RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7550
(144 letters)
>gnl|CDD|214518 smart00105, ArfGap, Putative GTP-ase activating proteins for the
small GTPase, ARF. Putative zinc fingers with GTPase
activating proteins (GAPs) towards the small GTPase,
Arf. The GAP of ARD1 stimulates GTPase hydrolysis for
ARD1 but not ARFs.
Length = 119
Score = 148 bits (376), Expect = 2e-47
Identities = 59/111 (53%), Positives = 70/111 (63%), Gaps = 7/111 (6%)
Query: 15 FKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNWT 74
K LR+IP NK+CFDC A NPTW+SV GVF+CI+CS +HR LGVH+S VRS LD WT
Sbjct: 1 LKLLRSIPGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLD-TWT 59
Query: 75 WVQLRQMQLGGNANAVSFFNQHNC------TSKDAQQKYNSRAAQLYREKL 119
+LR +Q GGN NA S + + D QQKY S A Y EKL
Sbjct: 60 EEELRLLQKGGNENANSIWESNLDDFSLKPPDDDDQQKYESFIAAKYEEKL 110
>gnl|CDD|216485 pfam01412, ArfGap, Putative GTPase activating protein for Arf.
Putative zinc fingers with GTPase activating proteins
(GAPs) towards the small GTPase, Arf. The GAP of ARD1
stimulates GTPase hydrolysis for ARD1 but not ARFs.
Length = 117
Score = 145 bits (367), Expect = 6e-46
Identities = 51/111 (45%), Positives = 64/111 (57%), Gaps = 6/111 (5%)
Query: 14 IFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDTNW 73
+ ++LR +P NK C DC A NPTW+S+ G+FICI CS VHR LGVH+S VRS LD W
Sbjct: 3 LLRELRKLPGNKVCADCGAPNPTWASLNLGIFICIRCSGVHRSLGVHISKVRSLTLDK-W 61
Query: 74 TWVQLRQMQLGGNANAVSFFNQHNC-----TSKDAQQKYNSRAAQLYREKL 119
T QL M+ GGN A F+ + S ++K S Y EKL
Sbjct: 62 TPEQLEFMKAGGNKRANEFWEANLPPPKPPPSSSDREKRESFIRAKYVEKL 112
>gnl|CDD|227651 COG5347, COG5347, GTPase-activating protein that regulates ARFs
(ADP-ribosylation factors), involved in ARF-mediated
vesicular transport [Intracellular trafficking and
secretion].
Length = 319
Score = 139 bits (351), Expect = 3e-41
Identities = 52/114 (45%), Positives = 75/114 (65%), Gaps = 3/114 (2%)
Query: 8 KNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRST 67
K++ + K L++ +NK+C DC A NPTW+SV GVF+CIDC+ VHR LGVH+S V+S
Sbjct: 4 KSEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSL 63
Query: 68 QLDTNWTWVQLRQMQLGGNANAVSFFNQHN--CTSKDAQQKYNSRAAQLYREKL 119
LD NWT +LR+M++GGN+NA F+ ++ + KY+S A+ Y K
Sbjct: 64 TLD-NWTEEELRRMEVGGNSNANRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKK 116
>gnl|CDD|178661 PLN03114, PLN03114, ADP-ribosylation factor GTPase-activating
protein AGD10; Provisional.
Length = 395
Score = 138 bits (349), Expect = 2e-40
Identities = 67/114 (58%), Positives = 81/114 (71%), Gaps = 2/114 (1%)
Query: 7 NKNDIEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRS 66
N ND +FKKL+ NK CFDCNAKNPTW+SVTYG+F+CIDCSAVHR LGVH+SFVRS
Sbjct: 5 NLNDKISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRS 64
Query: 67 TQLDTNWTWVQLRQMQLGGNANAVSFFNQHNCTS-KDAQQKYNSRAAQLYREKL 119
T LD+ W+ QL+ M GGN A FF Q+ + + KY SRAA LY++ L
Sbjct: 65 TNLDS-WSSEQLKMMIYGGNNRAQVFFKQYGWSDGGKTEAKYTSRAADLYKQIL 117
>gnl|CDD|178666 PLN03119, PLN03119, putative ADP-ribosylation factor
GTPase-activating protein AGD14; Provisional.
Length = 648
Score = 50.2 bits (119), Expect = 4e-08
Identities = 33/114 (28%), Positives = 59/114 (51%), Gaps = 6/114 (5%)
Query: 12 EVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDT 71
E I + L +P N+ C +CN+ P + T+ F+C+ CS +HR H V+S + +
Sbjct: 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREF-THR--VKSVSM-S 66
Query: 72 NWTWVQLRQMQLGGNANAVSFFNQHNCTSKDAQQKYNSRAAQLYREKLQHAAVQ 125
+T ++ +Q GGN A + + N + + NS A ++ RE +++ VQ
Sbjct: 67 KFTSKEVEVLQNGGNQRAREIYLK-NWDHQRQRLPENSNAERV-REFIKNVYVQ 118
>gnl|CDD|178677 PLN03131, PLN03131, hypothetical protein; Provisional.
