RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy66
(164 letters)
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 58.8 bits (143), Expect = 8e-11
Identities = 35/141 (24%), Positives = 55/141 (39%), Gaps = 9/141 (6%)
Query: 7 VYVSEISLPAYRGLFASLGPVFVSLGVLFVYYAGYML-------HWQIVCYFCAATACIS 59
+Y+SEI+ RG SL + ++ G+L G L W+I A +
Sbjct: 124 MYISEIAPKKLRGALGSLYQLGITFGILVAAIIGLGLNKYSNSDGWRIPLGLQFVPAILL 183
Query: 60 FIIVTFMPETPAWYASKGLVVKSSASLNWLRNSSAIANAEIADILQSISEREDDKKSCGQ 119
I + F+PE+P W KG + ++ A L LR S + EI + S+ ER + +
Sbjct: 184 LIGLLFLPESPRWLVLKGKLEEARAVLAKLRGVS-DVDQEIQEEKDSL-ERSVEAEKASW 241
Query: 120 TLREFTPIRILTTRNVASLQC 140
LQ
Sbjct: 242 LELFRGKTVRQRLLMGVMLQI 262
>gnl|CDD|233165 TIGR00879, SP, MFS transporter, sugar porter (SP) family. This
model represent the sugar porter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 481
Score = 57.3 bits (139), Expect = 3e-10
Identities = 40/151 (26%), Positives = 63/151 (41%), Gaps = 12/151 (7%)
Query: 8 YVSEISLPAYRGLFASLGPVFVSLGVLFVY-------YAGYMLHWQIVCYFCAATACISF 60
Y+SEI+ A RG SL + ++ G+L Y L W+I A + F
Sbjct: 151 YLSEIAPKALRGALTSLYQLAITFGILVAYGFGSGKVSLNNTLGWRIPLGLQLIPAGLLF 210
Query: 61 IIVTFMPETPAWYASKGLVVKSSASLNWLRNSSAIANAEIADILQSISEREDDKKSCGQ- 119
+ + F+PE+P W KG V ++ SL LR +S + E+ D L+ I + +K Q
Sbjct: 211 LGLFFLPESPRWLVGKGRVEEARKSLARLRGTS-GEDKELLDELELIDIKRSIEKRSVQP 269
Query: 120 ---TLREFTPIRILTTRNVASLQCSIENSCN 147
+L T LQ + +
Sbjct: 270 SWGSLFSSTRRIRRRLFLGVVLQWFQQFTGI 300
>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 505
Score = 36.5 bits (85), Expect = 0.003
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 4 STYVYVSEISLPAYRGLFASLGPVFVSLGVLFVYYAGYML-HWQIVCYFCAATACISFII 62
V +E R + +L VF SLG++ + Y + W+ + + + F++
Sbjct: 200 QAVVLNTEFLPKKQRAIVGTLIQVFFSLGLVLLPLVAYFIPDWRWLQLAVSLPTFLFFLL 259
Query: 63 VTFMPETPAWYASKG 77
F+PE+P W S+G
Sbjct: 260 SWFVPESPRWLISQG 274
>gnl|CDD|182225 PRK10077, xylE, D-xylose transporter XylE; Provisional.
Length = 479
Score = 35.4 bits (82), Expect = 0.007
Identities = 25/116 (21%), Positives = 48/116 (41%), Gaps = 13/116 (11%)
Query: 7 VYVSEISLPAYRGLFASLGPVFVSLGVLFVYYAGY------------MLHWQIVCYFCAA 54
+Y++EI+ RG S + G L VY+ Y W+ + A
Sbjct: 143 MYIAEIAPAHIRGKLVSFNQFAIIFGQLVVYFVNYFIARSGDASWLNTDGWRYMFASEAI 202
Query: 55 TACISFIIVTFMPETPAWYASKGLVVKSSASLNWLRNSSAIANAEIADILQSISER 110
A + +++ F+PETP + S+G ++ L + + +A + +I S+
Sbjct: 203 PALLFLMLLYFVPETPRYLMSRGKQEQAEGILRKI-MGNTLATQALQEIKHSLDHG 257
>gnl|CDD|200518 cd11257, Sema_4B, The Sema domain, a protein interacting module, of
semaphorin 4B (Sema4B). Sema4B, expressed in T and B
cells, is an immune semaphorin. It functions as a
negative regulatory of basophils through T cell-basophil
contacts and it significantly inhibits IL-4 and IL-6
production from basophils in response to various
stimuli, including IL-3 and papain. In addition, T
cell-derived Sema4B suppresses basophil-mediated Th2
skewing and humoral memory responses. Sema4B may be also
involved in lung cancer cell mobility by inducing the
degradation of CLCP1 (CUB, LCCL-homology, coagulation
factor V/VIII homology domains protein). Sema4B is
characterized by a PDZ-binding motif at the
carboxy-terminus, which mediates interaction with the
post-synaptic density protein PSD-95/SAP90, which is
thought to play a central role during synaptogenesis and
in the structure and function of post-synaptic
specializations of excitatory synapses. Sema4B belongs
to class 4 transmembrane semaphorin family proteins.
