RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13345
(276 letters)
>gnl|CDD|214983 smart01027, Beta-Casp, Beta-Casp domain. The beta-CASP domain is
found C terminal to the beta-lactamase domain in
pre-mRNA 3'-end-processing endonuclease. The active site
of this enzyme is located at the interface of these two
domains.
Length = 126
Score = 93.4 bits (233), Expect = 6e-24
Identities = 34/88 (38%), Positives = 47/88 (53%), Gaps = 4/88 (4%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAE---LAKVPSPKVVLVSTPDMECGFSRD 90
EWMSD++ K FE NPF FK++K SL E L PKV++ S+ + G SR
Sbjct: 40 PEWMSDEIRKRFE-QGRNPFDFKNLKFVKSLEESKRLNDYKGPKVIIASSGMLTGGRSRH 98
Query: 91 LFFQWCSSPENSIIITNRTSPGTLARDL 118
+ P N++I+T + GTL R L
Sbjct: 99 YLKRLAPDPRNTVILTGYQAEGTLGRKL 126
Score = 42.5 bits (101), Expect = 3e-05
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 208 VVLVSTPDMECGFSRDLFFQWCSSPENSIIIT 239
V++ S+ + G SR + P N++I+T
Sbjct: 83 VIIASSGMLTGGRSRHYLKRLAPDPRNTVILT 114
>gnl|CDD|220932 pfam10996, Beta-Casp, Beta-Casp domain. The beta-CASP domain is
found C terminal to the beta-lactamase domain in
pre-mRNA 3'-end-processing endonuclease. The active site
of this enzyme is located at the interface of these two
domains.
Length = 124
Score = 81.5 bits (202), Expect = 2e-19
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 34 IEWMSDKLMKSFEGARNNPF-HFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLF 92
EW+SD K F PF + K V+ EL + PKV++ S+ +E G S
Sbjct: 40 PEWLSDS-AKEFLLRGAFPFDNLKFVRSVDESKELNNLGGPKVIIASSGMLEGGRSLHYL 98
Query: 93 FQWCSSPENSIIITNRTSPGTLARDL 118
+ P+N++I+T + GTL R L
Sbjct: 99 KKLAPDPKNTVILTGYQAEGTLGRKL 124
Score = 41.5 bits (98), Expect = 5e-05
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 208 VVLVSTPDMECGFSRDLFFQWCSSPENSIIIT 239
V++ S+ +E G S + P+N++I+T
Sbjct: 81 VIIASSGMLEGGRSLHYLKKLAPDPKNTVILT 112
>gnl|CDD|222032 pfam13299, CPSF100_C, Cleavage and polyadenylation factor 2
C-terminal. This family lies at the C-terminus of many
fungal and plant cleavage and polyadenylation
specificity factor subunit 2 proteins. The exact
function of the domain is not known, but is likely to
function as a binding domain for the protein within the
overall CPSF complex.
Length = 152
Score = 76.1 bits (188), Expect = 3e-17
Identities = 39/161 (24%), Positives = 54/161 (33%), Gaps = 47/161 (29%)
Query: 120 ELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQ------EKEKIPPHDTSFINEL 173
E K E E K + D+ H FI +L
Sbjct: 32 ESDTPEETETSAKAIETEETETESSDDKLELSPELDELPTLEALTSATRSAHQPLFIGDL 91
Query: 174 QLSDFKQTLQRNGIDCEFM-DGVLICCRGTVAVRRVVLVSTPDMECGFSRDLFFQWCSSP 232
+L+D K+ L GI EF +G L+ C G VAVR+
Sbjct: 92 RLADLKKALASAGIQAEFKGEGTLV-CNGKVAVRK------------------------- 125
Query: 233 ENSIIITNRNRADDSDSNVIVLEGCLSDEYYRVQQLLYDQY 273
S + IV+EG LS YY V++L+Y+Q
Sbjct: 126 --------------SATGRIVIEGTLSPSYYEVRKLIYEQL 152
>gnl|CDD|224696 COG1782, COG1782, Predicted metal-dependent RNase, consists of a
metallo-beta-lactamase domain and an RNA-binding KH
domain [General function prediction only].
