RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy610
(128 letters)
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 41.1 bits (97), Expect = 1e-05
Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 51 AKPGTFFARDNVSNFIGWSRRGLGVFECLLFETDDLIMRKNEKHVILCLLEII 103
F +N++ + ++ + LGV + F+ +DL+ +EK V+ L +I
Sbjct: 53 NPLSRFKRLENINLALNFAEK-LGVPV-VNFDAEDLVEDGDEKLVLGLLWSLI 103
>gnl|CDD|227526 COG5199, SCP1, Calponin [Cytoskeleton].
Length = 178
Score = 39.9 bits (93), Expect = 7e-05
Identities = 27/107 (25%), Positives = 47/107 (43%), Gaps = 14/107 (13%)
Query: 2 CPLFFCPQHANNVRRYAEEHMAKRQAQGKDVHSIAISVLNLPPVKHLPGAKPGT------ 55
CP + V + E + ++ D+ S+ + L + L A P
Sbjct: 8 CP--GMDKQQKEVTLWIETVLGEKFEPPGDLLSLLKDGVRL--CRILNEASPLDIKYKES 63
Query: 56 ---FFARDNVSNFIGWSRRGLGVFECLLFETDDLIMRKNEKHVILCL 99
F +N+S+FI ++ L V E LF+T+DL K+ + V++CL
Sbjct: 64 KMPFVQMENISSFINGLKK-LRVPEYELFQTNDLFEAKDLRQVVICL 109
>gnl|CDD|215849 pfam00307, CH, Calponin homology (CH) domain. The CH domain is
found in both cytoskeletal proteins and signal
transduction proteins. The CH domain is involved in
actin binding in some members of the family. However in
calponins there is evidence that the CH domain is not
involved in its actin binding activity. Most member
proteins have from two to four copies of the CH domain,
however some proteins such as calponin have only a
single copy.
Length = 104
Score = 35.7 bits (83), Expect = 0.001
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 52 KPGTFFARDNVSNFIGWSRRGLGVFECLLFETDDLIMRKNEKHVILCLLEII 103
F +N++ + ++ + LGV + E +DL+ NEK V+ L ++
Sbjct: 51 NKNRFDKLENLNLALEFAEKKLGV--PKVLEPEDLVEDGNEKLVLTLLAQLF 100
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 31.1 bits (71), Expect = 0.049
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 46 KHLPGAKPGTFFARDNVSNFIGWSRRGLGVFECLLFETDDLI-MRKNEKHVILCL 99
K A F +N++ + ++ + G LFE +DL+ K VI L
Sbjct: 46 KKKVAASLSRFKKIENINLALSFAEKLGGKVV--LFEPEDLVEGPKLILGVIWTL 98
>gnl|CDD|241326 cd13172, RanBD2_RanBP2_insect-like, Ran-binding protein 2, Ran
binding domain repeat 2. RanBP2 (also called E3
SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and
nuclear pore complex (NPC) protein Nup358) is a giant
nucleoporin that localizes to the cytosolic face of the
NPC. RanBP2 contains a leucine-rich region, 8
zinc-finger motifs, a cyclophilin A homologous domain,
and 4 RanBDs. Ran is a Ras-like nuclear small GTPase,
which regulates receptor-mediated transport between the
nucleus and the cytoplasm. RanGTP hydrolysis is
stimulated by RanGAP together with the Ran-binding
domain containing acessory proteins RanBP1 and RanBP2.
These accessory proteins stabilize the active GTP-bound
form of Ran. All eukaryotic cells contain RanBP1, but in
vertebrates however, the main RanBP seems to be RanBP2.
There is no RanBP2 ortholog in yeast. Transport complex
disassembly is accomplished by a small ubiquitin-related
modifier-1 (SUMO-1)-modified version of RanGAP that is
bound to RanBP2. RanBP1 acts as a second line of defense
against exported RanGTP-importin complexes which have
escaped from dissociation by RanBP2. RanBP2 also
interacts with the importin subunit beta-1. RabBD shares
structural similarity to the PH domain, but lacks
detectable sequence similarity. The members here include
insects and nematodes. The second RanBD is present in
this hierarchy.
