RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy312
(90 letters)
>gnl|CDD|203401 pfam06179, Med22, Surfeit locus protein 5 subunit 22 of Mediator
complex. This family consists of several eukaryotic
Surfeit locus protein 5 (SURF5) sequences. The human
Surfeit locus has been mapped on chromosome 9q34.1. The
locus includes six tightly clustered housekeeping genes
(Surf1-6), and the gene organisation is similar in
human, mouse and chicken Surfeit locus. The Med22
subunit of Mediator complex is part of the essential
core head region.
Length = 108
Score = 98.1 bits (245), Expect = 2e-28
Identities = 34/79 (43%), Positives = 49/79 (62%)
Query: 1 MTQCELDLYEMHVRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQT 60
T ++YEM VRA +VRA E LLKL +IK++ ILNDF +NE I Q + F ++Q
Sbjct: 30 KTVAAQEVYEMEVRAAQLVRAVEDLLKLTREIKEFWILNDFSPLNEEIKQQEEEFESEQE 89
Query: 61 ECDQKLMNLRDDMAADLYD 79
E DQ L L + ++ +L +
Sbjct: 90 ETDQLLAELLEKLSEELIE 108
>gnl|CDD|212566 cd11684, DHR2_DOCK, Dock Homology Region 2, a GEF domain, of
Dedicator of Cytokinesis proteins. DOCK proteins
comprise a family of atypical guanine nucleotide
exchange factors (GEFs) that lack the conventional Dbl
homology (DH) domain. As GEFs, they activate the small
GTPases Rac and Cdc42 by exchanging bound GDP for free
GTP. They are also called the CZH (CED-5, Dock180, and
MBC-zizimin homology) family, after the first family
members identified. Dock180 was first isolated as a
binding partner for the adaptor protein Crk. The
Caenorhabditis elegans protein, Ced-5, is essential for
cell migration and phagocytosis, while the Drosophila
ortholog, Myoblast city (MBC), is necessary for
myoblast fusion and dorsal closure. DOCKs are divided
into four classes (A-D) based on sequence similarity
and domain architecture: class A includes Dock1 (or
Dock180), 2 and 5; class B includes Dock3 and 4; class
C includes Dock6, 7, and 8; and class D includes Dock9,
10 and 11. All DOCKs contain two homology domains: the
DHR-1 (Dock homology region-1), also called CZH1, and
DHR-2 (also called CZH2 or Docker). This alignment
model represents the DHR-2 domain of DOCK proteins,
which contains the catalytic GEF activity for Rac
and/or Cdc42.
Length = 392
Score = 34.6 bits (80), Expect = 0.003
Identities = 17/73 (23%), Positives = 24/73 (32%), Gaps = 9/73 (12%)
Query: 7 DLYEMHVRAGNIVRAGESLLKLVSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECDQKL 66
L ++H GN V A LL L L +QT ++K
Sbjct: 9 KLADLHEERGNYVEAALCLLLHADLYAWDLKALVPAL-------AESLSFPEQTSFERKE 61
Query: 67 MNLRDDMAADLYD 79
+ A DL+D
Sbjct: 62 ALYK--KAIDLFD 72
>gnl|CDD|233547 TIGR01730, RND_mfp, RND family efflux transporter, MFP subunit.
This model represents the MFP (membrane fusion protein)
component of the RND family of transporters. RND refers
to Resistance, Nodulation, and cell Division. It is, in
part, a subfamily of pfam00529 (Pfam release 7.5) but
hits substantial numbers of proteins missed by that
model. The related HlyD secretion protein, for which
pfam00529 is named, is outside the scope of this model.
Attributed functions imply outward transport. These
functions include nodulation, acriflavin resistance,
heavy metal efflux, and multidrug resistance proteins.
Most members of this family are found in Gram-negative
bacteria. The proposed function of MFP proteins is to
bring the inner and outer membranes together and enable
transport to the outside of the outer membrane. Note,
however, that a few members of this family are found in
Gram-positive bacteria, where there is no outer
membrane [Transport and binding proteins, Unknown
substrate].
Length = 322
Score = 28.4 bits (64), Expect = 0.39
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 10 EMHVRAGNIVRAGESLLKLVSDIKQ 34
++ VR G V+ G+ L +L D Q
Sbjct: 39 KISVREGQKVKKGQVLARLDDDDYQ 63
>gnl|CDD|214925 smart00941, PYNP_C, Pyrimidine nucleoside phosphorylase
C-terminal domain. This domain is found at the
C-terminal end of the large alpha/beta domain making up
various pyrimidine nucleoside phosphorylases. It has
slightly different conformations in different members
of this family. For example, in pyrimidine nucleoside
phosphorylase (PYNP) there is an added three-stranded
anti-parallel beta sheet as compared to other members
of the family, such as E. coli thymidine phosphorylase
(TP). The domain contains an alpha/ beta hammerhead
fold and residues in this domain seem to be important
in formation of the homodimer.
