RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5768
(652 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 = 57.6 bits (140), Expect = 4e-11
Identities = 17/43 (39%), Positives = 27/43 (62%)
Query: 439 ESIITTDITMPNALALDHQAEKLFWGDARLDKIERCDYDGTNR 481
+++++ + PN LA+D +L+W D LD IE + DGTNR
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 47.2 bits (113), Expect = 2e-07
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 92 HIAVDWIAQNIYWSDPKENVIEVARLTGQYR 122
+AVDWI +YW+D +VIEVA L G R
Sbjct: 13 GLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 44.1 bits (105), Expect = 2e-06
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 123 YVLISGGVDQPSALAVDPESGYLFWSESGKIPLIARAGLDGK 164
L+S G+ P+ LAVD G L+W++ G +I A LDG
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGL-DVIEVANLDGT 41
Score = 39.1 bits (92), Expect = 2e-04
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 392 RIVVVRLGQHDKPRGIDIDSCDSRIYWTNWNSHLPSIQRAFFSG 435
R ++ H P G+ +D + R+YWT+W L I+ A G
Sbjct: 1 RTLLSSGLGH--PNGLAVDWIEGRLYWTDW--GLDVIEVANLDG 40
Score = 36.4 bits (85), Expect = 0.002
Identities = 13/38 (34%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 37 LSKISSIAVWPVKGKMFWSNVTKQVVTIEMAFMDGTKR 74
L + +AV ++G+++W++ V IE+A +DGT R
Sbjct: 8 LGHPNGLAVDWIEGRLYWTDWGLDV--IEVANLDGTNR 43
Score = 31.4 bits (72), Expect = 0.087
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 348 HRVLLERQGSVEGLAYEYVHNYLYWTCNNDATINKIDLD 386
+L G GLA +++ LYWT I +LD
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLD 39
Score = 31.0 bits (71), Expect = 0.13
Identities = 8/39 (20%), Positives = 18/39 (46%)
Query: 310 STMMKNIIELSYDYKRKTLFYSDIQKGTINSVFFNGSNH 348
S+ + + L+ D+ L+++D I +G+N
Sbjct: 5 SSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 29.5 bits (67), Expect = 0.49
Identities = 7/43 (16%), Positives = 15/43 (34%), Gaps = 1/43 (2%)
Query: 481 RIVLSKISPLHPFDMAVYGEFIFWTDWVIHAVLRANKYTGEEV 523
++ S + + + ++WTDW V+ G
Sbjct: 2 TLLSSGLGHPNGLAVDWIEGRLYWTDWG-LDVIEVANLDGTNR 43
>gnl|CDD|238060 cd00112, LDLa, Low Density Lipoprotein Receptor Class A domain, a
cysteine-rich repeat that plays a central role in
mammalian cholesterol metabolism; the receptor protein
binds LDL and transports it into cells by endocytosis; 7
successive cysteine-rich repeats of about 40 amino acids
are present in the N-terminal of this multidomain
membrane protein; other homologous domains occur in
related receptors, including the very low-density
lipoprotein receptor and the LDL receptor-related
protein/alpha 2-macroglobulin receptor, and in proteins
which are functionally unrelated, such as the C9
component of complement; the binding of calcium is
required for in vitro formation of the native disulfide
isomer and is necessary in establishing and maintaining
the modular structure.
Length = 35
Score = 48.7 bits (117), Expect = 5e-08
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 593 CSEHDFKCSDGMCIPFNQTCDRVYNCHDKSDE 624
C ++F+C++G CIP + CD +C D SDE
Sbjct: 1 CPPNEFRCANGRCIPSSWVCDGEDDCGDGSDE 32
Score = 28.3 bits (64), Expect = 0.91
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 634 CRPGYFKCDNNKCILSS 650
C P F+C N +CI SS
Sbjct: 1 CPPNEFRCANGRCIPSS 17
>gnl|CDD|197566 smart00192, LDLa, Low-density lipoprotein receptor domain class A.
Cysteine-rich repeat in the low-density lipoprotein
(LDL) receptor that plays a central role in mammalian
cholesterol metabolism. The N-terminal type A repeats in
LDL receptor bind the lipoproteins. Other homologous
domains occur in related receptors, including the very
low-density lipoprotein receptor and the LDL
receptor-related protein/alpha 2-macroglobulin receptor,
and in proteins which are functionally unrelated, such
as the C9 component of complement. Mutations in the LDL
receptor gene cause familial hypercholesterolemia.
