RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12315
(120 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 = 153 bits (390), Expect = 3e-49
Identities = 65/100 (65%), Positives = 75/100 (75%)
Query: 11 HAETEEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKY 70
H E E +NKQINLEL ASYVYLSM+A+FDRD VALPG +K+F+ SDEE EHA KLIKY
Sbjct: 1 HEECEAALNKQINLELNASYVYLSMAAYFDRDDVALPGFAKFFRKLSDEEREHAEKLIKY 60
Query: 71 LNKRGGTLKLVDVKAPARQEWGTTEEAFSHALQLEKDVNQ 110
NKRGG + L D+K P + EWG+ EA AL LEK VNQ
Sbjct: 61 QNKRGGRVVLQDIKKPEKDEWGSGLEALELALDLEKLVNQ 100
>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 = 114 bits (286), Expect = 1e-33
Identities = 53/103 (51%), Positives = 72/103 (69%)
Query: 11 HAETEEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKY 70
+ E +N+Q+NLELYASY YLSM+ +FDRD VAL G++ +FK + EE EHA K KY
Sbjct: 1 SEKVEAAVNRQLNLELYASYTYLSMATYFDRDDVALKGVAHFFKEQAQEEREHAEKFYKY 60
Query: 71 LNKRGGTLKLVDVKAPARQEWGTTEEAFSHALQLEKDVNQVII 113
N+RGG ++L D++ P EWG T +A AL+LEK VNQ ++
Sbjct: 61 QNERGGRVELQDIEKPPSDEWGGTLDAMEAALKLEKFVNQALL 103
>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 = 107 bits (271), Expect = 3e-31
Identities = 43/100 (43%), Positives = 64/100 (64%), Gaps = 3/100 (3%)
Query: 13 ETEEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLN 72
+ E+ +N+QINLELY+SY+YL+M+A FD L G + +F+ + EE EHA K YLN
Sbjct: 3 KLEKALNEQINLELYSSYLYLAMAAWFDS--KGLDGFANFFRVQAQEEREHAMKFFDYLN 60
Query: 73 KRGGTLKLVDVKAPARQEWGTTEEAFSHALQLEKDVNQVI 112
RGG ++L ++AP E+ + E F AL+ E+ V + I
Sbjct: 61 DRGGRVELPAIEAP-PSEFESLLEVFEAALEHEQKVTESI 99
>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 = 90.4 bits (225), Expect = 1e-24
Identities = 37/101 (36%), Positives = 57/101 (56%), Gaps = 5/101 (4%)
Query: 15 EEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLNKR 74
E +N+Q+ EL ASY YL M+ +FD LPG++++F ++EE EHA KL + +
Sbjct: 1 IEALNEQLADELTASYQYLQMAWYFDG--PGLPGLAEFFDEQAEEEREHADKLAERILAL 58
Query: 75 GGTLKLVDVKAP---ARQEWGTTEEAFSHALQLEKDVNQVI 112
GG L V+ E+G+ EA AL+ EK+V + +
Sbjct: 59 GGKPVLTPVELLEIEPPDEFGSVLEALEAALEHEKEVTESL 99
>gnl|CDD|224445 COG1528, Ftn, Ferritin-like protein [Inorganic ion transport and
metabolism].
Length = 167
Score = 88.9 bits (221), Expect = 1e-23
Identities = 37/97 (38%), Positives = 57/97 (58%), Gaps = 3/97 (3%)
Query: 16 EKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLNKRG 75
E +N+Q+NLE YAS +YL M+A +LPG +K+ + + EE HA KL YLN+RG
Sbjct: 8 ELLNEQMNLEFYASNLYLQMAAWCSS--ESLPGFAKFLRAQAQEELTHAMKLFNYLNERG 65
Query: 76 GTLKLVDVKAPARQEWGTTEEAFSHALQLEKDVNQVI 112
+L ++AP ++ + +E F L+ E+ V I
Sbjct: 66 ARPELKAIEAP-PNKFSSLKELFEKTLEHEQKVTSSI 101
>gnl|CDD|182367 PRK10304, PRK10304, ferritin; Provisional.
