RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12373
(198 letters)
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 34.5 bits (80), Expect = 0.013
Identities = 16/95 (16%), Positives = 37/95 (38%), Gaps = 6/95 (6%)
Query: 28 CYIQLKNWTKIGQLLPHIKSATTF-IQYAKAK-EAMGSYRESVGAYERAEDYDNVVRVDL 85
Y + ++ K L +K + ++ E Y E+V Y++ +Y + + L
Sbjct: 51 LYAKYEDPEK---LEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKNGNYKEAISL-L 106
Query: 86 DHLNDIRHAVDIVKAKKCTEGAKRIADYCNKHGDF 120
L + A++ E +++ + +G F
Sbjct: 107 KKLKLYKDAIEYAVKSNDPELWEKLLNALLDNGRF 141
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 32.0 bits (73), Expect = 0.035
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 3/63 (4%)
Query: 15 LYESAGNYEKAATCYIQ-LKNWTKIGQLLPHIKSATTFIQYAKAKEAMGSYRESVGAYER 73
+ G+Y++A + L+ ++G+ H ++A A+ A+G Y E++ E+
Sbjct: 14 VLRRLGDYDEALELLEKALELARELGED--HPETARALNNLARLYLALGDYDEALEYLEK 71
Query: 74 AED 76
A
Sbjct: 72 ALA 74
>gnl|CDD|236058 PRK07579, PRK07579, hypothetical protein; Provisional.
Length = 245
Score = 30.6 bits (69), Expect = 0.42
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 66 ESVGAYERAEDYDNVVRVDLDHLNDIRHAVDIVKAKKCTEGAKRIADYCNKHG 118
+ G +D+ + +DLD RH ++ ++A T + A + ++ G
Sbjct: 178 ATEGNLNSKKDFKQLREIDLDERGTFRHFINRLRA--LTHDDYKNAYFVDESG 228
>gnl|CDD|128594 smart00299, CLH, Clathrin heavy chain repeat homology.
Length = 140
Score = 29.5 bits (67), Expect = 0.55
Identities = 10/63 (15%), Positives = 24/63 (38%)
Query: 55 AKAKEAMGSYRESVGAYERAEDYDNVVRVDLDHLNDIRHAVDIVKAKKCTEGAKRIADYC 114
K E Y E+V Y++ ++ + + ++HL + A++ + E +
Sbjct: 76 GKLCEKAKLYEEAVELYKKDGNFKDAIVTLIEHLGNYEKAIEYFVKQNNPELWAEVLKAL 135
Query: 115 NKH 117
Sbjct: 136 LDK 138
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-
[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence;
found in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate
to multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for
peroxisomal targeting signals, the Tom70p co-receptor
for mitochondrial targeting signals, Ser/Thr
phosphatase 5C and the p110 subunit of O-GlcNAc
transferase; three copies of the repeat are present
here.
Length = 100
Score = 28.9 bits (65), Expect = 0.74
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 11 GKWTLYESAGNYEKAATCYIQLKNWTKIGQLLPHIKSATTFIQYAKAKEAMGSYRESVGA 70
LY G+Y++A Y K +L P +A + A A +G Y E++
Sbjct: 5 NLGNLYYKLGDYDEALEYY------EKALELDP--DNADAYYNLAAAYYKLGKYEEALED 56
Query: 71 YERAEDYDN 79
YE+A + D
Sbjct: 57 YEKALELDP 65
>gnl|CDD|212567 cd11694, DHR2_DOCK_D, Dock Homology Region 2, a GEF domain, of
Class D Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided into
four classes (A-D) based on sequence similarity and
domain architecture; class D, also called the Zizimin
subfamily, includes Dock9, 10 and 11. Class D Docks are
specific GEFs for Cdc42. Dock9 plays important roles in
spine formation and dendritic growth. Dock10 and Dock11
are preferentially expressed in lymphocytes. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of class D DOCKs,
which contains the catalytic GEF activity for Cdc42.
Class D DOCKs also contain a Pleckstrin homology (PH)
domain at the N-terminus.
