RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7771
(193 letters)
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 31.2 bits (70), Expect = 0.36
Identities = 17/107 (15%), Positives = 31/107 (28%)
Query: 22 EALPQRQPLYQNPRYSESTHPVRQNYISPSLRTTRRAAKPNQPTSYSHQTAEYYRPNYQP 81
+ + +QP Y + P + A P QP + + AE + + P
Sbjct: 399 QPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAWQAEEQQSTFAP 458
Query: 82 SGQNQYYDPSYQPSNYQESYNPNPAAFKPSFDPSTFDPANFEPSYEP 128
Q QP+ + Y + +P+ P
Sbjct: 459 QSTYQTEQTYQQPAAQEPLYQQPQPVEQQPVVEPEPVVEETKPARPP 505
>gnl|CDD|178266 PLN02660, PLN02660, pantoate--beta-alanine ligase.
Length = 284
Score = 29.6 bits (67), Expect = 0.87
Identities = 18/71 (25%), Positives = 23/71 (32%), Gaps = 17/71 (23%)
Query: 104 NPAAFKPSFDPSTFDPANFEPSYEPSSFQPTALKKAPLPSKVTDH----DNSESRLERQS 159
NP F P D T+ P F K A L D + +
Sbjct: 57 NPGQFAPGEDLDTY----------PRDFDGDLRKLAAL---GVDAVFNPHDLYVYVSCLE 103
Query: 160 GGGGGHDTYVD 170
GG GH+T+V
Sbjct: 104 EGGAGHETWVR 114
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 29.3 bits (65), Expect = 1.2
Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 6/86 (6%)
Query: 47 YISPSLRTTRRAAKPNQP----TSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYN 102
YI P+ R A P P +S+ H+ +P QP+ QN P+ Q Q
Sbjct: 171 YIPPN--PPREAPAPGLPKTFTSSHGHRHRHAPKPTQQPTVQNPAQQPTVQNPAQQPQQQ 228
Query: 103 PNPAAFKPSFDPSTFDPANFEPSYEP 128
P +P+ P+ +PA P E
Sbjct: 229 PQQQPVQPAQQPTPQNPAQQPPQTEQ 254
>gnl|CDD|200456 cd11317, AmyAc_bac_euk_AmyA, Alpha amylase catalytic domain found
in bacterial and eukaryotic Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes AmyA proteins from bacteria, fungi, mammals,
insects, mollusks, and nematodes. The Alpha-amylase
family comprises the largest family of glycoside
hydrolases (GH), with the majority of enzymes acting on
starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 329
Score = 28.7 bits (65), Expect = 1.7
Identities = 15/35 (42%), Positives = 18/35 (51%), Gaps = 10/35 (28%)
Query: 141 LPSK-----VTDHDNSESRLERQSGGGGGHDTYVD 170
LPS+ V +HDN +R GGGG TY D
Sbjct: 224 LPSERAVVFVDNHDN-----QRGHGGGGDMLTYKD 253
>gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of
mammalian PITPNA, -B, and related proteins (Class I
PITPs). This subgroup includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of
mammalian Class 1 phosphatidylinositol transfer proteins
(PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta,
Drosophila vibrator, and related proteins. These are
single domain proteins belonging to the PITP family of
lipid transfer proteins, and to the SRPBCC domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. In vitro, PITPs bind phosphatidylinositol
(PtdIns), as well as phosphatidylcholine (PtdCho) but
with a lower affinity. They transfer these lipids from
one membrane compartment to another. The cellular roles
of PITPs include inositol lipid signaling, PtdIns
metabolism, and membrane trafficking. In addition,
PITPNB transfers sphingomyelin in vitro, with a low
affinity. PITPNA is found chiefly in the nucleus and
cytoplasm; it is enriched in the brain and predominantly
localized in the axons. A reduced expression of PITPNA
contributes to the neurodegenerative phenotype of the
mouse vibrator mutation. The role of PITPNA in vivo may
be to provide PtdIns for localized PI3K-dependent
signaling, thereby controlling the polarized extension
of axonal processes. PITPNA homozygous null mice die
soon after birth from complicated organ failure,
including intestinal and hepatic steatosis,
hypoglycemia, and spinocerebellar disease. PITPNB is
associated with the Golgi and ER, and is highly
expressed in the liver. Deletion of the PITPNB gene
results in embryonic lethality. The PtdIns and PtdCho
exchange activity of PITPNB is required for
COPI-mediated retrograde transport from the Golgi to the
ER. Drosophila vibrator localizes to the ER, and has an
essential role in cytokinesis during mitosis and
meiosis.
