RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2914
(158 letters)
>gnl|CDD|130902 TIGR01843, type_I_hlyD, type I secretion membrane fusion protein,
HlyD family. Type I secretion is an ABC transport
process that exports proteins, without cleavage of any
signal sequence, from the cytosol to extracellular
medium across both inner and outer membranes. The
secretion signal is found in the C-terminus of the
transported protein. This model represents the adaptor
protein between the ATP-binding cassette (ABC) protein
of the inner membrane and the outer membrane protein,
and is called the membrane fusion protein. This model
selects a subfamily closely related to HlyD; it is
defined narrowly and excludes, for example, colicin V
secretion protein CvaA and multidrug efflux proteins
[Protein fate, Protein and peptide secretion and
trafficking].
Length = 423
Score = 29.6 bits (67), Expect = 0.77
Identities = 19/151 (12%), Positives = 58/151 (38%), Gaps = 13/151 (8%)
Query: 1 MKSQSVMHSPRNSPFLSKVNSKDEDVHGSAMSLASVSSSIYSTPEERQSYE-----LRKL 55
+K Q + R S +++ + LA + + + + ++ + RKL
Sbjct: 128 IKGQQSLFESRKSTLRAQLELILAQIKQLEAELAGLQAQLQALRQQLEVISEELEARRKL 187
Query: 56 -------RRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEKLRSS 108
R EL++ + + +L + ++ + + QQ+ + E++
Sbjct: 188 KEKGLVSRLELLELERERAEAQGELGRLEAELEVLKRQIDELQLERQQIEQTFREEVLEE 247
Query: 109 FSKAFSRIVQIALKSPRLQEAANSSSKLTAP 139
++A +R+ ++ + + ++ + +P
Sbjct: 248 LTEAQARLAELRERLNKARD-RLQRLIIRSP 277
>gnl|CDD|220785 pfam10498, IFT57, Intra-flagellar transport protein 57. Eukaryotic
cilia and flagella are specialised organelles found at
the periphery of cells of diverse organisms.
Intra-flagellar transport (IFT) is required for the
assembly and maintenance of eukaryotic cilia and
flagella, and consists of the bidirectional movement of
large protein particles between the base and the distal
tip of the organelle. IFT particles contain multiple
copies of two distinct protein complexes, A and B, which
contain at least 6 and 11 protein subunits. IFT57 is
part of complex B but is not, however, required for the
core subunits to stay associated. This protein is known
as Huntington-interacting protein-1 in humans.
Length = 355
Score = 28.9 bits (65), Expect = 0.99
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 9/97 (9%)
Query: 15 FLSKVNSKDEDVHGSAM-SLASVSSSIYSTPEERQSYELRKLRRELVDAQEKVQTLSSQL 73
K ++KD H M L S S PE +Q L+KL ++L A EK+ + L
Sbjct: 205 VTIKTDAKDWRSHLEQMHQLKKAISK--SLPETKQY--LKKLSQDLSKALEKISSREKHL 260
Query: 74 NTN-SHVVSAFEQ---SLSNMTQRLQQLTVSAEEKLR 106
N +V + + +LS + ++ Q + E R
Sbjct: 261 NNQLEQLVQEYREARRTLSQVQEKYNQASQGVSELTR 297
Score = 26.6 bits (59), Expect = 6.0
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 51 ELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEK 104
E R+ RR L QEK S VS + L+ +++ L+Q+ EE+
Sbjct: 270 EYREARRTLSQVQEKYNQASQG-------VSELTRELNEISEELEQVKQEMEER 316
>gnl|CDD|171459 PRK12388, PRK12388, fructose-1,6-bisphosphatase II-like protein;
Reviewed.
Length = 321
Score = 28.8 bits (64), Expect = 1.0
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 97 LTVSAEEKLRS---SFSKAFSRIVQIALKSPRLQEAANSSSKLTAPKPSESTGDANGKVP 153
L++ + LR+ + K ++ + L PRL A +++L + GD V
Sbjct: 134 LSLPLADNLRNVARALGKPLDKLRMVTLDKPRLSAAIEEATQLGVKVFALPDGDVAASVL 193
Query: 154 TSQQ 157
T Q
Sbjct: 194 TCWQ 197
>gnl|CDD|148169 pfam06401, Alpha-2-MRAP_C, Alpha-2-macroglobulin RAP, C-terminal
domain. The alpha-2-macroglobulin receptor-associated
protein (RAP) is a intracellular glycoprotein that binds
to the 2-macroglobulin receptor and other members of the
low density lipoprotein receptor family. The protein
inhibits binding of all currently known ligands of these
receptors. Two different studies have provided
conflicted domain boundaries.
