RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5751
(232 letters)
>gnl|CDD|214531 smart00135, LY, Low-density lipoprotein-receptor YWTD domain. Type
"B" repeats in low-density lipoprotein (LDL) receptor
that plays a central role in mammalian cholesterol
metabolism. Also present in a variety of molecules
similar to gp300/megalin.
Length = 43
Score = 51.1 bits (123), Expect = 2e-09
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 79 KVIVSKDLVNPRGIVVHPYYRKLFWSDWNRSGPKIEWSNLDGTDR 123
+ ++S L +P G+ V +L+W+DW IE +NLDGT+R
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGL--DVIEVANLDGTNR 43
Score = 47.6 bits (114), Expect = 4e-08
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 38 VITTNIRSPEGLTFDWVNRVLYWTDSQMDTISMANLN 74
++++ + P GL DW+ LYWTD +D I +ANL+
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLD 39
Score = 34.1 bits (79), Expect = 0.003
Identities = 11/32 (34%), Positives = 14/32 (43%)
Query: 131 DLKLPNSLAVDFRTDELCWVDADSKSLECMTI 162
L PN LAVD+ L W D +E +
Sbjct: 7 GLGHPNGLAVDWIEGRLYWTDWGLDVIEVANL 38
Score = 32.6 bits (75), Expect = 0.012
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 178 FGLSITDEKYYWTDWKTNRIESANKEG 204
+ + + YWTDW + IE AN +G
Sbjct: 14 LAVDWIEGRLYWTDWGLDVIEVANLDG 40
Score = 29.9 bits (68), Expect = 0.12
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 4 GITVDCVEGQVYYSSVADKSSIKRAHLDGKNV 35
G+ VD +EG++Y++ I+ A+LDG N
Sbjct: 13 GLAVDWIEGRLYWTD-WGLDVIEVANLDGTNR 43
>gnl|CDD|215683 pfam00058, Ldl_recept_b, Low-density lipoprotein receptor repeat
class B. This domain is also known as the YWTD motif
after the most conserved region of the repeat. The YWTD
repeat is found in multiple tandem repeats and has been
predicted to form a beta-propeller structure.
Length = 42
Score = 42.2 bits (100), Expect = 4e-06
Identities = 19/40 (47%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 58 LYWTD-SQMDTISMANLNDDQPKVIVSKDLVNPRGIVVHP 96
LYWTD S +IS+A+LN + + S+DL P GI V P
Sbjct: 3 LYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 34.5 bits (80), Expect = 0.002
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 2/43 (4%)
Query: 99 RKLFWSDWNRSGPKIEWSNLDGTDREIFLKAADLKLPNSLAVD 141
+L+W+D + I ++L+G+DR DL+ PN +AVD
Sbjct: 1 GRLYWTDSS-LRASISVADLNGSDRRTLFS-EDLQWPNGIAVD 41
Score = 32.9 bits (76), Expect = 0.008
Identities = 10/42 (23%), Positives = 25/42 (59%)
Query: 12 GQVYYSSVADKSSIKRAHLDGKNVEDVITTNIRSPEGLTFDW 53
G++Y++ + ++SI A L+G + + + +++ P G+ D
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
>gnl|CDD|238765 cd01488, Uba3_RUB, Ubiquitin activating enzyme (E1) subunit UBA3.
UBA3 is part of the heterodimeric activating enzyme
(E1), specific for the Rub family of ubiquitin-like
proteins (Ubls). E1 enzymes are part of a conjugation
cascade to attach Ub or Ubls, covalently to substrate
proteins. consisting of activating (E1), conjugating
(E2), and/or ligating (E3) enzymes. E1 activates
ubiquitin(-like) by C-terminal adenylation, and
subsequently forms a highly reactive thioester bond
between its catalytic cysteine and Ubls C-terminus. E1
also associates with E2 and promotes ubiquitin transfer
to the E2's catalytic cysteine. Post-translational
modification by Rub family of ubiquitin-like proteins
(Ublps) activates SCF ubiquitin ligases and is involved
in cell cycle control, signaling and embryogenesis. UBA3
contains both the nucleotide-binding motif involved in
adenylation and the catalytic cysteine involved in the
thioester intermediate and Ublp transfer to E2.
