RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5288
(186 letters)
>gnl|CDD|205602 pfam13424, TPR_12, Tetratricopeptide repeat.
Length = 78
Score = 30.8 bits (70), Expect = 0.080
Identities = 15/66 (22%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 86 AANCYKKSNPAEAIKAIERAVEIHTDMG-RFIMVAKHHENIAEIYEKELEDQEKAIDHYQ 144
A + + EA++ +E+A+E+ ++G A+ N+A +Y L D ++A+++ +
Sbjct: 12 ALVLRRLGDYDEALELLEKALELARELGEDHPETARALNNLARLYL-ALGDYDEALEYLE 70
Query: 145 HAADCY 150
A
Sbjct: 71 KALALR 76
>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 = 31.2 bits (71), Expect = 0.087
Identities = 26/100 (26%), Positives = 46/100 (46%), Gaps = 12/100 (12%)
Query: 47 GNLFKLGKKWNDGGNAFLQAGTLHLKNNNKHDAGLCFVDAANCYKKSNPAEAIKAIERAV 106
GNL+ +++ + +A L + +A + AA YK EA++ E+A+
Sbjct: 7 GNLYYKLGDYDEALEYYEKALEL-----DPDNADAYYNLAAAYYKLGKYEEALEDYEKAL 61
Query: 107 EIHTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDHYQHA 146
E+ D AK + N+ Y K L E+A++ Y+ A
Sbjct: 62 ELDPDN------AKAYYNLGLAYYK-LGKYEEALEAYEKA 94
>gnl|CDD|217149 pfam02621, VitK2_biosynth, Menaquinone biosynthesis. This family
includes two enzymes which are involved in menaquinone
biosynthesis. One which catalyzes the conversion of
cyclic de-hypoxanthine futalosine to
1,4-dihydroxy-6-naphthoate, and one which may be
involved in the conversion of chorismate to futalosine.
These enzymes comprise two domains with alpha/beta
structures, a large domain and a small domain. A pocket
between the two domains may form the active site, a
conserved histidine located within this pocket could be
the catalytic base.
Length = 248
Score = 32.1 bits (74), Expect = 0.10
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 80 GLCFVDAANCYKKSNPAEAIKAIERAVEIHTDMGRFIMVAKHHENIAEIYEKELEDQEKA 139
GL FV ++ E K +E A+ + KH E IAE + EK
Sbjct: 165 GLPFVFGLWVVRRDLGLELAKELEEALRKSKEYAL-----KHPEEIAEYAAERAGLDEKF 219
Query: 140 IDHY 143
I+ Y
Sbjct: 220 IELY 223
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 30.4 bits (69), Expect = 0.11
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 86 AANCYKKSNPAEAIKAIERAVEIHTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDHYQH 145
+K + EAI+A E+A+E+ D A+ + N+A Y K +D E+A++ +
Sbjct: 10 GNALFKLGDYDEAIEAYEKALELDPD------NAEAYYNLALAYLKLGKDYEEALEDLEK 63
Query: 146 A 146
A
Sbjct: 64 A 64
>gnl|CDD|185694 cd08024, GH16_CCF, Coelomic cytolytic factor, member of glycosyl
hydrolase family 16. Subgroup of glucanases of unknown
function that are related to beta-GRP (beta-1,3-glucan
recognition protein), but contain active site residues.
Beta-GRPs are one group of pattern recognition
receptors (PRRs), also referred to as biosensor
proteins, that complexes with pathogen-associated
beta-1,3-glucans and then transduces signals necessary
for activation of an appropriate innate immune
response. Beta-GRPs are present in insects and lack all
catalytic residues. This subgroup contains related
proteins that still contain the active site and are
widely distributed in eukaryotes. Their structures
adopt a jelly roll fold with a deep active site channel
harboring the catalytic residues, like those of other
glycosyl hydrolase family 16 members.
