RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13635
(357 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 = 55.7 bits (135), Expect = 1e-10
Identities = 21/36 (58%), Positives = 27/36 (75%)
Query: 175 VEHPDGVAVDWVARNLYWTDTGTDRIEVCRLEGTHR 210
+ HP+G+AVDW+ LYWTD G D IEV L+GT+R
Sbjct: 8 LGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 52.6 bits (127), Expect = 1e-09
Identities = 18/41 (43%), Positives = 24/41 (58%)
Query: 258 LVKDRLGWPNGITLDVDNEKLYWCDAKTDKIEMIDFDGNNR 298
L+ LG PNG+ +D +LYW D D IE+ + DG NR
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 51.8 bits (125), Expect = 3e-09
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 111 VITNGLITPDGLAIDWLTEKLYWTDSETNKLEVSSLDGKKR 151
++++GL P+GLA+DW+ +LYWTD + +EV++LDG R
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVANLDGTNR 43
Score = 46.8 bits (112), Expect = 2e-07
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 211 KVLVNTDLVEPRAITLSPAHGYLFWSDWNEKRPKIERSLLNGGER 255
+ L+++ L P + + G L+W+DW IE + L+G R
Sbjct: 1 RTLLSSGLGHPNGLAVDWIEGRLYWTDW--GLDVIEVANLDGTNR 43
Score = 39.1 bits (92), Expect = 1e-04
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 301 LINENLPHVFGISL--LGDYVYWTDWQRRSIDRVNKITGNDR 340
L++ L H G+++ + +YWTDW I+ N + G +R
Sbjct: 3 LLSSGLGHPNGLAVDWIEGRLYWTDWGLDVIEVAN-LDGTNR 43
Score = 31.8 bits (73), Expect = 0.030
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 75 AIDYYYKKSMVCWTDHGTEMISCCTFDGNNV 105
A+D+ + + WTD G ++I DG N
Sbjct: 15 AVDWIEGR--LYWTDWGLDVIEVANLDGTNR 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 = 46.0 bits (110), Expect = 3e-07
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 231 GYLFWSDWNEKRPKIERSLLNGGERVLLVKDRLGWPNGITLD 272
G L+W+D + R I + LNG +R L + L WPNGI +D
Sbjct: 1 GRLYWTDSSL-RASISVADLNGSDRRTLFSEDLQWPNGIAVD 41
Score = 39.8 bits (94), Expect = 4e-05
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 188 RNLYWTDTGTD-RIEVCRLEGTHRKVLVNTDLVEPRAITLSP 228
LYWTD+ I V L G+ R+ L + DL P I + P
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAVDP 42
Score = 38.3 bits (90), Expect = 2e-04
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 129 EKLYWTDSET-NKLEVSSLDGKKRKVLYWEDIDQPRAIA 166
+LYWTDS + V+ L+G R+ L+ ED+ P IA
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIA 39
Score = 35.2 bits (82), Expect = 0.002
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 276 EKLYWCDAKTD-KIEMIDFDGNNRRELINENLPHVFGISL 314
+LYW D+ I + D +G++RR L +E+L GI++
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLFSEDLQWPNGIAV 40
Score = 31.8 bits (73), Expect = 0.030
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 87 WTDHGTEM-ISCCTFDGNNVGSKHNVITNGLITPDGLAIDW 126
WTD IS +G + + + L P+G+A+D
Sbjct: 5 WTDSSLRASISVADLNG---SDRRTLFSEDLQWPNGIAVDP 42
Score = 27.9 bits (63), Expect = 0.78
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 317 DYVYWTDWQRRSIDRVNKITGNDREVII 344
+YWTD R+ V + G+DR +
Sbjct: 1 GRLYWTDSSLRASISVADLNGSDRRTLF 28
>gnl|CDD|225926 COG3391, COG3391, Uncharacterized conserved protein [Function
unknown].
