RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6676
(144 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 32.4 bits (74), Expect = 0.005
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 71 NLKTHLLTHTDIKPYNCAACGKVFRR 96
NL+ H+ THT KPY C CGK F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 31.2 bits (71), Expect = 0.015
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 44 LAVHKILHLEESPHKCPVCSRSFNQ 68
L H H E P+KCPVC +SF+
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 29.7 bits (67), Expect = 0.054
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 22 IHSKEKPFKCTECGKGF 38
H+ EKP+KC CGK F
Sbjct: 8 THTGEKPYKCPVCGKSF 24
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.4 bits (81), Expect = 0.006
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 56 PHKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAA--CGKVFRRNCDLRRHSLTHNLGSAT 113
P CP C+ SF++ +L H+ +HT KP C+ C K F R +L RH TH+ +
Sbjct: 33 PDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHNNPSD 92
Query: 114 STSSGS 119
S
Sbjct: 93 LNSKSL 98
Score = 28.5 bits (63), Expect = 1.5
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 6/59 (10%)
Query: 55 SPHKCPVCSRSFNQRSNLKTHLLT--HT--DIKPYNC--AACGKVFRRNCDLRRHSLTH 107
P K C+ SF++ S L HL + H+ +KP++C + CGK+F RN L+RH L H
Sbjct: 288 LPIKSKQCNISFSRSSPLTRHLRSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLH 346
Score = 26.6 bits (58), Expect = 5.2
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 24 SKEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSR--SFNQRSNLKTHLLTHT 80
+ +P C C F + L H H E P +C SF++ L HL TH
Sbjct: 29 NAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHH 87
Score = 26.6 bits (58), Expect = 5.3
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 62 CSRSFNQRSNLKTHLLTHT--DIKPYNCAACGKVFRRNCDLRRHSLTH 107
C R+F + SNL H++TH C K F R+ +L H H
Sbjct: 394 CIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFNRHYNLIPHKKIH 441
>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 = 31.2 bits (71), Expect = 0.015
Identities = 14/22 (63%), Positives = 18/22 (81%)
Query: 58 KCPVCSRSFNQRSNLKTHLLTH 79
KCP C +SF+++SNLK HL TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 26.5 bits (59), Expect = 0.85
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 87 CAACGKVFRRNCDLRRHSLTH 107
C CGK F R +L+RH TH
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
Score = 25.0 bits (55), Expect = 2.4
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 30 KCTECGKGFCQSRTLAVHKILH 51
KC +CGK F + L H H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|192286 pfam09416, UPF1_Zn_bind, RNA helicase (UPF2 interacting domain).
UPF1 is an essential RNA helicase that detects mRNAs
containing premature stop codons and triggers their
degradation. This domain contains 3 zinc binding motifs
and forms interactions with another protein (UPF2) that
is also involved nonsense-mediated mRNA decay (NMD).
Length = 152
Score = 33.2 bits (76), Expect = 0.020
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 22 IHSKEKPFKCTECGKGFCQSR--TLAVHKILHLEESPHK 58
IH+ KC C K FC + T H + HL +S HK
Sbjct: 8 IHNPACVVKCNSCNKWFCNGKGGTSGSHIVNHLVKSKHK 46
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 30.1 bits (68), Expect = 0.033
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 57 HKCPVCSRSFNQRSNLKTHLLTH 79
++CP C + F +S L+ H+ TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.0 bits (60), Expect = 0.54
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 29 FKCTECGKGFCQSRTLAVHKILH 51
++C ECGK F L H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.7 bits (59), Expect = 0.77
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 85 YNCAACGKVFRRNCDLRRHSLTH 107
Y C CGKVF+ LR H TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 28.8 bits (65), Expect = 0.16
Identities = 8/35 (22%), Positives = 15/35 (42%), Gaps = 7/35 (20%)
Query: 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCS 63
++CT CG F + ++ ++ CP C
Sbjct: 6 YRCTACGHRFEVLQKMS-------DDPLATCPECG 33
>gnl|CDD|203007 pfam04423, Rad50_zn_hook, Rad50 zinc hook motif. The Mre11
complex (Mre11 Rad50 Nbs1) is central to chromosomal
maintenance and functions in homologous recombination,
telomere maintenance and sister chromatid association.
