RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13905
(248 letters)
>gnl|CDD|216424 pfam01302, CAP_GLY, CAP-Gly domain. Cytoskeleton-associated
proteins (CAPs) are involved in the organisation of
microtubules and transportation of vesicles and
organelles along the cytoskeletal network. A conserved
motif, CAP-Gly, has been identified in a number of CAPs,
including CLIP-170 and dynactins. The crystal structure
of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain
was recently solved. The domain contains three
beta-strands. The most conserved sequence, GKNDG, is
located in two consecutive sharp turns on the surface,
forming the entrance to a groove.
Length = 67
Score = 108 bits (273), Expect = 7e-31
Identities = 34/68 (50%), Positives = 47/68 (69%), Gaps = 1/68 (1%)
Query: 165 VGKRCKINDSDVRFGTVMFVGETKFSSGVWVGVKLDEPFGKNNGTVKDVKYFECEENYGM 224
VG R ++ R GTV +VG F+ G+WVGV+LDEP GKN+G+V V+YFEC YG+
Sbjct: 1 VGDRVEVLGGG-RRGTVRYVGPVPFAPGLWVGVELDEPRGKNDGSVDGVRYFECPPKYGI 59
Query: 225 FVKPGRLT 232
FV+P ++
Sbjct: 60 FVRPSKVE 67
>gnl|CDD|214997 smart01052, CAP_GLY, Cytoskeleton-associated proteins (CAPs) are
involved in the organisation of microtubules and
transportation of vesicles and organelles along the
cytoskeletal network. A conserved motif, CAP-Gly, has
been identified in a number of CAPs, including CLIP-170
and dynactins. The crystal structure of Caenorhabditis
elegans F53F4.3 protein CAP-Gly domain was recently
solved. The domain contains three beta-strands. The most
conserved sequence, GKNDG, is located in two consecutive
sharp turns on the surface, forming the entrance to a
groove.
Length = 68
Score = 101 bits (253), Expect = 7e-28
Identities = 36/69 (52%), Positives = 49/69 (71%), Gaps = 2/69 (2%)
Query: 165 VGKRCKINDSDVRFGTVMFVGETKFSSGVWVGVKLDEP-FGKNNGTVKDVKYFECEENYG 223
VG R ++ R GTV +VG T F+ GVWVGV+LDEP GKN+G+VK V+YFEC +G
Sbjct: 1 VGDRVEVGGGGRR-GTVRYVGPTPFAPGVWVGVELDEPLRGKNDGSVKGVRYFECPPKHG 59
Query: 224 MFVKPGRLT 232
+FV+P ++
Sbjct: 60 IFVRPSKVE 68
>gnl|CDD|227569 COG5244, NIP100, Dynactin complex subunit involved in mitotic
spindle partitioning in anaphase B [Cell division and
chromosome partitioning].
Length = 669
Score = 68.6 bits (167), Expect = 3e-13
Identities = 30/66 (45%), Positives = 49/66 (74%), Gaps = 3/66 (4%)
Query: 163 IEVGKRCKINDSDVRFGTVMFVGETKFSSGVWVGVKLDEPFGKNNGTVKDVKYFECEENY 222
+ V R + D +FGTV F+G+TKF G+W+G++LD+P GKN+G+V V+YF C++ +
Sbjct: 4 LSVNDRVLLGD---KFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRH 60
Query: 223 GMFVKP 228
G+F++P
Sbjct: 61 GIFIRP 66
>gnl|CDD|176384 cd01789, Alp11_N, Ubiquitin-like domain of Alp11 tubulin-folding
cofactor B. Alp11, also known as tubulin-folding
cofactor B, is one of at least three proteins required
for the proper folding of tubulins prior to their
incorporation into microtubules. These cofactors are
necessary for the biogenesis of microtubules and for
cell viability. Alp11 has three domains including an
N-terminal ubiquitin-like domain (represented by this
CD) which executes the essential function, a central
coiled-coil domain necessary for maintenance of
cellular alpha-tubulin levels, and a C-terminal
CLIP-170 domain is required for efficient binding to
alpha-tubulin.
Length = 84
Score = 54.7 bits (132), Expect = 4e-10
Identities = 33/81 (40%), Positives = 47/81 (58%), Gaps = 3/81 (3%)
Query: 16 TVELYITNSKDKHESCLNLKKLKLNNTIGELKQKLELLTGQMSSNMTISLYNRNHDLVSH 75
TV + IT+S D KK TI ELK+KLEL+ G +S+M + L++ + LVS
Sbjct: 1 TVTVNITSSADSFSF---EKKYSRGLTIAELKKKLELVVGTPASSMRLQLFDGDDKLVSK 57
Query: 76 LSDNSMLLGQYPVENEMTLFV 96
L D+ LLG YPV++ + V
Sbjct: 58 LDDDDALLGSYPVDDGCRIHV 78
>gnl|CDD|216447 pfam01346, FKBP_N, Domain amino terminal to FKBP-type
peptidyl-prolyl isomerase. This family is only found at
the amino terminus of pfam00254. This domain is of
unknown function.
Length = 124
Score = 28.7 bits (65), Expect = 1.4
Identities = 14/67 (20%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 92 MTLFVEGNYLTDGLESSETKYVLPEEKYKEHKENLKNFMMKQKEERLRREALLKENNEEK 151
++G L D L E K L +E+ ++ + + + +++ + ++A +EN
Sbjct: 47 KDALLQG--LQDALAGKELK--LTDEEIQKALQAFQKKLQAKQQAKAEKKA--EENKAAG 100
Query: 152 DKCLEEN 158
+ L EN
Sbjct: 101 EAFLAEN 107
>gnl|CDD|223950 COG1019, COG1019, Predicted nucleotidyltransferase [General
function prediction only].
