RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4796
(274 letters)
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 33.1 bits (76), Expect = 0.007
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 108 LQRHLLTHTGEKPFACHLCPYRASR 132
L+RH+ THTGEKP+ C +C S
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 30.8 bits (70), Expect = 0.051
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 209 KTHVMTHTGDKPFACSYCDYTCNQ 232
+ H+ THTG+KP+ C C + +
Sbjct: 3 RRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 29.7 bits (67), Expect = 0.13
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 81 KNHLSSHLGWKPYKCPHCDHCFTQ 104
+ H+ +H G KPYKCP C F+
Sbjct: 3 RRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 27.0 bits (60), Expect = 0.92
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 235 NLQTHLRIHKTEREYACGKCAYRTA 259
NL+ H+R H E+ Y C C +
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFS 25
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.6 bits (64), Expect = 0.26
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 93 YKCPHCDHCFTQKVVLQRHLLTH 115
Y+CP C F K L+ H+ TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 27.8 bits (62), Expect = 0.51
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 221 FACSYCDYTCNQSSNLQTHLRIH 243
+ C C S L+ H+R H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 0.37
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 94 KCPHCDHCFTQKVVLQRHLLTH 115
KCP C F++K L+RHL TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.1 bits (63), Expect = 0.43
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 223 CSYCDYTCNQSSNLQTHLRIH 243
C C + ++ SNL+ HLR H
Sbjct: 2 CPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|233304 TIGR01180, aman2_put, alpha-1,2-mannosidase, putative. The
identification of members of this family as putative
alpha-1,2-mannosidases is based on an unpublished
characterization of the aman2 gene in Bacillus sp. M-90
by Maruyama,Y., Nakajima,M. and Nakajima,T. (Genbank
accession BAA76709, pid g4587313). Most members of this
family appear to have signal sequences. Members from the
dental pathogen Porphyromonas gingivalis have been
described as immunoreactive with periodontitis patient
serum [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 750
Score = 31.4 bits (71), Expect = 0.61
Identities = 17/89 (19%), Positives = 30/89 (33%), Gaps = 9/89 (10%)
Query: 4 LAGDEDSSGLLSGQDKASPGPPPADVTCLHCSLTTPCVMKDMIRH--GRLCEFNSVVTSA 61
L G+EDS L + + G P D + +P + I G + T
Sbjct: 650 LPGNEDSGWLSAWAVFSMLGFYPVDPGSPGYPIGSPVFLSVTIGLPTGLHAPATAADTPY 709
Query: 62 KLQFLCLFCSYVATARIAIKNHLSSHLGW 90
SY+ ++ K +L+ +
Sbjct: 710 I-------NSYIVEVKLWGKPYLTHEILH 731
>gnl|CDD|225366 COG2808, PaiB, Transcriptional regulator [Transcription].
Length = 209
Score = 29.3 bits (66), Expect = 1.6
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 112 LLTHTGEKPFACHLCPY----RASRKYYITAHL 140
L+T G PFA HL P+ + + AHL
Sbjct: 27 LVTSGGGGPFATHL-PFLLNEEEGGEGVLIAHL 58
>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 = 26.1 bits (57), Expect = 2.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 93 YKCPHCDHCFTQKVVLQRHLLTH 115
+KCP C F+ K L+RHL H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|217097 pfam02548, Pantoate_transf, Ketopantoate
hydroxymethyltransferase. Ketopantoate
hydroxymethyltransferase (EC:2.1.2.11) is the first
enzyme in the pantothenate biosynthesis pathway.
Length = 261
Score = 28.2 bits (64), Expect = 4.3
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 37 TTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCL---FCSYVATARIAIKN 82
T P +++MI H + +V A F+ F SY A+ A++N
Sbjct: 56 TLPVTLEEMIYHTK-----AVARGAPRAFVVADMPFGSYEASPEQALRN 99
>gnl|CDD|236694 PRK10436, PRK10436, hypothetical protein; Provisional.
Length = 462
Score = 28.4 bits (64), Expect = 5.2
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 66 LCLFCSYVATARIAIKNHLSSHLGW----KPYKCPHCDHCFT 103
LC C A+ I + ++ W ++ C+HC+
Sbjct: 357 LCPHCRQQASEPIHLPPNI-----WPGPLPHWQAVGCEHCYH 393
>gnl|CDD|184688 PRK14457, PRK14457, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 345
Score = 28.0 bits (63), Expect = 5.4
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 84 LSSHLGWKPYKCP-HCDHCFTQKVVLQRHLLTH 115
+SS +G CP CD C T K L+R L H
Sbjct: 105 VSSQVG-----CPMACDFCATGKGGLKRSLKAH 132
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 28.1 bits (63), Expect = 7.1
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 11/41 (26%)
Query: 89 GWKPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYR 129
G+ +CP+CD T H CH C Y+
Sbjct: 442 GYIA-ECPNCDSPLT----------LHKATGQLRCHYCGYQ 471
>gnl|CDD|234723 PRK00311, panB, 3-methyl-2-oxobutanoate hydroxymethyltransferase;
Reviewed.
Length = 264
Score = 27.3 bits (62), Expect = 7.6
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 37 TTPCVMKDMIRHGRLCEFNSVVTSAKLQFLCL---FCSYVATARIAIKN 82
T P + DMI H + +V A + F SY A+ A++N
Sbjct: 55 TLPVTLDDMIYHTK-----AVARGAPRALVVADMPFGSYQASPEQALRN 98
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 27.7 bits (61), Expect = 8.1
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 91 KPYKCPHCDHCFTQKVVLQRHLLTHTGEKPFACHLCPYRASRK 133
+P CP+C F++ L RH+ +HTGEKP C S
Sbjct: 32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFS 74
>gnl|CDD|178497 PLN02909, PLN02909, Endoglucanase.
Length = 486
Score = 27.5 bits (61), Expect = 8.4
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 209 KTHVMTHTGDKPFACSYCDY 228
K H T+ G+ PF CSY Y
Sbjct: 219 KAHKGTYDGECPFYCSYSGY 238
>gnl|CDD|235391 PRK05290, PRK05290, hybrid cluster protein; Provisional.
Length = 546
Score = 27.4 bits (62), Expect = 8.6
Identities = 7/23 (30%), Positives = 8/23 (34%)
Query: 161 CVHCSEPISSDMSEIIEHCLVCP 183
H D S +IE L P
Sbjct: 334 VKHIEGDGKKDFSPVIEKALELP 356
>gnl|CDD|227003 COG4656, RnfC, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfC [Energy production and conversion].
Length = 529
Score = 27.3 bits (61), Expect = 9.2
Identities = 16/83 (19%), Positives = 29/83 (34%), Gaps = 21/83 (25%)
Query: 9 DSSGLLSGQDKASPGPPPADVTCLHCSLTTPCV-------MKDMI-RHGRLCEFNSVVTS 60
++GLL+ K P + +C+ CSL C + + + +
Sbjct: 346 TTNGLLA-LTKKELLEPIKEQSCIRCSL---CADACPVNLLPQQLYWFAKGEQH----DE 397
Query: 61 AKLQFL-----CLFCSYVATARI 78
+ L C C+YV + I
Sbjct: 398 EEEHNLLDCIECGACAYVCPSNI 420
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
0.325 0.135 0.452
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,733,304
Number of extensions: 1070049
Number of successful extensions: 1334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1334
Number of HSP's successfully gapped: 49
Length of query: 274
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 179
Effective length of database: 6,723,972
Effective search space: 1203590988
Effective search space used: 1203590988
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 (21.7 bits)
S2: 58 (26.1 bits)