Length = 165
Score = 45.0 bits (106), Expect = 7e-07
Identities = 31/101 (30%), Positives = 51/101 (50%), Gaps = 3/101 (2%)
Query: 12 AETEEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYL 71
E EK+N+Q+NLELY+S +Y MSA G + + + + EE H +L YL
Sbjct: 4 PEMIEKLNEQMNLELYSSLLYQQMSAWCSYH--TFEGAAAFLRRHAQEEMTHMQRLFDYL 61
Query: 72 NKRGGTLKLVDVKAPARQEWGTTEEAFSHALQLEKDVNQVI 112
G ++ V++P E+ + +E F + E+ + Q I
Sbjct: 62 TDTGNLPRINTVESPF-AEYSSLDELFQETYKHEQLITQKI 101
>gnl|CDD|153097 cd00657, Ferritin_like, Ferritin-like superfamily of
diiron-containing four-helix-bundle proteins.
Ferritin-like, diiron-carboxylate proteins participate
in a range of functions including iron regulation,
mono-oxygenation, and reactive radical production. These
proteins are characterized by the fact that they
catalyze dioxygen-dependent oxidation-hydroxylation
reactions within diiron centers; one exception is
manganese catalase, which catalyzes peroxide-dependent
oxidation-reduction within a dimanganese center.
Diiron-carboxylate proteins are further characterized by
the presence of duplicate metal ligands, glutamates and
histidines (ExxH) and two additional glutamates within a
four-helix bundle. Outside of these conserved residues
there is little obvious homology. Members include
bacterioferritin, ferritin, rubrerythrin, aromatic and
alkene monooxygenase hydroxylases (AAMH), ribonucleotide
reductase R2 (RNRR2), acyl-ACP-desaturases
(Acyl_ACP_Desat), manganese (Mn) catalases,
demethoxyubiquinone hydroxylases (DMQH), DNA protecting
proteins (DPS), and ubiquinol oxidases (AOX), and the
aerobic cyclase system, Fe-containing subunit (ACSF).
Length = 130
Score = 41.7 bits (98), Expect = 7e-06
Identities = 23/100 (23%), Positives = 34/100 (34%), Gaps = 9/100 (9%)
Query: 16 EKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLNKRG 75
+N + E A Y ++A P + +DEE HA L + L + G
Sbjct: 1 RLLNDALAGEYAAIIAYGQLAARAPD-----PDLKDELLEIADEERRHADALAERLRELG 55
Query: 76 GTLKLVDVKAPAR----QEWGTTEEAFSHALQLEKDVNQV 111
GT L A + EA AL++E
Sbjct: 56 GTPPLPPAHLLAAYALPKTSDDPAEALRAALEVEARAIAA 95
>gnl|CDD|217284 pfam02915, Rubrerythrin, Rubrerythrin. This domain has a
ferritin-like fold.
Length = 137
Score = 32.4 bits (74), Expect = 0.025
Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 5/79 (6%)
Query: 47 PGISKYFKHASDEESEHAHKLIKYLNKRGGTLKLVDVK-----APARQEWGTTEEAFSHA 101
P I++ F+ ++EE HA L K L L+L +K T E A
Sbjct: 29 PQIAELFEEMAEEERRHAGFLNKLLKDLFLGLELGILKEHVEYTFFPVADELTRENLKEA 88
Query: 102 LQLEKDVNQVIIYFFTSLA 120
++ + F+ +A
Sbjct: 89 IEGAMLEEKEAYPFYIEIA 107
>gnl|CDD|184983 PRK15022, PRK15022, ferritin-like protein; Provisional.
