RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy509
(158 letters)
>gnl|CDD|214499 smart00064, FYVE, Protein present in Fab1, YOTB, Vac1, and EEA1.
The FYVE zinc finger is named after four proteins where
it was first found: Fab1, YOTB/ZK632.12, Vac1, and
EEA1. The FYVE finger has been shown to bind two Zn2+
ions. The FYVE finger has eight potential zinc
coordinating cysteine positions. The FYVE finger is
structurally related to the PHD finger and the RING
finger. Many members of this family also include two
histidines in a motif R+HHC+XCG, where + represents a
charged residue and X any residue. The FYVE finger
functions in the membrane recruitment of cytosolic
proteins by binding to phosphatidylinositol 3-phosphate
(PI3P), which is prominent on endosomes. The R+HHC+XCG
motif is critical for PI3P binding.
Length = 68
Score = 86.3 bits (214), Expect = 3e-23
Identities = 32/65 (49%), Positives = 41/65 (63%), Gaps = 3/65 (4%)
Query: 23 APEWMDG---DTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCE 79
P W+ C C F+L +R+HHCR CG++FC CSSK LPK GIE+ VRVC+
Sbjct: 1 RPHWIPDEEVSNCMGCGKEFNLTKRRHHCRNCGRIFCSKCSSKKAPLPKLGIERPVRVCD 60
Query: 80 DCHEK 84
DC+E
Sbjct: 61 DCYEN 65
>gnl|CDD|216454 pfam01363, FYVE, FYVE zinc finger. The FYVE zinc finger is named
after four proteins that it has been found in: Fab1,
YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been
shown to bind two Zn++ ions. The FYVE finger has eight
potential zinc coordinating cysteine positions. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. We have included members which do
not conserve these histidine residues but are clearly
related.
Length = 68
Score = 84.8 bits (210), Expect = 1e-22
Identities = 33/68 (48%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 24 PEWMDGDT---CHRCRTTFSLVQRKHHCRACGQVFCQLCSSK-STSLPKFGIEKEVRVCE 79
P W+ C C FS +R+HHCR CG+VFC CSSK LPK GI K VRVC+
Sbjct: 1 PRWVPDSDVTNCMGCGKPFSFFRRRHHCRNCGKVFCSSCSSKKIALLPKLGINKPVRVCD 60
Query: 80 DCHEKFTN 87
DC++K
Sbjct: 61 DCYDKLQK 68
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in
Fab1, YOTB, Vac1, and EEA1;.
Length = 57
Score = 81.3 bits (201), Expect = 2e-21
Identities = 27/57 (47%), Positives = 35/57 (61%)
Query: 28 DGDTCHRCRTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEK 84
D +C C F+L +R+HHCR CG++FC CSS LP G K VRVC+ C+E
Sbjct: 1 DASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYEL 57
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 36.6 bits (84), Expect = 0.004
Identities = 24/79 (30%), Positives = 33/79 (41%), Gaps = 17/79 (21%)
Query: 24 PEWM----DGDTCHRCRTTF-----SLVQRKHHCRACGQVFCQLCSSKST-------SLP 67
P W D+C C F L R HHCR+CG C C +K + P
Sbjct: 451 PSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKP 510
Query: 68 KFGIEKEVR-VCEDCHEKF 85
E E R VC+ C++++
Sbjct: 511 GSSDEAEERLVCDTCYKEY 529
>gnl|CDD|145783 pfam02809, UIM, Ubiquitin interaction motif. This motif is called
the ubiquitin interaction motif. One of the proteins
containing this motif is a receptor for
poly-ubiquitination chains for the proteasome. This
motif has a pattern of conservation characteristic of an
alpha helix.
Length = 18
Score = 32.4 bits (76), Expect = 0.006
Identities = 13/17 (76%), Positives = 14/17 (82%)
Query: 135 KEEEELQLALALSQSEA 151
EEE+LQLALALS EA
Sbjct: 2 SEEEDLQLALALSLEEA 18
Score = 26.2 bits (60), Expect = 0.85
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 136 EEEELQLALALSQSEAES 153
EE L LAL+ S E+
Sbjct: 1 MSEEEDLQLALALSLEEA 18
>gnl|CDD|197845 smart00726, UIM, Ubiquitin-interacting motif. Present in
proteasome subunit S5a and other ubiquitin-associated
proteins.
Length = 20
Score = 30.6 bits (71), Expect = 0.024
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 136 EEEELQLALALSQSEAESN 154
E+E+LQ AL LS EAE +
Sbjct: 2 EDEDLQRALELSLQEAEES 20
>gnl|CDD|217297 pfam02945, Endonuclease_7, Recombination endonuclease VII.