Length = 637
Score = 45.0 bits (107), Expect = 2e-05
Identities = 23/113 (20%), Positives = 46/113 (40%), Gaps = 13/113 (11%)
Query: 35 EWMSDKLMKSFEGARNNPF---HFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
E+++ +L + NPF FK V+ E+ + P ++L ++ + G +
Sbjct: 460 EYLNKELRERIFHEGENPFLSEIFKRVEGSDERQEIIESDEPAIILATSGMLNGGPVVEY 519
Query: 92 FFQWCSSPENSIIITNRTSPGTLAR---------DLIELGGNRTLTLQVKKRI 135
F P+N++I + GTL R + G +T ++V +
Sbjct: 520 FKHLAPDPKNTLIFVGYQAEGTLGRRIQSGAKEIPIPGEDG-KTEVIKVNMEV 571
>gnl|CDD|224157 COG1236, YSH1, Predicted exonuclease of the beta-lactamase fold
involved in RNA processing [Translation, ribosomal
structure and biogenesis].
Length = 427
Score = 44.3 bits (105), Expect = 4e-05
Identities = 27/111 (24%), Positives = 46/111 (41%), Gaps = 9/111 (8%)
Query: 34 IEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDM-ECGFSRDLF 92
I L+K E F+ V+ + P VV ++ P M + G SR
Sbjct: 265 IGLDLPDLLKVAES------RFRFVESRRNSMREGIDKGPAVV-LAAPGMLKGGRSRYYL 317
Query: 93 FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELE 143
S +N +++ + GTL R L+E GG ++ +++ EEL+
Sbjct: 318 KHLLSDEKNWVLLPGYQAEGTLGRVLLE-GGTSVHIKGIEIKVKARVEELD 367
Score = 30.1 bits (68), Expect = 1.2
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 207 RVVLVSTPDM-ECGFSRDLFFQWCSSPENSIIITNR 241
V+++ P M + G SR S +N +++
Sbjct: 298 PAVVLAAPGMLKGGRSRYYLKHLLSDEKNWVLLPGY 333
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 36.8 bits (86), Expect = 0.011
Identities = 27/129 (20%), Positives = 52/129 (40%), Gaps = 18/129 (13%)
Query: 35 EWMSDKLMKSFEGARNNPF---HFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
E+++ +L + NPF F V+ E+ + P ++L ++ + G +
Sbjct: 454 EYLNKELRERIFHEGENPFLSEIFHRVEGSDERREIIESDEPAIILATSGMLNGGPVVEY 513
Query: 92 FFQWCSSPENSIIITNRTSPGTLARDL------IELGG-NRTLTLQVKKRIR-LEG---- 139
F P NS++ + GTL R + I L +T T+++ + +EG
Sbjct: 514 FKLLAPDPRNSLVFVGYQAEGTLGRRIQSGWREIPLTDDGKTETIKINMEVETIEGFSGH 573
Query: 140 ---EELEEY 145
+L Y
Sbjct: 574 SDRRQLMNY 582
>gnl|CDD|218100 pfam04466, Terminase_3, Phage terminase large subunit. Initiation
of packaging of double-stranded viral DNA involves the
specific interaction of the prohead with viral DNA in a
process mediated by a phage-encoded terminase protein.
The terminase enzymes are usually hetero-oligomers
composed of a small and a large subunit. This region is
found on the large subunit and possess an endonuclease
and ATPase activity that require Mg2+ and a neutral or
slightly basic reaction. This region is also found in
bacterial sequences.