The Rad50 coiled-coil region contains a dimer interface
at the apex of the coiled coils in which pairs of
conserved Cys-X-X-Cys motifs form interlocking hooks
that bind one Zn ion. This alignment includes the zinc
hook motif and a short stretch of coiled-coil on either
side.
Length = 54
Score = 28.8 bits (65), Expect = 0.18
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 48 KILHLEESPHKCPVCSRSF 66
I L+E+ CPVC R
Sbjct: 12 AIEELKEAKGCCPVCGRPL 30
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 30.2 bits (68), Expect = 0.20
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 55 SPHKCPVCSRSFNQRSNLKTHL--LTHTDIKPYNCAACGKVFRRNCDLRRH 103
SP+ CP+C F+ +LK H+ H+ + P CGK FR H
Sbjct: 72 SPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPV----CGKEFRNTDSTLDH 118
Score = 25.6 bits (56), Expect = 6.6
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 2/49 (4%)
Query: 28 PFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHL 76
P+ C C F S +L H + E CPVC + F + H+
Sbjct: 73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHV 119
>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 = 28.0 bits (62), Expect = 0.23
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 57 HKCPVCSRSFNQRSNLKTHLLTH 79
KCP+C +SF+ + LK HL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 24.9 bits (54), Expect = 3.1
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 85 YNCAACGKVFRRNCDLRRHSLTH 107
+ C CGK F L+RH H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>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 = 30.9 bits (70), Expect = 0.23
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 1/38 (2%)
Query: 45 AVHKILHLEESPHKCPVCSRSFNQRSNLKTHL-LTHTD 81
K + S + C VC F+ L H TH+
Sbjct: 62 QSKKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTHSI 99
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 28.9 bits (64), Expect = 0.24
Identities = 12/32 (37%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 57 HKCPVCSRSFNQRSNLKTHLLTH-TDIKPYNC 87
++CP+C + +R ++ THL H T++K NC
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNC 37
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 30.8 bits (69), Expect = 0.24
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 21/73 (28%)
Query: 52 LEESPHKCPV--CSRSFNQRSNLKTHLL-------TH-------TDI-----KPYNCAAC 90
+ P+KCPV C++ + ++ LK H+L H +I KPY C C
Sbjct: 345 KDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVC 404
Query: 91 GKVFRRNCDLRRH 103
K ++ L+ H
Sbjct: 405 DKRYKNLNGLKYH 417
Score = 29.7 bits (66), Expect = 0.53
Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 21/77 (27%)
Query: 26 EKPFKC--TECGKGFCQSRTLAVHK-------------------ILHLEESPHKCPVCSR 64
KP+KC C K + L H I ++ P++C VC +
Sbjct: 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDK 406
Query: 65 SFNQRSNLKTHLLTHTD 81
+ + LK H D
Sbjct: 407 RYKNLNGLKYHRKHSHD 423
>gnl|CDD|177300 PHA00732, PHA00732, hypothetical protein.
Length = 79
Score = 28.6 bits (64), Expect = 0.33
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRSFNQRSNLKTHLLTHTDI 82
FKC CG F A+ + + KCPVC++S+ + L H + DI
Sbjct: 2 FKCPICG--FTTVTLFALKQHARRNHTLTKCPVCNKSYRR---LNQHFYSQYDI 50
>gnl|CDD|132661 TIGR03622, urea_t_UrtB_arc, urea ABC transporter, permease protein
UrtB. Members of this protein family are ABC
transporter permease subunits restricted to the Archaea.
