RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12656
(291 letters)
>gnl|CDD|201683 pfam01245, Ribosomal_L19, Ribosomal protein L19.
Length = 113
Score = 62.9 bits (154), Expect = 1e-12
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 8/107 (7%)
Query: 64 NQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGL 121
+ +++E + K D+P F VG + V K + NK R F G+ I KR GL
Sbjct: 1 MNLIKEIEAEQLKK-----DLPEFRVGDTVKVHVKIK-EGNKERIQVFEGVVIAKRGRGL 54
Query: 122 RHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
F +R + +G+E + ++ P I I V+R K L YLRD
Sbjct: 55 NSTFTVRKISQGVGVERVFPLHSPRIDKIEVVRRGKVRRAKLYYLRD 101
>gnl|CDD|223412 COG0335, RplS, Ribosomal protein L19 [Translation, ribosomal
structure and biogenesis].
Length = 115
Score = 48.4 bits (116), Expect = 2e-07
Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 83 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 140
DIPSF G + V + +K R F G+ I +R G+ F +R + +G+E +
Sbjct: 17 DIPSFRPGDTVRVHVKIV-EGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVF 75
Query: 141 DMYDPTIHNITVLRLEKRLDDDLLYLRD 168
++ P I +I V+R K L YLR+
Sbjct: 76 PLHSPLIESIEVVRRGKVRRAKLYYLRE 103
>gnl|CDD|130096 TIGR01024, rplS_bact, ribosomal protein L19, bacterial type. This
model describes bacterial ribosomoal protein L19 and its
chloroplast equivalent. Putative mitochondrial L19 are
found in several species (but not Saccharomyces
cerevisiae) and score between trusted and noise cutoffs
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 44.2 bits (105), Expect = 6e-06
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 3/88 (3%)
Query: 83 DIPSFFVGSILSVTSADKHDPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGIEIAY 140
D+P F VG + V + K R F G+ I +R G+ F +R + +G+E +
Sbjct: 15 DLPDFRVGDTVRVHVKIV-EGKKERIQVFEGVVIARRGGGIGETFTVRKISYGVGVERIF 73
Query: 141 DMYDPTIHNITVLRLEKRLDDDLLYLRD 168
++ P I +I V+R K L YLR+
Sbjct: 74 PLHSPNIDSIEVVRRGKVRRAKLYYLRE 101
>gnl|CDD|235418 PRK05338, rplS, 50S ribosomal protein L19; Provisional.
Length = 116
Score = 38.5 bits (91), Expect = 5e-04
Identities = 25/78 (32%), Positives = 38/78 (48%), Gaps = 11/78 (14%)
Query: 83 DIPSFFVGSILSVTSADKH----DPNKTR--KFVGICIQKRYCGLRHEFVLRNVVDNLGI 136
DIP F G + V H + NK R F G+ I +R GL F +R + +G+
Sbjct: 15 DIPEFRPGDTVRV-----HVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGV 69
Query: 137 EIAYDMYDPTIHNITVLR 154
E + ++ P I +I V+R
Sbjct: 70 ERTFPLHSPRIDSIEVVR 87
>gnl|CDD|177023 CHL00084, rpl19, ribosomal protein L19.
Length = 117
Score = 33.8 bits (78), Expect = 0.026
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 82 IDIPSFFVGSI----LSVTSADKHDPNKTRKFVGICIQKRYCGLRHEFVLRNVVDNLGIE 137
++P VG + + +K + + + G I K+ GL +R V +G+E
Sbjct: 18 KNLPKIRVGDTVKVGVLIQEGNK---ERVQFYEGTVIAKKNSGLNTTITVRKVFQGIGVE 74
Query: 138 IAYDMYDPTIHNITVLRLEKRLDDDLLYLRD 168
+ ++ P + +I VLR K L YLR+
Sbjct: 75 RVFLLHSPKLASIEVLRRSKVRRAKLYYLRN 105
>gnl|CDD|202620 pfam03411, Peptidase_M74, Penicillin-insensitive murein
endopeptidase.
Length = 240
Score = 33.3 bits (76), Expect = 0.085
Identities = 14/66 (21%), Positives = 30/66 (45%)
Query: 54 FLPDPELKFRNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGIC 113
+L P+ ++ + + + D++ R + + I S+ DP+ TR FV
Sbjct: 88 WLQMPKTRWTSAQLLRPQALDLVSRDGKHVDSTLWKPEIFSLIKLAAQDPDVTRIFVNPA 147
Query: 114 IQKRYC 119
I+++ C
Sbjct: 148 IKQQLC 153
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 33.5 bits (77), Expect = 0.14
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 165 YLRDALPQYSTFPFDMEPEY-LLDGAPVPINDIKVKLKPRP-WVGRWERKGYKGIDDVDQ 222
LRD P Y P EP Y G V ++++ +K R W RWE G G++ V++
Sbjct: 304 KLRD--PGYVLAPAQCEPFYQFFQGETVDVDELPIKFFDRSGWTYRWEGGGAHGLERVNE 361
>gnl|CDD|226293 COG3770, MepA, Murein endopeptidase [Cell envelope biogenesis,
outer membrane].