Length = 158
Score = 28.8 bits (65), Expect = 1.5
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 98 GNYLTDGLESSE---TKYVLPEEKYKEHKENLKNFMMKQKEER 137
G+ +T GL S E K E Y+ NL+NF+ K +
Sbjct: 32 GDRVTIGLTSDELAKKKKKEKIEPYEVRLRNLRNFLESIKADY 74
>gnl|CDD|166227 PLN02586, PLN02586, probable cinnamyl alcohol dehydrogenase.
Length = 360
Score = 29.5 bits (66), Expect = 1.7
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 144 LKENNEEKDKCLEENILKDIEVGKRCKIN-------DSDVRFGTVMFVGET 187
+KE E D C + NI DIE+ + +IN SDVR+ V+ V +
Sbjct: 306 IKETQEMLDFCAKHNITADIELIRMDEINTAMERLAKSDVRYRFVIDVANS 356
>gnl|CDD|237147 PRK12586, PRK12586, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 145
Score = 27.8 bits (62), Expect = 3.2
Identities = 8/43 (18%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 98 GNYLTDGLESSETKYVLPEEKYKEHKENLKNFMMKQKEERLRR 140
G Y+ ++ +L + E L+ K++EE ++
Sbjct: 99 GAYMYRKNDAHTHASILLSSNEQNSTEALQL-RAKKREEHRKK 140
>gnl|CDD|227807 COG5520, COG5520, O-Glycosyl hydrolase [Cell envelope biogenesis,
outer membrane].
Length = 433
Score = 28.3 bits (63), Expect = 4.3
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 182 MFVGETKFSSGVWVGVKLDEPFGKNNGTVKDVKYFECEENYGMFVKPG 229
M G F + VW ++LD G N+G Y C ++ FV+ G
Sbjct: 296 MTEGG--FQAYVWWNIRLDYGGGPNHGGNSKRGY--CMAHFSKFVQNG 339
>gnl|CDD|201540 pfam00992, Troponin, Troponin. Troponin (Tn) contains three
subunits, Ca2+ binding (TnC), inhibitory (TnI), and
tropomyosin binding (TnT). this Pfam contains members of
the TnT subunit. Troponin is a complex of three
proteins, Ca2+ binding (TnC), inhibitory (TnI), and
tropomyosin binding (TnT). The troponin complex
regulates Ca++ induced muscle contraction. This family
includes troponin T and troponin I. Troponin I binds to
actin and troponin T binds to tropomyosin.
Length = 131
Score = 27.1 bits (61), Expect = 4.5
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 123 KENLKNFMMKQKEERLRREALLKENNEEKDKCLEENI 159
K +LK+ ++ + E L E KE EEK+K L E
Sbjct: 1 KRHLKSLLLLKAAEELEFEQRKKE--EEKEKYLAERC 35
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 27.0 bits (61), Expect = 5.5
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 123 KENLKNFMMKQKEERLRREALLKENNEEKDKCLEENILKDIEVGKRCKINDSDVRFGTV 181
K NLK ++ E + L E +K L+ + V + K + FG+V
Sbjct: 41 KGNLKQLEARRAELEAKAAEELAEAEALAEK------LEGLTVTIKAKAGEDGKLFGSV 93
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 27.7 bits (61), Expect = 5.7
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 144 LKENNEEKDKCLEENILKDIEVGKRCKIND-------SDVRFGTVMFVGET 187
+KE E + C + I+ DIE+ K IN SDVR+ V+ V +
Sbjct: 301 MKETQEMLEFCAKHKIVSDIELIKMSDINSAMDRLAKSDVRYRFVIDVANS 351
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.0 bits (63), Expect = 5.9
Identities = 13/26 (50%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 115 PEEKYKEHKENLKNFMMKQKEERLRR 140
EE KE E LK K + ERLRR
Sbjct: 260 EEELAKEEAERLK----KLEAERLRR 281
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. 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
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 27.5 bits (61), Expect = 6.7
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 115 PEEKYKEHKENLKNFMMKQKEERLRREALLK 145
PEE+ K K +LK ++ Q EE LR AL +
Sbjct: 290 PEERRKLGKAHLKRAILGQ-EEALRLHALCR 319
>gnl|CDD|184695 PRK14471, PRK14471, F0F1 ATP synthase subunit B; Provisional.
Length = 164
Score = 26.7 bits (59), Expect = 8.1
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 106 ESSETKYVLPEEKYKEHKENLKNFMMK-QKEERLRREALLKENNEEKDKCLEE 157
E S + E+ ++ +NL+ + KE R R+A+LKE E K+K + +
Sbjct: 41 EDSIKNALASAEEARKEMQNLQADNERLLKEARAERDAILKEAREIKEKMIAD 93
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 27.3 bits (60), Expect = 8.9
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 116 EEKYKEHKENLKNFMMKQKEERLRREALLKENNEEKDKCLEE 157
EE+ E E + +KE + + E +EEK K EE
Sbjct: 242 EEEEFELDEEHEEAEEDKKEALEK---IGAEGDEEKFKFDEE 280
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 0.135 0.382
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,514,846
Number of extensions: 1172566
Number of successful extensions: 1194
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1181
Number of HSP's successfully gapped: 83
Length of query: 248
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 154
Effective length of database: 6,768,326
Effective search space: 1042322204
Effective search space used: 1042322204
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 (21.9 bits)
S2: 58 (26.0 bits)