RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1450
(187 letters)
>gnl|CDD|217322 pfam03022, MRJP, Major royal jelly protein. Royal jelly is the
food of queen bee larvae, and is responsible for the
high reproductive ability of the queen. Major royal
jelly proteins make up around 90% of larval jelly
proteins. This family also the sequence-related yellow
protein of drosophila which controls pigmentation of the
adult cuticle and larval mouth parts.
Length = 285
Score = 94.7 bits (236), Expect = 6e-24
Identities = 32/82 (39%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 106 TSVFRVEVDECGRLWVLDTGKLNAFGETPKVVCPPQIVVYDLNQGDKVILRHKFPDSQIA 165
SV+R+ VDEC RLWVLD+G +N + PK +CPP+++V+DL DK++ R + P
Sbjct: 1 VSVYRIAVDECDRLWVLDSGIVN-TLQPPKQICPPKLLVFDLAT-DKLLKRFELPADVAK 58
Query: 166 ANSLPLTIVIDTRNPQCTRQYA 187
NS + +V+D + C +
Sbjct: 59 GNSRLVNLVVDVGDDTCDDTFV 80
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 27.9 bits (63), Expect = 2.9
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 116 CGRLWVLDTGKLNAFGETPKVVCPPQI-VVYDLN 148
L +L GK+ A G +V+ + VY ++
Sbjct: 206 ADHLILLKDGKIVAQGTPEEVLTEENLREVYGVD 239
>gnl|CDD|187783 cd09652, Cas6-I-III, CRISPR/Cas system-associated RAMP superfamily
protein Cas6. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas6 is an endoribonuclease that generates crRNAs,
predicted subunit of Cascade complex; RAMP superfamily
protein; Possesses double RRM/ferredoxin fold.
Length = 190
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/45 (24%), Positives = 17/45 (37%)
Query: 54 KEKRIFVTTPKLRTGIPVTLSTLSSKRSKDGSPLLEPFPNWDAHS 98
+EK+I +T P + T + P EPFP +
Sbjct: 69 EEKKIKEDEVTFKTLSPTVIRTKGEENKYYYVPDDEPFPELLFEN 113
>gnl|CDD|173866 cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial
lipoprotein Lpqw contains type 2 periplasmic binding
fold. LpqW is one of key players in synthesis and
transport of the unique components of the mycobacterial
cell wall which is a complex structure rich in two
related lipoglycans, the phosphatidylinositol mannosides
(PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly
conserved lipoprotein that transport intermediates from
a pathway for mature PIMs production into a pathway for
LAMs biosynthesis, thus controlling the relative
abundance of these two essential components of cell
wall. LpqW is thought to have been adapted by the
cell-wall biosynthesis machinery of mycobacteria and
other closely related pathogens, evolving to play an
important role in PIMs/LAMs biosynthesis. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the LpqW protein. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 486
Score = 27.7 bits (62), Expect = 4.3
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 15/73 (20%)
Query: 89 EPFPNWDAHS-EGNCDG--------LTSVFRVEVDECGRLWVLDTGKLNAFGETPKVVCP 139
E P ++ HS GN L S FR + D V + + G
Sbjct: 8 ELGPGFNPHSAAGNSTYTSALASLVLPSAFRYDPDG---TDVPNP---DYVGSVEVTSDD 61
Query: 140 PQIVVYDLNQGDK 152
PQ V Y +N +
Sbjct: 62 PQTVTYTINPEAQ 74
>gnl|CDD|179812 PRK04293, PRK04293, adenylosuccinate synthetase; Provisional.
Length = 333
Score = 27.2 bits (61), Expect = 5.0
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 31 ASSVAILDVDVFDPANYGNASGNK---EKRIFVTTPKLRTGIPVTL 73
A+ +AI +D D YG +K E + F+ + G+PVTL
Sbjct: 274 ATQIAITKLDKLDKEAYGVTEYDKLPPEAKKFIEEIEEELGVPVTL 319
>gnl|CDD|213534 TIGR00486, YbgI_SA1388, dinuclear metal center protein, YbgI/SA1388
family. The characterization of this family of
uncharacterized proteins as orthologous is tentative.