Length = 75
Score = 24.8 bits (55), Expect = 3.2
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 10 EMHVRAGNIVRAGESLLKL 28
+H + G+ V+ GE L +
Sbjct: 35 VLHKKLGDRVKKGEPLATI 53
>gnl|CDD|185017 PRK15057, PRK15057, UDP-glucose 6-dehydrogenase; Provisional.
Length = 388
Score = 25.4 bits (55), Expect = 4.5
Identities = 14/45 (31%), Positives = 23/45 (51%)
Query: 42 PSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYT 86
P + E NS+L R T Q + + + MA +L D+ ++ YT
Sbjct: 337 PVMKEDSFFNSRLERDLATFKQQADVIISNRMAEELKDVADKVYT 381
>gnl|CDD|184253 PRK13697, PRK13697, cytochrome c6; Provisional.
Length = 111
Score = 24.7 bits (54), Expect = 6.8
Identities = 9/24 (37%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 12 HVRAGNIVRAGESLLKLVSDIKQY 35
H N+V AG++L K +D+++Y
Sbjct: 43 HAGGKNLVNAGKTLKK--ADLEKY 64
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
Miro is one of few Rho subfamilies that lack this
feature.
Length = 180
Score = 24.9 bits (55), Expect = 7.0
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 4/35 (11%)
Query: 29 VSDIKQYLILNDFPSVNEAITQNSKLFRTKQTECD 63
V ++YLIL + EAI N + CD
Sbjct: 49 VPGQEKYLILREVGEDEEAILLNDA----ELAACD 79
>gnl|CDD|214378 CHL00160, rpl9, ribosomal protein L9; Provisional.
Length = 153
Score = 24.3 bits (53), Expect = 8.2
Identities = 19/60 (31%), Positives = 23/60 (38%), Gaps = 4/60 (6%)
Query: 32 IKQYLILNDFPSVNEAITQNS-KLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTSVYK 90
+ YLI N V TQ S K + Q D KL ++ LEE SV K
Sbjct: 31 ARNYLIPNKMAKVA---TQGSLKQQKMYQKILDLKLKEAKEKCLKVKQLLEEIQKFSVKK 87
>gnl|CDD|205240 pfam13059, DUF3922, Protein of unknown function (DUF3992). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 87 and 98 amino
acids in length.
Length = 79
Score = 23.8 bits (51), Expect = 9.1
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 8/58 (13%)
Query: 33 KQYLILNDFPSVNEAITQNSKLFRTKQTECDQKLMNLRDDMAADLYDLEEEYYTSVYK 90
+QY + D ++ EA T+ LF KQ +C D + + D EYYT YK
Sbjct: 21 EQYNVETDKIAIIEA-TEEYYLFLVKQEDC-------YDVVKVETVDTNIEYYTKAYK 70
>gnl|CDD|235289 PRK04350, PRK04350, thymidine phosphorylase; Provisional.
Length = 490
Score = 24.4 bits (54), Expect = 9.3
Identities = 6/22 (27%), Positives = 15/22 (68%)
Query: 10 EMHVRAGNIVRAGESLLKLVSD 31
++HV+ G+ V+ G+ L + ++
Sbjct: 442 DLHVKVGDKVKKGDPLYTIHAE 463
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 24.7 bits (54), Expect = 9.9
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 16 GNIVRAGESLLKLV 29
G+IV+ GE+LLK++
Sbjct: 60 GDIVKVGETLLKIM 73
>gnl|CDD|213892 TIGR04171, RNR_1b_NrdF, ribonucleoside-diphosphate reductase, class
1b, beta subunit. Members of this family are NrdF, the
beta subunit of class 1b ribonucleotide reductase. This
form uses a dimanganese moiety associated with a
tyrosine radical to reduce the cellular requirement for
iron [Purines, pyrimidines, nucleosides, and
nucleotides, 2'-Deoxyribonucleotide metabolism].
Length = 313
Score = 24.4 bits (54), Expect = 9.9
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 58 KQTECDQKLMNLRDDMAADLYDLEEEYYTSVY 89
+Q E + +L + LY+ EE+Y +Y
Sbjct: 209 EQEELKDWMYDLLYE----LYENEEKYTEELY 236
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
0.318 0.133 0.368
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,333,256
Number of extensions: 332029
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 332
Number of HSP's successfully gapped: 26
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.0 bits)