RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15458
(176 letters)
>gnl|CDD|153114 cd01056, Euk_Ferritin, eukaryotic ferritins. Eukaryotic Ferritin
(Euk_Ferritin) domain. Ferritins are the primary iron
storage proteins of most living organisms and members of
a broad superfamily of ferritin-like diiron-carboxylate
proteins. The iron-free (apoferritin) ferritin molecule
is a protein shell composed of 24 protein chains
arranged in 432 symmetry. Iron storage involves the
uptake of iron (II) at the protein shell, its oxidation
by molecular oxygen at the dinuclear ferroxidase
centers, and the movement of iron (III) into the cavity
for deposition as ferrihydrite; the protein shell can
hold up to 4500 iron atoms. In vertebrates, two types of
chains (subunits) have been characterized, H or M (fast)
and L (slow), which differ in rates of iron uptake and
mineralization. Fe(II) oxidation in the H/M subunits
take place initially at the ferroxidase center, a
carboxylate-bridged diiron center, located within the
subunit four-helix bundle. In a complementary role,
negatively charged residues on the protein shell inner
surface of the L subunits promote ferrihydrite
nucleation. Most plant ferritins combine both oxidase
and nucleation functions in one chain: they have four
interior glutamate residues as well as seven ferroxidase
center residues.
Length = 161
Score = 151 bits (384), Expect = 2e-47
Identities = 58/178 (32%), Positives = 81/178 (45%), Gaps = 24/178 (13%)
Query: 3 HSCTNLMMQQVQKELNASLTYLAMGVHFSRDCVNRPGFAKF------SSRVLVRSGGEHA 56
C + +Q+ ELNAS YL+M +F RD V PGFAKF R EHA
Sbjct: 2 EECEAALNKQINLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEER-------EHA 54
Query: 57 IKFSSSYLTMRGNLTDYHHHQGVNKMTWNSAAHAVQDALNLETQVTESIRKIIIECEQGT 116
K Y RG + K W S A++ AL+LE V +S+ +
Sbjct: 55 EKL-IKYQNKRGGRVVLQDIKKPEKDEWGSGLEALELALDLEKLVNQSLLDLHKLA---- 109
Query: 117 NNVHDLESVNDYHLSDWLTGEFLDEQYKGQRKLAGMLSTMRKTEGTHGKLTEFLMDKE 174
ND HL+D+L EFL+EQ + +KLAG ++ +++ L E+L DK
Sbjct: 110 ------SEHNDPHLADFLESEFLEEQVESIKKLAGYITNLKRVGKPQSGLGEYLFDKY 161
>gnl|CDD|153098 cd00904, Ferritin, Ferritin iron storage proteins. Ferritins are
the primary iron storage proteins of most living
organisms and members of a broad superfamily of
ferritin-like diiron-carboxylate proteins. The iron-free
(apoferritin) ferritin molecule is a protein shell
composed of 24 protein chains arranged in 432 symmetry.
Iron storage involves the uptake of iron (II) at the
protein shell, its oxidation by molecular oxygen at the
dinuclear ferroxidase centers, and the movement of iron
(III) into the cavity for deposition as ferrihydrite;
the protein shell can hold up to 4500 iron atoms. In
vertebrates, two types of chains (subunits) have been
characterized, H or M (fast) and L (slow), which differ
in rates of iron uptake and mineralization. Bacterial
non-heme ferritins are composed only of H chains. Fe(II)
oxidation in the H/M subunits take place initially at
the ferroxidase center, a carboxylate-bridged diiron
center, located within the subunit four-helix bundle. In
a complementary role, negatively charged residues on the
protein shell inner surface of the L subunits promote
ferrihydrite nucleation. Most plant ferritins combine
both oxidase and nucleation functions in one chain: they
have four interior glutamate residues as well as seven
ferroxidase center residues.
Length = 160
Score = 73.8 bits (181), Expect = 4e-17
Identities = 50/164 (30%), Positives = 76/164 (46%), Gaps = 14/164 (8%)
Query: 11 QQVQKELNASLTYLAMGVHFSRDCVNRPGFAKFSSRVLVRSGGEHAIKFSSSYLTMRGNL 70
+Q+ EL AS TYL+M +F RD V G A F + + EHA KF Y RG
Sbjct: 10 RQLNLELYASYTYLSMATYFDRDDVALKGVAHFF-KEQAQEEREHAEKFYK-YQNERGGR 67
Query: 71 TDYHHHQGVNKMTWNSAAHAVQDALNLETQVTESIRKIIIECEQGTNNVHDLESVN-DYH 129
+ + W A++ AL LE V +++ ++H+L S D H
Sbjct: 68 VELQDIEKPPSDEWGGTLDAMEAALKLEKFVNQALL-----------DLHELASEEKDPH 116
Query: 130 LSDWLTGEFLDEQYKGQRKLAGMLSTMRKTEGTHGKLTEFLMDK 173
L D+L FLDEQ K +++ +L+ + + G E+L D+
Sbjct: 117 LCDFLESHFLDEQVKEIKQVGDILTNLERLNGQQAGSGEYLFDR 160
>gnl|CDD|215791 pfam00210, Ferritin, Ferritin-like domain. This family contains
ferritins and other ferritin-like proteins such as
members of the DPS family and bacterioferritins.
