RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2920
(325 letters)
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 62.4 bits (152), Expect = 1e-12
Identities = 29/82 (35%), Positives = 44/82 (53%), Gaps = 14/82 (17%)
Query: 28 VRYSITQGNDNHTFALKNPTTHEIRNSTESKSGVLLVTSGDIDREEVAQYSLVITATDVK 87
V YSI GND+ F++ + ++G + T+ +DREE +Y+L + ATD
Sbjct: 13 VTYSILSGNDDGLFSI------------DPETGEI-TTTKPLDREEQPEYTLTVEATDGG 59
Query: 88 GINK-AETHVTVDVLDENDNSP 108
G + VT+ VLD NDN+P
Sbjct: 60 GPPLSSTATVTITVLDVNDNAP 81
Score = 30.4 bits (69), Expect = 0.25
Identities = 26/68 (38%), Positives = 30/68 (44%), Gaps = 12/68 (17%)
Query: 143 SATDADGD---KVAYKLA--VPSNLVVIVPQTGELLLTGDPPSDDVE----YELTVEAHD 193
SATDAD KV Y + L I P+TGE+ T D E Y LTVEA D
Sbjct: 1 SATDADSGENGKVTYSILSGNDDGLFSIDPETGEITTTK---PLDREEQPEYTLTVEATD 57
Query: 194 LQSPSRYA 201
P +
Sbjct: 58 GGGPPLSS 65
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 61.6 bits (150), Expect = 3e-12
Identities = 37/107 (34%), Positives = 53/107 (49%), Gaps = 16/107 (14%)
Query: 1 MENSKSGTGVKGLPILVASSHKHPHQLVRYSITQGNDNHTFALKNPTTHEIRNSTESKSG 60
EN+ GT V L + + V YSI GN++ F++ +P+T EI
Sbjct: 7 PENAPPGTVV--LTVSATDPDSGENGEVTYSIVSGNEDGLFSI-DPSTGEIT-------- 55
Query: 61 VLLVTSGDIDREEVAQYSLVITATDVKGINK-AETHVTVDVLDENDN 106
T+ +DREE + Y+L +TATD G + VT+ VLD NDN
Sbjct: 56 ----TAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
Score = 40.8 bits (96), Expect = 7e-05
Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 8/72 (11%)
Query: 137 SSIGSVSATDADGD---KVAYKLA--VPSNLVVIVPQTGELLLTG--DPPSDDVEYELTV 189
+ + +VSATD D +V Y + L I P TGE+ D Y LTV
Sbjct: 14 TVVLTVSATDPDSGENGEVTYSIVSGNEDGLFSIDPSTGEITTAKPLDREEQS-SYTLTV 72
Query: 190 EAHDLQSPSRYA 201
A D P +
Sbjct: 73 TATDGGGPPLSS 84
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 45.0 bits (107), Expect = 2e-06
Identities = 28/104 (26%), Positives = 43/104 (41%), Gaps = 20/104 (19%)
Query: 1 MENSKSGTGVKGLPILVASSHKH--PHQLVRYSITQGNDNHTFALKNPTTHEIRNSTESK 58
EN+ GT + V ++ P+ + YSI G F + +
Sbjct: 6 PENAPVGT----EVLTVTATDADLGPNGRIFYSILGGGPGGWFRI------------DPD 49
Query: 59 SGVLLVTSGDIDREEVAQYSLVITATDVKGINK-AETHVTVDVL 101
+G L T +DRE + +Y L + ATD G + T VT+ VL
Sbjct: 50 TGDLSTT-KPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
Score = 36.1 bits (84), Expect = 0.003
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 137 SSIGSVSATDADGD---KVAYKLA--VPSNLVVIVPQTGELLLTG--DPPSDDVEYELTV 189
+ + +V+ATDAD ++ Y + P I P TG+L T D S EYELTV
Sbjct: 13 TEVLTVTATDADLGPNGRIFYSILGGGPGGWFRIDPDTGDLSTTKPLDRESIG-EYELTV 71
Query: 190 EAHDLQSPSRYAREPAQVWLQ 210
A D P + + +
Sbjct: 72 LATDSGGPPLSSTTTVTITVL 92
>gnl|CDD|214795 smart00736, CADG, Dystroglycan-type cadherin-like domains.
Cadherin-homologous domains present in metazoan
dystroglycans and alpha/epsilon sarcoglycans, yeast
Axl2p and in a very large protein from magnetotactic
bacteria. Likely to bind calcium ions.
Length = 97
Score = 33.5 bits (77), Expect = 0.024
Identities = 24/68 (35%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 138 SIGSVSATDADGDKVAYKL------AVPSNLVVIVPQTGELLLTGDPPSDDV-EYELTVE 190
+I S + TDADGD + Y A+PS + TG L+G P + DV L V
Sbjct: 18 TIPSSTFTDADGDTLTYSATLSDGSALPS-WLSFDSDTG--TLSGTPTNSDVGSLSLKVT 74
Query: 191 AHDLQSPS 198
A D S
Sbjct: 75 ATDSSGAS 82
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 30.2 bits (68), Expect = 1.3
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 4/54 (7%)
Query: 225 IDRKSEAPHRIEKRRVTR-AVRPTKRIDFSETDGEMEGRIVFALE---KETERE 274
+ R R R + T+ E + R VF L+ K ER+
Sbjct: 52 SRSPNRYYRPRGDRSYRRDDRRSGRNTKEPLTEAERDDRTVFVLQLALKARERD 105
>gnl|CDD|235212 PRK04043, tolB, translocation protein TolB; Provisional.