Semaphorins are regulatory molecules in the development
of the nervous system and in axonal guidance. They also
play important roles in other biological processes, such
as angiogenesis, immune regulation, respiration systems
and cancer. The Sema domain is located at the N-terminus
and contains four disulfide bonds formed by eight
conserved cysteine residues. It serves as a
receptor-recognition and -binding module.
Length = 464
Score = 32.1 bits (73), Expect = 0.11
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 65 FMPETPAWYASKGL--VVKSSASLNWLRNSSAIANAEIADILQSISEREDDK 114
F P Y S G +K+ SLNWL++ + + +A I + L + +DDK
Sbjct: 149 FQGNDPIIYRSLGSGTPLKTENSLNWLQDPAFVGSAYIQESLPKL-VGDDDK 199
>gnl|CDD|119392 cd06174, MFS, The Major Facilitator Superfamily (MFS) is a large
and diverse group of secondary transporters that
includes uniporters, symporters, and antiporters. MFS
proteins facilitate the transport across cytoplasmic or
internal membranes of a variety of substrates including
ions, sugar phosphates, drugs, neurotransmitters,
nucleosides, amino acids, and peptides. They do so using
the electrochemical potential of the transported
substrates. Uniporters transport a single substrate,
while symporters and antiporters transport two
substrates in the same or in opposite directions,
respectively, across membranes. MFS proteins are
typically 400 to 600 amino acids in length, and the
majority contain 12 transmembrane alpha helices (TMs)
connected by hydrophilic loops. The N- and C-terminal
halves of these proteins display weak similarity and may
be the result of a gene duplication/fusion event. Based
on kinetic studies and the structures of a few bacterial
superfamily members, GlpT (glycerol-3-phosphate
transporter), LacY (lactose permease), and EmrD
(multidrug transporter), MFS proteins are thought to
function through a single substrate binding site,
alternating-access mechanism involving a rocker-switch
type of movement. Bacterial members function primarily
for nutrient uptake, and as drug-efflux pumps to confer
antibiotic resistance. Some MFS proteins have medical
significance in humans such as the glucose transporter
Glut4, which is impaired in type II diabetes, and
glucose-6-phosphate transporter (G6PT), which causes
glycogen storage disease when mutated.
Length = 352
Score = 30.4 bits (69), Expect = 0.37
Identities = 13/71 (18%), Positives = 25/71 (35%), Gaps = 4/71 (5%)
Query: 1 MGSSTYVYVSEISLPAYRGLFASLGPVFVSLGVLFVYYAGYMLH----WQIVCYFCAATA 56
+ + ++E P RG L LG L G +L W+ + A
Sbjct: 104 LYPAAAALIAEWFPPKERGRALGLFSAGFGLGALLGPLLGGLLAESLGWRWLFLILAILG 163
Query: 57 CISFIIVTFMP 67
+ +++ F+
Sbjct: 164 LLLALLLLFLL 174
Score = 28.0 bits (63), Expect = 2.4
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 4/71 (5%)
Query: 1 MGSSTYVYVSEISLPAYRGLFASLGPVFVSLG-VLFVYYAGYMLH---WQIVCYFCAATA 56
+ SE++ P RG + L F SLG L AG +L + V AA A
Sbjct: 282 AFPALLTLASELAPPEARGTASGLFNTFGSLGGALGPLLAGLLLDTGGYGGVFLILAALA 341
Query: 57 CISFIIVTFMP 67
++ +++ +P
Sbjct: 342 LLAALLLLLLP 352
>gnl|CDD|198368 cd07796, FGGY_NHO1_plant, Arabidopsis NHO1 and related proteins;
belongs to the FGGY family of carbohydrate kinases.
This subgroup includes Arabidopsis NHO1 (also known as
NONHOST1, or noh-host resistant 1) and other putative
plant glycerol kinases, which share strong homology with
glycerol kinases from bacteria, fungi, and animals.
