RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy111
(85 letters)
>gnl|CDD|214829 smart00812, Alpha_L_fucos, Alpha-L-fucosidase. O-Glycosyl
hydrolases (EC 3.2.1.-) are a widespread group of
enzymes that hydrolyse the glycosidic bond between two
or more carbohydrates, or between a carbohydrate and a
non-carbohydrate moiety. A classification system for
glycosyl hydrolases, based on sequence similarity, has
led to the definition of 85 different families. This
classification is available on the CAZy
(CArbohydrate-Active EnZymes) web site. Because the fold
of proteins is better conserved than their sequences,
some of the families can be grouped in 'clans'. Family
29 encompasses alpha-L-fucosidases, which is a lysosomal
enzyme responsible for hydrolyzing the alpha-1,6-linked
fucose joined to the reducing-end N-acetylglucosamine of
the carbohydrate moieties of glycoproteins. Deficiency
of alpha-L-fucosidase results in the lysosomal storage
disease fucosidosis.
Length = 384
Score = 83.9 bits (208), Expect = 7e-21
Identities = 31/74 (41%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 2 VVVNDRWCNTCLCKHGGYLTCEDKYNPGKFQSRKFENCFTLDKYSWGYRRDANIDDILNM 61
VVVNDRW CKHGG+ T E++ PGK +E C T+ SWGYRR+ ++ D +
Sbjct: 229 VVVNDRWGG-TGCKHGGFYTDEERGAPGKLLPHPWETCTTIG-KSWGYRRNESLSDYKSP 286
Query: 62 TEVLQTMMNTVSFG 75
E+++ +++ VS G
Sbjct: 287 KELIRDLVDIVSKG 300
>gnl|CDD|216307 pfam01120, Alpha_L_fucos, Alpha-L-fucosidase.
Length = 320
Score = 63.4 bits (155), Expect = 1e-13
Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 2 VVVNDRWCNTCLCKHGGYLTCEDKYNPGKFQSRKFENCFTLDKYSWGYRRDANIDDILNM 61
VVVNDRW GG ++ PG+ +E C T+ SWGYRR D +
Sbjct: 211 VVVNDRWGYGP--YGGGDYETPERGLPGELLDHPWETCMTIG-GSWGYRRLVTDSDYKSP 267
Query: 62 TEVLQTMMNTVSFG 75
E+++ +++ VS G
Sbjct: 268 KEIIRMLVDAVSKG 281
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 30.1 bits (68), Expect = 0.095
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 14/50 (28%)
Query: 36 FENCFTLDKYSWGYRRDANIDDILNMTEVLQTM-MNTVSFGDKTLSILFS 84
NC + D +TEVL T NT + GDKT ++ S
Sbjct: 38 VTNCEA-----------GTVQDA--ITEVLATQHTNTRAKGDKTYHLIVS 74
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 27.4 bits (60), Expect = 0.93
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 26 YNPGKFQSRKFENCF-TLDKYSW-GYRRDANIDDILNMTEVLQTMMNT 71
Y P + SRK +N T D+ GY +++ I I+ + ++ T NT
Sbjct: 677 YKPYAYDSRKAKNYQDTFDRNDMHGYMKNSPISTIVPSSHMMHTKGNT 724
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 27.2 bits (61), Expect = 1.1
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 21/49 (42%)
Query: 19 YLTCED----KYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ CE +YN TL+ KY + NI D+L+MT
Sbjct: 753 YVPCEVCHGKRYNR-----------ETLEVKY-----KGKNIADVLDMT 785
>gnl|CDD|129571 TIGR00479, rumA, 23S rRNA (uracil-5-)-methyltransferase RumA. This
protein family was first proposed to be RNA
methyltransferases by homology to the TrmA family. The
member from E. coli has now been shown to act as the 23S
RNA methyltransferase for the conserved U1939. The gene
is now designated rumA and was previously designated
ygcA [Protein synthesis, tRNA and rRNA base
modification].
Length = 431
Score = 26.7 bits (59), Expect = 1.6
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 29 GKFQSRKFENCFTLDKYSWGYRRDA 53
GKF S E T+ WGYR A
Sbjct: 93 GKFTSEPIEPLPTIGGDPWGYRNKA 117
>gnl|CDD|188250 TIGR02802, Pal_lipo, peptidoglycan-associated lipoprotein.
Members of this protein are Pal (also called OprL), the
Peptidoglycan-Associated Lipoprotein of the Tol-Pal
system. The system appears to be involved both in the
maintenance of outer membrane integrity and in the
import of certain organic molecules as nutrients.
Members of this family contain a hydrodrophobic
lipoprotein signal sequence, a conserved N-terminal
cleavage and modification site, a poorly conserved
low-complexity region, together comprising about 65
amino acids, and a well-conserved C-terminal domain.
The seed alignment for this model includes only the
conserved C-terminal domain.
Length = 104
Score = 25.2 bits (56), Expect = 3.1
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 48 GYRRDANIDDILNMTEVLQTMMNTVSFG 75
G RR + D L V + + TVS+G
Sbjct: 53 GERRANAVKDYLQSKGVSASQIETVSYG 80
>gnl|CDD|234734 PRK00349, uvrA, excinuclease ABC subunit A; Reviewed.
Length = 943
Score = 25.8 bits (58), Expect = 3.2
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 21/49 (42%)
Query: 19 YLTCE----DKYNPGKFQSRKFENCFTLD-KYSWGYRRDANIDDILNMT 62
Y+ C+ +YN E TL+ KY + NI D+L+MT
Sbjct: 761 YVPCDVCKGKRYNR--------E---TLEVKY-----KGKNIADVLDMT 793
>gnl|CDD|217837 pfam04003, Utp12, Dip2/Utp12 Family. This domain is found at the
C-terminus of proteins containing WD40 repeats. These
proteins are part of the U3 ribonucleoprotein the yeast
protein is called Utp12 or DIP2.
Length = 109
Score = 25.2 bits (56), Expect = 3.5
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 7 RWCNTCLCKHGGYLT 21
RW L HG YL
Sbjct: 54 RWLKFLLRIHGKYLV 68
>gnl|CDD|241424 cd13270, PH1_TAPP1_2, Tandem PH-domain-containing proteins 1 and
2 Pleckstrin homology (PH) domain, N-terminal repeat.
The binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain binds
PtdIns(3,4)P2. They also contain a C-terminal
PDZ-binding motif that interacts with several
PDZ-binding proteins, including PTPN13 (known
previously as PTPL1 or FAP-1) as well as the
scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 118
Score = 25.1 bits (55), Expect = 4.3
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 15 KHGGYLTCEDKYNPGKFQSRKF 36
+ G+L E+ N GKF R F
Sbjct: 9 RTCGFLDIEENENSGKFLRRYF 30
>gnl|CDD|176218 cd08256, Zn_ADH2, Alcohol dehydrogenases of the MDR family. This
group has the characteristic catalytic and structural
zinc-binding sites of the zinc-dependent alcohol
dehydrogenases of the MDR family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability.
Length = 350
Score = 25.1 bits (55), Expect = 4.8
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 9 CNTC-LCKHGGYLTCEDKYNPGKFQSR 34
C C C G Y C+ K++ FQ+
Sbjct: 100 CWNCRFCNRGQYWMCQ-KHDLYGFQNN 125
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 0.137 0.449
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,072,322
Number of extensions: 302679
Number of successful extensions: 234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 230
Number of HSP's successfully gapped: 14
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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 (22.0 bits)
S2: 53 (24.2 bits)