RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780446|ref|YP_003064859.1| hypothetical protein
CLIBASIA_01655 [Candidatus Liberibacter asiaticus str. psy62]
(171 letters)
>gnl|CDD|144199 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 29.4 bits (67), Expect = 0.49
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 48 VNKDGKFKPIGYLPSDRLKVFEFKYPCLYKEDQEQV 83
V D ++K YL S R+ VFEF P + E+ V
Sbjct: 362 VKADDRYK---YLHS-RITVFEFPNPFPFDENGNPV 393
>gnl|CDD|146172 pfam03393, Pneumo_matrix, Pneumovirus matrix protein.
Length = 252
Score = 29.5 bits (66), Expect = 0.55
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 140 AIPNAKIAPYQGIILL 155
AI NAKI PY G+IL+
Sbjct: 188 AITNAKIIPYAGLILV 203
>gnl|CDD|73019 cd03260, ABC_PstB_phosphate_transporter, Phosphate uptake is of
fundamental importance in the cell physiology of
bacteria because phosphate is required as a nutrient.
The Pst system of E. coli comprises four distinct
subunits encoded by the pstS, pstA, pstB, and pstC
genes. The PstS protein is a phosphate-binding protein
located in the periplasmic space. P stA and PstC are
hydrophobic and they form the transmembrane portion of
the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD)..
Length = 227
Score = 28.6 bits (64), Expect = 0.88
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 11/55 (20%)
Query: 118 GIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNN--WIRC 170
G GK STL+R + IP AP +G +LLD + I ++ + +R
Sbjct: 36 GCGK------STLLRLLNRLNDLIPG---APDEGEVLLDGKDIYDLDVDVLELRR 81
>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporters is the obligatory coupling of ATP
hydrolysis to substrate translocation. ABC transporters
are a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins..
Length = 269
Score = 28.2 bits (63), Expect = 1.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 8/41 (19%)
Query: 123 SNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEI 163
S S STL+RC+ N I P G +L+D + I +
Sbjct: 59 SGSGKSTLLRCI--------NRLIEPTSGKVLIDGQDIAAM 91
>gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding
components of the bacterial periplasmic histidine and
glutamine permeases, repectively. Histidine permease is
a multisubunit complex containing the HisQ and HisM
integral membrane subunits and two copies of HisP. HisP
has properties intermediate between those of integral
and peripheral membrane proteins and is accessible from
both sides of the membrane, presumably by its
interaction with HisQ and HisM. The two HisP subunits
form a homodimer within the complex. The domain
structure of the amino acid uptake systems is typical
for prokaryote extracellular solute binding
protein-dependent uptake systems. All of the amino acid
uptake systems also have at least one, and in a few
cases, two extracellular solute binding proteins located
in the periplasm of Gram-negative bacteria, or attached
to the cell membrane of Gram-positive bacteria. The
best-studied member of the PAAT (polar amino acid
transport) family is the HisJQMP system of S.
typhimurium, where HisJ is the extracellular solute
binding proteins and HisP is the ABC protein..
Length = 213
Score = 28.2 bits (63), Expect = 1.3
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 123 SNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIRC 170
S S STL+RC+ L E P G I++D K+ + + N
Sbjct: 35 SGSGKSTLLRCINLLE--------EPDSGTIIIDGLKLTDDKKNINEL 74
>gnl|CDD|35278 KOG0055, KOG0055, KOG0055, Multidrug/pheromone exporter, ABC
superfamily [Secondary metabolites biosynthesis,
transport and catabolism].
Length = 1228
Score = 27.9 bits (62), Expect = 1.6
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 148 PYQGIILLDDRKINEIQNNWIR 169
P G +L+D I + W+R
Sbjct: 405 PTSGEVLIDGEDIRNLNLKWLR 426
>gnl|CDD|73056 cd03297, ABC_ModC_molybdenum_transporter, ModC is an ABC-type
transporter and the ATPase component of a molybdate
transport system that also includes the periplasmic
binding protein ModA and the membrane protein ModB. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 214
Score = 27.9 bits (62), Expect = 1.6
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 10/55 (18%)
Query: 113 PYPFLGIGKNSNSVASTLIRCM-GLKELAIPNAKIAPYQGIILLDDRKINEIQNN 166
GI S + STL+RC+ GL++ P G I+L+ + + +
Sbjct: 22 NEEVTGIFGASGAGKSTLLRCIAGLEK---------PDGGTIVLNGTVLFDSRKK 67
>gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor)
[Signal transduction mechanisms].
