RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15323
(139 letters)
>gnl|CDD|238123 cd00202, ZnF_GATA, Zinc finger DNA binding domain; binds
specifically to DNA consensus sequence [AT]GATA[AG]
promoter elements; a subset of family members may also
bind protein; zinc-finger consensus topology is
C-X(2)-C-X(17)-C-X(2)-C.
Length = 54
Score = 67.0 bits (164), Expect = 4e-16
Identities = 31/62 (50%), Positives = 38/62 (61%), Gaps = 10/62 (16%)
Query: 65 CTNCGTRMTTLWRRN-NDGEPVCNACGLYYKLHNVNRPLAMRHLAMRPLAMRKDGIQTRK 123
C+NCGT T LWRR + G +CNACGLY+K H V RPL+ R +KD I+ R
Sbjct: 2 CSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKR---------KKDQIKRRN 52
Query: 124 RK 125
RK
Sbjct: 53 RK 54
Score = 62.4 bits (152), Expect = 3e-14
Identities = 27/52 (51%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 10 ECVNCGAISTPLWRRDG-TGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRR 60
C NCG +TPLWRR G LCNACGLY K +G+ RPL K K R
Sbjct: 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGVMRPLSKRKKDQIKRRN 52
>gnl|CDD|214648 smart00401, ZnF_GATA, zinc finger binding to DNA consensus sequence
[AT]GATA[AG].
Length = 52
Score = 57.4 bits (139), Expect = 2e-12
Identities = 29/59 (49%), Positives = 35/59 (59%), Gaps = 10/59 (16%)
Query: 62 GLCCTNCGTRMTTLWRRNNDGE-PVCNACGLYYKLHNVNRPLAMRHLAMRPLAMRKDGI 119
G C+NCGT T LWRR G +CNACGLYYK H + RPL+++KDGI
Sbjct: 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLK---------RPLSLKKDGI 52
Score = 54.3 bits (131), Expect = 4e-11
Identities = 27/51 (52%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 6 GEGRECVNCGAISTPLWRRDGTGH-YLCNACGLYHKMNG-MNRPLVKPSKR 54
G GR C NCG TPLWRR +G+ LCNACGLY+K +G + RPL
Sbjct: 1 GSGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGLKRPLSLKKDG 51
>gnl|CDD|109380 pfam00320, GATA, GATA zinc finger. This domain uses four
cysteine residues to coordinate a zinc ion. This domain
binds to DNA. Two GATA zinc fingers are found in the
GATA transcription factors. However there are several
proteins which only contains a single copy of the
domain.
Length = 36
Score = 53.4 bits (129), Expect = 5e-11
Identities = 21/36 (58%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 65 CTNCGTRMTTLWRRNNDGEP-VCNACGLYYKLHNVN 99
C+NCGT T LWRR DG +CNACGLYY+ H +
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGLYYRKHGLK 36
Score = 52.7 bits (127), Expect = 1e-10
Identities = 20/36 (55%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 11 CVNCGAISTPLWRRDGTGHY-LCNACGLYHKMNGMN 45
C NCG TPLWRR G+ LCNACGLY++ +G+
Sbjct: 1 CSNCGTTKTPLWRRGPDGNRTLCNACGLYYRKHGLK 36
>gnl|CDD|227928 COG5641, GAT1, GATA Zn-finger-containing transcription factor
[Transcription].