Length = 330
Score = 31.1 bits (71), Expect = 0.30
Identities = 23/78 (29%), Positives = 30/78 (38%), Gaps = 15/78 (19%)
Query: 32 GGNK-----TDEAIDLYVRAGNLF---KLGKKWNDGGNAFLQAGTLHLKNNNKHDAGLCF 83
GGN T++ + YVR G L+ L G FL G +L G C
Sbjct: 24 GGNGEFQWYTNDRSNSYVRDGKLYIKPTLTADTF--GEDFLTLGNGNLDGLA--PWGTC- 78
Query: 84 VDAAN--CYKKSNPAEAI 99
+ AN CY+ N I
Sbjct: 79 TNNANNGCYRTGNAGGII 96
>gnl|CDD|238525 cd01092, APP-like, Similar to Prolidase and Aminopeptidase P. The
members of this subfamily presumably catalyse hydrolysis
of Xaa-Pro dipeptides and/or release of any N-terminal
amino acid, including proline, that is linked with
proline.
Length = 208
Score = 29.8 bits (68), Expect = 0.54
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 109 HTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDH 142
+D+ R + V + + + EIYE LE Q+ AI
Sbjct: 89 CSDITRTVAVGEPSDELKEIYEIVLEAQQAAIKA 122
>gnl|CDD|181182 PRK07960, fliI, flagellum-specific ATP synthase; Validated.
Length = 455
Score = 30.1 bits (68), Expect = 0.59
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 160 NKCLIKIANYSALTD-HLDKAIKLYEQL 186
N+ L+ + Y+ +D LDKAI L+ QL
Sbjct: 401 NRDLVSVGAYAKGSDPMLDKAIALWPQL 428
>gnl|CDD|215993 pfam00557, Peptidase_M24, Metallopeptidase family M24. This family
contains metallopeptidases. It also contains
non-peptidase homologues such as the N terminal domain
of Spt16 which is a histone H3-H4 binding module.
Length = 208
Score = 28.4 bits (64), Expect = 1.6
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 109 HTDMGRFIMVAKHHENIAEIYEKELEDQEKAID 141
H+D+ R +V K E+YE LE QE AI
Sbjct: 89 HSDITRTFVVGKPTPEQRELYEAVLEAQEAAIA 121
>gnl|CDD|184463 PRK14030, PRK14030, glutamate dehydrogenase; Provisional.
Length = 445
Score = 27.9 bits (62), Expect = 3.2
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 36 TDEAIDLYVRAGNLFKLGKKWNDGGNA 62
T EAID ++ A LF GK N GG A
Sbjct: 349 TAEAIDKFIAAKQLFAPGKAVNAGGVA 375
>gnl|CDD|223085 COG0006, PepP, Xaa-Pro aminopeptidase [Amino acid transport and
metabolism].
Length = 384
Score = 27.8 bits (62), Expect = 3.8
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 109 HTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDH 142
+D+ R + K + EIYE LE QE AI
Sbjct: 248 CSDITRTFPIGKPSDEQREIYEAVLEAQEAAIAA 281
>gnl|CDD|221958 pfam13176, TPR_7, Tetratricopeptide repeat.
Length = 36
Score = 24.9 bits (55), Expect = 4.1
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 124 NIAEIYEKELEDQEKAIDHYQHAADCYAGEENK 156
N+ +Y K L D EKAI Y+ A E++
Sbjct: 4 NLGRLYRK-LGDYEKAISLYERALALAKDPEDR 35
>gnl|CDD|227497 COG5169, HSF1, Heat shock transcription factor [Transcription].
Length = 282
Score = 27.0 bits (60), Expect = 5.6
Identities = 8/46 (17%), Positives = 14/46 (30%)
Query: 132 ELEDQEKAIDHYQHAADCYAGEENKSSANKCLIKIANYSALTDHLD 177
EL K + Q GE + N + + + + D
Sbjct: 202 ELFGAYKEVAEPQSPTQHQRGEPGQRFHNSVVPLADSKNEVDQKGD 247
>gnl|CDD|215946 pfam00491, Arginase, Arginase family.
Length = 268
Score = 26.8 bits (60), Expect = 6.3
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 59 GGNAFLQAGT-LHLKNNNKHDAGLCFVDAANCYKKSNPAEAIKAIERAVEIHTDMGRFIM 117
G +A +A L L + GL VD + +P + ++ IE AV G+F +
Sbjct: 23 GPDAIREASANLELYELYELSLGLKVVDLGDVAVPPDPEDVLERIEEAVAAILAAGKFPL 82
Query: 118 V 118
V
Sbjct: 83 V 83
>gnl|CDD|172776 PRK14288, PRK14288, chaperone protein DnaJ; Provisional.