Length = 705
Score = 47.9 bits (113), Expect = 3e-07
Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 12 EVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSAVHRGLGVHLSFVRSTQLDT 71
E I + L +P N+ C +CN+ P + + FIC+ CS +HR H V+S + +
Sbjct: 11 EKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREF-THR--VKSVSM-S 66
Query: 72 NWTWVQLRQMQLGGNANA 89
+T + +Q GGN A
Sbjct: 67 KFTSQDVEALQNGGNQRA 84
>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
Length = 448
Score = 29.5 bits (67), Expect = 0.49
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 4 EGPNKNDIEVIFKKLRNIPT 23
E NKN IE+I K RN P
Sbjct: 406 ETENKNTIEIIIAKQRNGPV 425
>gnl|CDD|224034 COG1109, {ManB}, Phosphomannomutase [Carbohydrate transport and
metabolism].
Length = 464
Score = 29.2 bits (66), Expect = 0.65
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 106 KYNSRAAQLYREKLQHAAVQAMKIHGTKLFLDAMHG 141
K A Y E ++ +K+ G K+ +D +G
Sbjct: 153 KRIPDALDRYIEFIKSLVDVDLKLRGLKVVVDCANG 188
>gnl|CDD|173065 PRK14601, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 183
Score = 28.3 bits (63), Expect = 1.3
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 16 KKLRNIPTNKECFDCNAKNPTWSSVTYGVFICIDCSA-VHRGLGVHLSFVRSTQLDTN 72
+ I T KE K T S V+YG+FI + CSA + +G L + + D+N
Sbjct: 3 VAIEGIITKKEPTFIVLK--TASGVSYGIFISLFCSAKIQKGEKHELFITQIIKEDSN 58
>gnl|CDD|221443 pfam12150, MFP2b, Cytosolic motility protein. This domain family
is found in eukaryotes, and is approximately 50 amino
acids in length. These proteins are found in nematodes.
They complex with MSP (major sperm protein) to allow
motility. Their action is quite similar to the action of
bacterial actin molecules.
Length = 362
Score = 26.9 bits (59), Expect = 4.1
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 9/49 (18%)
Query: 4 EGPNKNDIEVIFKKLRNIPTNKECFDCNAKNPT---------WSSVTYG 43
G ++ +IF+ L+ P EC +C ++ P W+ G
Sbjct: 151 SGSALANMLIIFRNLKGGPPYCECEECKSEPPKPIVRVTLDEWADFRCG 199
>gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4.
Glycoside hydrolases cleave glycosidic bonds to release
smaller sugars from oligo- or polysaccharides. Some
bacteria simultaneously translocate and phosphorylate
disaccharides via the phosphoenolpyruvate-dependent
phosphotransferase system (PEP-PTS). After
translocation, these phospho-disaccharides may be
hydrolyzed by GH4 glycoside hydrolases. Other organisms
(such as archaea and Thermotoga maritima) lack the
PEP-PTS system, but have several enzymes normally
associated with the PEP-PTS operon. GH4 family members
include 6-phospho-beta-glucosidases,
6-phospho-alpha-glucosidases,
alpha-glucosidases/alpha-glucuronidases (only from
Thermotoga), and alpha-galactosidases. They require two
cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+),
for activity. Some also require reducing conditions. GH4
glycoside hydrolases are part of the NAD(P)-binding
Rossmann fold superfamily, which includes a wide variety
of protein families including the NAD(P)-binding domains
of alcohol dehydrogenases, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate
dehydrogenases, formate/glycerate dehydrogenases,
siroheme synthases, 6-phosphogluconate dehydrogenases,
aminoacid dehydrogenases, repressor rex, and NAD-binding
potassium channel domains, among others.
Length = 425
Score = 26.7 bits (59), Expect = 4.5
Identities = 7/39 (17%), Positives = 12/39 (30%)
Query: 11 IEVIFKKLRNIPTNKECFDCNAKNPTWSSVTYGVFICID 49
E + +K ++ T D + YGV
Sbjct: 215 DEWVEEKSKDWKTENPFVDQLSPAAIDFYRFYGVLPNPY 253
>gnl|CDD|147475 pfam05306, DUF733, Protein of unknown function (DUF733). This
family consists of several uncharacterized Drosophila
melanogaster proteins of unknown function.
Length = 89
Score = 25.3 bits (56), Expect = 6.5
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 114 LYREKLQHAAVQAMKIHGTKLFL 136
LYR++L+ + M++ TK+ L
Sbjct: 11 LYRQELRRRNAEYMRLSRTKIHL 33
>gnl|CDD|236754 PRK10760, PRK10760, murein hydrolase B; Provisional.