Length = 258
Score = 28.2 bits (63), Expect = 2.3
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 113 DPSTFDPANFEPSYEPSSFQPTALKKAPL 141
D S DP +++ +P+ FQ + PL
Sbjct: 144 DRSQVDPKDYKADEDPAKFQSEKTGRGPL 172
>gnl|CDD|177847 PLN02196, PLN02196, abscisic acid 8'-hydroxylase.
Length = 463
Score = 28.4 bits (63), Expect = 2.5
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 113 DPSTFDPANFEPSYEPSSFQP 133
DP FDP+ FE + +P++F P
Sbjct: 383 DPGKFDPSRFEVAPKPNTFMP 403
>gnl|CDD|236571 PRK09565, PRK09565, hypothetical protein; Reviewed.
Length = 533
Score = 28.2 bits (63), Expect = 2.8
Identities = 18/79 (22%), Positives = 24/79 (30%), Gaps = 13/79 (16%)
Query: 112 FDPSTFDPANFEPSYEPSSFQPTALKK----APLPSK----VTDHDNSESRLERQSGGGG 163
FDPS+ A F Y F P+ L +P+ D + + G G
Sbjct: 228 FDPSSSKFAEFGRFYVGRRFPPSDLGAFLAGERVPTATPEDAADGGTGGTHDAEEFGEHG 287
Query: 164 GHDTYVDFGAHTGHHGSFG 182
H G G G
Sbjct: 288 HHG-----GHPGGEDGEHP 301
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 28.1 bits (63), Expect = 3.1
Identities = 21/94 (22%), Positives = 28/94 (29%), Gaps = 2/94 (2%)
Query: 50 PSLRTTRRAAKPNQPTSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYNPNPAAFK 109
P + P +P QP+ Q Q P QP + Q + P P
Sbjct: 101 PRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPVHSA 160
Query: 110 PSFDPSTFDPAN--FEPSYEPSSFQPTALKKAPL 141
P F PA P EP + + K
Sbjct: 161 PQPAQQAFQPAEPVAAPQPEPVAEPAPVMDKPKR 194
>gnl|CDD|171613 PRK12621, flgB, flagellar basal body rod protein FlgB; Provisional.
Length = 136
Score = 27.0 bits (60), Expect = 4.2
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 114 PSTFDPANFEPSYEPSSFQPT 134
P+ FDP FEP + +F+P
Sbjct: 70 PAVFDPEGFEPEWS-KAFKPR 89
>gnl|CDD|217990 pfam04257, Exonuc_V_gamma, Exodeoxyribonuclease V, gamma subunit.
The Exodeoxyribonuclease V enzyme is a multi-subunit
enzyme comprised of the proteins RecB, RecC (this
family) and RecD. This enzyme plays an important role in
homologous genetic recombination, repair of double
strand DNA breaks resistance to UV irradiation and
chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes
ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of
ssDNA or dsDNA and unwinding of dsDNA. This family
consists of two AAA domains.