Length = 81
Score = 30.5 bits (69), Expect = 0.094
Identities = 18/77 (23%), Positives = 25/77 (32%), Gaps = 13/77 (16%)
Query: 22 TAPEWM-----DGDTCHRCRTTFSLVQRKH--HCRACGQVFCQLCSSKSTSLPKFGIEKE 74
TA E+ G C C+ H G V LC +T+L K
Sbjct: 11 TAEEYWAIYEAQGGRCAICQRANGGTPALAVDHDHKTGHVRGLLCGPCNTALGKL----- 65
Query: 75 VRVCEDCHEKFTNYYRS 91
R + E+ +Y S
Sbjct: 66 -RDDPEALERAIDYLES 81
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 29.2 bits (66), Expect = 0.87
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 90 RSPTPGAAGSKSEEMLPAEYLNS--SLALQPQVPPPKATGGKTEEELKEEEELQL 142
R+ P + E EY L + P T KTEEEL +EE +L
Sbjct: 219 RTVKPPPKPPMTPEEKDDEYDQRVRELTFDRRAQPTDRT--KTEEELAKEEAERL 271
>gnl|CDD|223572 COG0498, ThrC, Threonine synthase [Amino acid transport and
metabolism].
Length = 411
Score = 29.2 bits (66), Expect = 1.0
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 32 CHRCRTTFSLVQRKHHCRACG 52
C +C FS + C CG
Sbjct: 8 CLKCGREFSQALLQGLCPDCG 28
>gnl|CDD|221121 pfam11489, DUF3210, Protein of unknown function (DUF3210). This is
a family of proteins conserved in yeasts. The function
is not known. The Schizosaccharomyces pombe member is
SPBC18E5.07 and the Saccharomyces cerevisiae member is
AIM21.
Length = 671
Score = 28.7 bits (64), Expect = 1.6
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 110 LNSSLALQPQVPPPKATGGKTEEELKEEEE 139
LN LAL PQ P K + K+EE+
Sbjct: 590 LNGRLALGPQAPKKVLESPKEPSKEKKEED 619
>gnl|CDD|222211 pfam13542, HTH_Tnp_ISL3, Helix-turn-helix domain of transposase
family ISL3.
Length = 65
Score = 26.5 bits (59), Expect = 1.9
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 26 WMDGDTCHRCRTTFSLVQRKHHCRACGQVF 55
+ L +R++ C+ CG+ F
Sbjct: 25 IRHLPIGGK-PVYLRLRKRRYRCKECGKTF 53
>gnl|CDD|216353 pfam01190, Pollen_Ole_e_I, Pollen proteins Ole e I like.
Length = 95
Score = 27.0 bits (60), Expect = 1.9
Identities = 9/44 (20%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 52 GQVFCQLCSSKSTSLPKFGIEK-EVRV-CEDCHEKFTNYYRSPT 93
G V+C C + L + + +V++ C+D + + T
Sbjct: 3 GSVYCDTCRASGFELSAYPLPGAKVKIECKDGDGRVVTSAEAVT 46
>gnl|CDD|215864 pfam00335, Tetraspannin, Tetraspanin family.
Length = 221
Score = 27.8 bits (62), Expect = 2.2
Identities = 9/68 (13%), Positives = 16/68 (23%), Gaps = 14/68 (20%)
Query: 36 RTTFSLVQRKHHCRACG-----------QVFCQLCSSKSTSLPKFGIEKEVRV-CEDCHE 83
+Q+ C CG + S + + E C E
Sbjct: 126 TEAIDELQKSLEC--CGVNSYTDWLDSQYFSPSSSNPDSDCCCWNNDTSNLNIYTEGCKE 183
Query: 84 KFTNYYRS 91
K + +
Sbjct: 184 KLLEFLKK 191
>gnl|CDD|115907 pfam07282, OrfB_Zn_ribbon, Putative transposase DNA-binding
domain. This putative domain is found at the
C-terminus of a large number of transposase proteins.
This domain contains four conserved cysteines
suggestive of a zinc binding domain. Given the need for
transposases to bind DNA as well as the large number of
DNA-binding zinc fingers we hypothesise this domain is
DNA-binding.