Length = 387
Score = 31.2 bits (71), Expect = 0.49
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 140 EELEEYQKKKDKEAKDKQEKEKIPPH 165
EEL +YQ KKDK ++ K PH
Sbjct: 351 EELNKYQYKKDKNGALIPDEMKKDPH 376
>gnl|CDD|236080 PRK07734, motB, flagellar motor protein MotB; Reviewed.
Length = 259
Score = 30.9 bits (70), Expect = 0.59
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 137 LEGEELEEYQKKKDKEAKDKQEKEKIPPHDTSFINELQLSDFKQT 181
LE E+ ++ ++ + K+ K+ +E + + +I E QLS QT
Sbjct: 85 LEAEQAKKKEEAEAKKKKEMEELKAVQKKIDQYIKEKQLSSSLQT 129
>gnl|CDD|213736 TIGR02773, addB_Gpos, helicase-exonuclease AddAB, AddB subunit.
DNA repair is accomplished by several different systems
in prokaryotes. Recombinational repair of
double-stranded DNA breaks involves the RecBCD pathway
in some lineages, and AddAB (also called RexAB) in
other. The AddA protein is conserved between the
firmicutes and the alphaproteobacteria, while the
partner protein is not. Nevertheless, the partner is
designated AddB in both systems. This model describes
the AddB protein as found Bacillus subtilis and related
species. Although the RexB protein of Streptococcus and
Lactococcus is considered to be orthologous,
functionally equivalent, and merely named differently,
all members of this protein family have a P-loop
nucleotide binding motif GxxGxGK[ST] at the N-terminus,
unlike RexB proteins, and a CxxCxxxxxC motif at the
C-terminus, both of which may be relevant to function
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1160
Score = 31.2 bits (71), Expect = 0.65
Identities = 14/71 (19%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 104 IITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEKIP 163
++ P R+LI+ N L +K + R E+ +Y++ + + Q E+I
Sbjct: 405 LLFPLNEPFIDVRELIDQLENYVLAYGIKGKKRWWKEDWFQYRRFRGLDDDFAQTDEEI- 463
Query: 164 PHDTSFINELQ 174
+N+ +
Sbjct: 464 -EMQEMLNDTR 473
>gnl|CDD|234944 PRK01345, PRK01345, heat shock protein HtpX; Provisional.
Length = 317
Score = 30.0 bits (68), Expect = 1.4
Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 8/51 (15%)
Query: 36 WMSDKLMKSFEGA-----RNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTP 81
W SDK++ GA R+ P ++ V LA A +P PKV ++ P
Sbjct: 46 WNSDKMVLRMYGAQEVDERSAPELYRMV---RDLARRAGLPMPKVYIIDNP 93
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 30.0 bits (68), Expect = 1.4
Identities = 23/58 (39%), Positives = 27/58 (46%), Gaps = 6/58 (10%)
Query: 110 SPG--TLARDLIEL----GGNRTLTLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEK 161
SPG L R L EL KK I GE+LEE K EAK ++E+EK
Sbjct: 83 SPGEQGLQRKLKELEREQKEEEVREKHNKKIIEKFGEDLEEVYKFMKGEAKVEEEEEK 140
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 29.8 bits (68), Expect = 1.6
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 103 IIITNRTSPGTLARDLIELGGNRTLTLQ------VKKRI-RLEGEELEEYQKKKDKEAKD 155
II+ R+S LA++ E R + + R+ RL E+E+ +K+ + K+
Sbjct: 371 IIVLIRSSK-DLAKEAKEKLMERFELSEIQADAILDMRLRRLTKLEVEKLEKELKELEKE 429
Query: 156 KQEKEKIPP 164
++ EKI
Sbjct: 430 IEDLEKILA 438
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 29.2 bits (66), Expect = 2.9
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 128 TLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKEK-----IPPHD 166
LQ +K + +E + +K K +E K K+E EK IPP +
Sbjct: 552 ELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAE 595
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 28.5 bits (64), Expect = 3.0
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 132 KKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTS 168
KK + + E +E ++KKDK+ K + K
Sbjct: 154 KKEKKKKKEVKKEKKEKKDKKEKMVEPKGSKKKKKKK 190
>gnl|CDD|237722 PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis
protein NifN; Provisional.