Length = 359
Score = 26.2 bits (58), Expect = 8.1
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 72 NWTWVQLR-QMQLGGN-ANAVSFFNQHNCTSKDAQQKY 107
N W++ R + N N V F+NQ+ A Q Y
Sbjct: 109 NGAWLRYRKKFITPDNVQNGVVFWNQYEDALNRAWQVY 146
>gnl|CDD|238582 cd01177, IPT_NFkappaB, IPT domain of the transcription factor
NFkappaB and related transcription factors. NFkappaB is
considered a central regulator of stress responses,
activated by different stressful conditions, including
physical stress, oxidative stress, and exposure to
certain chemicals. NFkappaB blocking cell apoptosis in
several cell types, gives it an important role in cell
proliferation and differentiation.
Length = 102
Score = 25.0 bits (55), Expect = 8.5
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 4 EGPNKNDIEVIFKKLRNIPTNKECF 28
+ K DI+V F + T E F
Sbjct: 24 DKVQKEDIQVRFFEEDEEETVWEAF 48
>gnl|CDD|176802 cd08968, MeNeil2_N, N-terminal domain of metazoan Nei-like
glycosylase 2 (NEIL2). This family contains the
N-terminal domain of the metazoan protein Neil2. It
belongs to the FpgNei_N, [N-terminal domain of Fpg
(formamidopyrimidine-DNA glycosylase, MutM)_Nei
(endonuclease VIII)] domain superfamily. DNA
glycosylases maintain genome integrity by recognizing
base lesions created by ionizing radiation, alkylating
or oxidizing agents, and endogenous reactive oxygen
species. They initiate the base-excision repair process,
which is completed with the help of enzymes such as
phosphodiesterases, AP endonucleases, DNA polymerases
and DNA ligases. DNA glycosylases cleave the N-glycosyl
bond between the sugar and the damaged base, creating an
AP (apurinic/apyrimidinic) site. Most FpgNei DNA
glycosylases use their N-terminal proline residue as the
key catalytic nucleophile, and the reaction proceeds via
a Schiff base intermediate. NEIL2 repairs
5-hydroxyuracil (5-OHU) and other oxidized derivatives
of cytosine, but it shows preference for DNA bubble
structures. In addition to this MeNeil2_N domain, NEIL2
contains a helix-two turn-helix (H2TH) domain and a
characteristic CHCC zinc finger motif. Neil2 is one of
three homologs found in eukaryotes.
Length = 126
Score = 25.5 bits (56), Expect = 8.8
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 114 LYREKLQHAAVQAMKIHGTKLFL 136
+ LQ +Q ++HG LFL
Sbjct: 32 INPNDLQGLRLQDSQVHGKNLFL 54
>gnl|CDD|204552 pfam10764, Gin, Inhibitor of sigma-G Gin. Gin allows sigma-F to
delay late forespore transcription by preventing
sigma-G to take over before the cell has reached a
critical stage of development. Gin is also known as
CsfB.
Length = 46
Score = 24.1 bits (53), Expect = 9.1
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 27 CFDCNAKNPTWSSVTYGVFICIDC 50
C C + YG FIC +C
Sbjct: 2 CIICEQPKNEGIHL-YGKFICTEC 24
>gnl|CDD|238657 cd01347, ligand_gated_channel, TonB dependent/Ligand-Gated channels
are created by a monomeric 22 strand (22,24)
anti-parallel beta-barrel. Ligands apparently bind to
the large extracellular loops. The N-terminal 150-200
residues form a plug from the periplasmic end of barrel.
Energy (proton-motive force) and TonB-dependent
conformational alteration of channel (parts of plug, and
loops 7 and 8) allow passage of ligand. FepA residues
12-18 form the TonB box, which mediates the interaction
with the TonB-containing inner membrane complex. TonB
preferentially interacts with ligand-bound receptors.
Transport thru the channel may resemble passage thru an
air lock. In this model, ligand binding leads to
closure of the extracellular end of pore, then a
TonB-mediated signal facillitates opening of the
interior side of pore, deforming the N-terminal plug and
allowing passage of the ligand to the periplasm. Such a
mechanism would prevent the free diffusion of small
molecules thru the pore.
Length = 635
Score = 25.9 bits (57), Expect = 9.3
Identities = 7/39 (17%), Positives = 11/39 (28%), Gaps = 2/39 (5%)
Query: 52 AVHRG--LGVHLSFVRSTQLDTNWTWVQLRQMQLGGNAN 88
A RG L L ++T+ + G
Sbjct: 486 ARIRGVELEASYDLTDGLGLTGSYTYTDTEVKRTDGATT 524
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
0.321 0.132 0.419
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,864,906
Number of extensions: 549001
Number of successful extensions: 463
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 18
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
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 (21.9 bits)
S2: 54 (24.6 bits)