Length = 69
Score = 26.0 bits (58), Expect = 3.2
Identities = 10/27 (37%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 31 TCHRC--RTTFSLVQRKHHCRACGQVF 55
TC C + SL R C CG V
Sbjct: 30 TCSVCGHKNKESLSGRTFKCPNCGFVA 56
>gnl|CDD|224246 COG1327, COG1327, Predicted transcriptional regulator, consists
of a Zn-ribbon and ATP-cone domains [Transcription].
Length = 156
Score = 26.8 bits (60), Expect = 4.0
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 76 RVCEDCHEKFTNYYR 90
R C +C E+FT + R
Sbjct: 29 RECLECGERFTTFER 43
>gnl|CDD|216328 pfam01147, Crust_neurohorm, Crustacean CHH/MIH/GIH neurohormone
family.
Length = 73
Score = 25.2 bits (56), Expect = 5.2
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 4/21 (19%)
Query: 72 EKEVRVCEDCHEKFTNYYRSP 92
+K RVCEDC N +R P
Sbjct: 17 KKLDRVCEDC----YNLFREP 33
>gnl|CDD|224416 COG1499, NMD3, NMD protein affecting ribosome stability and mRNA
decay [Translation, ribosomal structure and biogenesis].
Length = 355
Score = 27.0 bits (60), Expect = 5.4
Identities = 18/89 (20%), Positives = 26/89 (29%), Gaps = 17/89 (19%)
Query: 27 MDGDTCHRC-RTTFSLVQRKHHCRACGQVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEKF 85
C RC R+ L+ C C ++T L + E V VC C
Sbjct: 4 ASTILCVRCGRSVDPLIDG----------LCGDCYVETTPLIEIPDEVNVEVCRHCGAYR 53
Query: 86 T--NYYRSPTPGAAGSKSEEMLPAEYLNS 112
+ ++ E L E L
Sbjct: 54 IRGRWVDEE----GANRLLEALEDEVLRR 78
>gnl|CDD|221306 pfam11906, DUF3426, Protein of unknown function (DUF3426). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 262 to 463 amino acids in
length.
Length = 149
Score = 26.1 bits (58), Expect = 6.8
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 105 LPAEYLNSSLALQPQVPP 122
LP +YL LA Q +PP
Sbjct: 107 LPEDYLAPELAGQAGLPP 124
>gnl|CDD|234774 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 25.9 bits (58), Expect = 6.9
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 76 RVCEDCHEKFTNYYR 90
R C C ++FT + R
Sbjct: 29 RECLACGKRFTTFER 43
>gnl|CDD|239127 cd02662, Peptidase_C19F, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 240
Score = 26.2 bits (58), Expect = 7.3
Identities = 6/26 (23%), Positives = 10/26 (38%)
Query: 15 DAMFSADTAPEWMDGDTCHRCRTTFS 40
+ + E +D C RC+T
Sbjct: 99 EHCLDDFLSTEIIDDYKCDRCQTVIV 124
>gnl|CDD|185434 PTZ00083, PTZ00083, 40S ribosomal protein S27; Provisional.
Length = 85
Score = 25.0 bits (55), Expect = 8.7
Identities = 10/29 (34%), Positives = 10/29 (34%), Gaps = 3/29 (10%)
Query: 32 CHRCR---TTFSLVQRKHHCRACGQVFCQ 57
C C T FS Q C C CQ
Sbjct: 38 CPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66
>gnl|CDD|224032 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
DnaJ-type Zn finger domain [DNA replication,
recombination, and repair].
Length = 715
Score = 26.2 bits (58), Expect = 8.9
Identities = 13/66 (19%), Positives = 20/66 (30%), Gaps = 12/66 (18%)
Query: 29 GDTCHRCRTTFSLVQRKHHCRACG----QVFCQLCSSKSTSLPKFGIEKEVRVCEDCHEK 84
C +CR + V C CG + C +C + +C +C K
Sbjct: 53 EIPCPKCRGKGT-VTVYDTCPECGGTGKVLTCDICGDIIVPWEEG-------LCPECRRK 104
Query: 85 FTNYYR 90
Y
Sbjct: 105 PKIVYV 110
>gnl|CDD|178274 PLN02669, PLN02669, xylulokinase.
Length = 556
Score = 26.3 bits (58), Expect = 9.1
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 18 FSADTAPEWMDGDTCHRCR 36
FS +P WMD T +CR
Sbjct: 130 FSTKDSPIWMDSSTTKQCR 148
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
0.314 0.128 0.388
Gapped
Lambda K H
0.267 0.0633 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,649,190
Number of extensions: 642920
Number of successful extensions: 685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 675
Number of HSP's successfully gapped: 59
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
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 (22.0 bits)
S2: 55 (25.2 bits)