Length = 455
Score = 28.7 bits (65), Expect = 3.2
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 7/29 (24%)
Query: 65 AELAKVPSPKVVLVSTPD----MECGFSR 89
ELA P +V VSTPD +E G++
Sbjct: 123 PELADTP---IVYVSTPDFKGALEDGWAA 148
>gnl|CDD|169691 PRK09173, PRK09173, F0F1 ATP synthase subunit B; Validated.
Length = 159
Score = 28.2 bits (63), Expect = 3.3
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 111 PGTLARDLIELGGNRTLTLQVKKRIRLEGEE-LEEYQKKKDKEAKDKQE 158
PG +AR L L +R+R E ++ L EYQ+K+ + K+ +
Sbjct: 24 PGMIARSLDARADRIKNELAEARRLREEAQQLLAEYQRKRKEAEKEAAD 72
>gnl|CDD|215214 PLN02381, PLN02381, valyl-tRNA synthetase.
Length = 1066
Score = 29.1 bits (65), Expect = 3.6
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 128 TLQVKKRIRLEGEELEEYQKKKDKEAKDKQEKE 160
T ++ L EELE +KKK+++AK+K+ K+
Sbjct: 4 TESEAEKKILTEEELER-KKKKEEKAKEKELKK 35
>gnl|CDD|240292 PTZ00148, PTZ00148, 40S ribosomal protein S8; Provisional.
Length = 205
Score = 28.4 bits (64), Expect = 3.6
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 137 LEGEELEEYQKKKDKEAK 154
LEG+ELE Y KK +K+ K
Sbjct: 188 LEGKELEFYLKKLEKKKK 205
>gnl|CDD|130488 TIGR01421, gluta_reduc_1, glutathione-disulfide reductase,
animal/bacterial. The tripeptide glutathione is an
important reductant, e.g., for maintaining the cellular
thiol/disulfide status and for protecting against
reactive oxygen species such as hydrogen peroxide.
Glutathione-disulfide reductase regenerates reduced
glutathione from oxidized glutathione (glutathione
disulfide) + NADPH. This model represents one of two
closely related subfamilies of glutathione-disulfide
reductase. Both are closely related to trypanothione
reductase, and separate models are built so each of the
three can describe proteins with conserved function.
This model describes glutathione-disulfide reductases of
animals, yeast, and a number of animal-resident bacteria
[Energy metabolism, Electron transport].
Length = 450
Score = 28.7 bits (64), Expect = 3.7
Identities = 31/157 (19%), Positives = 53/157 (33%), Gaps = 30/157 (19%)
Query: 39 DKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKV---------VLVST--------- 80
D + G V + A K + +V +L++T
Sbjct: 87 DAYVDRLNGIYQKNLEKNKVDVIFGHARFTKDGTVEVNGRDYTAPHILIATGGKPSFPEN 146
Query: 81 -PDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIELGGNRTL-TLQVKKRIRLE 138
P E G D FF P+ +I+ G +A +EL G L L + + +
Sbjct: 147 IPGAELGTDSDGFFALEELPKRVVIV----GAGYIA---VELAG--VLHGLGSETHLVIR 197
Query: 139 GEE-LEEYQKKKDKEAKDKQEKEKIPPHDTSFINELQ 174
E L + + ++ EKE I H S +++
Sbjct: 198 HERVLRSFDSMISETITEEYEKEGINVHKLSKPVKVE 234
>gnl|CDD|226491 COG4002, COG4002, Predicted phosphotransacetylase [General function
prediction only].