Length = 205
Score = 28.5 bits (64), Expect = 1.2
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 7/84 (8%)
Query: 51 ELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQR------LQQLTVSAEEK 104
EL L+RE +EK+ +S L T S E +S + L +EK
Sbjct: 25 ELDALKREFQHHKEKIDEYNSLLETLSRTEEIHENVISPSEENDIKEESLHNKHNELKEK 84
Query: 105 LRSSFSKAFSRIVQIALKSPRLQE 128
LR + F R+ +++ + P E
Sbjct: 85 LR-EINDGFDRLRRVSHEGPDSSE 107
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 28.4 bits (64), Expect = 1.6
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 45 EERQSYELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEK 104
E R EL++L R L+ +E + L+ + E+ LSN + L + EE
Sbjct: 73 ERRN--ELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEEL 130
Query: 105 LR 106
+
Sbjct: 131 IA 132
>gnl|CDD|234501 TIGR04211, SH3_and_anchor, SH3 domain protein. Members of this
protein family have a signal peptide, a strongly
conserved SH3 domain, a variable region, and then a
C-terminal hydrophobic transmembrane alpha helix region.
Length = 198
Score = 27.7 bits (62), Expect = 2.2
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 5/78 (6%)
Query: 52 LRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEKLRSSFSK 111
L +L++EL + QE++ L QL +Q LS + L++L + S
Sbjct: 68 LPELQQELAELQEELAELQEQLAELQQENQELKQELSTLEAELERLQKELARIKQLS--- 124
Query: 112 AFSRIVQIALKSPRLQEA 129
+ +++ ++ L+E
Sbjct: 125 --ANAIELDEENRELREE 140
>gnl|CDD|223024 PHA03252, PHA03252, DNA packaging tegument protein UL25;
Provisional.
Length = 589
Score = 28.1 bits (63), Expect = 2.3
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 53 RKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLS 88
R+L EL D Q+++QT L + VS E L
Sbjct: 57 RRLGEELDDLQKRLQTECEDLRSR---VSEAEALLL 89
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 27.7 bits (62), Expect = 2.8
Identities = 20/107 (18%), Positives = 37/107 (34%), Gaps = 8/107 (7%)
Query: 32 SLASVSSSIYSTPEERQSYELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQS---LS 88
L +S E + E + LS LN + ++A L+
Sbjct: 33 LLQEAVNSKRQEEAEPAAEEAELQAELIQQELAINDQLSQALNQQTERLNALASDDRQLA 92
Query: 89 NMTQRLQQLTVSAEE---KLRSSFSKAFSRIVQIAL--KSPRLQEAA 130
N+ +L Q + + E LR S + + Q+ ++ + QE
Sbjct: 93 NLLLQLLQSSRTIREQIAVLRGSLLLSRILLQQLGPLPEAGQPQEQF 139
>gnl|CDD|224665 COG1751, COG1751, Uncharacterized conserved protein [Function
unknown].
Length = 186
Score = 27.5 bits (61), Expect = 2.8
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 61 DAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEKLRSSFSKAFSRIVQIA 120
+ +++++ +++ T SH +S E+S+S L + A E LR F + V+I
Sbjct: 74 EVRKELKERGAKVLTQSHALSGVERSISRKFGGYSPLEIIA-ETLR-MFGQGVKVCVEIT 131
Query: 121 L 121
+
Sbjct: 132 I 132
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 27.3 bits (61), Expect = 3.5
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 51 ELRKLRRELVDA-QEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEK 104
LR+L EL +++ +L + S +S + L + Q LQ+LT++ E
Sbjct: 193 SLRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAIEAL 247
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 27.2 bits (61), Expect = 4.6
Identities = 16/88 (18%), Positives = 36/88 (40%), Gaps = 16/88 (18%)
Query: 16 LSKVNSKDEDVHGSAMSLASVSSSIYSTPEERQSYELRKLRRELVDAQEKVQTLSSQLNT 75
++K N+K + ++ ++ T E + E +L+DA+EK+ L +L
Sbjct: 477 VTKSNAKLVPDD--YIRRQTLKNAERFTTPELKELE-----EKLLDAEEKILALEYEL-- 527
Query: 76 NSHVVSAFEQSLSNMTQRLQQLTVSAEE 103
F++ + + +L A+
Sbjct: 528 -------FDELREKILAHINELQALAKA 548
>gnl|CDD|234897 PRK01096, PRK01096, deoxyguanosinetriphosphate
triphosphohydrolase-like protein; Provisional.
Length = 440
Score = 27.2 bits (61), Expect = 4.9
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 91 TQRL-QQLTVSAEEKLRSSFSKAFSRIV 117
+RL ++ S +E RS F K + RI+
Sbjct: 9 RERLGKKGKTSKDELGRSPFHKDYDRII 36
>gnl|CDD|213852 TIGR03707, PPK2_P_aer, polyphosphate kinase 2, PA0141 family.