Length = 167
Score = 31.8 bits (72), Expect = 0.053
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 7/90 (7%)
Query: 16 EKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLNKRG 75
K+N Q+NLE YAS +YL +S +L G + + + + ++ ++ G
Sbjct: 8 LKLNSQMNLEFYASNLYLHLSEWCSEQ--SLNGTATFLRAQAQSNVTQMMRMFNFMKSAG 65
Query: 76 GT--LKLVDVKAPARQEWGTTEEAFSHALQ 103
T +K +DV ++ + EE F L+
Sbjct: 66 ATPIVKAIDVPG---EKLNSLEELFQKTLE 92
>gnl|CDD|153105 cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding
domain. Rubrerythrin-like domain, similar to
rubrerythrin, a nonheme iron binding domain found in
many air-sensitive bacteria and archaea, and member of
a broad superfamily of ferritin-like diiron-carboxylate
proteins. Rubrerythrin is thought to reduce hydrogen
peroxide as part of an oxidative stress protection
system. The rubrerythrin protein has two domains, a
binuclear metal center located within a four-helix
bundle of the rubrerythrin domain, and a rubredoxin
domain. The Rubrerythrin-like domains in this CD are
singular domains (no C-terminus rubredoxin domain) and
are phylogenetically distinct from rubrerythrin domains
of rubrerythrin-rubredoxin proteins.
Length = 123
Score = 30.0 bits (68), Expect = 0.14
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 13 ETEEKINKQINLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHA 64
+ EE + E +YL+M+ R+ P +++ K + EE+EHA
Sbjct: 1 DLEEDLEANFKGETTEVGMYLAMARVAQRE--GYPEVAEELKRIAMEEAEHA 50
>gnl|CDD|153104 cd01045, Ferritin_like_AB, Uncharacterized family of ferritin-like
proteins found in archaea and bacteria. Ferritin-like
domain found in archaea and bacteria (Ferritin_like_AB).
This uncharacterized domain is a member of a broad
superfamily of ferritin-like diiron-carboxylate proteins
whose function is unknown. This family includes unknown
or hypothetical proteins which were sequenced from
mostly anaerobic or microaerophilic metal-metabolizing
and/or nitrogen-fixing microbes. The family includes
sequences from ferric-, sulfate-, and arsenic-reducing
bacteria, Geobacter, Magnetospirillum, Desulfovibrio,
and Desulfitobacterium. Also included are several
nitrogen-fixing endosymbiotic bacteria, Rhizobium,
Mesorhizobium, and Bradyrhizobium; also phototrophic
purple nonsulfur bacteria, Rhodobacter and
Rhodopseudomonas, as well as, obligate thermophiles,
Thermotoga, Thermoanaerobacter, and Pyrococcus. The
conserved residues of a diiron center are present in
this uncharacterized domain.
Length = 139
Score = 30.0 bits (68), Expect = 0.15
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 18/99 (18%)
Query: 22 INLELYASYVYLSMSAHFDRDVVALPGISKYFKHASDEESEHAHKLIKYLNKRGGT---- 77
I +E A+ YL ++ + K F+ ++EE EHA +L + K G
Sbjct: 7 IKMEEEAAEFYLELAEKAKDPELK-----KLFEELAEEEKEHAERLEELYEKLFGEELPE 61
Query: 78 LKLVDVKAPARQE---------WGTTEEAFSHALQLEKD 107
L+ D K +E EA A+++EKD
Sbjct: 62 LEPEDYKEEVEEEPEFKKALESLMDPLEALRLAIEIEKD 100
>gnl|CDD|153100 cd01041, Rubrerythrin, Rubrerythrin, ferritin-like diiron-binding
domain. Rubrerythrin domain is a nonheme iron binding
domain found in many air-sensitive bacteria and archaea
and member of a broad superfamily of ferritin-like
diiron-carboxylate proteins. The homodimeric
rubrerythrin protein contains a binuclear metal center
located within a four helix bundle. Many, but not all,
rubrerythrin proteins have a second domain with a
rubredoxin-like hexacoordinated iron center.
Rubrerythrin is thought to reduce hydrogen peroxide as
part of an oxidative stress protection system but its
function is still poorly understood.
