct: 481 C 481
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 27.7 bits (62), Expect = 0.35
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 65 DLKNHHNLHTGKRPYTCPWCSRTFAN 90
+L+ H HTG++PY CP C ++F++
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 27.0 bits (60), Expect = 0.59
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 38 LRMHLVVHRDTKAYQCVTCGKSFRR 62
LR H+ H K Y+C CGKSF
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 27.8 bits (62), Expect = 0.44
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 51 YQCVTCGKSFRRSKDLKNH 69
YQC+ CG FR+ K++ H
Sbjct: 2 YQCLRCGGIFRKKKEVIEH 20
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 30.1 bits (69), Expect = 0.44
Identities = 14/61 (22%), Positives = 18/61 (29%), Gaps = 25/61 (40%)
Query: 24 GCPHCPMKLNTRRTLRMHLVVHRDTKAYQCVTCGKSFRRSKDLKNHHNLHTGKRPYTCPW 83
CPHC L +HR + +C HH + P CP
Sbjct: 392 ECPHCDASL----------TLHRFQRRLRC---------------HHCGYQEPIPKACPE 426
Query: 84 C 84
C
Sbjct: 427 C 427
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or
more acidic residues. The function of members of this
family is unknown.
Length = 104
Score = 28.8 bits (65), Expect = 0.51
Identities = 15/37 (40%), Positives = 15/37 (40%), Gaps = 12/37 (32%)
Query: 48 TKAYQCVTCGKSFRRSKDLKNHHNLHTGKRPYTCPWC 84
TK C TCGK F DL K P CP C
Sbjct: 8 TK-RTCPTCGKRFY---DL--------NKDPIVCPKC 32
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.1 bits (67), Expect = 0.51
Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 25/93 (26%)
Query: 32 LNTRRTLRMHLVVHRDTKAYQC--VTCGKSFRRSKDLKNHHNLH---------------- 73
N RM V D K Y+C C K ++ LK +H LH
Sbjct: 333 RNIDTPSRMLKVK--DGKPYKCPVEGCNKKYKNQNGLK-YHMLHGHQNQKLHENPSPEKM 389
Query: 74 ----TGKRPYTCPWCSRTFANGSNCRSHKRRMH 102
+PY C C + + N + + H++ H
Sbjct: 390 NIFSAKDKPYRCEVCDKRYKNLNGLKYHRKHSH 422
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 29.7 bits (66), Expect = 0.73
Identities = 19/84 (22%), Positives = 28/84 (33%), Gaps = 3/84 (3%)
Query: 56 CGKSFRRSKDLKNHHNLHTGKRPYTCPW--CSRTFANGSNCRSHKRRMHPEELKLYESSL 113
CGK F R+ LK H LHT P S F+ N + ++LK + S
Sbjct: 329 CGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQSLQQYKDLKNDKKSE 388
Query: 114 GIVHKEKKKFDVSLHPPPQPPEDH 137
+ + + H
Sbjct: 389 TLSNS-CIRNFKRDSNLSLHIITH 411
>gnl|CDD|187638 cd08933, RDH_SDR_c, retinal dehydrogenase-like, classical (c) SDR.
These classical SDRs includes members identified as
retinol dehydrogenases, which convert retinol to
retinal, a property that overlaps with 17betaHSD
activity. 17beta-dehydrogenases are a group of isozymes
that catalyze activation and inactivation of estrogen
and androgens, and include members of the short-chain
dehydrogenases/reductase family. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 261
Score = 27.9 bits (62), Expect = 2.1
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 124 DVSLHPPPQPPEDHNVQ 140
+ HPP Q ++ + Q
Sbjct: 94 NAGWHPPHQTTDETSAQ 110
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large subunit,
gpA, products of the Nu1 and A genes, respectively.
Terminase is involved in the site-specific binding and
cutting of the DNA in the initial stages of packaging.
It is now known that gpA is actively involved in late
stages of packaging, including DNA translocation, and
that this enzyme contains separate functional domains
for its early and late packaging activities.
Length = 552
Score = 28.0 bits (63), Expect = 2.2
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 25 CPHCPMK-LNTRRTLRMHLVVHRDTKAYQCVTCG 57
CPHC + L+ +T Y C CG
Sbjct: 203 CPHCGEEQELRWERLKWDKGEAPETARYVCPHCG 236
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 2.6
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 51 YQCVTCGKSFRRSKDLKNHHNLH 73
Y+C CGK F+ L+ H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 24.0 bits (52), Expect = 7.1
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 23 YGCPHCPMKLNTRRTLRMHLVVH 45
Y CP C ++ LR H+ H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 27.6 bits (62), Expect = 2.9
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 80 TCPWCSRTFANGSNCRSHKRRMHPEELK 107
TCP C A G C + R + P EL
Sbjct: 144 TCPKCGGEDARGDQCENCGRTLDPTELI 171
>gnl|CDD|223915 COG0846, SIR2, NAD-dependent protein deacetylases, SIR2 family
[Transcription].
Length = 250
Score = 26.9 bits (60), Expect = 5.1
Identities = 8/36 (22%), Positives = 12/36 (33%), Gaps = 4/36 (11%)
Query: 49 KAYQCVTCGKSFRRSKDLKNHHNLHTGKRPYTCPWC 84
K +C CG + +K + CP C
Sbjct: 121 KRVRCSKCGNQYYDEDVIKFIED----GLIPRCPKC 152
>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 = 24.1 bits (52), Expect = 6.5
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 79 YTCPWCSRTFANGSNCRSHKRRMH 102
+ CP C ++F++ + H R+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|203053 pfam04606, Ogr_Delta, Ogr/Delta-like zinc finger. This is a
viral family of phage zinc-binding transcriptional
activators, which also contains cryptic members in some
bacterial genomes. The P4 phage delta protein contains
two such domains attached covalently, while the P2
phage Ogr proteins possess one domain but function as
dimers. All the members of this family have the
following consensus sequence:
C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This
family also includes zinc fingers in recombinase
proteins.
Length = 47
Score = 24.5 bits (54), Expect = 7.3
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 25 CPHCPMKLNTRRTLRMHLVVHRDTKAYQC--VTCGKSFRRS 63
CPHC K R + R+ +V YQC CG +F +
Sbjct: 2 CPHCGAKARIRTSRRLSALVRELY--YQCTNPECGHTFVTN 40
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 26.4 bits (59), Expect = 8.2
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 80 TCPWCSRTFANGSNCRSHKRRMHPEELKLYESSLG----IVHKEKKKF 123
TCP+C A G C R + P EL S++ + +E+ F
Sbjct: 138 TCPYCGSEDARGDQCEVCGRPLEPTELINPRSAISGSTPELKEEEHYF 185
>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 = 23.7 bits (52), Expect = 8.4
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 53 CVTCGKSFRRSKDLKNHHN 71
CV C K F+ L+NH
Sbjct: 4 CVACDKYFKSENALENHLK 22
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing
archaeal-type C2H2 Zn-finger [General function
prediction only].
Length = 65
Score = 24.6 bits (53), Expect = 9.8
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 36 RTLRMHLVVHRDTKAY-QCVTCGKSFRRSKDLKNHHN 71
L+ V RD + + +C CG FRR KD H N
Sbjct: 2 VRLKAIKVRDRDGEEFLRCPRCGMVFRRRKDYIRHVN 38
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
0.324 0.138 0.465
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,795,831
Number of extensions: 643455
Number of successful extensions: 904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 895
Number of HSP's successfully gapped: 50
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.1 bits)