Length = 376
Score = 30.0 bits (68), Expect = 0.82
Identities = 17/72 (23%), Positives = 24/72 (33%), Gaps = 18/72 (25%)
Query: 6 LTLDRGKWTLYESAGNYEKAATCYIQLKNWTKIGQLLPHIKSATTFIQYAKAKEAMGSYR 65
L + +YE ++E+ A CY L Y K E M S +
Sbjct: 65 GELYKLIIPIYEKRRDFEQLADCYRTLH------------------RAYEKVVEVMESGK 106
Query: 66 ESVGAYERAEDY 77
+G Y R Y
Sbjct: 107 RLLGTYYRVAFY 118
>gnl|CDD|237953 PRK15378, PRK15378, inositol phosphate phosphatase SopB;
Provisional.
Length = 564
Score = 29.9 bits (67), Expect = 0.99
Identities = 14/62 (22%), Positives = 21/62 (33%)
Query: 11 GKWTLYESAGNYEKAATCYIQLKNWTKIGQLLPHIKSATTFIQYAKAKEAMGSYRESVGA 70
K +A + A + + W I L H T Q A+ +G+ A
Sbjct: 150 AKEAHRFAALAFSDAQVKQLNNQPWQTIKNTLSHNGHHYTNTQLPAAEMKIGAKDIFPKA 209
Query: 71 YE 72
YE
Sbjct: 210 YE 211
>gnl|CDD|184804 PRK14720, PRK14720, transcript cleavage factor/unknown domain
fusion protein; Provisional.
Length = 906
Score = 29.4 bits (66), Expect = 1.5
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 114 CNKHGDFGAAIHFL-ILSKCYQDAFNLSQQHKKLHEFGKFLLEEDEPNPVELKRLAIHFE 172
C+K +G L L++ Y ++KKL + L++ D NP +K+LA +E
Sbjct: 106 CDKILLYGENKLALRTLAEAYAKL----NENKKLKGVWERLVKADRDNPEIVKKLATSYE 161
Query: 173 ED 174
E+
Sbjct: 162 EE 163
>gnl|CDD|151989 pfam11553, DUF3231, Protein of unknown function (DUF3231). This
bacterial family of proteins has no known function.
Length = 166
Score = 28.4 bits (64), Expect = 1.7
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 129 LSKCYQDAFNLSQQHKKLHEFGKFLLEEDEPNP 161
+ K Q A +LS +H K L EE P P
Sbjct: 48 IKKYLQRALDLSNKHIK--ILSSLLKEEGLPLP 78
>gnl|CDD|185766 cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of
human Brox1 and related proteins. This family contains
the Bro1-like domain of a single-domain protein, human
Brox, and related domains. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of Brox. Human Brox can bind
to human immunodeficiency virus type 1 (HIV-1)
nucleocapsid. In addition to a Bro1-like domain, Brox
also has a C-terminal thioester-linkage site for
isoprenoid lipids (CaaX motif). This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 353
Score = 28.1 bits (63), Expect = 3.0
Identities = 20/72 (27%), Positives = 28/72 (38%), Gaps = 12/72 (16%)
Query: 16 YESAGNYEKAATCYIQLK-----NWTKIGQLLPHIKSATTFIQYA-------KAKEAMGS 63
YE+A ++KA L W K QL A + + K EA+ S
Sbjct: 211 YETAKLFQKADDSLSSLDPEYSGKWRKYLQLKSVFYLAYAYCYHGETLLAKDKCGEAIRS 270
Query: 64 YRESVGAYERAE 75
+ES Y +AE
Sbjct: 271 LQESEKLYNKAE 282
>gnl|CDD|183292 PRK11728, PRK11728, hydroxyglutarate oxidase; Provisional.
Length = 393
Score = 28.2 bits (64), Expect = 3.2
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 99 KAKKCTEGAKRIADYCNKHG 118
KA+ C G + +C++HG
Sbjct: 63 KARFCRRGNEATKAFCDQHG 82
>gnl|CDD|222424 pfam13862, BCIP, p21-C-terminal region-binding protein. This
family of p21-binding proteins is important as a
modulator of p21 activity. The domain binds the
C-terminal region of p21 in a ternary complex with CDK2,
which results in inhibition of the kinase activity of
CDK2.
Length = 189
Score = 27.5 bits (62), Expect = 3.9
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 115 NKHGDFGAAIHFLILSKCYQDAFNLSQQHKK 145
K F H+LILSK Y++ + KK
Sbjct: 148 EKPYKFT---HYLILSKVYKENDPNKKAKKK 175
>gnl|CDD|227610 COG5290, COG5290, IkappaB kinase complex, IKAP component
[Transcription].