Length = 134
Score = 29.5 bits (67), Expect = 0.24
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 46 LPGISKYFKHASDEESEHAHKLIKYLNKRGGT 77
I++ F+ ++ E EHA K L GG
Sbjct: 32 YEQIARLFRATAENEKEHAKGHFKLLKGLGGG 63
>gnl|CDD|239652 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis.
Length = 538
Score = 29.9 bits (68), Expect = 0.30
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 42 DVVALPGISKYFKHASDEESEHAHKLIKYLNKRGGTLKLVDVKAPARQEWGTTEEAFSHA 101
DVV G S Y + +DE E A K I ++ GG +K ++ R+ + A+ +
Sbjct: 386 DVVDPLGGSYYVEALTDEIEEEAWKYIDKIDAMGGMIKAIEDGYFQRE---IADAAYKYQ 442
Query: 102 LQLEKDVNQVI 112
++E V+
Sbjct: 443 KEIESGERIVV 453
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 27.6 bits (61), Expect = 1.9
Identities = 10/49 (20%), Positives = 12/49 (24%)
Query: 42 DVVALPGISKYFKHASDEESEHAHKLIKYLNKRGGTLKLVDVKAPARQE 90
V G F+ E LI K + VD E
Sbjct: 2855 FEVEDSGDLYKFEEGLLELIVGHAPLIYAHKKSLENERNVDRLGSKENE 2903
>gnl|CDD|224386 COG1469, COG1469, Uncharacterized conserved protein [Function
unknown].
Length = 289
Score = 26.9 bits (60), Expect = 2.7
Identities = 9/39 (23%), Positives = 14/39 (35%)
Query: 41 RDVVALPGISKYFKHASDEESEHAHKLIKYLNKRGGTLK 79
R +V + + +EES H H G L+
Sbjct: 250 RRLVEDFPDAAFTVEVENEESIHPHDAFAERVATKGELR 288
>gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
Length = 555
Score = 26.4 bits (59), Expect = 4.2
Identities = 15/33 (45%), Positives = 17/33 (51%), Gaps = 2/33 (6%)
Query: 55 HASDEESEHAHKLIKYLNKRGGTLKLVDVKAPA 87
A D E E LI +NK G LK+ VKAP
Sbjct: 261 IAEDVEGEALQTLI--INKLRGGLKVCAVKAPG 291
>gnl|CDD|143944 pfam00178, Ets, Ets-domain.
Length = 85
Score = 25.4 bits (56), Expect = 4.4
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 57 SDEESEHAHKLIKYLNKRGGTLKLVDVKAPARQEWG 92
+D+++ I++ + G KLVD + AR WG
Sbjct: 13 TDQDNRD---FIRWTGRDKGEFKLVDPEEVARL-WG 44
>gnl|CDD|153099 cd00907, Bacterioferritin, Bacterioferritin, ferritin-like
diiron-binding domain. Bacterioferritins, also known as
cytochrome b1, are members of a broad superfamily of
ferritin-like diiron-carboxylate proteins. Similar to
ferritin in architecture, Bfr forms an oligomer of 24
subunits that assembles to form a hollow sphere with 432
symmetry. Up to 12 heme cofactor groups (iron
protoporphyrin IX or coproporphyrin III) are bound
between dimer pairs. The role of the heme is unknown,
although it may be involved in mediating iron-core
reduction and iron release. Each subunit is composed of
a four-helix bundle which carries a diiron ferroxidase
center; it is here that initial oxidation of ferrous
iron by molecular oxygen occurs, facilitating the
detoxification of iron, protection against dioxygen and
radical products, and storage of ferric-hydroxyphosphate
at the core. Some bacterioferritins are composed of two
subunit types, one conferring heme-binding ability
(alpha) and the other (beta) bestowing ferroxidase
activity.
