RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4644
(351 letters)
>gnl|CDD|227528 COG5201, SKP1, SCF ubiquitin ligase, SKP1 component
[Posttranslational modification, protein turnover,
chaperones].
Length = 158
Score = 158 bits (402), Expect = 6e-48
Identities = 79/158 (50%), Positives = 101/158 (63%), Gaps = 4/158 (2%)
Query: 1 MPNIKLQSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQW 60
M I+L+S DGEIF VD IA+ S+ IK M+ D +P PNV S++L KV +W
Sbjct: 1 MSMIELESIDGEIFRVDENIAERSILIKNMLCDST---ACNYPIPAPNVRSSVLMKVQEW 57
Query: 61 ATYHKDDPPPPEDDENKEKRTDDISSWDADFLKVDQGTLFELILAANYLDIKGLLDVTCK 120
+H E+D K WD F++VDQ L E+ LAANYL+IK LLD+ CK
Sbjct: 58 MEHHTSSLSEDENDLEIRKSKP-SDFWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCK 116
Query: 121 TVANMIKGKTPEEIRKTFNIKNDFTQAEEEQVRKENEW 158
VA MI+GK+PEEIR+TFNI+NDFT EE ++RKENEW
Sbjct: 117 IVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEW 154
Score = 155 bits (392), Expect = 2e-46
Identities = 79/161 (49%), Positives = 102/161 (63%), Gaps = 4/161 (2%)
Query: 191 SAILRKSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQWA 250
S I +S DGEIF VD IA+ S+ IK M+ D +P PNV S++L KV +W
Sbjct: 2 SMIELESIDGEIFRVDENIAERSILIKNMLCDST---ACNYPIPAPNVRSSVLMKVQEWM 58
Query: 251 TYHKDDPPPPEDDENKEKRTDDISSWDADFLKVDQGTLFELILAANYLDIKGLLDVTCKT 310
+H E+D K WD F++VDQ L E+ LAANYL+IK LLD+ CK
Sbjct: 59 EHHTSSLSEDENDLEIRKSKP-SDFWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKI 117
Query: 311 VANMIKGKTPEEIRKTFNIKNDFTQAEEEQVRKENEWCEEK 351
VA MI+GK+PEEIR+TFNI+NDFT EE ++RKENEW E++
Sbjct: 118 VAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAEDR 158
>gnl|CDD|201810 pfam01466, Skp1, Skp1 family, dimerisation domain.
Length = 78
Score = 141 bits (359), Expect = 2e-42
Identities = 54/78 (69%), Positives = 66/78 (84%)
Query: 273 ISSWDADFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKND 332
+ WDA+F+ VDQ TLF+LILAANYL+IKGLLD+ C+ VA+MIKGKTPEEIR+ F I+ND
Sbjct: 1 LKEWDAEFVDVDQDTLFDLILAANYLNIKGLLDLACQKVADMIKGKTPEEIREIFGIEND 60
Query: 333 FTQAEEEQVRKENEWCEE 350
FT EEE++RKENEW E
Sbjct: 61 FTPEEEEEIRKENEWAFE 78
Score = 139 bits (352), Expect = 2e-41
Identities = 53/76 (69%), Positives = 65/76 (85%)
Query: 84 ISSWDADFLKVDQGTLFELILAANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKND 143
+ WDA+F+ VDQ TLF+LILAANYL+IKGLLD+ C+ VA+MIKGKTPEEIR+ F I+ND
Sbjct: 1 LKEWDAEFVDVDQDTLFDLILAANYLNIKGLLDLACQKVADMIKGKTPEEIREIFGIEND 60
Query: 144 FTQAEEEQVRKENEWC 159
FT EEE++RKENEW
Sbjct: 61 FTPEEEEEIRKENEWA 76
Score = 36.0 bits (84), Expect = 0.003
Identities = 16/19 (84%), Positives = 18/19 (94%)
Query: 160 TLFELILAANYLDIKGLED 178
TLF+LILAANYL+IKGL D
Sbjct: 15 TLFDLILAANYLNIKGLLD 33
>gnl|CDD|214704 smart00512, Skp1, Found in Skp1 protein family. Family of Skp1
(kinetochore protein required for cell cycle
progression) and elongin C (subunit of RNA polymerase II
transcription factor SIII) homologues.
Length = 104
Score = 136 bits (345), Expect = 5e-40
Identities = 65/111 (58%), Positives = 80/111 (72%), Gaps = 7/111 (6%)
Query: 1 MPNIKLQSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQW 60
IKL SSDGE+F V+ E+A+ S TIK M+EDLG++DE+ +PLPNV S IL KVI++
Sbjct: 1 SKYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEY 60
Query: 61 ATYHKDDPPPPEDDENKEKRTDDISSWDADFLKVDQGTLFELILAANYLDI 111
+H DDPP D DDI +WDA+FLK+DQ TLFELILAANYLDI
Sbjct: 61 CEHHVDDPPSVADK-------DDIPTWDAEFLKIDQETLFELILAANYLDI 104
Score = 130 bits (329), Expect = 1e-37
Identities = 62/105 (59%), Positives = 77/105 (73%), Gaps = 7/105 (6%)
Query: 196 KSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQWATYHKD 255
SSDGE+F V+ E+A+ S TIK M+EDLG++DE+ +PLPNV S IL KVI++ +H D
Sbjct: 7 ISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVD 66
Query: 256 DPPPPEDDENKEKRTDDISSWDADFLKVDQGTLFELILAANYLDI 300
DPP D DDI +WDA+FLK+DQ TLFELILAANYLDI
Sbjct: 67 DPPSVADK-------DDIPTWDAEFLKIDQETLFELILAANYLDI 104
>gnl|CDD|217800 pfam03931, Skp1_POZ, Skp1 family, tetramerisation domain.