Length = 381
Score = 46.8 bits (111), Expect = 9e-06
Identities = 39/215 (18%), Positives = 73/215 (33%), Gaps = 32/215 (14%)
Query: 98 CTFDGNNVGSKHNVITNGLIT-------PDGLAIDWLTEKLYWTDSETNKLEVSSLDGKK 150
T D N V S + TN ++ P GLA+D + +Y ++ VS +D
Sbjct: 91 TTGDSNTV-SVIDTATNTVLGSIPVGLGPVGLAVDPDGKYVYVANAGNGNNTVSVIDAAT 149
Query: 151 RKVLYWEDIDQPRAIASYKLPTIEVEHPDGVAVDWVARNLYWTDTGTDRIEVCRLEG--- 207
KV + P GVAVD +Y T++ + + V G
Sbjct: 150 NKVTATIPVG---------------NTPTGVAVDPDGNKVYVTNSDDNTVSVIDTSGNSV 194
Query: 208 -THRKVLVNTDLVEPRAITLSPAHGYLFWSDWNEKRPKIERSLLNGGERVLLVKDR---L 263
+ P I + P ++ ++ + ++ + D
Sbjct: 195 VRGSVGSLVGVGTGPAGIAVDPDGNRVYVANDGSGSNNV--LKIDTATGNVTATDLPVGS 252
Query: 264 GWPNGITLDVDNEKLYWCDAKTDKIEMIDFDGNNR 298
G P G+ +D + Y +++ + +ID +
Sbjct: 253 GAPRGVAVDPAGKAAYVANSQGGTVSVIDGATDRV 287
Score = 35.7 bits (82), Expect = 0.029
Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 2/86 (2%)
Query: 259 VKDRLGWPNGITLDVDNEKLYWCDAKTDKIEMIDFDGNNRRELIN-ENLPHVFGISLLGD 317
+ +P G+ ++ K+Y ++ + +ID N I P + G
Sbjct: 69 LSVGGVYPAGVAVNPAGNKVYVTTGDSNTVSVIDTATNTVLGSIPVGLGPVGLAVDPDGK 128
Query: 318 YVYWTDWQRRSIDRVNKITGNDREVI 343
YVY + + + V+ I +V
Sbjct: 129 YVYVANAGNGN-NTVSVIDAATNKVT 153
>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 = 35.7 bits (83), Expect = 0.023
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 250 LNGGERVLLVKDRLGWPNGITLDVDNEKLYWCDAKTDKIEMIDFDGN-----NRRELI 302
L+ +V V D + NG+ D + LY+ D+ T +I D+D + NRR
Sbjct: 119 LDPDGKVERVLDGITISNGLAWSPDGKTLYFADSPTRRIWAFDYDADGGLISNRRVFA 176
Score = 33.8 bits (78), Expect = 0.085
Identities = 27/83 (32%), Positives = 35/83 (42%), Gaps = 22/83 (26%)
Query: 112 ITNGL-ITPDGLAIDWLTEKLYWTDSETNKLEVSSLDGKKRKVLYWEDIDQPRAIASYKL 170
I+NGL +PDG + LY+ DS T ++ D I R A +K
Sbjct: 134 ISNGLAWSPDG-------KTLYFADSPTRRIWAFDYDADGGL------ISNRRVFADFK- 179
Query: 171 PTIEVEHPDGVAVD-----WVAR 188
PDG+AVD WVAR
Sbjct: 180 --DGDGEPDGMAVDAEGNVWVAR 200
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 33.9 bits (78), Expect = 0.11
Identities = 35/167 (20%), Positives = 53/167 (31%), Gaps = 32/167 (19%)
Query: 151 RKVLYWEDIDQPRAIASYKLPTIEV---EHPDGVAVDWVARNLYWTDTGTDRIEVCRLEG 207
R L W DI R I T + P G + + D G R+ C
Sbjct: 36 RGALLWVDILGGR-IHRLDPETGKKRVFPSPGGFS------SGALIDAG-GRLIACEHGV 87
Query: 208 THR------KVLVNTDLVEPRAITLSP------AHGYLFWSD-WNEKRPKIERS------ 248
K+ + + + + P G +++ D K E
Sbjct: 88 RLLDPDTGGKITLLAEPEDGLPLN-RPNDGVVDPDGRIWFGDMGYFDLGKSEERPTGSLY 146
Query: 249 -LLNGGERVLLVKDRLGWPNGITLDVDNEKLYWCDAKTDKIEMIDFD 294
+ G V L+ D L PNG+ D + LY D ++I D D
Sbjct: 147 RVDPDGGVVRLLDDDLTIPNGLAFSPDGKTLYVADTPANRIHRYDLD 193
Score = 30.8 bits (70), Expect = 1.0
Identities = 24/95 (25%), Positives = 34/95 (35%), Gaps = 11/95 (11%)
Query: 111 VITNGLITPDGLAIDWLTEKLYWTDSETNKLEVSSLDGKKRKVLYWEDIDQPRAIASYKL 170
++ + L P+GLA + LY D+ N++ LD I R +
Sbjct: 157 LLDDDLTIPNGLAFSPDGKTLYVADTPANRIHRYDLDPATG------PIGGRRGFVDF-- 208
Query: 171 PTIEVEHPDGVAVDWVARNLYWTDTGTDRIEVCRL 205
E PDG+AVD A W V R
Sbjct: 209 -DEEPGLPDGMAVD--ADGNLWVAAVWGGGRVVRF 240
>gnl|CDD|215497 PLN02919, PLN02919, haloacid dehalogenase-like hydrolase family
protein.