Length = 256
Score = 28.3 bits (63), Expect = 4.5
Identities = 9/44 (20%), Positives = 23/44 (52%)
Query: 110 SPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKDKEA 153
+ G R I +G N+ + ++ ++++ EG ++E K ++
Sbjct: 11 ARGMAIRVAIGIGENKEVVVKAYEKLKEEGIDVELVDNKDPEKV 54
>gnl|CDD|220600 pfam10147, CR6_interact, Growth arrest and DNA-damage-inducible
proteins-interacting protein 1. Members of this family
of proteins act as negative regulators of G1 to S cell
cycle phase progression by inhibiting cyclin-dependent
kinases. Inhibitory effects are additive with GADD45
proteins but occur also in the absence of GADD45
proteins. Furthermore, they act as a repressor of the
orphan nuclear receptor NR4A1 by inhibiting AB
domain-mediated transcriptional activity.
Length = 217
Score = 27.9 bits (62), Expect = 5.4
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 140 EELEEYQKKKDKEAKDKQEKEK 161
++ E+ +KKK KEAK ++++EK
Sbjct: 185 QQKEKEEKKKVKEAKRREKEEK 206
>gnl|CDD|237844 PRK14873, PRK14873, primosome assembly protein PriA; Provisional.
Length = 665
Score = 28.4 bits (64), Expect = 5.6
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 63 SLAELAKVPSPKVVLVSTPDM 83
L L +V SP+ VL TP++
Sbjct: 72 KLRWLERVVSPEPVL--TPEI 90
>gnl|CDD|215149 PLN02265, PLN02265, probable phenylalanyl-tRNA synthetase beta
chain.
Length = 597
Score = 28.1 bits (63), Expect = 5.8
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 218 CGFSRDLFFQWCSSPENSIIITNRNRADDSDSNVIV 253
GF+ L + CS EN NR DD +S VI+
Sbjct: 413 AGFTEVLTWILCSHKEN---FAMLNREDDGNSAVII 445
>gnl|CDD|234582 PRK00028, infC, translation initiation factor IF-3; Reviewed.
Length = 177
Score = 27.4 bits (62), Expect = 6.3
Identities = 16/30 (53%), Positives = 17/30 (56%), Gaps = 9/30 (30%)
Query: 146 QKKKDKEAKDKQE----KE-----KIPPHD 166
QKKK KEAK KQ+ KE KI HD
Sbjct: 75 QKKKQKEAKKKQKVIEVKEIKFRPKIDEHD 104
>gnl|CDD|220371 pfam09736, Bud13, Pre-mRNA-splicing factor of RES complex. This
entry is characterized by proteins with alternating
conserved and low-complexity regions. Bud13 together
with Snu17p and a newly identified factor,
Pml1p/Ylr016c, form a novel trimeric complex. called The
RES complex, pre-mRNA retention and splicing complex.
Subunits of this complex are not essential for viability
of yeasts but they are required for efficient splicing
in vitro and in vivo. Furthermore, inactivation of this
complex causes pre-mRNA leakage from the nucleus. Bud13
contains a unique, phylogenetically conserved C-terminal
region of unknown function.
Length = 141
Score = 26.9 bits (60), Expect = 6.6
Identities = 10/28 (35%), Positives = 21/28 (75%)
Query: 133 KRIRLEGEELEEYQKKKDKEAKDKQEKE 160
+ I +E + E+ ++K++KE K+++EKE
Sbjct: 10 RIIDIEEKREEKEREKEEKERKEEKEKE 37
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 27.3 bits (61), Expect = 7.3
Identities = 8/37 (21%), Positives = 18/37 (48%)
Query: 132 KKRIRLEGEELEEYQKKKDKEAKDKQEKEKIPPHDTS 168
K + + ++ ++ + KKD + DK EK+ +
Sbjct: 85 KWKKKKSKKKKDKDKDKKDDKKDDKSEKKDEKEAEDK 121
>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed.