Length = 61
Score = 81.2 bits (201), Expect = 1e-19
Identities = 37/65 (56%), Positives = 46/65 (70%), Gaps = 4/65 (6%)
Query: 2 PNIKLQSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQWA 61
IKL SSDGEIF V+ E+A+ S TIK M+EDLG++D +PLPNV S IL KVI+W
Sbjct: 1 KLIKLTSSDGEIFEVEREVARQSKTIKAMIEDLGVDDP----IPLPNVTSKILAKVIEWC 56
Query: 62 TYHKD 66
+HK
Sbjct: 57 KHHKV 61
Score = 74.6 bits (184), Expect = 3e-17
Identities = 34/60 (56%), Positives = 43/60 (71%), Gaps = 4/60 (6%)
Query: 196 KSSDGEIFNVDFEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQWATYHKD 255
SSDGEIF V+ E+A+ S TIK M+EDLG++D +PLPNV S IL KVI+W +HK
Sbjct: 6 TSSDGEIFEVEREVARQSKTIKAMIEDLGVDDP----IPLPNVTSKILAKVIEWCKHHKV 61
Score = 25.7 bits (57), Expect = 8.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 180 DEEIVPLPNVNSAILRK 196
++ +PLPNV S IL K
Sbjct: 35 VDDPIPLPNVTSKILAK 51
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 28.5 bits (64), Expect = 6.2
Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 6/140 (4%)
Query: 147 AEEEQVRKENEWCTLFELILAANYLDIKGLEDEDEEIVPLPNVNSAILRKSSDGEIFNVD 206
E+ + EW +L E + Y K + EE L A ++ +
Sbjct: 297 REKSDSKVVREWSSLLESLKEKGY--FKDNLEGSEEYKELLEKAEAYFSSTASSPGEEIL 354
Query: 207 FEIAKSSVTIKTMVEDLGLEDEDEEIVPLPNVNSAILRKVIQWATYHKDDPPPPEDDENK 266
+ ++ +DL ED+D + N++ L +Q K D ++D N+
Sbjct: 355 DLLQLDLEELRDEEQDLPPEDDDSWL----NISPDELDSELQERQGDKKDLKSNKEDANE 410
Query: 267 EKRTDDISSWDADFLKVDQG 286
+++ S +FL
Sbjct: 411 VDDLEEVVSSMEEFLNKVSS 430
>gnl|CDD|117609 pfam09043, Lys-AminoMut_A, D-Lysine 5,6-aminomutase alpha
subunit. Members of his family are involved in the 1,2
rearrangement of the terminal amino group of DL-lysine
and of L-beta-lysine, using adenosylcobalamin (AdoCbl)
and pyridoxal-5'-phosphate as cofactors. The structure
is predominantly a PLP-binding TIM barrel domain, with
several additional alpha-helices and beta-strands at
the N and C termini. These helices and strands form an
intertwined accessory clamp structure that wraps around
the sides of the TIM barrel and extends up toward the
Ado ligand of the Cbl cofactor, providing most of the
interactions observed between the protein and the Ado
ligand of the Cbl, suggesting that its role is mainly
in stabilising AdoCbl in the precatalytic resting
state.
Length = 509
Score = 28.2 bits (63), Expect = 6.9
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 17 DFEIAKSSVTI-KTMVEDLGLEDEDEEIVPLPNV 49
+F ++VT+ +T+ LG++ DE+ VPLPNV
Sbjct: 24 EFIERHTTVTVERTVCRLLGIDGVDEDGVPLPNV 57
Score = 28.2 bits (63), Expect = 6.9
Identities = 14/34 (41%), Positives = 23/34 (67%), Gaps = 1/34 (2%)
Query: 206 DFEIAKSSVTI-KTMVEDLGLEDEDEEIVPLPNV 238
+F ++VT+ +T+ LG++ DE+ VPLPNV
Sbjct: 24 EFIERHTTVTVERTVCRLLGIDGVDEDGVPLPNV 57
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 28.3 bits (64), Expect = 7.0
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 9/83 (10%)
Query: 163 ELILAANYLDIKGLEDEDEEIVPLPNVNSAILRKSSDGEIFNVDFEIAKSSVTI---KTM 219
EL N L G+ +E ++ L IL E V + + I +
Sbjct: 480 ELEALRNALAGGGILEEGVLVLDLSEGVKRIL------EKLGVPHRVRDGKIVIEEAYPL 533
Query: 220 VEDLGLEDEDEEIVPLPNVNSAI 242
+ LGL++ +E L + ++ +
Sbjct: 534 LYSLGLDELEELKKKLDDGSNVL 556
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
0.312 0.133 0.381
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,828,083
Number of extensions: 1919546
Number of successful extensions: 1539
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1531
Number of HSP's successfully gapped: 42
Length of query: 351
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 253
Effective length of database: 6,590,910
Effective search space: 1667500230
Effective search space used: 1667500230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 59 (26.5 bits)