Length = 142
Score = 72.7 bits (179), Expect = 7e-17
Identities = 43/151 (28%), Positives = 67/151 (44%), Gaps = 18/151 (11%)
Query: 11 QQVQKELNASLTYLAMGVHFSRDCVNRPGFAKFSSRVLVRSGGEHAIKFSSSYLTMRG-- 68
+Q+ EL AS YL M +F D PG A+F EHA K + + G
Sbjct: 6 EQLADELTASYQYLQMAWYF--DGPGLPGLAEFF-DEQAEEEREHADKLAE-RILALGGK 61
Query: 69 -NLTDYHHHQGVNKMTWNSAAHAVQDALNLETQVTESIRKIIIECEQGTNNVHDLESVND 127
LT + + S A++ AL E +VTES+R++I E+ D
Sbjct: 62 PVLTPVELLEIEPPDEFGSVLEALEAALEHEKEVTESLRELIELAEE----------EGD 111
Query: 128 YHLSDWLTGEFLDEQYKGQRKLAGMLSTMRK 158
Y +D+L FL+EQ + + L +L +++
Sbjct: 112 YATADFLE-WFLEEQEEHEWFLEALLEKLKR 141
>gnl|CDD|153113 cd01055, Nonheme_Ferritin, nonheme-containing ferritins. Nonheme
Ferritin domain, found in archaea and bacteria, is a
member of a broad superfamily of ferritin-like
diiron-carboxylate proteins. The ferritin protein shell
is composed of 24 protein subunits arranged in 432
symmetry. Each protein subunit, a four-helix bundle with
a fifth short terminal helix, contains a dinuclear
ferroxidase center (H type). Unique to this group of
proteins is a third metal site in the ferroxidase
center. Iron storage involves the uptake of iron (II) at
the protein shell, its oxidation by molecular oxygen at
the ferroxidase centers, and the movement of iron (III)
into the cavity for deposition as ferrihydrite.
Length = 156
Score = 56.0 bits (136), Expect = 2e-10
Identities = 47/180 (26%), Positives = 69/180 (38%), Gaps = 48/180 (26%)
Query: 11 QQVQKELNASLTYLAMGVHFSRDCVNRPGFAKFSSRVLVRSGGE--HAIKFSSSYLTMRG 68
+Q+ EL +S YLAM F GFA F V++ E HA+KF
Sbjct: 10 EQINLELYSSYLYLAMAAWFDS--KGLDGFANF---FRVQAQEEREHAMKF--------- 55
Query: 69 NLTDYHHHQGVN---------KMTWNSAAHAVQDALNLETQVTESIRKIIIECEQGTNNV 119
DY + +G + S + AL E +VTESI NN+
Sbjct: 56 --FDYLNDRGGRVELPAIEAPPSEFESLLEVFEAALEHEQKVTESI-----------NNL 102
Query: 120 HDL-ESVNDY---HLSDWLTGEFLDEQYKGQRKLAGMLSTMRKTEGTHGKLTEFLMDKEF 175
DL DY + W F+ EQ + + +L ++ G L +++DKE
Sbjct: 103 VDLALEEKDYATFNFLQW----FVKEQVEEEALARDILDKLKLAGDDGGGL--YMLDKEL 156
>gnl|CDD|224445 COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and
metabolism].
