RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12011
(94 letters)
>gnl|CDD|179545 PRK03147, PRK03147, thiol-disulfide oxidoreductase; Provisional.
Length = 173
Score = 28.0 bits (63), Expect = 0.56
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 34 CDLCDKEYKYKRNLYSHKKDE 54
C C+KE Y LY K++
Sbjct: 73 CKPCEKEMPYMNELYPKYKEK 93
>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
subunit.
Length = 1079
Score = 28.0 bits (62), Expect = 0.77
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 7/62 (11%)
Query: 33 ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKR-KGNLKSHLAIRHECYLDDS 91
ACD+C + R Y +++ + Q CPQC + KR KG+ + DD
Sbjct: 38 ACDVC--AFPVCRPCYEYERKDGNQ----SCPQCKTKYKRHKGSPAILGDEEEDGDADDG 91
Query: 92 AN 93
A+
Sbjct: 92 AS 93
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 27.7 bits (61), Expect = 0.81
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 1 MSSQNLQVHFCGLFPESFLTWSNLKPNLNGMFACDLCDKEYKYKRNL 47
M + Q H GLFP L S+L N++ + C+ + RN+
Sbjct: 261 MLNFGFQFHLEGLFPLRILNESDLDINVSEVDGAIACNTSFIDDRNI 307
>gnl|CDD|223064 PHA03375, PHA03375, hypothetical protein; Provisional.
Length = 844
Score = 27.5 bits (61), Expect = 0.99
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 55 CGQEPRFQCPQCSYRTKRKG------NLKSHLAIRHECYL 88
G+E R + + +R G N +H I+H C L
Sbjct: 714 HGRERRLKVDRLVFRAISDGLFDYSKNTVAHTKIKHTCAL 753
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 24.3 bits (53), Expect = 2.6
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 46 NLYSHKKDECGQEPRFQCPQCSYRTKR 72
NL H + G++P ++CP C
Sbjct: 1 NLRRHMRTHTGEKP-YKCPVCGKSFSS 26
>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 = 2.9
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 61 FQCPQCSYRTKRKGNLKSHLAIRH 84
F+CP C K LK HL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 23.7 bits (52), Expect = 3.9
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 61 FQCPQCSYRTKRKGNLKSHLAIRHE 85
++C C Y + K L+ HL + H
Sbjct: 1 YKCSHCPYSSTPK-KLERHLKLHHG 24
>gnl|CDD|222774 PHA00028, rep, RNA replicase, beta subunit.
Length = 561
Score = 25.9 bits (57), Expect = 4.0
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 20 TWSNLKPNLNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRF 61
KP+L + D+ Y L+SHK++ C R+
Sbjct: 465 KKKRRKPDLADTKKDRVRDERIAYLYALFSHKEELCDDNGRY 506
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 24.0 bits (52), Expect = 4.3
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 61 FQCPQCSYRTKRKGNLKSHLAI 82
++CP+C K K L+ H+
Sbjct: 1 YRCPECGKVFKSKSALREHMRT 22
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 25.5 bits (56), Expect = 5.4
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 10/53 (18%)
Query: 34 CDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQC--SYRTKRKGN-LKSHLAIR 83
C C KEYK + H + CP+C +G + A+
Sbjct: 121 CPDCAKEYKDPLDRRFHAQPIA-------CPRCGPQLNFVSRGGHAEQDDALL 166
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 24.1 bits (52), Expect = 6.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 63 CPQCSYRTKRKGNLKSHLAIRH 84
CP C ++ NL+ HL +RH
Sbjct: 27 CPICQAVIRQSRNLRRHLELRH 48
>gnl|CDD|226756 COG4306, COG4306, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 160
Score = 24.9 bits (54), Expect = 6.7
Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 28 LNGMFACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCS 67
LNG A D+ + S CG+ QCP CS
Sbjct: 11 LNGHVATTAADQSPELMEAFCSK----CGEATITQCPICS 46
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 25.1 bits (56), Expect = 7.8
Identities = 5/14 (35%), Positives = 7/14 (50%), Gaps = 2/14 (14%)
Query: 54 ECGQEPRFQCPQCS 67
+CG +CP C
Sbjct: 386 DCGW--VAECPHCD 397
>gnl|CDD|215121 PLN02189, PLN02189, cellulose synthase.
Length = 1040
Score = 25.0 bits (54), Expect = 8.0
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 33 ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKR 72
AC+ C + R Y +++ E Q CPQC R KR
Sbjct: 55 ACNECG--FPVCRPCYEYERREGTQ----NCPQCKTRYKR 88
>gnl|CDD|234080 TIGR02987, met_A_Alw26, type II restriction m6 adenine DNA
methyltransferase, Alw26I/Eco31I/Esp3I family. Members
of this family are the m6-adenine DNA methyltransferase
protein, or domain of a fusion protein that also carries
m5 cytosine methyltransferase activity, of type II
restriction systems of the Alw26I/Eco31I/Esp3I family. A
methyltransferase of this family is alway accompanied by
a type II restriction endonuclease from the
Alw26I/Eco31I/Esp3I family (TIGR02986) and by an
adenine-specific modification methyltransferase. Members
of this family are unusual in that regions of similarity
to homologs outside this family are circularly permuted
[DNA metabolism, Restriction/modification].
Length = 524
Score = 24.7 bits (54), Expect = 8.8
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 35 DLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKRK 73
+ E +K+ + + KK + R QCSY +++
Sbjct: 350 NESSSEDIFKKFIKNSKKSRHIRMKRIVWRQCSYMKQKR 388
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 24.8 bits (54), Expect = 9.2
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 33 ACDLCDKEYKYKRNLYSHKKDECGQEPRFQCPQCSYRTKR-KGN 75
AC+ C + R Y +++ E Q CPQC R KR KG+
Sbjct: 57 ACNEC--AFPVCRPCYEYERREGNQ----ACPQCKTRYKRIKGS 94
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
0.323 0.136 0.457
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,320,521
Number of extensions: 312075
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 33
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)