Length = 1243
Score = 28.0 bits (62), Expect = 4.3
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 37 KIGQLLPHIKSATTFIQYAKAKEAMGSYRESVGAYERAEDY 77
KI ++ I AKA E G Y E+ GAY+ A +
Sbjct: 924 KINIFAGNLVDNLYHISAAKAYEVEGKYIEAHGAYDSALMW 964
>gnl|CDD|222086 pfam13378, MR_MLE_C, Enolase C-terminal domain-like. This domain
appears at the C-terminus of many of the proteins that
carry the MR_MLE, pfam01188 and MR_MLE_N pfam02746
domains. EC:4.2.1.40.
Length = 111
Score = 26.8 bits (60), Expect = 4.3
Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 6/32 (18%)
Query: 92 RHAVDIV--KAKKC---TEGAKRIADYCNKHG 118
AVDI+ + TE A +IA G
Sbjct: 16 AGAVDIIQPDVTRVGGITE-ALKIAALAEAFG 46
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 27.4 bits (61), Expect = 4.7
Identities = 15/41 (36%), Positives = 19/41 (46%)
Query: 128 ILSKCYQDAFNLSQQHKKLHEFGKFLLEEDEPNPVELKRLA 168
I S+C Q A L + L + L E DE +EL LA
Sbjct: 153 IKSRCQQQACPLPSNEESLQWLQQALPESDERERIELLTLA 193
>gnl|CDD|234114 TIGR03121, one_C_dehyd_A, formylmethanofuran dehydrogenase subunit
A. Members of this largely archaeal protein family are
subunit A of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit A. Note
that this model does not distinguish tungsten (FwdA)
from molybdenum-containing (FmdA) forms of this enzyme;
a single gene from this family is expressed
constitutively in Methanobacterium thermoautotrophicum,
which has both tungsten and molybdenum forms and may
work interchangeably.
Length = 556
Score = 27.7 bits (62), Expect = 4.8
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 62 GSYRESVGAYERAEDYDNVVRVDLDHLNDIR-HAVDIVKAKKCTEGAKRIADYCNKH 117
G+Y ++ + AE L HL ++ H+ + GA++IADY N +
Sbjct: 242 GNYETTLDTLDAAEGVKPNRNQVL-HLTHVQFHSYGGTSWRDFESGAEKIADYVNAN 297
>gnl|CDD|240391 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 27.6 bits (62), Expect = 4.9
Identities = 13/64 (20%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 108 KRIADYCNKHGDFGAAIHFLILS-KCYQDAFNLSQQHKKLHEFGKFLLEEDEPNPVELKR 166
+ I +C + G ++++ + YQ+ N+ K F K LLE +++
Sbjct: 241 EEIIKFCYEKG-------IVLMADEVYQE--NIYDGEKPFISFRKVLLELPAEYNTDVEL 291
Query: 167 LAIH 170
++ H
Sbjct: 292 VSFH 295
>gnl|CDD|201261 pfam00489, IL6, Interleukin-6/G-CSF/MGF family.
Length = 154
Score = 26.6 bits (59), Expect = 5.6
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 10/42 (23%)
Query: 129 LSKCYQDAFN----LSQQHKKLHEFGKFL------LEEDEPN 160
L C+Q FN L+Q L E+ +L ++ N
Sbjct: 42 LDGCFQSGFNQETCLTQITTGLLEYQGYLQALQNIYPGNKEN 83
>gnl|CDD|239121 cd02656, MIT, MIT: domain contained within Microtubule
Interacting and Trafficking molecules. The MIT domain
is found in sorting nexins, the nuclear thiol protease
PalBH, the AAA protein spastin and archaebacterial
proteins with similar domain architecture, vacuolar
sorting proteins and others. The molecular function of
the MIT domain is unclear.
Length = 75
Score = 25.3 bits (56), Expect = 6.6
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 43 PHIKSATTFIQYAKAKEAMGSYRESVGAYERAEDY 77
++ A I+ A ++ G+Y E++ Y+ A DY
Sbjct: 1 ELLQQAKELIKQAVKEDEDGNYEEALELYKEALDY 35
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 24.5 bits (54), Expect = 7.0
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 15 LYESAGNYEKAATCYIQL 32
LY G+YEKA + Y +
Sbjct: 8 LYRKLGDYEKAISLYERA 25
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
0.319 0.134 0.411
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,970,180
Number of extensions: 919758
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 888
Number of HSP's successfully gapped: 41
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)