Length = 33
Score = 48.4 bits (116), Expect = 6e-08
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 593 CSEHDFKCSDGMCIPFNQTCDRVYNCHDKSDE 624
C +F+C +G CIP + CD V +C D SDE
Sbjct: 2 CPPGEFQCDNGRCIPSSWVCDGVDDCGDGSDE 33
Score = 28.4 bits (64), Expect = 0.89
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 634 CRPGYFKCDNNKCILSS 650
C PG F+CDN +CI SS
Sbjct: 2 CPPGEFQCDNGRCIPSS 18
>gnl|CDD|200964 pfam00057, Ldl_recept_a, Low-density lipoprotein receptor domain
class A.
Length = 37
Score = 45.7 bits (109), Expect = 7e-07
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 591 TVCSEHDFKCSDGMCIPFNQTCDRVYNCHDKSDE 624
+ C +F+C G CIP + CD +C D SDE
Sbjct: 1 STCGPDEFQCGSGECIPMSWVCDGDPDCEDGSDE 34
>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 = 41.0 bits (97), Expect = 4e-05
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 100 QNIYWSDPK-ENVIEVARLTGQYRYVLISGGVDQPSALAVDP 140
+YW+D I VA L G R L S + P+ +AVDP
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 40.2 bits (95), Expect = 7e-05
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 415 RIYWTNWNSHLPSIQRAFFSGFGTESIITTDITMPNALALDH 456
R+YWT+ + SI A +G ++ + D+ PN +A+D
Sbjct: 2 RLYWTDSSLR-ASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 34.5 bits (80), Expect = 0.007
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 500 EFIFWTDWVIHAVLRANKYTGEEVYTL-RKNIRRPMGIV 537
++WTD + A + G + TL ++++ P GI
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIA 39
Score = 32.1 bits (74), Expect = 0.041
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 14/52 (26%)
Query: 50 GKMFWSNVTKQVVTIEMAFMDGTKRETVVSQKKYPAVTACNLH----IAVDW 97
G+++W++ +I +A ++G+ R T+ S+ +L IAVD
Sbjct: 1 GRLYWTDS-SLRASISVADLNGSDRRTLFSE---------DLQWPNGIAVDP 42
Score = 29.8 bits (68), Expect = 0.32
Identities = 12/42 (28%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 143 GYLFWSESGKIPLIARAGLDGKKQ-TILAQEIIMPIKDITLD 183
G L+W++S I+ A L+G + T+ ++++ P I +D
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWP-NGIAVD 41
>gnl|CDD|176475 cd08638, DNA_pol_A_theta, DNA polymerase theta is a low-fidelity
family A enzyme implicated in translesion synthesis and
in somatic hypermutation. DNA polymerase theta is a
low-fidelity family A enzyme implicated in translesion
synthesis (TLS) and in somatic hypermutation (SHM).
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
Pol theta is an exception among family A polymerases and
generates processive single base substitutions. Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
(pol I) ,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. Polymerase theta mostly has
amino-terminal helicase domain, a carboxy-terminal
polymerase domain and an intervening space region.
Length = 373
Score = 36.4 bits (85), Expect = 0.043
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 453 ALDHQAEKLFWGDARLDKIERCDYDGTNRIVLSKISPLHPF 493
L+ Q L A+L ++E Y T++ VL ++ LHP
Sbjct: 8 ELERQRALL---QAKLKELEEEAYRSTSKEVLEQLKRLHPL 45
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 35.8 bits (83), Expect = 0.058
Identities = 44/207 (21%), Positives = 69/207 (33%), Gaps = 26/207 (12%)
Query: 321 YDYKRKTLFYSDIQKGTINSVFFNGSNHRVLLERQGSVEGLAYEYVHNYLYWTCNNDATI 380
+D R L + DI G I+ + RV G G + C + +
Sbjct: 32 WDPDRGALLWVDILGGRIHRLDPETGKKRVFPSPGGFSSGALIDA--GGRLIAC--EHGV 87
Query: 381 NKIDLDSPKAQRIVVVRLGQHDKP--RGIDID-SCDSRIYWT---------NWNSHLPSI 428
+D D+ ++ + P R D D RI++ + S+
Sbjct: 88 RLLDPDTGGKITLLAEP--EDGLPLNRPNDGVVDPDGRIWFGDMGYFDLGKSEERPTGSL 145
Query: 429 QRAFFSGFGTESIITTDITMPNALALDHQAEKLFWGDARLDKIERCDYD-------GTNR 481
R G ++ D+T+PN LA + L+ D ++I R D D G
Sbjct: 146 YR-VDPDGGVVRLLDDDLTIPNGLAFSPDGKTLYVADTPANRIHRYDLDPATGPIGGRRG 204
Query: 482 IVLSKISPLHPFDMAVYGEFIFWTDWV 508
V P P MAV + W V
Sbjct: 205 FVDFDEEPGLPDGMAVDADGNLWVAAV 231
>gnl|CDD|225926 COG3391, COG3391, Uncharacterized conserved protein [Function
unknown].