Length = 419
Score = 30.0 bits (68), Expect = 1.6
Identities = 26/109 (23%), Positives = 39/109 (35%), Gaps = 11/109 (10%)
Query: 86 VKGINKAETHVTVDVLDENDNSPVFSQKVYRFIVGDLKSSLNSNVSHWKKFSSIGSVSAT 145
VK K V D D ND + +K ++ +V DLK S + VS K SS
Sbjct: 24 VKKGQKLPKIVVEDASDLNDAN--LKKKFFKILVNDLKVSSHFEVSENKDQSSGDINYNE 81
Query: 146 DADGD-----KVAYKLAVPSNLVVIV----PQTGELLLTGDPPSDDVEY 185
D + + + L + V TG L D + ++
Sbjct: 82 LKDKKVDLVFRYSLANKNGNKLSLRVKLYDVNTGSLKFEKDYTINSLDR 130
>gnl|CDD|211364 cd09253, AP-4_Mu4_Cterm, C-terminal domain of medium Mu4 subunit in
adaptor protein (AP) complex AP-4. AP complexes
participate in the formation of intracellular coated
transport vesicles and select cargo molecules for
incorporation into the coated vesicles in the late
secretory and endocytic pathways. There are four AP
complexes, AP-1, AP-2, AP-3, and AP-4, described in
various eukaryotic organisms. Each AP complex consists
of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
family corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 4 (AP-4) medium
mu4 subunit. AP-4 plays a role in signal-mediated
trafficking of integral membrane proteins in mammalian
cells. Unlike other AP complexes, AP-4 is found only in
mammals and plants. It is believed to be part of a
nonclathrin coat, since it might function independently
of clathrin, a scaffolding protein participating in the
formation of coated vesicles. Recruitment of AP-4 to the
trans-Golgi network (TGN) membrane is regulated by a
small GTPase, ADP-ribosylation factor 1 (ARF1) or a
related protein. Membrane-anchored cargo molecules
interact with adaptors through short sorting signals in
their cytosolic segments. One of the most important
sorting signals binding to mu subunits of AP complexes
are tyrosine-based endocytotic signals, which are of the
form Y-X-X-Phi, where Y is tyrosine, X is any amino acid
and Phi is a bulky hydrophobic residue that can be Leu,
Ile, Met, Phe, or Val. However, AP-4 does not bind most
canonical tyrosine-based signals except for two
naturally occurring ones from the lysosomal membrane
proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif,
where X can be any residue, from the cytosolic tails of
amyloid precursor protein (APP) family members in a
distinct way.
Length = 271
Score = 29.5 bits (67), Expect = 2.4
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 6 SGTGVKGLPILVASSHKHPHQLVRYSITQGN 36
SG VK L I SS +PH+ VRY ITQ +
Sbjct: 236 SGLQVKYLRISEKSSSYNPHRWVRY-ITQSS 265
>gnl|CDD|222549 pfam14111, DUF4283, Domain of unknown function (DUF4283). This
domain family is found in plants, and is approximately
100 amino acids in length. Considering the very diverse
range of other domains it is associated with it is
possible that this domain is a binding/guiding region.
There are two highly conserved tryptophan residues.
Length = 153
Score = 28.3 bits (64), Expect = 2.8
Identities = 18/86 (20%), Positives = 31/86 (36%), Gaps = 13/86 (15%)
Query: 237 KRRVTRAVRPTKRIDFSETDGEMEGRIVFALEKETEREKFKIRDENPWITVDENGDVRVK 296
+ + +A + + G +F E E + E+ + PW+ G +
Sbjct: 35 RSWMAKAWGLKGGLGVASLGD---GLFLFEFESEEDAER--VLRRGPWLF---GGWALIL 86
Query: 297 KRWDFEELGP----EKTIDFWVTINN 318
+RW E+G K I WV I
Sbjct: 87 ERWS-PEVGCSEEELKRIPVWVRIYG 111
>gnl|CDD|238774 cd01516, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
glpX-encoded. A dimeric enzyme dependent on Mg(2+).
glpX-encoded FPBase (FBPase class II) differs from other
members of the inositol-phosphatase superfamily by
permutation of secondary structure elements. The core
structure around the active site is well preserved. In
E. coli, FBPase II is part of the glp regulon, which
mediates growth on glycerol or sn-glycerol 3-phosphate
as the sole carbon source.