Length = 291
Score = 33.9 bits (78), Expect = 0.051
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 17/60 (28%)
Query: 65 MDTISMANLND---------DQPKVIVSKDLVNPR--GIVVHPYYRKL------FWSDWN 107
MDTI ++NLN +PK V+ VN R G+ V P++ K+ F+ +N
Sbjct: 31 MDTIDVSNLNRQFLFREKDIGKPKAEVAAKFVNDRVPGVNVTPHFGKIQDKDEEFYRQFN 90
>gnl|CDD|143441 cd07123, ALDH_F4-17_P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, ALDH families 4 and 17.
Delta(1)-pyrroline-5-carboxylate dehydrogenase
(EC=1.5.1.12 ), families 4 and 17: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), also known as ALDH4A1 in humans,
is a mitochondrial homodimer involved in proline
degradation and catalyzes the NAD + -dependent
conversion of P5C to glutamate. This is a necessary step
in the pathway interconnecting the urea and
tricarboxylic acid cycles. The preferred substrate is
glutamic gamma-semialdehyde, other substrates include
succinic, glutaric and adipic semialdehydes. Also
included in this CD is the Aldh17 Drosophila
melanogaster (Q9VUC0) P5CDH and similar sequences.
Length = 522
Score = 32.2 bits (74), Expect = 0.23
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 112 KIEWSNLDGTDR-EIFLKAADL 132
+ EW+ + DR IFLKAADL
Sbjct: 82 RKEWARMPFEDRAAIFLKAADL 103
>gnl|CDD|202944 pfam04253, TFR_dimer, Transferrin receptor-like dimerisation
domain. This domain is involved in dimerisation of the
transferrin receptor as shown in its crystal structure.
Length = 122
Score = 29.5 bits (67), Expect = 0.62
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 21/78 (26%)
Query: 48 GLTFDWVN---------------RVLYWTDSQMDTISMANLNDDQPKVI-VSKDLVNPRG 91
GL+ D + + W + + + +++ ND +++ V + +NP G
Sbjct: 1 GLSLDPLFSAVKKFKKAAKELESWIKNWDNFEPNPLAVRRWND---RLMRVERAFLNPYG 57
Query: 92 IVVHPYYRKLFW--SDWN 107
+ P+YR + + S WN
Sbjct: 58 LPGRPFYRHVIFGPSLWN 75
>gnl|CDD|148156 pfam06380, DUF1072, Protein of unknown function (DUF1072). This
family consists of several Barley yellow dwarf virus
proteins of unknown function.
Length = 39
Score = 26.6 bits (59), Expect = 1.5
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 210 IALDMMGTTYMYGIAAVPSSCPG 232
IA+ ++ T + G+ AV C G
Sbjct: 7 IAVCVLALTVLTGLGAVAGCCVG 29
>gnl|CDD|233324 TIGR01236, D1pyr5carbox1, delta-1-pyrroline-5-carboxylate
dehydrogenase, group 1. This model represents one of
two related branches of delta-1-pyrroline-5-carboxylate
dehydrogenase. The two branches are not as closely
related to each other as some aldehyde dehydrogenases
are to this branch, and separate models are built for
this reason. The enzyme is the second of two in the
degradation of proline to glutamate [Energy metabolism,
Amino acids and amines].
Length = 532
Score = 29.0 bits (65), Expect = 2.5
Identities = 15/22 (68%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 112 KIEWSNLDGTDR-EIFLKAADL 132
K EWS L DR IFLKAADL
Sbjct: 82 KKEWSLLPFYDRAAIFLKAADL 103
>gnl|CDD|143423 cd07105, ALDH_SaliADH, Salicylaldehyde dehydrogenase, DoxF-like.