Several lines of evidence suggest this protein is
functionally analogous, as well as homologous, to the
UrtB subunit of the Corynebacterium glutamicum urea
transporter. All members of the operon show sequence
similarity to urea transport subunits, the gene is
located near the urease structural subunits in two of
three species, and partial phylogenetic profiling
identifies this permease subunit as closely matching the
profile of urea utilization.
Length = 283
Score = 29.8 bits (67), Expect = 0.44
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 101 RRHSLTHNLGSATSTSSGSTTATLLSVSPT---SFIVESMV 138
R + T +GS + +G+ A + +++P F+VE+ V
Sbjct: 180 RMYVTTFAIGSGLAGLTGALYAPIGAITPDRGSIFLVEAFV 220
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 29.6 bits (67), Expect = 0.57
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 58 KCPVCSRS--FNQRSN-LKTHLLTHTDIKPYNCAACG 91
+CP C ++ + L+ H + + P +C CG
Sbjct: 446 ECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECG 482
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 29.6 bits (67), Expect = 0.66
Identities = 17/92 (18%), Positives = 31/92 (33%), Gaps = 8/92 (8%)
Query: 51 HLEESPHKCPVCSRSFNQ-RSNLKTHLLTHTDIKPYNCAACGKVFRRNCDLRRHSLTHNL 109
L ES C C R+F++ +S L+ + I+ K + + + L
Sbjct: 5 RLNESLSSCDKCIRAFHRGKSKLRQRFIRSFPIENVQ-----KFMEKIDEWDIQRILPGL 59
Query: 110 GSATSTSSGSTTATLLSVSPTSFIVESMVNME 141
A+ T S+ + E + N
Sbjct: 60 EKASKILESGPPNTRSSLLLA--LYECLCNPA 89
>gnl|CDD|177367 PHA02513, V1, structural protein V1; Reviewed.
Length = 135
Score = 27.9 bits (62), Expect = 1.1
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 104 SLTHNLGSATSTSSGSTTATLLSVSPTSFIV 134
S +NL S T+ S T ATLL++ P +I+
Sbjct: 89 SQVNNLTSGTAPSVTGTNATLLNLVPLFYIL 119
>gnl|CDD|237417 PRK13533, PRK13533, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 487
Score = 28.3 bits (64), Expect = 1.3
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 3/26 (11%)
Query: 42 RTLAVHKILHLEES---PHKCPVCSR 64
R L V LE+ P CPVCS+
Sbjct: 257 RYLTVTGTYRLEDLEYLPCSCPVCSK 282
>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 = 26.1 bits (57), Expect = 1.7
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 54 ESPHKCPVCSRSFNQRSNLKTHL 76
E P CP+C Q NL+ HL
Sbjct: 22 EQPATCPICQAVIRQSRNLRRHL 44
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 25.9 bits (57), Expect = 2.2
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 85 YNCAACGKVFRRNCDLRRHSL-THNLGSAT 113
Y C CG +FR+ ++ H L H T
Sbjct: 2 YQCLRCGGIFRKKKEVIEHLLSVHKQNKLT 31
>gnl|CDD|222704 pfam14353, CpXC, CpXC protein. This presumed domain is
functionally uncharacterized. This domain is found in
bacteria and archaea, and is typically between 122 and
134 amino acids in length. It contains four conserved
cysteines forming two CpXC motifs.