Length = 309
Score = 29.1 bits (66), Expect = 3.4
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 257 GEMEGRIVFALEKETER-EKFKIRDENPWITVDE 289
GEM+GR++ E+E R + I D N +T+D+
Sbjct: 225 GEMQGRLLPRNEEERARAREMGITDPNKILTLDD 258
>gnl|CDD|240985 cd12541, RRM2_La, RNA recognition motif 2 in La autoantigen (La or
LARP3) and similar proteins. This subgroup corresponds
to the RRM2 of La autoantigen, also termed Lupus La
protein, or La ribonucleoprotein, or Sjoegren syndrome
type B antigen (SS-B), a highly abundant nuclear
phosphoprotein and well conserved in eukaryotes. It
specifically binds the 3'-terminal UUU-OH motif of
nascent RNA polymerase III transcripts and protects them
from exonucleolytic degradation by 3' exonucleases. In
addition, La can directly facilitate the translation
and/or metabolism of many UUU-3' OH-lacking cellular and
viral mRNAs, through binding internal RNA sequences
within the untranslated regions of target mRNAs. La
contains an N-terminal La motif (LAM), followed by two
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition, it possesses a short basic motif (SBM) and a
nuclear localization signal (NLS) at the C-terminus. .
Length = 76
Score = 26.8 bits (60), Expect = 3.7
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 10/42 (23%)
Query: 250 IDFSETDGEMEGRIVF--------ALEKETEREKFKIRDENP 283
+DF+ G+ EG + F ALEK E + KI+
Sbjct: 31 VDFAR--GQTEGYVRFKEENAAKEALEKLKEAKNLKIKGSEV 70
>gnl|CDD|217491 pfam03320, FBPase_glpX, Bacterial fructose-1,6-bisphosphatase,
glpX-encoded.
Length = 308
Score = 28.2 bits (64), Expect = 5.7
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 256 DGEMEGRIVFALEKETER-EKFKIRDENPWITVDE 289
GEM+GR+V ++E R +K I D + T+D+
Sbjct: 223 GGEMQGRLVPRNDEERARAKKMGIDDLDRVYTLDD 257
>gnl|CDD|182166 PRK09955, rihB, ribonucleoside hydrolase 2; Provisional.
Length = 313
Score = 28.4 bits (63), Expect = 5.7
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 6/52 (11%)
Query: 24 PHQLVRYSITQGNDNHTFALKNPTTHEIRNSTESKSGV------LLVTSGDI 69
P ++R I N + L P + ES V L+ + GDI
Sbjct: 68 PQPIMRQQIVADNIHGETGLDGPVFEPLTRQAESTHAVKYIIDTLMASDGDI 119
>gnl|CDD|221476 pfam12234, Rav1p_C, RAVE protein 1 C terminal. This domain family
is found in eukaryotes, and is typically between 621 and
644 amino acids in length. This family is the C terminal
region of the protein RAVE (regulator of the ATPase of
vacuolar and endosomal membranes). Rav1p is involved in
regulating the glucose dependent assembly and
disassembly of vacuolar ATPase V1 and V0 subunits.
Length = 629
Score = 28.1 bits (63), Expect = 6.6
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 47 TTHEIRNSTESKSGVLLVTSG 67
T H I +ST K G L+V SG
Sbjct: 127 TPHPIGDSTWLKDGNLVVASG 147
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 27.9 bits (62), Expect = 7.1
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 13 LPILVASSHKHPHQ--LVRYSITQGNDNH 39
LP+L A H P Q ++R +I QGN H
Sbjct: 238 LPLLHAMHHGTPEQAAMIRTAIEQGNGRH 266
>gnl|CDD|214751 smart00634, BID_1, Bacterial Ig-like domain (group 1).
Length = 92
Score = 26.5 bits (59), Expect = 7.2
Identities = 11/55 (20%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 75 AQYSLVITATDVKGINKAETHVTVDVLDENDNSPVFSQKVYRFIVGDLKSSLNSN 129
+ +L +T V D N N PV Q+V +L+
Sbjct: 1 SVTTLTADKDTAVANGSDAITLTATVTDANGN-PVAGQEVTFTTPSGGALTLSKG 54
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 28.0 bits (62), Expect = 8.2
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 166 VPQTGELLLTGDPPSDD 182
+PQ GE+LL G S D
Sbjct: 393 IPQEGEILLDGAAVSAD 409
>gnl|CDD|214905 smart00909, Germane, Sporulation and spore germination. The
GerMN domain is a region of approximately 100 residues
that is found, duplicated, in the Bacillus GerM protein
and is implicated in both sporulation and spore
germination. The domain is found in a number of
different bacterial species both alone and in
association with other domains such as Amidase_3
pfam01520 Gmad1 and Gmad2. It is predicted to have a
novel alpha-beta fold.
Length = 84
Score = 26.1 bits (58), Expect = 9.5
Identities = 10/34 (29%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 66 SGDIDREEVAQYSLVITATDVKGINKAETHVTVD 99
S + E++ LV+T T+ G++K + + VD
Sbjct: 51 SAGSEAEQLLLAQLVLTLTEFPGVDKVQ--ILVD 82
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
0.312 0.130 0.372
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,408,798
Number of extensions: 1577392
Number of successful extensions: 1020
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1014
Number of HSP's successfully gapped: 37
Length of query: 325
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 228
Effective length of database: 6,635,264
Effective search space: 1512840192
Effective search space used: 1512840192
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: 59 (26.5 bits)