Salicylaldehyde dehydrogenase (DoxF, SaliADH,
EC=1.2.1.65) involved in the upper naphthalene catabolic
pathway of Pseudomonas strain C18 and other similar
sequences are present in this CD.
Length = 432
Score = 28.7 bits (65), Expect = 2.9
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 114 EWSNLDGTDR-EIFLKAADLKLPNSLAVDFRTDELC 148
WS ++R +I LKAADL ++ R DE
Sbjct: 15 AWSKTPPSERRDILLKAADL-------LESRRDEFI 43
>gnl|CDD|188666 cd08711, RGS_RGS8, Regulator of G protein signaling (RGS) domain
found in the RGS8 protein. The RGS (Regulator of
G-protein Signaling) domain is an essential part of the
RGS8 protein. RGS8 is a member of R4/RGS subfamily of
RGS family, a diverse group of multifunctional proteins
that regulate cellular signaling events downstream of
G-protein coupled receptors (GPCRs). RGS proteins play
critical regulatory roles as GTPase activating proteins
(GAPs) of the heterotrimeric G-protein G-alpha subunits.
The RGS domain controls G-protein signaling by
accelerating the GTPase activity of the G-alpha subunit
which leads to G protein deactivation and promotes
desensitization. As a major G-protein regulator, RGS
domain containing proteins are involved in many crucial
cellular processes such as regulation of intracellular
trafficking, glial differentiation, embryonic axis
formation, skeletal and muscle development, and cell
migration during early embryogenesis. RGS8 is involved
in G-protein-gated potassium channels regulation and
predominantly expressed in the brain. RGS8 also is
selectively expressed in the hematopoietic system (NK
cells).
Length = 125
Score = 27.4 bits (60), Expect = 3.9
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 116 SNLDGTDREIFLKAADLKLPNSLAVDFRTDELCWVDADSKSLECMTIRNRVRRKVYS 172
+ L IF + D++ P + +DF+T E + SL C ++ + KV+S
Sbjct: 54 AKLVSKAHRIFEEFVDVQAPREVNIDFQTREATRKNLQEPSLTCF---DQAQGKVHS 107
>gnl|CDD|182912 PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional.
Length = 330
Score = 27.6 bits (62), Expect = 6.2
Identities = 19/81 (23%), Positives = 30/81 (37%), Gaps = 9/81 (11%)
Query: 24 SIKRAHLDGKNVEDVITT--NIRSPEGLTFDWVNRVLYWTDSQMDTISMANLNDD----- 76
S+ DG I + D NR L+ + D I + L+DD
Sbjct: 105 SVSPLDKDG-IPVAPIQIIEGLEGCHSANIDPDNRTLWVPCLKEDRIRLFTLSDDGHLVA 163
Query: 77 -QPKVIVSKDLVNPRGIVVHP 96
+P + + + PR +V HP
Sbjct: 164 QEPAEVTTVEGAGPRHMVFHP 184
>gnl|CDD|237028 PRK12267, PRK12267, methionyl-tRNA synthetase; Reviewed.
Length = 648
Score = 27.5 bits (62), Expect = 6.9
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 125 IFLKAADLKLPNSLAV 140
I L A L LP +
Sbjct: 274 IMLMALGLPLPKKVFA 289
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 26.8 bits (60), Expect = 9.7
Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 17 SSVADKSSIKRAHLDGKNVEDVITTNIR 44
SS A S IK AH GK++E VI T R
Sbjct: 130 SSAA-LSVIKTAHEQGKDIE-VIATETR 155
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
0.318 0.134 0.420
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,771,949
Number of extensions: 1078265
Number of successful extensions: 746
Number of sequences better than 10.0: 1
Number of HSP's gapped: 743
Number of HSP's successfully gapped: 27
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
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 (21.7 bits)
S2: 57 (25.6 bits)