Length = 498
Score = 52.6 bits (126), Expect = 6e-09
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 14/66 (21%)
Query: 65 CTNCGTRMTTLWRR-----NNDGEPVCNACGLYYKLHNVNRPLAMRHLAMRPLAMRKDGI 119
C+NC T T LWRR + G +CNACGLY KLH R P++++ D I
Sbjct: 161 CSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPR---------APISLKSDSI 211
Query: 120 QTRKRK 125
++R +
Sbjct: 212 KSRSSR 217
Score = 51.4 bits (123), Expect = 2e-08
Identities = 27/93 (29%), Positives = 35/93 (37%), Gaps = 6/93 (6%)
Query: 13 NCGAISTPLWRR-DGTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCCTNCGTR 71
+ +TPLWRR + CNA G K G RPL K ++R C NC +
Sbjct: 303 LTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPL--LPKPDPNSKRSNATCMNCSST 360
Query: 72 MTTLWRRNNDGEPVCNACGLYYKLHNVNRPLAM 104
T + N+ G KL N R
Sbjct: 361 PTN---KILSPPTTSNSPGAQVKLPNQTRSTGA 390
Score = 49.9 bits (119), Expect = 5e-08
Identities = 32/115 (27%), Positives = 42/115 (36%), Gaps = 22/115 (19%)
Query: 11 CVNCGAISTPLWRRD-----GTGHYLCNACGLYHKMNGMNRPLVKPSKRLTATRRLGLCC 65
C NC STPLWRR G+ LCNACGLY K++G R + +R
Sbjct: 161 CSNCKTTSTPLWRRASSESSLPGNNLCNACGLYLKLHGSPRAPISLKSDSIKSRSSRSSH 220
Query: 66 TNC--------GTRM--------TTLWRRNNDGEPV-CNACGLYYKLHNVNRPLA 103
N + T W G + +A L + +N PL
Sbjct: 221 NNNDSNGENANTESIGNSSASKLTKSWEERPQGRQLLSDAGSLSPRSNNPKSPLL 275
Score = 34.1 bits (78), Expect = 0.015
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 65 CTNCGTR-MTTLWRRN-NDGEPVCNACGLYYKLHNVNRPLAMRHLAM 109
+ T T LWRR + CNA G K RPL +
Sbjct: 300 RSTLTTSTATPLWRRTSDKSSFSCNASGSALKPPGSKRPLLPKPDPN 346
Score = 26.8 bits (59), Expect = 4.6
Identities = 7/34 (20%), Positives = 10/34 (29%), Gaps = 1/34 (2%)
Query: 19 TPLWRRDGTGHYLCNACGL-YHKMNGMNRPLVKP 51
L+R C+ + HK N N
Sbjct: 6 DSLFRSPPDLFLSCDINSIDLHKHNLPNAAPNIE 39
>gnl|CDD|184886 PRK14892, PRK14892, putative transcription elongation factor
Elf1; Provisional.
Length = 99
Score = 31.9 bits (73), Expect = 0.033
Identities = 10/33 (30%), Positives = 14/33 (42%)
Query: 10 ECVNCGAISTPLWRRDGTGHYLCNACGLYHKMN 42
EC CG +S + + C CGLY +
Sbjct: 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTEFE 55
Score = 27.7 bits (62), Expect = 1.0
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 46 RPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDGEPVCNACGLYYKL 95
+ +++P +L C CG ++ + N C CGLY +
Sbjct: 9 KKIIRPKPKLPKI----FECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54
>gnl|CDD|203895 pfam08271, TF_Zn_Ribbon, TFIIB zinc-binding. The transcription
factor TFIIB contains a zinc-binding motif near the
N-terminus. This domain is involved in the interaction
with RNA pol II and TFIIF and plays a crucial role in
selecting the transcription initiation site. The domain
adopts a zinc ribbon like structure.
Length = 40
Score = 27.2 bits (61), Expect = 0.49
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACGL 91
C NCG+ GE VC CGL
Sbjct: 3 CPNCGSTEIV--FDYERGEYVCTECGL 27
Score = 24.6 bits (54), Expect = 5.7
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 11 CVNCGAISTPLWRRDGTGHYLCNACGL 37
C NCG ST + G Y+C CGL
Sbjct: 3 CPNCG--STEIVFDYERGEYVCTECGL 27
>gnl|CDD|235832 PRK06567, PRK06567, putative bifunctional glutamate synthase
subunit beta/2-polyprenylphenol hydroxylase; Validated.
Length = 1028
Score = 29.1 bits (65), Expect = 0.78
Identities = 15/38 (39%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 27 TGHYLCNACG---LYHKMNGMNRPLVKPSKRLTATRRL 61
TGH +CN C +Y K + +N PL++ S L T +L
Sbjct: 319 TGHRICNDCSKACIYQKQDPVNIPLIE-SNILEETLKL 355
>gnl|CDD|220888 pfam10846, DUF2722, Protein of unknown function (DUF2722). This
eukaryotic family of proteins has no known function.
Length = 373
Score = 27.9 bits (62), Expect = 2.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 92 YYKLHNVNRPLAMRHLAMR 110
YYKL N N+ + + A+
Sbjct: 63 YYKLENANKSIELLKTALN 81
>gnl|CDD|227652 COG5349, COG5349, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 126
Score = 26.9 bits (60), Expect = 2.1
Identities = 21/56 (37%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 43 GMNRPLVKPSKRLTATRRLGL--CCTNCGTRMTTLWRRNNDGEPVCNACGLYYKLH 96
G RP+V P KR GL C CG L+R P C ACGL Y
Sbjct: 7 GAKRPVVTPIKR-------GLRGRCPRCGE--GRLFRGFLKVVPACEACGLDYGFA 53
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 27.7 bits (62), Expect = 2.1
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACGL 91
C CG+ T + GE VC CGL
Sbjct: 4 CPECGS--TNIITDYERGEIVCADCGL 28
>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 = 25.2 bits (56), Expect = 2.6
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACG 90
C +CG L + ++D C CG
Sbjct: 8 CEDCGHTFEVLQKISDDPLATCPECG 33
>gnl|CDD|178882 PRK00124, PRK00124, hypothetical protein; Validated.