Length = 5019
Score = 27.0 bits (59), Expect = 3.1
Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 25 FAHRLLVVFDSNKEFVAELDGLVVNKDGKFKP----IGYLPSDRLKVFE--FKYPCLYKE 78
F +++ D EF+AE D + G+ P I + L + + FK CLY
Sbjct: 2942 FLKKIIKYVDEAHEFIAEFDAIGSRGKGEHFPRDQEIKFFAKVLLPLIDQYFKNHCLYFL 3001
Query: 79 DQEQVVLCSS 88
LCS
Sbjct: 3002 SAALKPLCSG 3011
>gnl|CDD|73017 cd03258, ABC_MetN_methionine_transporter, MetN (also known as YusC)
is an ABC-type transporter encoded by metN of the metNPQ
operon in Bacillus subtilis that is involved in
methionine transport. Other members of this system
include the MetP permease and the MetQ substrate
binding protein. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 233
Score = 26.7 bits (59), Expect = 3.4
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 117 LGIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIR 169
GI S + STLIRC+ E P G +L+D + + +R
Sbjct: 34 FGIIGRSGAGKSTLIRCINGLE--------RPTSGSVLVDGTDLTLLSGKELR 78
>gnl|CDD|31330 COG1135, AbcC, ABC-type metal ion transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 339
Score = 26.4 bits (58), Expect = 4.7
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 117 LGIGKNSNSVASTLIRCMGLKELAIPNAKIAPYQGIILLDDRKINEIQNNWIR 169
GI S + STL+R + L E P G + +D + + + +R
Sbjct: 35 FGIIGYSGAGKSTLLRLINLLE--------RPTSGSVFVDGQDLTALSEAELR 79
>gnl|CDD|176034 cd08388, C2A_Synaptotagmin-4-11, C2A domain first repeat present in
Synaptotagmins 4 and 11. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmins 4 and 11, class 4
synaptotagmins, are located in the brain. Their
functions are unknown. They are distinguished from the
other synaptotagmins by having and Asp to Ser
substitution in their C2A domains. Previously all
synaptotagmins were thought to be calcium sensors in the
regulation of neurotransmitter release and hormone
secretion, but it has been shown that not all of them
bind calcium. Of the 17 identified synaptotagmins only
8 bind calcium (1-3, 5-7, 9, 10). The function of the
two C2 domains that bind calcium are: regulating the
fusion step of synaptic vesicle exocytosis (C2A) and
binding to phosphatidyl-inositol-3,4,5-triphosphate
(PIP3) in the absence of calcium ions and to
phosphatidylinositol bisphosphate (PIP2) in their
presence (C2B). C2B also regulates also the recycling
step of synaptic vesicles. C2 domains fold into an
8-standed beta-sandwich that can adopt 2 structural
arrangements: Type I and Type II, distinguished by a
circular permutation involving their N- and C-terminal
beta strands. Many C2 domains are Ca2+-dependent
membrane-targeting modules that bind a wide variety of
substances including bind phospholipids, inositol
polyphosphates, and intracellular proteins. Most C2
domain proteins are either signal transduction enzymes
that contain a single C2 domain, such as protein kinase
C, or membrane trafficking proteins which contain at
least two C2 domains, such as synaptotagmin 1. However,
there are a few exceptions to this including RIM
isoforms and some splice variants of piccolo/aczonin and
intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the first C2
repeat, C2A, and has a type-I topology.
Length = 128
Score = 26.2 bits (58), Expect = 5.5
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 129 TLIRCMGLKELAIPNAKIAPYQGIILLDDRK 159
+I C L + + PY + LL +++
Sbjct: 21 NIIECRDLPAMDEQSGTSDPYVKLQLLPEKE 51
>gnl|CDD|73008 cd03249, ABC_MTABC3_MDL1_MDL2, MTABC3 (also known as ABCB6) is a
mitochondrial ATP-binding cassette protein involved in
iron homeostasis and one of four ABC transporters
expressed in the mitochondrial inner membrane, the other
three being MDL1(ABC7), MDL2, and ATM1. In fact, the
yeast MDL1 (multidrug resistance-like protein 1) and
MDL2 (multidrug resistance-like protein 2) transporters
are also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1 and
is thought to have a role in resistance to oxidative
stress. Interestingly, subfamily B is more closely
related to the carboxyl-terminal component of subfamily
C than the two halves of ABCC molecules are with one
another..
Length = 238
Score = 25.9 bits (57), Expect = 5.9
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 148 PYQGIILLDDRKINEIQNNWIR 169
P G ILLD I ++ W+R
Sbjct: 55 PTSGEILLDGVDIRDLNLRWLR 76
>gnl|CDD|36542 KOG1328, KOG1328, KOG1328, Synaptic vesicle protein BAIAP3,
involved in vesicle priming/regulation [Intracellular
trafficking, secretion, and vesicular transport, Signal
transduction mechanisms].
Length = 1103
Score = 25.8 bits (56), Expect = 6.9
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 122 NSNSVA--STLIRCMGLKELAIPNAKIAPYQ 150
N NS +L++C+G + K P++
Sbjct: 441 NRNSGERLESLLKCLGALRESPFYQKYCPFK 471
>gnl|CDD|37338 KOG2127, KOG2127, KOG2127, Calmodulin-binding protein CRAG,
contains DENN domain [Signal transduction mechanisms].
Length = 1020
Score = 25.3 bits (55), Expect = 8.6
Identities = 15/88 (17%), Positives = 29/88 (32%), Gaps = 1/88 (1%)
Query: 31 VVFDSNKEFVAELDGLVVNKDGKFKPIGYLPSDRLKVFEFK-YPCLYKEDQEQVVLCSSS 89
V+ D + ++V DG ++ LP V + E + + S
Sbjct: 770 VMLDQSLQWVGLSDGKMIPSIPGPVTSLVLPYLSPLVLRKELESLDENEGDTVLSVSSFP 829
Query: 90 EECVMSRWNAAVHTKEILNEKNMPYPFL 117
+ WN + + + N+P L
Sbjct: 830 NHHPIIFWNLVWYFRRLDLRSNLPGLVL 857
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.321 0.137 0.408
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,014,689
Number of extensions: 98372
Number of successful extensions: 198
Number of sequences better than 10.0: 1
Number of HSP's gapped: 198
Number of HSP's successfully gapped: 20
Length of query: 171
Length of database: 6,263,737
Length adjustment: 87
Effective length of query: 84
Effective length of database: 4,383,754
Effective search space: 368235336
Effective search space used: 368235336
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 (24.7 bits)