Length = 113
Score = 29.7 bits (67), Expect = 0.21
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 68 WSRRGLGVFECLLFETDD----LIMRKNEKHVILCLLEIISGEKFEISKTPPKKL 118
W RGLG + L + D+ L+MR+ + + C + +F+ PK L
Sbjct: 21 WKERGLGNIKLLRNKEDNNKVRLLMRREQVLKVCCNQRLTKDMEFKYLTNNPKAL 75
>gnl|CDD|241342 cd13188, FERM_C_PTPN14_PTPN21, Protein tyrosine phosphatase
non-receptor proteins 14 and 21 (PTPN14 and 21) FERM
domain. This CD contains PTP members: pez/PTPN14 and
PTPN21. A number of mutations in Pez have been shown to
be associated with breast and colorectal cancer. The
PTPN protein family belong to larger family of PTPs.
PTPs are known to be signaling molecules that regulate
a variety of cellular processes including cell growth,
differentiation, mitotic cycle, and oncogenic
transformation. The members are composed of a
N-terminal FERM domain and a C-terminal PTP catalytic
domain. The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. Like most other ERM members they have a
phosphoinositide-binding site in their FERM domain. The
FERM C domain is the third structural domain within the
FERM domain. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a
link between the membrane and cytoskeleton and are
involved in signal transduction pathways. The FERM
domain is also found in protein tyrosine phosphatases
(PTPs) , the tyrosine kinases FAK and JAK, in addition
to other proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 111
Score = 29.6 bits (67), Expect = 0.21
Identities = 21/80 (26%), Positives = 30/80 (37%), Gaps = 11/80 (13%)
Query: 17 YAEEHMAKRQAQGKDVHSIAISVLNLPPVKHLPGAKPGTFFARDNVSNFIGWSRRGLGVF 76
Y EE + QG D+ I S + VKH G P F D + I ++ V
Sbjct: 21 YGEESYPAKDNQGNDIF-IGASFEGI-FVKHKNGRPPVVFKWNDIGN--ISHNKSFFSV- 75
Query: 77 EC------LLFETDDLIMRK 90
E + F+ +D K
Sbjct: 76 ELINKEETIQFQMEDAETAK 95
>gnl|CDD|216678 pfam01750, HycI, Hydrogenase maturation protease. The family
consists of hydrogenase maturation proteases. In E. coli
HypI the hydrogenase maturation protease is involved in
processing of HypE the large subunit of hydrogenases 3,
by cleavage of its C-terminal.
Length = 128
Score = 27.2 bits (61), Expect = 1.5
Identities = 17/73 (23%), Positives = 29/73 (39%), Gaps = 12/73 (16%)
Query: 50 GAKPGT--FFARDNVSNFIGWSRRG---LGVFECL--LFETDDLIMRKNEKHVILCLLEI 102
G +PGT + V F+ + LG+ E L L E ++ K VIL ++
Sbjct: 48 GLEPGTVRILDVEEVPKFLKAKKMSAHQLGLQEVLRLLEELGEI-----PKEVILGGVQP 102
Query: 103 ISGEKFEISKTPP 115
+ E + +
Sbjct: 103 VILEDYGGELSEE 115
>gnl|CDD|235535 PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated.
Length = 284
Score = 27.4 bits (62), Expect = 1.8
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 12 NNVRRYAEEHMAKRQAQGKDVHSIAI 37
+N+ + E + + +AQGK+V I I
Sbjct: 92 SNIIKKVLELIKELEAQGKEVKLIVI 117
>gnl|CDD|223302 COG0224, AtpG, F0F1-type ATP synthase, gamma subunit [Energy
production and conversion].
Length = 287
Score = 27.6 bits (62), Expect = 1.9
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 6 FCPQHANNVRRYAEEHMAKRQAQGKDVHSIAI 37
C +N+ + E + + + +GK+V I I
Sbjct: 84 LCGGFNSNIFKKVENLIKELKNKGKEVKLILI 115
>gnl|CDD|233292 TIGR01146, ATPsyn_F1gamma, ATP synthase, F1 gamma subunit. This
model describes the ATP synthase gamma subunit in
bacteria and its equivalents in organelles, namely,
mitochondria and chloroplast. F1/F0-ATP synthase is a
multisubunit, membrane associated enzyme found in
bacteria and organelles of higher eukaryotes, namely,
mitochondria and chloroplast. This enzyme is principally
involed in the synthesis of ATP from ADP and inorganic
phosphate by coupling the energy derived from the proton
electrochemical gradient across the biological membrane.