Members are found in all three domains of life. Several
members (from Bacillus subtilis, Listeria monocytogenes,
and Mycobacterium tuberculosis - all classified as
Firmicutes within the Eubacteria) share a long insert
relative to other members [Unknown function, General].
Length = 249
Score = 27.0 bits (60), Expect = 6.1
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 10/52 (19%)
Query: 54 KEKRIFVTTPKLRTGIPVTLSTLSSKRSKDGSPLLEPFPNWDAHSEGNCDGL 105
KR+ R I + ++ L N DAH GN D L
Sbjct: 71 PLKRLIRGIKPGRLKILL----------QNDISLYSAHTNLDAHDGGNNDAL 112
>gnl|CDD|133065 cd06915, NTP_transferase_WcbM_like, WcbM_like is a subfamily of
nucleotidyl transferases. WcbM protein of Burkholderia
mallei is involved in the biosynthesis, export or
translocation of capsule. It is a subfamily of
nucleotidyl transferases that transfer nucleotides onto
phosphosugars.
Length = 223
Score = 26.7 bits (60), Expect = 7.1
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 94 WDAHSEGNCDGLTSVFRVE-VDECGRLWVLDTGKLNAFGET 133
A D ++ RV G + V G++ AF E
Sbjct: 116 LAALRASGADATMALRRVPDASRYGNVTVDGDGRVIAFVEK 156
>gnl|CDD|234020 TIGR02801, tolR, TolR protein. The model describes the inner
membrane protein TolR, part of the TolR/TolQ complex
that transduces energy from the proton-motive force,
through TolA, to an outer membrane complex made up of
TolB and Pal (peptidoglycan-associated lipoprotein).
The complex is required to maintain outer membrane
integrity, and defects may cause a defect in the import
of some organic compounds in addition to the resulting
morphologic. While several gene pairs homologous to
talR and tolQ may be found in a single genome, but the
scope of this model is set to favor finding only bone
fide TolR, supported by operon structure as well as by
score [Transport and binding proteins, Other, Cellular
processes, Pathogenesis].
Length = 129
Score = 26.0 bits (58), Expect = 7.5
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 58 IF-VTTPKLRTGIPVTLSTLSSK--RSKDGSPLL 88
IF VT P L G+ V L S+K +SKD P+
Sbjct: 20 IFMVTAPLLTQGVKVDLPKSSAKPLQSKDKKPIT 53
>gnl|CDD|238849 cd01751, PLAT_LH2, PLAT/ LH2 domain of plant lipoxygenase related
proteins. Lipoxygenases are nonheme, nonsulfur iron
dioxygenases that act on lipid substrates containing one
or more (Z,Z)-1,4-pentadiene moieties. In plants, the
immediate products are involved in defense mechanisms
against pathogens and may be precursors of metabolic
regulators. The generally proposed function of PLAT/LH2
domains is to mediate interaction with lipids or
membrane bound proteins.
Length = 137
Score = 26.1 bits (58), Expect = 8.9
Identities = 11/72 (15%), Positives = 20/72 (27%), Gaps = 13/72 (18%)
Query: 1 MTVLHEWS--SVDYVWPSSQDRDNAIRDGKYNASSVAILDVDVFDPANYG---------- 48
L S ++ P+S A+ + S + + + G
Sbjct: 63 GKSLAGESAYEAEFEVPASFGPPGAVLVKNEHHSEFFLKSITLEGFGGSGTITFVCNSWV 122
Query: 49 -NASGNKEKRIF 59
+KRIF
Sbjct: 123 YPKKDYPDKRIF 134
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
0.317 0.134 0.414
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,368,574
Number of extensions: 833074
Number of successful extensions: 616
Number of sequences better than 10.0: 1
Number of HSP's gapped: 614
Number of HSP's successfully gapped: 14
Length of query: 187
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 96
Effective length of database: 6,901,388
Effective search space: 662533248
Effective search space used: 662533248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.3 bits)