Length = 167
Score = 43.4 bits (103), Expect = 7e-06
Identities = 43/172 (25%), Positives = 70/172 (40%), Gaps = 22/172 (12%)
Query: 7 NLMMQQVQKELNASLTYLAMGVHFSRDCVNRPGFAKFSSRVLVRSGGEHAIKFSSSYLTM 66
L+ +Q+ E AS YL M S + + PGFAKF R + HA+K +YL
Sbjct: 8 ELLNEQMNLEFYASNLYLQMAAWCSSESL--PGFAKF-LRAQAQEELTHAMKL-FNYLNE 63
Query: 67 RGNLTDYHHHQGVN--KMTWNSAAHAVQDALNLETQVTESIRKIIIECEQGTNNVHDLES 124
RG + + ++S + L E +VT SI ++ + D +
Sbjct: 64 RGARP---ELKAIEAPPNKFSSLKELFEKTLEHEQKVTSSINELAEVARE----EKDYAT 116
Query: 125 VNDYHLSDWLTGEFLDEQYKGQRKLAGMLSTMRKTEGTHGKLTEFLMDKEFL 176
N W F+ EQ + ++ +L + G G+ +L+DKE
Sbjct: 117 FN---FLQW----FVAEQVEEEKLFKTILDKLELA-GNDGE-GLYLIDKELK 159
>gnl|CDD|233789 TIGR02225, recomb_XerD, tyrosine recombinase XerD. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerD, one of two closely related
chromosomal proteins along with XerC (TIGR02224). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and with homologs of XerD on other replicons,
the chomosomal copy was preferred for building this
model. This model does not detect all XerD, as some
apparent XerD examples score below the trusted and noise
cutoff scores. XerC and XerD interact with cell division
protein FtsK [DNA metabolism, DNA replication,
recombination, and repair].
Length = 291
Score = 28.7 bits (65), Expect = 1.5
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 120 HDLESVNDYHLSDWLTGEFLDEQYKGQRKLAGMLSTMRK 158
DLE V+ + D+L L E R +A LS +R
Sbjct: 37 IDLEEVDRGDIVDFL--AELKEAGLSARSIARALSALRS 73
>gnl|CDD|225312 COG2514, COG2514, Predicted ring-cleavage extradiol dioxygenase
[General function prediction only].
Length = 265
Score = 28.8 bits (65), Expect = 1.5
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 2/16 (12%)
Query: 72 DYHHHQGVNKMTWNSA 87
DYHHH N TWNS
Sbjct: 208 DYHHHLAAN--TWNSR 221
>gnl|CDD|233282 TIGR01130, ER_PDI_fam, protein disulfide isomerase, eukaryotic.
This model represents eukaryotic protein disulfide
isomerases retained in the endoplasmic reticulum (ER)
and closely related forms. Some members have been
assigned alternative or additional functions such as
prolyl 4-hydroxylase and
dolichyl-diphosphooligosaccharide-protein
glycotransferase. Members of this family have at least
two protein-disulfide domains, each similar to
thioredoxin but with the redox-active disulfide in the
motif PWCGHCK, and an ER retention signal at the extreme
C-terminus (KDEL, HDEL, and similar motifs).
Length = 462
Score = 27.3 bits (61), Expect = 4.2
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 7/46 (15%)
Query: 136 GEFLDEQYKGQRKLAGMLSTMRKTEG-------THGKLTEFLMDKE 174
GE Y G R G++ M+K G T L FL D +
Sbjct: 85 GEDSVSDYNGPRDADGIVKYMKKQSGPAVKEIETVADLEAFLADDD 130
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 27.6 bits (62), Expect = 4.3
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 96 NLETQVTESIRKIIIECEQGTNNVHDLESVNDYHLSDWLTGEFLDEQYKGQRKLAGMLST 155
+E E++R IIE + T L+ V+ H+ +G ++ +L G
Sbjct: 634 IIEVLGIEALRNAIIEEIKITLEEQGLDFVDIRHMGL--SGARMNIS--QIVQLIGQQGV 689
Query: 156 MRKTEG 161
M +
Sbjct: 690 MGEKIS 695
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 27.0 bits (60), Expect = 6.4
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 6/40 (15%)
Query: 128 YHLSDWLTGEFLDEQYKGQRKLAGMLSTMRKTEGTHGKLT 167
YH DW+ + L +Y AG + RK G+HG+ T
Sbjct: 243 YHRGDWIDPKELPIRY------AGYSTCFRKEAGSHGRDT 276
>gnl|CDD|221728 pfam12708, Pectate_lyase_3, Pectate lyase superfamily protein.
This family of proteins possesses a beta helical
structure like Pectate lyase. This family is most
closely related to glycosyl hydrolase family 28.
Length = 222
Score = 26.2 bits (58), Expect = 8.4
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 48 LVRSGGEHAIKFSSSYLTMRGNLTDYHHHQGVNKMTWNS 86
LV +GG+ F S T+R + G+ + W
Sbjct: 168 LVFNGGDDGATFGSQQFTIRNLTFNNACSTGIG-IDWGW 205
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 0.130 0.384
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,475,023
Number of extensions: 730786
Number of successful extensions: 551
Number of sequences better than 10.0: 1
Number of HSP's gapped: 542
Number of HSP's successfully gapped: 17
Length of query: 176
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 86
Effective length of database: 6,945,742
Effective search space: 597333812
Effective search space used: 597333812
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: 56 (25.5 bits)