Length = 1057
Score = 31.7 bits (72), Expect = 0.72
Identities = 16/38 (42%), Positives = 25/38 (65%)
Query: 111 VITNGLITPDGLAIDWLTEKLYWTDSETNKLEVSSLDG 148
++T+ L P LAID L +L+ +DS N++ V+ LDG
Sbjct: 562 LLTSPLKFPGKLAIDLLNNRLFISDSNHNRIVVTDLDG 599
Score = 29.4 bits (66), Expect = 3.6
Identities = 12/39 (30%), Positives = 23/39 (58%)
Query: 258 LVKDRLGWPNGITLDVDNEKLYWCDAKTDKIEMIDFDGN 296
L+ L +P + +D+ N +L+ D+ ++I + D DGN
Sbjct: 562 LLTSPLKFPGKLAIDLLNNRLFISDSNHNRIVVTDLDGN 600
>gnl|CDD|163414 TIGR03702, lip_kinase_YegS, lipid kinase YegS. Members of this
protein family are designated YegS, an apparent lipid
kinase family in the Proteobacteria. Bakali, et al.
report phosphatidylglycerol kinase activity for the
member from Escherichia coli, but refrain from calling
that activity synonymous with its biological role. Note
that a broader, subfamily-type model (TIGR00147),
includes this family but also multiple paralogs in some
species and varied functions [Unknown function, Enzymes
of unknown specificity].
Length = 293
Score = 30.8 bits (70), Expect = 1.0
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 239 NEKRPKIERSLLNGGERVLLVKDRLGW-----PNGITLDVDNEKL 278
E P +L G + V+ RL W P +T ++D E L
Sbjct: 224 PELLPATLSTLFGGDKNPEFVRARLPWLEIEAPQPLTFNLDGEPL 268
>gnl|CDD|234377 TIGR03866, PQQ_ABC_repeats, PQQ-dependent catabolism-associated
beta-propeller protein. Members of this protein family
consist of seven repeats each of the YVTN family
beta-propeller repeat (see TIGR02276). Members occur
invariably as part of a transport operon that is
associated with PQQ-dependent catabolism of alcohols
such as phenylethanol.
Length = 300
Score = 28.5 bits (64), Expect = 5.0
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 266 PNGITLDVDNEKLYWCDAKTDKIEMID 292
P GIT D + LY C + +D +++ID
Sbjct: 33 PRGITFSKDGKLLYVCASDSDTVQVID 59
>gnl|CDD|185767 cd09244, BRO1_Rhophilin, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin and related domains.
This family contains the Bro1-like domain of
RhoA-binding proteins, Rhophilin-1 and -2, and related
domains. It belongs to the BRO1_Alix_like superfamily
which also includes the Bro1-like domains of mammalian
Alix (apoptosis-linked gene-2 interacting protein X),
His-Domain type N23 protein tyrosine phosphatase
(HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20
(also known as PalA) from Saccharomyces cerevisiae,
Ustilago maydis Rim23 (also known as PalC), and related
domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound
RhoA. Bro1-like domains are boomerang-shaped, and part
of the domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 and -2, contain an N-terminal Rho-binding
domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. Their PDZ domains have limited homology.
Rhophilin-1 and -2 have different activities. The
Drosophila knockout of Rhophilin-1 is embryonic lethal,
suggesting an essential role in embryonic development.
Roles of Rhophilin-2 may include limiting stress fiber
formation or increasing the turnover of F-actin in the
absence of high levels of RhoA signaling activity. The
isolated Bro1-like domain of Rhophilin-1 binds human
immunodeficiency virus type 1 (HIV-1) nucleocapsid. This
family lacks the V-shaped (V) domain found in many
members of the BRO1_Alix _like superfamily.
Length = 350
Score = 28.5 bits (64), Expect = 5.5
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 10 VHKMMFITNTK------WVNYIFLVVHFWYALSHHVAAQMLLFATSKDIRIANLSRPL 61
VHK+M K W++ + + + AL+H+ AA LL + + A+L L
Sbjct: 214 VHKLMNQEPVKDYIPYSWISLVEVKSEHYKALAHYYAAMGLLLEERRLLGKAHLKEAL 271
>gnl|CDD|224600 COG1686, DacC, D-alanyl-D-alanine carboxypeptidase [Cell envelope
biogenesis, outer membrane].