Members of this protein family are designated
polyphosphate kinase 2 (PPK2) after the characterized
protein in Pseudomonas aeruginosa. This family
comprises one of three well-separated clades in the
larger family described by pfam03976. PA0141 from this
family has been shown capable of operating in reverse,
with GDP preferred (over ADP) as a substrate, producing
GTP (or ATP) by transfer of a phosphate residue from
polyphosphate. Most species with a member of this
family also encode a polyphosphate kinase 1 (PPK1)
[Central intermediary metabolism, Phosphorus
compounds].
Length = 230
Score = 26.8 bits (60), Expect = 5.0
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 47 RQSYE--LRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFE 84
R+ YE L +L+ ELV QE V+ T + +V FE
Sbjct: 4 RKEYEAELERLQIELVKLQEWVK------ETGARIVIVFE 37
>gnl|CDD|221584 pfam12455, Dynactin, Dynein associated protein. This domain family
is found in eukaryotes, and is approximately 280 amino
acids in length. The family is found in association with
pfam01302. There is a single completely conserved
residue E that may be functionally important. Dynactin
has been associated with Dynein, a kinesin protein which
is involved in organelle transport, mitotic spindle
assembly and chromosome segregation. Dynactin anchors
Dynein to specific subcellular structures.
Length = 274
Score = 26.5 bits (59), Expect = 5.6
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 104 KLRSSFSKAFSRIVQIALKSPRLQEAANSSSKLTA 138
KL++S SKA ++ + + L+ ++AA + L A
Sbjct: 32 KLQASASKAQAKTIDLELRRLEAEQAAEHLAILKA 66
>gnl|CDD|181196 PRK08010, PRK08010, pyridine nucleotide-disulfide oxidoreductase;
Provisional.
Length = 441
Score = 26.9 bits (59), Expect = 5.7
Identities = 18/75 (24%), Positives = 36/75 (48%)
Query: 4 QSVMHSPRNSPFLSKVNSKDEDVHGSAMSLASVSSSIYSTPEERQSYELRKLRRELVDAQ 63
++V +S +P LS+V +E S + V+ + + P R + R + + +VD +
Sbjct: 326 KNVPYSVFMTPPLSRVGMTEEQARESGADIQVVTLPVAAIPRARVMNDTRGVLKAIVDNK 385
Query: 64 EKVQTLSSQLNTNSH 78
+ +S L +SH
Sbjct: 386 TQRILGASLLCVDSH 400
>gnl|CDD|218848 pfam05996, Fe_bilin_red, Ferredoxin-dependent bilin reductase.
This family consists of several different but closely
related proteins which include
phycocyanobilin:ferredoxin oxidoreductase EC:1.3.7.5
(PcyA), 15,16-dihydrobiliverdin:ferredoxin
oxidoreductase EC:1.3.7.2 (PebA) and
phycoerythrobilin:ferredoxin oxidoreductase EC:1.3.7.3
(PebB). Phytobilins are linear tetrapyrrole precursors
of the light-harvesting prosthetic groups of the
phytochrome photoreceptors of plants and the
phycobiliprotein photosynthetic antennae of
cyanobacteria, red algae, and cryptomonads. It is known
that that phytobilins are synthesised from heme via the
intermediary of biliverdin IX alpha (BV), which is
reduced subsequently by ferredoxin-dependent bilin
reductases with different double-bond specificities.
Length = 228
Score = 26.3 bits (59), Expect = 6.4
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 48 QSYELRKLRRELVDAQEKVQTL 69
QS RKLR E DA E +Q L
Sbjct: 43 QSPGFRKLRLERADAGESLQVL 64
>gnl|CDD|226396 COG3879, COG3879, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 247
Score = 26.2 bits (58), Expect = 6.9
Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 29 SAMSLASVSSSI----YSTPEERQSYELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFE 84
AM LA V + R++ +L L +EL Q+KV TL++++ + + +
Sbjct: 26 LAMLLAGVMLAAVFQTSKGESVRRARDL-DLVKELRSLQKKVNTLAAEVEDLENKLDSVR 84
Query: 85 QSLSNMTQRLQ 95
+S+ L+
Sbjct: 85 RSVLTDDAALE 95
>gnl|CDD|179807 PRK04280, PRK04280, arginine repressor; Provisional.