Length = 381
Score = 34.1 bits (78), Expect = 0.20
Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 7/111 (6%)
Query: 318 ELSYDYKRKTLFYSDIQKGTINSVFFNGSNHRVLLERQGSV----EGLAYEYVHNYLYWT 373
L+ D K ++ ++ G + + ++V V G+A + N +Y T
Sbjct: 120 GLAVDPDGKYVYVANAGNGNNTVSVIDAATNKVTAT--IPVGNTPTGVAVDPDGNKVYVT 177
Query: 374 CNNDATINKIDLDSPKAQR-IVVVRLGQHDKPRGIDIDSCDSRIYWTNWNS 423
++D T++ ID R V +G P GI +D +R+Y N S
Sbjct: 178 NSDDNTVSVIDTSGNSVVRGSVGSLVGVGTGPAGIAVDPDGNRVYVANDGS 228
>gnl|CDD|180659 PRK06690, PRK06690, acetyl-CoA acetyltransferase; Provisional.
Length = 361
Score = 33.6 bits (77), Expect = 0.28
Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 194 LSKGNIH--IISLSNLSDVSTISMKPYGDSYLKDIKIYSKDAQ-TGTNPCGVNNGGCAEL 250
L KG IH I+S + L D S Y + + + T N CGVN+G CA L
Sbjct: 166 LEKGYIHEEILSFNGLLDESIKKEMNYERIIKRTKPAFLHNGTVTAGNSCGVNDGACAVL 225
Query: 251 CL 252
+
Sbjct: 226 VM 227
>gnl|CDD|219847 pfam08450, SGL, SMP-30/Gluconolaconase/LRE-like region. This
family describes a region that is found in proteins
expressed by a variety of eukaryotic and prokaryotic
species. These proteins include various enzymes, such as
senescence marker protein 30 (SMP-30), gluconolactonase
and luciferin-regenerating enzyme (LRE). SMP-30 is known
to hydrolyse diisopropyl phosphorofluoridate in the
liver, and has been noted as having sequence similarity,
in the region described in this family, with PON1 and
LRE.
Length = 245
Score = 32.6 bits (75), Expect = 0.43
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 437 GTESIITTDITMPNALALDHQAEKLFWGDARLDKIERCDYDGTNRIVLSKISPLHPF 493
G + IT+ N LA + L++ D+ +I DYD IS F
Sbjct: 123 GKVERVLDGITISNGLAWSPDGKTLYFADSPTRRIWAFDYDADG----GLISNRRVF 175
>gnl|CDD|185070 PRK15115, PRK15115, response regulator GlrR; Provisional.
Length = 444
Score = 32.9 bits (75), Expect = 0.50
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 127 SGGVDQPSALAVDPESGYLFWSESGKIPLIARAGLDGKKQTILAQEIIMPI---KDITLD 183
+G V L E G LF E G +P L K +L + + P+ +DI +D
Sbjct: 214 TGAVSNREGLFQAAEGGTLFLDEIGDMPA----PLQVKLLRVLQERKVRPLGSNRDIDID 269
Query: 184 LKFFSAFYRNLSK 196
++ SA +R+L K
Sbjct: 270 VRIISATHRDLPK 282
>gnl|CDD|205157 pfam12947, EGF_3, EGF domain. This family includes a variety of
EGF-like domain homologues. This family includes the
C-terminal domain of the malaria parasite MSP1 protein.
Length = 36
Score = 29.0 bits (66), Expect = 0.51
Identities = 15/37 (40%), Positives = 16/37 (43%), Gaps = 3/37 (8%)
Query: 240 CGVNNGGCAE--LCLYNGVSAVCACAHGVVAQDGKSC 274
C NNGGC C G S C C G DG +C
Sbjct: 1 CAENNGGCHPNATCTNTGGSFTCTCKSGYTG-DGVTC 36
>gnl|CDD|173479 PTZ00214, PTZ00214, high cysteine membrane protein Group 4;
Provisional.
Length = 800
Score = 32.2 bits (73), Expect = 0.99
Identities = 23/56 (41%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 228 IYSKDAQTGTNP--CG--VNNG--GCAELCLYNGVSAVCA-CAHGVVAQDGKSCSE 276
I+SK+ + CG N G GCA C YN + C C+ G + DGKSCSE
Sbjct: 339 IFSKNDDNNGDGYLCGDATNGGVSGCAT-CGYNSGAVTCTRCSAGYLGVDGKSCSE 393
>gnl|CDD|99943 cd05511, Bromo_TFIID, Bromodomain, TFIID-like subfamily. Human
TAFII250 (or TAF250) is the largest subunit of TFIID, a
large multi-domain complex, which initiates the assembly
of the transcription machinery. TAFII250 contains two
bromodomains that specifically bind to acetylated
histone H4. Bromodomains are 110 amino acid long
domains, that are found in many chromatin associated
proteins. Bromodomains can interact specifically with
acetylated lysine.