Nonhost resistance of plants refers to the phenomenon
observed when all members of a plant species are
typically resistant to a specific parasite. NHO1 is
required for nonspecific resistance to nonhost
Pseudomonas bacteria, it is also required for resistance
to the fungal pathogen Botrytis cinerea. This subgroup
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 503
Score = 30.3 bits (68), Expect = 0.44
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 67 PETPAWYASKGLVVKSSASLNWLRNSSAIANAEIADILQSISEREDDKKSCGQT 120
P+ P YA +G + + A++ WLR+S I++S SE E K+ T
Sbjct: 301 PDAPTNYALEGSIAIAGAAVQWLRDSLG--------IIKSASEIESLAKTVNNT 346
>gnl|CDD|130366 TIGR01299, synapt_SV2, synaptic vesicle protein SV2. This model
describes a tightly conserved subfamily of the larger
family of sugar (and other) transporters described by
PFAM model pfam00083. Members of this subfamily include
closely related forms SV2A and SV2B of synaptic vesicle
protein from vertebrates and a more distantly related
homolog (below trusted cutoff) from Drosophila
melanogaster. Members are predicted to have two sets of
six transmembrane helices.
Length = 742
Score = 29.6 bits (66), Expect = 0.80
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 39 AGYMLH-WQIVCYFCAATACISFIIVTFMPETPAWYASKG 77
+ Y H W++ CA + +TFMPE+P ++ G
Sbjct: 326 SAYQFHSWRVFVIVCAFPCVFAIGALTFMPESPRFFLENG 365
>gnl|CDD|227005 COG4658, RnfD, Predicted NADH:ubiquinone oxidoreductase, subunit
RnfD [Energy production and conversion].
Length = 338
Score = 29.3 bits (66), Expect = 0.84
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 5/64 (7%)
Query: 12 ISLPAYRGLFASLG----PVFVSLGVLFVYYAGYMLHWQIVCYFCAATACISFIIVTFMP 67
+ P + G A G + LG LF+ + + W I F ++ + F P
Sbjct: 192 LQAPIFSGKLAGAGWEWVNLAFLLGGLFLLWVKA-IRWHIPVSFLVTLFLLALLTWLFSP 250
Query: 68 ETPA 71
ET A
Sbjct: 251 ETLA 254
>gnl|CDD|240348 PTZ00294, PTZ00294, glycerol kinase-like protein; Provisional.
Length = 504
Score = 29.6 bits (67), Expect = 0.88
Identities = 12/45 (26%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 67 PETPAWYASKGLVVKSSASLNWLRNSSAIAN--AEIADILQSISE 109
P P YA +G + + A + WLR++ + + +EI + +S+ +
Sbjct: 298 PNGPTVYALEGSIAVAGAGVEWLRDNMGLISHPSEIEKLARSVKD 342
>gnl|CDD|237212 PRK12808, PRK12808, flagellin; Provisional.
Length = 476
Score = 29.2 bits (65), Expect = 0.97
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 74 ASKGLVVKSSASLNWLRNSSAIANAEIADILQSISEREDDKKSCGQTL 121
ASK LV K A+ NS A + + I +++ D++ + G TL
Sbjct: 364 ASKVLVPKLEAAKKATTNSKADSLDAVKAIDEALKTVADNRATLGATL 411
>gnl|CDD|225958 COG3424, BcsA, Predicted naringenin-chalcone synthase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 356
Score = 27.7 bits (62), Expect = 2.7
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 1 MGSSTYVYVSEISL-----PAYRGLFASLGPVFVSLGVLFVYYAG 40
M S+T ++V E +L RGL ++GP F S VL + G
Sbjct: 311 MSSATVLFVLEDTLQKAPKSGSRGLMFAMGPGFCSELVLLDWEGG 355
>gnl|CDD|212664 cd07792, FGGY_GK1-3_metazoa, Metazoan glycerol kinase 1 and 3-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan glycerol kinases (GKs), coded by X
chromosome-linked GK genes, and glycerol kinase
(GK)-like proteins, coded by autosomal testis-specific
GK-like genes (GK-like genes, GK1 and GK3). Sequence
comparison shows that metazoan GKs and GK-like proteins
in this family are closely related to the bacterial GKs,
which catalyze the Mg-ATP dependent phosphorylation of
glycerol to yield glycerol 3-phosphate (G3P). The
metazoan GKs do have GK enzymatic activity. However, the
GK-like metazoan proteins do not exhibit GK activity and
their biological functions are not yet clear. Some of
them lack important functional residues involved in the
binding of ADP and Mg2+, which may result in the loss of
GK catalytic function. Others that have conserved
catalytic residues have lost their GK activity as well;
the reason remains unclear. It has been suggested the
conserved catalytic residues might facilitate them
performing a distinct function. GKs belong to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 504
Score = 27.3 bits (61), Expect = 3.8
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 67 PETPAWYASKGLVVKSSASLNWLRN 91
P+ P YA +G V + A++ WLR+
Sbjct: 301 PDKPTIYALEGSVAIAGAAIRWLRD 325
>gnl|CDD|109608 pfam00558, Vpu, Vpu protein. The Vpu protein contains an
N-terminal transmembrane spanning region and a
C-terminal cytoplasmic region. The HIV-1 Vpu protein
stimulates virus production by enhancing the release of
viral particles from infected cells. The VPU protein
binds specifically to CD4.