A brief description of this multisubunit enzyme complex:
F1 and F0 represent two major clusters of subunits. The
gamma subunit is the part of F1 cluster. Surrounding the
gamma subunit in a cylinder-like structure are three
alpha and three subunits in an alternating fashion. This
is the central catalytic unit whose different
conformations permit the binding of ADP and inorganic
phosphate and release of ATP [Energy metabolism,
ATP-proton motive force interconversion].
Length = 286
Score = 26.9 bits (60), Expect = 3.0
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 14/68 (20%)
Query: 7 CPQHANNVRRYAEEHMAKRQAQGKDVHSIAISVLNLPPVKHLPGAKPGTFFARDNVSNFI 66
C + +NV + + +A GK+V + I G K +FF R N +
Sbjct: 87 CGGYNSNVLKRVRARAKELKAAGKEVKLVVI------------GRKGRSFFKRRG-DNIV 133
Query: 67 GWSRRGLG 74
S GL
Sbjct: 134 A-SVTGLS 140
>gnl|CDD|215808 pfam00231, ATP-synt, ATP synthase.
Length = 288
Score = 26.8 bits (60), Expect = 3.6
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 13/57 (22%)
Query: 12 NNVRRYAEEHMAKRQAQGKDVHSIAISVLNLPPVKHLPGAKPGTFFARDNVSNFIGW 68
+NV + A E + + +A+GK+V I I G K FF R N I
Sbjct: 93 SNVIKAALELIKELKAEGKEVDLIVI------------GKKGRDFFKRRGK-NIIAE 136
>gnl|CDD|223752 COG0680, HyaD, Ni,Fe-hydrogenase maturation factor [Energy
production and conversion].
Length = 160
Score = 26.5 bits (59), Expect = 3.7
Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 8/73 (10%)
Query: 48 LPGAKPGTF--FARDNVSNFIGWSRRG---LGVFECLLFETDDLIMRKNEKHVILCLLEI 102
L G +PG + + + S+ L + E LL +L ++ + I
Sbjct: 66 LFGLEPGEVRIIDPEEIPAYSSASKDSAHELPLSE-LLALLKELG--GLPVLILGVQVPI 122
Query: 103 ISGEKFEISKTPP 115
+S +F +P
Sbjct: 123 VSLPEFGGGLSPE 135
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 26.8 bits (59), Expect = 4.0
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 60 DNVSNFIGWSRRGLGVFECLLFETDDLIMRKNEKHVILCLLEIIS 104
DN++ F+ +G+ E FE DL +KN VI C+ +IS
Sbjct: 103 DNINAFLDLIEH-VGLPESFHFELQDLYEKKNIPKVIYCIHALIS 146
>gnl|CDD|220422 pfam09818, ABC_ATPase, Predicted ATPase of the ABC class. Members
of this family include various bacterial predicted ABC
class ATPases.
Length = 447
Score = 26.0 bits (58), Expect = 7.7
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 29 GKDVHSIAISVLNLPPVKHLPGAKPGTFFARDNVS 63
G+ VH + IS P + +LP K T F+ ++ S
Sbjct: 293 GRSVHGVDIS----PFINNLPPGKDTTDFSTEDAS 323
>gnl|CDD|226459 COG3950, COG3950, Predicted ATP-binding protein involved in
virulence [General function prediction only].
Length = 440
Score = 25.7 bits (56), Expect = 8.0
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 3/49 (6%)
Query: 76 FECLLFETDD---LIMRKNEKHVILCLLEIISGEKFEISKTPPKKLNTY 121
F+ L E DD IM ++ V + ++E + +K T K
Sbjct: 60 FKSLKIELDDIELCIMSQSNPTVAVAVVEYENDKKRTWVLTKNKNKELD 108
>gnl|CDD|180749 PRK06920, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1107
Score = 25.9 bits (57), Expect = 8.3
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 88 MRKNEKHVILCLLEIISGEKFEISKTPPKKLNTYTILPS 126
+ +++ V CLL + SG K P K + Y + S
Sbjct: 196 INQSDALVHECLLSVESGTKMTDPDRPRLKTDQYYLKSS 234
>gnl|CDD|227760 COG5473, COG5473, Predicted integral membrane protein [Function
unknown].
Length = 290
Score = 25.5 bits (56), Expect = 9.0
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 51 AKPGTF--FARDNVSNFIGWSRRGLGVFECLLF 81
A P T F R ++ +GW+ LG ++F
Sbjct: 167 APPVTISTFFRLVLTTGLGWALIFLGNLIGVVF 199
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
0.324 0.140 0.434
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,561,571
Number of extensions: 575576
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 24
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)