Length = 153
Score = 25.6 bits (57), Expect = 6.0
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 51 KYFKHASDEESEHAHKLIK---YLNKRGGTLKLVDVKAPARQEWGTTEEAFSHALQLEKD 107
+ F+ S EE +HA KLI+ +L G L + E E + L LE +
Sbjct: 41 ERFRKESIEEMKHADKLIERILFL---EGLPNLQRLGKLRIGE--DVPEMLENDLALEYE 95
Query: 108 V 108
Sbjct: 96 A 96
>gnl|CDD|238868 cd01830, XynE_like, SGNH_hydrolase subfamily, similar to the
putative arylesterase/acylhydrolase from the rumen
anaerobe Prevotella bryantii XynE. The P. bryantii XynE
gene is located in a xylanase gene cluster. SGNH
hydrolases are a diverse family of lipases and
esterases. The tertiary fold of the enzyme is
substantially different from that of the alpha/beta
hydrolase family and unique among all known hydrolases;
its active site closely resembles the Ser-His-Asp(Glu)
triad found in other serine hydrolases.
Length = 204
Score = 25.7 bits (57), Expect = 6.6
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 37 AHFDRDVVALPGIS 50
A FDRDV++ PG+
Sbjct: 63 ARFDRDVLSQPGVR 76
>gnl|CDD|224508 COG1592, COG1592, Rubrerythrin [Energy production and
conversion].
Length = 166
Score = 25.4 bits (56), Expect = 6.7
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 46 LPGISKYFKHASDEESEHAHKLIKYLNKRGGTL 78
P I++ F+ ++ E+ HA +K L K L
Sbjct: 35 YPEIARLFRAIAEAEAVHAKNHLKLLGKLLLVL 67
>gnl|CDD|234573 PRK00013, groEL, chaperonin GroEL; Reviewed.
Length = 542
Score = 25.5 bits (57), Expect = 7.9
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 71 LNKRGGTLKLVDVKAP 86
+NK GTLK+V VKAP
Sbjct: 263 VNKLRGTLKVVAVKAP 278
>gnl|CDD|183779 PRK12830, PRK12830, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Reviewed.
Length = 417
Score = 25.6 bits (57), Expect = 8.5
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 16 EKINKQINLELYASYVYL--SMSAHFDRDVVALPG 48
K+ L ASY Y ++ F + VV LPG
Sbjct: 86 GKVKS-----LRASY-YFMGALLGRFKKAVVGLPG 114
>gnl|CDD|189027 cd09857, PIN_EXO1, PIN domain of Exonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Exonuclease-1 (EXO1) is involved
in multiple, eukaryotic DNA metabolic pathways,
including DNA replication processes (5' flap DNA
endonuclease activity and double stranded DNA
5'-exonuclease activity), DNA repair processes (DNA
mismatch repair (MMR) and post-replication repair
(PRR)), recombination, and telomere integrity. EXO1
functions in the MMS2 error-free branch of the PRR
pathway in the maintenance and repair of stalled
replication forks. Studies also suggest that EXO1 plays
both structural and catalytic roles during MMR-mediated
mutation avoidance. EXO1 belongs to the FEN1-EXO1-like
family of structure-specific, 5' nucleases. These
nucleases contain a PIN (PilT N terminus) domain with a
helical arch/clamp region (I domain) of variable length
(approximately 43 residues in EXO1 PIN domains) and a
H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA binding. Nucleases within this group
also have a carboxylate-rich active site that is
involved in binding essential divalent metal ion
cofactors (Mg2+/Mn2+). EXO1 nucleases also have
C-terminal Mlh1- and Msh2-binding domains which allow
interaction with MMR and PRR proteins, respectively.
Length = 210
Score = 25.1 bits (56), Expect = 9.8
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 51 KYFKHASDEESEHAHKLIKYLNKRG 75
+ F+ A D E AH+LIK L K G
Sbjct: 117 ECFQRAVDITPEMAHELIKALRKEG 141
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
0.317 0.130 0.364
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,909,696
Number of extensions: 499856
Number of successful extensions: 529
Number of sequences better than 10.0: 1
Number of HSP's gapped: 519
Number of HSP's successfully gapped: 48
Length of query: 120
Length of database: 10,937,602
Length adjustment: 83
Effective length of query: 37
Effective length of database: 7,256,220
Effective search space: 268480140
Effective search space used: 268480140
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: 53 (24.2 bits)