Length = 81
Score = 25.8 bits (57), Expect = 4.7
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 20/72 (27%)
Query: 42 MLHWQIVCYFCAATACISFIIVTFMPETPAWYASKGLVVKSSASLNWLRNSSAIANAEIA 101
ML +I+ A I I+V W +V + + + EI
Sbjct: 1 MLLLEIIGLIALIVALIINIVV--------W----TIVYRE-----YRKIKK---QREIL 40
Query: 102 DILQSISEREDD 113
+++ I ER +D
Sbjct: 41 RLIKRIRERAED 52
>gnl|CDD|220031 pfam08818, DUF1801, Domain of unknown function (DU1801). This
large family of bacterial proteins is uncharacterized.
They contain a presumed domain about 110 amino acids in
length.
Length = 101
Score = 26.1 bits (58), Expect = 5.6
Identities = 8/72 (11%), Positives = 21/72 (29%), Gaps = 2/72 (2%)
Query: 40 GYMLHWQIVCYFCAATACISFIIV--TFMPETPAWYASKGLVVKSSASLNWLRNSSAIAN 97
Y H + F A +S + + + + K S + + I
Sbjct: 30 AYTYHGKPFVGFAAFKKHVSLYFMPGALLKDFEEELLAALGKGKMGKSCLRFKKLADIDE 89
Query: 98 AEIADILQSISE 109
+ ++++
Sbjct: 90 ELLKELIREAIA 101
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 26.5 bits (59), Expect = 7.2
Identities = 14/79 (17%), Positives = 26/79 (32%), Gaps = 10/79 (12%)
Query: 78 LVVKSSASLNWLRNSSAIA---NAEI----ADILQSISEREDDKKSCGQTLREFTPIR-- 128
L K + + ++ E + L+SI ED K++ + LRE+
Sbjct: 118 LEYKPDSIGVLEKFKKSLTKKTREEFQDNYRETLESIKALEDIKRNLLELLREYGAELLK 177
Query: 129 -ILTTRNVASLQCSIENSC 146
T ++ S
Sbjct: 178 EYDKTGHIYSELLEFLAFL 196
>gnl|CDD|176491 cd08761, Cyt_b561_CYB561D2_like, Eukaryotic cytochrome b(561),
including the CYB561D2 gene product. Cytochrome
b(561), as found in eukaryotes, similar to and
including the human CYB561D2 gene product. CYB561D2 is
a candidate tumor suppressor. The protein might act as
a ferric-chelate reductase, catalyzing the reduction of
Fe(3+) to Fe(2+), such as associated with the transport
of iron from the endosome to the cytoplasm. It is
assumed that this protein uses ascorbate as the
electron donor. Belongs to the cytochrome b(561)
family, which are secretory vesicle-specific electron
transport proteins. Cytochromes b(561) are integral
membrane proteins that bind two heme groups
non-covalently, and may have six alpha-helical
trans-membrane segments.
Length = 183
Score = 26.1 bits (58), Expect = 8.1
Identities = 8/70 (11%), Positives = 21/70 (30%)
Query: 27 VFVSLGVLFVYYAGYMLHWQIVCYFCAATACISFIIVTFMPETPAWYASKGLVVKSSASL 86
VF + + + W + ++ ++ P + ++ V+ L
Sbjct: 5 VFAAFLLYIARPGTSLFSWHPLLMSLGFLLLMTEALLLLQPTSSLTKLARKTKVRLHWIL 64
Query: 87 NWLRNSSAIA 96
L +A
Sbjct: 65 QLLALLCILA 74
>gnl|CDD|238799 cd01558, D-AAT_like, D-Alanine aminotransferase (D-AAT_like):
D-amino acid aminotransferase catalyzes transamination
between D-amino acids and their respective alpha-keto
acids. It plays a major role in the synthesis of
bacterial cell wall components like D-alanine and
D-glutamate in addition to other D-amino acids. The
enzyme like other members of this superfamily requires
PLP as a cofactor. Members of this subgroup are found in
all three forms of life.
Length = 270
Score = 26.0 bits (58), Expect = 9.9
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 60 FIIVTFMPETPAWYASKGLVVKSSASLNWLR 90
II +P PA KG+ V + + WLR
Sbjct: 108 VIITQPLPLPPAELLEKGVRVITVPDIRWLR 138
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
0.325 0.135 0.423
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,945,016
Number of extensions: 682460
Number of successful extensions: 1012
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1003
Number of HSP's successfully gapped: 59
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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: 40 (21.7 bits)
S2: 55 (24.9 bits)