Length = 369
Score = 27.0 bits (59), Expect = 7.1
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 128 IYEKELEDQEKAIDHYQHAADCYAGEENKSSANKCLIKIANY 169
IY K L +++ + HA+ Y GE +KS C+ KI ++
Sbjct: 326 IYPKSLNKEQQELLEKLHASFGYEGEPHKSVLETCISKIKDW 367
>gnl|CDD|205256 pfam13075, DUF3939, Protein of unknown function (DUF3939). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 150 amino acids in length.
Length = 140
Score = 26.3 bits (58), Expect = 7.7
Identities = 14/30 (46%), Positives = 16/30 (53%)
Query: 127 EIYEKELEDQEKAIDHYQHAADCYAGEENK 156
EI+E+E D ID Q A D Y EE K
Sbjct: 67 EIFEEEERDLPYEIDIVQVAVDQYVDEEGK 96
>gnl|CDD|238514 cd01066, APP_MetAP, A family including aminopeptidase P,
aminopeptidase M, and prolidase. Also known as
metallopeptidase family M24. This family of enzymes is
able to cleave amido-, imido- and amidino-containing
bonds. Members exibit relatively narrow substrate
specificity compared to other metallo-aminopeptidases,
suggesting they play roles in regulation of biological
processes rather than general protein degradation.
Length = 207
Score = 26.6 bits (59), Expect = 7.7
Identities = 10/41 (24%), Positives = 18/41 (43%)
Query: 109 HTDMGRFIMVAKHHENIAEIYEKELEDQEKAIDHYQHAADC 149
H D+ R ++ + + E+YE E QE A+ +
Sbjct: 88 HADLTRTFVIGEPSDEQRELYEAVREAQEAALAALRPGVTA 128
>gnl|CDD|215959 pfam00508, PPV_E2_N, E2 (early) protein, N terminal.
Length = 201
Score = 26.3 bits (59), Expect = 7.9
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 123 ENIAEIYEKELEDQEKAIDHYQH 145
E + E+YEK+ D E I+H++
Sbjct: 12 EQLLELYEKDSTDLEDQIEHWKL 34
>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 = 26.9 bits (60), Expect = 8.1
Identities = 20/103 (19%), Positives = 39/103 (37%), Gaps = 9/103 (8%)
Query: 69 LHLKNNNKHDAGLCFVDAANCYKKSNPAEAIKAIERAVEIHTDMGRFIM---VAKHHENI 125
LH + N +A LC + A+ Y +KA+ A+ ++
Sbjct: 13 LHEERGNYVEAALCLLLHADLYAWD-----LKALVPALAESLSFPEQTSFERKEALYKKA 67
Query: 126 AEIYEKELEDQEKAIDHYQHAADCYAGEENKSSANKCLIKIAN 168
++++K + E AI Y+ Y + + ++ KIA
Sbjct: 68 IDLFDKG-KAWEFAIALYKELIPQYENNFDYAKLSEVHRKIAK 109
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 26.3 bits (59), Expect = 9.7
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 94 NPAEAIKAIERAVEIHTDMGRFIMVAKHHENIAEI---YE 130
N +EA + +RAV+I +M ++ A E + I YE
Sbjct: 111 NRSEARECFQRAVDITPEMAHELIKALRKEGVEYIVAPYE 150
>gnl|CDD|181834 PRK09414, PRK09414, glutamate dehydrogenase; Provisional.
Length = 445
Score = 26.6 bits (60), Expect = 9.8
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 36 TDEAIDLYVRAGNLFKLGKKWNDGGNA 62
T EAI++++ AG LF GK N GG A
Sbjct: 349 TPEAIEVFLEAGVLFAPGKAANAGGVA 375
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 0.129 0.370
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: 9,132,206
Number of extensions: 833930
Number of successful extensions: 900
Number of sequences better than 10.0: 1
Number of HSP's gapped: 887
Number of HSP's successfully gapped: 63
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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: 56 (25.3 bits)