Length = 756
Score = 28.0 bits (63), Expect = 4.4
Identities = 6/23 (26%), Positives = 7/23 (30%)
Query: 117 FDPANFEPSYEPSSFQPTALKKA 139
F P F S+ L A
Sbjct: 704 FSPRYFTEDGRLFSYDREWLAAA 726
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 27.3 bits (61), Expect = 5.5
Identities = 14/97 (14%), Positives = 28/97 (28%), Gaps = 5/97 (5%)
Query: 61 PNQPTSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSNYQESYNPNPAAFKPSFDPSTFDPA 120
P P+ S + + P + + NP+P P P
Sbjct: 192 PGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPP---PGPAAPPPPPV 248
Query: 121 NFEPSYEPSSFQPTALKKAPLPSKVTDHDNSESRLER 157
P S+ +PT + P+ + + + +
Sbjct: 249 QQVPP--LSTAKPTPPSASATPAPIGGITLDDDAIAK 283
>gnl|CDD|220032 pfam08819, DUF1802, Domain of unknown function (DUF1802). The
function of this family is unknown. This region is
found associated with a pfam04471 suggesting they could
be part of a restriction modification system..
Length = 177
Score = 26.9 bits (60), Expect = 5.8
Identities = 7/18 (38%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 64 PTSYSHQTAEYYRPNYQP 81
PT HQ E RP ++
Sbjct: 45 PT-VFHQNPELLRPEFRD 61
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 27.3 bits (60), Expect = 6.1
Identities = 20/85 (23%), Positives = 30/85 (35%), Gaps = 5/85 (5%)
Query: 65 TSYSHQTAEYYRPNYQPSGQNQYYDPSY-QPSNYQESYNPNPAAFKPSFDPSTFDPANFE 123
++ + A + Y G +P Y N YN P + P +P +P
Sbjct: 400 SNAAQSNAGFSNAGYSNPG---NSNPGYNNAPNSNTPYNNPPNSNTPYSNPPNSNPPYSN 456
Query: 124 PSYEPSSFQPTALKKAPLPSKVTDH 148
Y + + L AP PS DH
Sbjct: 457 LPYSNTPYSNAPLSNAP-PSSAKDH 480
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 26.8 bits (60), Expect = 6.3
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 4/26 (15%)
Query: 1 MSLLINLCTILLTLTTLMLQ-AEALP 25
++L I T LLT+T +L E+LP
Sbjct: 27 VTLGI---TTLLTMTVFLLLIRESLP 49
>gnl|CDD|237216 PRK12821, PRK12821, aspartyl/glutamyl-tRNA amidotransferase subunit
C-like protein; Provisional.
Length = 477
Score = 27.2 bits (60), Expect = 6.8
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 111 SFDPST-FDPANFEPSYEPSSFQPTALKK 138
SF D N +P Y P S PT L+K
Sbjct: 423 SFKQVEKIDTTNVKPMYAPFSNSPTPLRK 451
>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
Provisional.
Length = 494
Score = 26.9 bits (60), Expect = 7.7
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 108 FKPSFDPSTFDPANFEPSYEPSSFQPTALKK 138
FKP+F+P T EPS E + P LKK
Sbjct: 415 FKPAFNPYT------EPSMEIFGYHPG-LKK 438
>gnl|CDD|225401 COG2845, COG2845, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 354
Score = 26.7 bits (59), Expect = 9.7
Identities = 16/102 (15%), Positives = 26/102 (25%), Gaps = 15/102 (14%)
Query: 45 QNYISPSLRTTRRAAKPNQP--------TSYSHQTAEYYRPNYQPSGQNQYYDPSYQPSN 96
QN I+ T +P ++ Q P ++ P
Sbjct: 23 QNVINAFFAQTYHRQEPLGRRTVFEWLRGGFALQE----NPYQNREWILRFRQGFPPPIA 78
Query: 97 YQESYNPNP-AAFKPSFDPSTFDPANFEPSYEPSSFQPTALK 137
P A+ P A EP+ ++ A K
Sbjct: 79 KVGPSLDMPRASAASEVAPRPGATA--EPATTIAAKSRDADK 118
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 0.129 0.396
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,817,114
Number of extensions: 867745
Number of successful extensions: 696
Number of sequences better than 10.0: 1
Number of HSP's gapped: 675
Number of HSP's successfully gapped: 48
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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: 56 (25.5 bits)