Length = 457
Score = 27.6 bits (62), Expect = 7.4
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 245 DDSDSNVIVLEGCLSDEYYRV 265
DD +NV +LE L EYY V
Sbjct: 9 DDIPANVKLLEAKLLAEYYTV 29
>gnl|CDD|99912 cd00145, POLBc, DNA polymerase type-B family catalytic domain.
DNA-directed DNA polymerases elongate DNA by adding
nucleotide triphosphate (dNTP) residues to the 5'-end of
the growing chain of DNA. DNA-directed DNA polymerases
are multifunctional with both synthetic (polymerase) and
degradative modes (exonucleases) and play roles in the
processes of DNA replication, repair, and recombination.
DNA-dependent DNA polymerases can be classified in six
main groups based upon their phylogenetic relationships
with E. coli polymerase I (class A), E. coli polymerase
II (class B), E. coli polymerase III (class C),
euryarchaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB, and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family B
DNA polymerases include E. coli DNA polymerase II, some
eubacterial phage DNA polymerases, nuclear replicative
DNA polymerases (alpha, delta, epsilon, and zeta), and
eukaryotic viral and plasmid-borne enzymes. DNA
polymerase is made up of distinct domains and
sub-domains. The polymerase domain of DNA polymerase
type B (Pol domain) is responsible for the
template-directed polymerization of dNTPs onto the
growing primer strand of duplex DNA that is usually
magnesium dependent. In general, the architecture of the
Pol domain has been likened to a right hand with
fingers, thumb, and palm sub-domains with a deep groove
to accommodate the nucleic acid substrate. There are a
few conserved motifs in the Pol domain of family B DNA
polymerases. The conserved aspartic acid residues in the
DTDS motifs of the palm sub-domain is crucial for
binding to divalent metal ion and is suggested to be
important for polymerase catalysis.
Length = 323
Score = 27.3 bits (61), Expect = 8.7
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 2/76 (2%)
Query: 102 SIIITNRTSPGTLARDLIELGGNRTLTLQVKKRIRLEGEELEEYQKKKD--KEAKDKQEK 159
SIIIT SP TL + + + + +G ++ + EAK + +
Sbjct: 30 SIIITYNLSPTTLVGNGEIAAPEDYIGVGFRSPKDRKGLLPRILEELLNFRDEAKKRMKA 89
Query: 160 EKIPPHDTSFINELQL 175
K+ P + + Q
Sbjct: 90 AKLAPEERVLYDNRQQ 105
>gnl|CDD|239738 cd03769, SR_IS607_transposase_like, Serine Recombinase (SR) family,
IS607-like transposase subfamily, catalytic domain;
members contain a DNA binding domain with homology to
MerR/SoxR located N-terminal to the catalytic domain.
Serine recombinases catalyze site-specific recombination
of DNA molecules by a concerted, four-strand cleavage
and rejoining mechanism which involves a transient
phosphoserine linkage between DNA and the enzyme. They
are functionally versatile and include resolvases,
invertases, integrases, and transposases. This subfamily
is composed of proteins that catalyze the transposition
of insertion sequence (IS) elements such as IS607 from
Helicobacter and IS1535 from Mycobacterium, and similar
proteins from other bacteria and several archaeal
species. IS elements are DNA segments that move to new
sites in prokaryotic and eukaryotic genomes causing
insertion mutations and gene rearrangements.
Length = 134
Score = 26.5 bits (59), Expect = 9.7
Identities = 9/47 (19%), Positives = 22/47 (46%)
Query: 74 KVVLVSTPDMECGFSRDLFFQWCSSPENSIIITNRTSPGTLARDLIE 120
+ V+++ D F +L + + I++ N+ L ++L+E
Sbjct: 64 ERVVITYKDRLARFGFELLEELFKAYGVEIVVINQEENEELEQELVE 110
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 0.408
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,981,489
Number of extensions: 1323247
Number of successful extensions: 1984
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1953
Number of HSP's successfully gapped: 66
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
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: 58 (26.0 bits)