Length = 128
Score = 26.5 bits (59), Expect = 3.3
Identities = 10/61 (16%), Positives = 17/61 (27%), Gaps = 9/61 (14%)
Query: 58 KCPVCSRSFNQRSNLKTHLLTHTDIKP---------YNCAACGKVFRRNCDLRRHSLTHN 108
CP C F + +++ + C +CG FR + H
Sbjct: 3 TCPSCGHEFEAEVWTSVNADEDPELREAILDGTLFTFTCPSCGHEFRLDYPFLYHDPEKK 62
Query: 109 L 109
Sbjct: 63 F 63
>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 = 25.2 bits (56), Expect = 3.5
Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 29 FKCTECGKGFCQSRTLAVHKILHLEESPHKCPVCSRS 65
++C +CG F + ++ ++ CP C
Sbjct: 6 YRCEDCGHTFEVLQKIS-------DDPLTTCPECGGD 35
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 27.0 bits (60), Expect = 4.6
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 58 KCPVCS--RSFNQRSN-LKTHLLTHTDIKPYNCAACG 91
CP C +++++ L+ H + + P C CG
Sbjct: 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCG 260
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 27.0 bits (59), Expect = 4.6
Identities = 12/50 (24%), Positives = 14/50 (28%), Gaps = 8/50 (16%)
Query: 23 HSKEKPFKCTECGKGFCQS-RTLAVHKIL-------HLEESPHKCPVCSR 64
KC C +T L +S KCP CSR
Sbjct: 269 QPPNISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSR 318
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and conversion].
Length = 166
Score = 26.1 bits (58), Expect = 5.5
Identities = 10/38 (26%), Positives = 14/38 (36%), Gaps = 13/38 (34%)
Query: 25 KEKPFKCTECGKGFCQSRTLAVHKILHLEESPHKCPVC 62
+ K + C CG H E+P CP+C
Sbjct: 131 EGKVWVCPVCG-------------YTHEGEAPEVCPIC 155
>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 = 24.1 bits (53), Expect = 5.7
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 56 PHKCPVCSRSFNQRSNLKTHLLT 78
C C + F + L+ HL +
Sbjct: 1 QFYCVACDKYFKSENALENHLKS 23
>gnl|CDD|232972 TIGR00432, arcsn_tRNA_tgt, tRNA-guanine transglycosylase,
archaeosine-15-forming. This tRNA-guanine
transglycosylase (tgt) differs from the tgt of E. coli
and other Bacteria in the site of action and the
modification that results. It exchanges
7-cyano-7-deazaguanine (preQ0) with guanine at position
15 of archaeal tRNA; this nucleotide is subsequently
converted to archaeosine, found exclusively in the
Archaea. This enzyme from Haloferax volcanii has been
purified, characterized, and partially sequenced and is
the basis for identifying this family. In contrast,
bacterial tgt catalyzes the exchange of preQ0 or preQ1
for the guanine base at position 34; this nucleotide is
subsequently modified to queuosine. Archeoglobus
fulgidus has both enzymes, while some other Archaea have
just this one [Protein synthesis, tRNA and rRNA base
modification].
Length = 540
Score = 26.5 bits (58), Expect = 6.5
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 5/27 (18%)
Query: 42 RTLAVHKILHLEE-----SPHKCPVCS 63
R L V+ LEE P CPVCS
Sbjct: 153 RYLTVYGTKKLEELNLQYFPCSCPVCS 179
>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 = 7.6
Identities = 10/17 (58%), Positives = 10/17 (58%)
Query: 87 CAACGKVFRRNCDLRRH 103
C CG VFRR D RH
Sbjct: 20 CPRCGMVFRRRKDYIRH 36
>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 = 23.6 bits (52), Expect = 9.5
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 59 CPVCSRSFNQRSNLKTHL 76
C +C+ +F S LK+HL
Sbjct: 3 CELCNVTFTSESQLKSHL 20
>gnl|CDD|226336 COG3815, COG3815, Predicted membrane protein [Function unknown].
Length = 113
Score = 25.2 bits (55), Expect = 9.8
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 57 HKCPVCSRSFNQRSNLKTHLLTHTDIKPYNCAACGKVF 94
HK VC+R F S + T L+ + P++ + +F
Sbjct: 23 HKMAVCARCFGIYSGVLTVLVIYLFELPFDFSQSSVLF 60
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
0.319 0.128 0.386
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,468,894
Number of extensions: 504740
Number of successful extensions: 734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 722
Number of HSP's successfully gapped: 85
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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 (21.8 bits)
S2: 54 (24.6 bits)