Length = 112
Score = 29.9 bits (68), Expect = 1.1
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 310 STMMKNIIELSYDYKRKTLFYSDIQKGTINSVFFNGSNHR 349
T+ K I + Y+ + F DI+ NSV +NG +
Sbjct: 44 QTIRKKI--SKHKYQSREEFLEDIELIVDNSVLYNGPDSV 81
>gnl|CDD|235212 PRK04043, tolB, translocation protein TolB; Provisional.
Length = 419
Score = 30.0 bits (68), Expect = 4.0
Identities = 28/124 (22%), Positives = 62/124 (50%), Gaps = 12/124 (9%)
Query: 72 TKRETVVSQKKYP-----AVTACNLHI---AVDWIAQNIYWS---DPKENVIEVARLTGQ 120
K T+ S +YP + N ++ ++DW+ + + +S PK++ I +A T
Sbjct: 120 EKDYTINSLDRYPFLAHKSAIDINDYLKAPSIDWMKRKVVFSKYTGPKKSNIVLADYTLT 179
Query: 121 YRYVLISGGVDQPSALAVDPESGYLFWSESGKIPLIARAGL-DGKKQTILAQEIIMPIKD 179
Y+ V++ GG++ A ++ + + S + P + + L GKK+ I + + ++ + D
Sbjct: 180 YQKVIVKGGLNIFPKWANKEQTAFYYTSYGERKPTLYKYNLYTGKKEKIASSQGMLVVSD 239
Query: 180 ITLD 183
++ D
Sbjct: 240 VSKD 243
>gnl|CDD|236594 PRK09618, flgD, flagellar basal body rod modification protein;
Provisional.
Length = 142
Score = 28.4 bits (64), Expect = 5.6
Identities = 8/40 (20%), Positives = 15/40 (37%), Gaps = 5/40 (12%)
Query: 94 AVDWIAQNIYWSDPKENVIE-----VARLTGQYRYVLISG 128
+ I + + W ++ V + G Y VL +G
Sbjct: 87 YSELIGKEVEWEGEDGEIVSGTVTSVKQKDGDYPLVLDNG 126
>gnl|CDD|193472 pfam12999, PRKCSH-like, Glucosidase II beta subunit-like. The
sequences found in this family are similar to a region
found in the beta-subunit of glucosidase II, which is
also known as protein kinase C substrate 80K-H (PRKCSH).
The enzyme catalyzes the sequential removal of two
alpha-1,3-linked glucose residues in the second step of
N-linked oligosaccharide processing. The beta subunit is
required for the solubility and stability of the
heterodimeric enzyme, and is involved in retaining the
enzyme within the endoplasmic reticulum.
Length = 176
Score = 28.6 bits (64), Expect = 8.2
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 13/65 (20%)
Query: 595 EHDFKC--SDGMCIPFNQTCDRVYNCHDKSDE--------GILYCAMRDCRPGY---FKC 641
++KC + + F+Q D +C D SDE G YCA PGY FK
Sbjct: 35 NGNWKCLNHSEIKLSFDQVNDDYCDCPDGSDEPGTNACSNGKFYCANEGFIPGYIPSFKV 94
Query: 642 DNNKC 646
D+ C
Sbjct: 95 DDGVC 99
>gnl|CDD|213273 cd05905, Dip2, Disco-interacting protein 2 (Dip2). Dip2 proteins
show sequence similarity to other members of the
adenylate forming enzyme family, including insect
luciferase, acetyl CoA ligases and the adenylation
domain of nonribosomal peptide synthetases (NRPS).
However, its function may have diverged from other
members of the superfamily. In mouse embryo, Dip2
homolog A plays an important role in the development of
both vertebrate and invertebrate nervous systems. Dip2A
appears to regulate cell growth and the arrangement of
cells in organs. Biochemically, Dip2A functions as a
receptor of FSTL1, an extracellular glycoprotein, and
may play a role as a cardiovascular protective agent.
Length = 556
Score = 29.0 bits (65), Expect = 9.2
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 248 AELCLYNGVSAVCACAHGVVAQDGKSCSEYDAFIMYSRV-NRIDSIH 293
+Y G AV + VV + SE ++F RV N I S H
Sbjct: 475 VHPMIYRGRIAVFSVTERVVVVAEQRGSEEESFQWVPRVLNAILSEH 521
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
0.320 0.135 0.420
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,483,960
Number of extensions: 3150880
Number of successful extensions: 2218
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2213
Number of HSP's successfully gapped: 39
Length of query: 652
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 549
Effective length of database: 6,369,140
Effective search space: 3496657860
Effective search space used: 3496657860
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 (21.8 bits)
S2: 62 (27.6 bits)