Length = 389
Score = 28.5 bits (64), Expect = 5.7
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 147 DGKKRKVLYWEDIDQPRAIASY-KLPTIEV 175
D KVLY ++ D R AS KL T V
Sbjct: 45 DADSGKVLYSKNADARRPPASLTKLMTAYV 74
>gnl|CDD|226156 COG3629, DnrI, DNA-binding transcriptional activator of the SARP
family [Signal transduction mechanisms].
Length = 280
Score = 28.2 bits (63), Expect = 6.6
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 15/61 (24%)
Query: 233 LFWSDWNEKRPKIE--------RSLLNGGERVLLVKDRLGWPNGITLDVDNEKLYWCDAK 284
L W D + R + R LL G+ +L + G+TL+ + DA
Sbjct: 49 LLWEDSDPSRARANLRTTLHNLRKLLGDGDVILATE-----GPGVTLNPGAD--ITIDAG 101
Query: 285 T 285
Sbjct: 102 R 102
>gnl|CDD|216527 pfam01488, Shikimate_DH, Shikimate / quinate 5-dehydrogenase. This
family contains both shikimate and quinate
dehydrogenases. Shikimate 5-dehydrogenase catalyzes the
conversion of shikimate to 5-dehydroshikimate. This
reaction is part of the shikimate pathway which is
involved in the biosynthesis of aromatic amino acids.
Quinate 5-dehydrogenase catalyzes the conversion of
quinate to 5-dehydroquinate. This reaction is part of
the quinate pathway where quinic acid is exploited as a
source of carbon in prokaryotes and microbial
eukaryotes. Both the shikimate and quinate pathways
share two common pathway metabolites 3-dehydroquinate
and dehydroshikimate.
Length = 133
Score = 27.3 bits (61), Expect = 6.9
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 134 TDSETNKLEVSSL-DGKKRKVLYWEDIDQPRAIASYKLPTIEVEHPD 179
T + T + + + K + L + DI PR I +L + V D
Sbjct: 82 TSAPTPIITKEMVEEALKARPLLFVDIAVPRDIEPEELEGVYVYTVD 128
>gnl|CDD|129806 TIGR00723, ttdB_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, beta region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase beta chain and the C-terminal
region of the class I fumarase (where the N-terminal
region is homologous to the tartrate dehydratase alpha
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 168
Score = 27.4 bits (61), Expect = 7.4
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 7/45 (15%)
Query: 149 KKRKVLYWEDIDQPRAIASYKLPTIEVEH--PDGVAVDWVARNLY 191
KK + + WED+ P AI ++ +EVE P VA+D +++
Sbjct: 127 KKVEGVAWEDLGMPEAI--WE---LEVEDFGPLIVAIDSHGNSIF 166
>gnl|CDD|185514 PTZ00212, PTZ00212, T-complex protein 1 subunit beta; Provisional.
Length = 533
Score = 28.1 bits (63), Expect = 9.2
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 140 KLEVSSLDGKKRKVLYWED-IDQPRAIASYKLPTIEVEHPDGVAVDWVAR 188
LE + D + + ED ++ R S KL T+E +H +AVD V R
Sbjct: 142 ALEEIAFDHGSDEEKFKEDLLNIARTTLSSKLLTVEKDHFAKLAVDAVLR 191
>gnl|CDD|147459 pfam05271, Tobravirus_2B, Tobravirus 2B protein. This family
consists of several tobravirus 2B proteins. It is known
that the 2B protein is required for transmission by both
Paratrichodorus pachydermus and P. anemones nematodes.
Length = 117
Score = 26.7 bits (59), Expect = 9.7
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 265 WPNGITLDVDNEKLYWCDAKTDKIEMIDFDGNNRRELIN 303
WPN D +L W D DK+E F +L +
Sbjct: 8 WPNDQLFLSDTYQLVWFDILRDKVEHKHFVSQVSTDLSS 46
>gnl|CDD|220975 pfam11086, DUF2878, Protein of unknown function (DUF2878). This
bacterial family of proteins has no known function.
Some members annotate the proteins as the permease
component of a Mn2+/Zn2+ transport system however this
cannot be confirmed.
Length = 152
Score = 27.2 bits (61), Expect = 9.7
Identities = 5/28 (17%), Positives = 12/28 (42%)
Query: 21 WVNYIFLVVHFWYALSHHVAAQMLLFAT 48
+ + L++H + S ++LL
Sbjct: 26 LLLALLLLLHLLLSPSRKADLRLLLLLA 53
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
0.321 0.138 0.443
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: 18,898,205
Number of extensions: 1854709
Number of successful extensions: 1527
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1515
Number of HSP's successfully gapped: 39
Length of query: 357
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 259
Effective length of database: 6,590,910
Effective search space: 1707045690
Effective search space used: 1707045690
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: 60 (26.8 bits)