Length = 151
Score = 26.7 bits (60), Expect = 3.0
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 93 YKLHNVNRPLAMRHLAMRPLAMRKDGIQT---RKRKPK 127
Y N+++ LAMR L +R+ GI+T + +
Sbjct: 97 YTNDNIDQLLAMRDLMA---TLRRSGIRTGGPKPFTQE 131
>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 = 3.2
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACG 90
C +CG L + ++D C CG
Sbjct: 8 CEDCGHTFEVLQKISDDPLTTCPECG 33
>gnl|CDD|178094 PLN02476, PLN02476, O-methyltransferase.
Length = 278
Score = 26.6 bits (58), Expect = 4.6
Identities = 23/83 (27%), Positives = 30/83 (36%), Gaps = 9/83 (10%)
Query: 44 MNRPLVKPSKRLTATRRLGLCCTNCGTRMTTLWRRNNDG-----EPVCNACGLY-YKLHN 97
+NRP V + L +RR NC ND + + LY Y L N
Sbjct: 22 LNRPTVSVCRSLKFSRR---LIGNCSIAPADPVVVANDDKYGNKQVISLTPRLYDYVLSN 78
Query: 98 VNRPLAMRHLAMRPLAMRKDGIQ 120
V P +R L MR +Q
Sbjct: 79 VREPKILRQLREETSKMRGSQMQ 101
>gnl|CDD|226060 COG3529, COG3529, Predicted nucleic-acid-binding protein
containing a Zn-ribbon domain [General function
prediction only].
Length = 66
Score = 24.8 bits (54), Expect = 6.1
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 4 QFGEGRECVNCGAIST-PLWRRDGTGHYLCNACG 36
+F G C C A T +WR + C CG
Sbjct: 6 RFIAGAVCPACQAQDTLAMWRENNVEIVECVKCG 39
>gnl|CDD|223924 COG0855, Ppk, Polyphosphate kinase [Inorganic ion transport and
metabolism].
Length = 696
Score = 26.1 bits (58), Expect = 7.0
Identities = 7/37 (18%), Positives = 15/37 (40%)
Query: 100 RPLAMRHLAMRPLAMRKDGIQTRKRKPKKQGGGGGGG 136
RP+ + L + P +R ++ +R+ G
Sbjct: 500 RPVRLNKLLVSPFTLRARILELIEREIAHAQAGKPAR 536
>gnl|CDD|235828 PRK06556, PRK06556, vitamin B12-dependent ribonucleotide reductase;
Validated.
Length = 953
Score = 26.1 bits (58), Expect = 8.0
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 7/27 (25%)
Query: 65 CTNCGTRMTTLWRRNNDGEP-VCNACG 90
C CGT+M RN G VC CG
Sbjct: 927 CPTCGTKM----VRN--GSCYVCEGCG 947
>gnl|CDD|225210 COG2331, COG2331, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 82
Score = 24.8 bits (54), Expect = 8.4
Identities = 9/26 (34%), Positives = 11/26 (42%)
Query: 65 CTNCGTRMTTLWRRNNDGEPVCNACG 90
CT CG R + +D C CG
Sbjct: 15 CTECGNRFDVVQAMTDDPLTTCEECG 40
>gnl|CDD|240135 cd04865, LigD_Pol_like_2, LigD_Pol_like_2: Polymerase (Pol) domain
of bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain
belongs to the archaeal/eukaryal primase (AEP)
superfamily. In prokaryotes, LigD along with Ku is
required for non-homologous end joining (NHEJ)-mediated
repair of DNA double-strand breaks (DSB). NHEJ-mediated
DNA DSB repair is error-prone. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The Pol domains of PaeLigD and Mycobacterium
tuberculosis (Mt)LigD are stimulated by manganese, are
error-prone, and prefer adding rNTPs to dNTPs in vitro;
however PaeLigD and MtLigD belong to other subgroups,
proteins in this subgroup await functional
characterization.
Length = 228
Score = 25.7 bits (57), Expect = 8.6
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 6/33 (18%)
Query: 101 PLAMRHLAMRPLAMRK--DGIQT----RKRKPK 127
P + +L RPL +++ DGI +K P
Sbjct: 13 PYLLPYLRDRPLVLKRYPDGIDGKGFYQKDVPA 45
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 0.140 0.475
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: 7,010,614
Number of extensions: 577380
Number of successful extensions: 797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 44
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.4 bits)