Length = 148
Score = 26.1 bits (58), Expect = 7.5
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 41 YSTPEERQSYELRKLRRELVDA 62
YS P +++ L+KL+R L+D+
Sbjct: 61 YSLPADQRFNPLQKLKRALMDS 82
>gnl|CDD|225953 COG3419, PilY1, Tfp pilus assembly protein, tip-associated adhesin
PilY1 [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 1036
Score = 26.3 bits (58), Expect = 8.3
Identities = 20/115 (17%), Positives = 34/115 (29%), Gaps = 3/115 (2%)
Query: 33 LASVSSSIYSTPEERQSYELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQ 92
LA VS ++P Y L A + + + + + +
Sbjct: 319 LAVVSKPNGTSPVGLNQYYLTTFYGGRCVAPRPNKNTKQPSVASQSTNAEYGADPTASSG 378
Query: 93 RLQQLTVSAEEKLRSSFSKAFSRIVQIALKSPRL---QEAANSSSKLTAPKPSES 144
+ + E + +S + FS I A S NSSS + S
Sbjct: 379 AANFFSAPSAESMVASIKRIFSAISGYASSSAGTALSSGWINSSSGESGSTDYLS 433
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a molecular
chaperone that interacts with unfolded proteins as they
emerge in the periplasm from the Sec translocation
machinery.
Length = 140
Score = 25.6 bits (57), Expect = 8.7
Identities = 14/73 (19%), Positives = 32/73 (43%), Gaps = 5/73 (6%)
Query: 51 ELRKLRRELVDAQEKVQTLSSQLNTNSHVVSA-----FEQSLSNMTQRLQQLTVSAEEKL 105
E +K + EL ++++Q L +L ++ +S E+ L Q Q+ ++ L
Sbjct: 26 EFKKRQAELEKLEKELQKLKEKLQKDAATLSEAAREKKEKELQKKVQEFQRKQQKLQQDL 85
Query: 106 RSSFSKAFSRIVQ 118
+ + +I+
Sbjct: 86 QKRQQEELQKILD 98
>gnl|CDD|185277 PRK15379, PRK15379, pathogenicity island 1 effector protein SopD;
Provisional.
Length = 317
Score = 26.2 bits (57), Expect = 8.9
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 10 PRNSPFLSKVNSKDEDVHGSAMSLASVSSSIYSTPE 45
P NS FL K+N D H M + + +Y T E
Sbjct: 265 PTNSGFLKKLNQDYNDYHAKKMFIDVILEKLYLTHE 300
>gnl|CDD|241471 cd13317, PH_PLEKHO1_PLEKHO2, Pleckstrin homology domain-containing
family O Pleckstrin homology domain. The PLEKHO family
members are PLEKHO1 (also called CKIP-1/Casein kinase
2-interacting protein 1/CK2-interacting protein 1) and
PLEKHO2 (PLEKHQ1/PH domain-containing family Q member
1). They both contain a single PH domain. PLEKHO1 acts
as a scaffold protein that functions in plasma membrane
recruitment, transcriptional activity modulation, and
posttranscriptional modification regulation. As an
adaptor protein it is involved in signaling pathways,
apoptosis, differentiation, cytoskeleton, and bone
formation. Not much is know about PLEKHO2. PH domains
have diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 101
Score = 25.2 bits (55), Expect = 9.7
Identities = 12/67 (17%), Positives = 22/67 (32%), Gaps = 3/67 (4%)
Query: 38 SSIYSTPEERQSYELRKLRRELVDAQEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQL 97
+ + +E++ ++L + Q S+ S N L+
Sbjct: 32 TQLLVYEKEQEVFDLEDYEL---CEYLRCQKSRSKKKRKSRFTLIRSPQPGNKVPDLKFQ 88
Query: 98 TVSAEEK 104
VS EEK
Sbjct: 89 AVSPEEK 95
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 26.1 bits (57), Expect = 10.0
Identities = 27/122 (22%), Positives = 51/122 (41%), Gaps = 14/122 (11%)
Query: 5 SVMHSPRNSPFLSKVNS--KDEDVHGSAMSLASVSSSIYSTPEERQSYELRKLRRELVDA 62
S + S NS F ++V+S D D A ++ S+ IY+ ++ S +
Sbjct: 3549 SPLESFNNSSF-NEVSSLGYDHDFENRAQAV-SMLCQIYAIVIQKHS---------SISP 3597
Query: 63 QEKVQTLSSQLNTNSHVVSAFEQSLSNMTQRLQQLTVSAEEKLRSSFSKAFSRIVQI-AL 121
Q++ + L +N S+ S+ + + + L +K S F +V + +L
Sbjct: 3598 TASFQSIFADLLSNKLFPSSIVSSIRDQQKGINDLIEYCRKKRELPESYCFKHLVSLQSL 3657
Query: 122 KS 123
KS
Sbjct: 3658 KS 3659
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
0.303 0.115 0.286
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,033,128
Number of extensions: 579985
Number of successful extensions: 676
Number of sequences better than 10.0: 1
Number of HSP's gapped: 670
Number of HSP's successfully gapped: 127
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 55 (24.9 bits)