Length = 284
Score = 32.0 bits (73), Expect = 0.28
Identities = 19/66 (28%), Positives = 33/66 (50%)
Query: 54 FLPDPELKFRNQVREKLERSDMIKRRSVIDIPSFFVGSILSVTSADKHDPNKTRKFVGIC 113
+L P+ ++ + RE+ + DM+KR+ P + S+ DP+ TR FV
Sbjct: 127 WLQMPKTRWTDAQRERPQALDMVKRKGKRVDPRLWTPQHASLIKLAASDPDVTRIFVNPA 186
Query: 114 IQKRYC 119
I+K+ C
Sbjct: 187 IKKKLC 192
>gnl|CDD|237463 PRK13668, PRK13668, hypothetical protein; Provisional.
Length = 267
Score = 31.5 bits (72), Expect = 0.41
Identities = 23/88 (26%), Positives = 35/88 (39%), Gaps = 20/88 (22%)
Query: 154 RLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPINDI----KVKLKPRPWVGRW 209
+L+KRL P + F FD E E L I V + P V +W
Sbjct: 9 KLKKRLSH---------PDW-DFSFDREKETLR------IERKDNKKGVTISLPPIVAKW 52
Query: 210 ERKGYKGIDDVDQHITEKMKGQKKKLEE 237
E K K ID++ ++ E + K++
Sbjct: 53 EEKKEKAIDEIVYYVEEALAAMADKVKL 80
>gnl|CDD|129509 TIGR00415, serS_MJ, seryl-tRNA synthetase, Methanococcus jannaschii
family. The seryl-tRNA synthetases from a few of the
Archaea, represented by this model, are very different
from the set of mutually more closely related seryl-tRNA
synthetases from Eubacteria, Eukaryotes, and other
Archaea. Although distantly homologous, the present set
differs enough not to be recognized by the pfam model
tRNA-synt_2b that recognizes the remainder of seryl-tRNA
synthetases among oither class II amino-acyl tRNA
synthetases [Protein synthesis, tRNA aminoacylation].
Length = 520
Score = 31.1 bits (70), Expect = 0.81
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 4/59 (6%)
Query: 166 LRDALPQYSTFPFDMEPEY-LLDGAPVPINDIKVKLKPRP-WVGRWERKGYKGIDDVDQ 222
++D P Y P EP Y +G + D +K R W RWE G KG+D V +
Sbjct: 305 IKD--PGYVIAPAQCEPFYQFFEGEVIDAEDKPIKFFDRSGWTYRWEAGGAKGLDRVHE 361
>gnl|CDD|227185 COG4848, COG4848, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 30.6 bits (69), Expect = 0.93
Identities = 24/112 (21%), Positives = 49/112 (43%), Gaps = 9/112 (8%)
Query: 150 ITVLRLEKRLDDDLLYLRDALPQYSTFPFDMEPEYLLDGAPVPINDIKVKLKPRPWVGRW 209
+T ++ +L++ L + TF +D E + L N + + P + ++
Sbjct: 1 MTTRKMRDQLEERLNHPN------RTFSYDREEDTL--RIEDTENKKGITIALPPIIAKY 52
Query: 210 ERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRT-IPEEEQEEI 260
ERKG + ID++ ++ E M K K E + + R T P++ ++
Sbjct: 53 ERKGERAIDEIVYYVQEGMAAMKGKTTEKGNEKRIYPVIRATSFPDKTKDGH 104
>gnl|CDD|236533 PRK09474, malE, maltose ABC transporter periplasmic protein;
Reviewed.
Length = 396
Score = 30.4 bits (69), Expect = 1.00
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 21 RNLSKNSPLQ--FENAENGEKKLSIPQENRFMYQE 53
L+K+ + +NA+NGE +IPQ + F Y
Sbjct: 335 EELAKDPRIAATMDNAQNGEIMPNIPQMSAFWYAM 369
>gnl|CDD|216950 pfam02259, FAT, FAT domain. The FAT domain is named after FRAP,
ATM and TRRAP.
Length = 350
Score = 30.4 bits (69), Expect = 1.2
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 241 KYDLMKEYRRTIPEEEQEEIFSEVFSELHQ 270
++D M EY ++ E + F + LH+
Sbjct: 13 QWDEMDEYLSSMKEASPDRSFYQALLALHR 42
>gnl|CDD|233454 TIGR01536, asn_synth_AEB, asparagine synthase
(glutamine-hydrolyzing). This model describes the
glutamine-hydrolysing asparagine synthase. A poorly
conserved C-terminal extension was removed from the
model. Bacterial members of the family tend to have a
long, poorly conserved insert lacking from archaeal and
eukaryotic sequences. Multiple isozymes have been
demonstrated, such as in Bacillus subtilis. Long-branch
members of the phylogenetic tree (which typically were
also second or third candidate members from their
genomes) were removed from the seed alignment and score
below trusted cutoff [Amino acid biosynthesis, Aspartate
family].
Length = 466
Score = 30.0 bits (68), Expect = 1.4
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 45 QENRFMYQEFLPDPELKFRNQVREKLERSDMIKRRSVIDIPSFFVGSILS 94
+ + ++ D E +++R LE + +KRR V D+P VG +LS
Sbjct: 216 ERYYWERRDEHTDSEEDLVDELRSLLEDA--VKRRLVADVP---VGVLLS 260
>gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X
DNA Polymerases. X family polymerases fill in short
gaps during DNA repair. They are relatively inaccurate
enzymes and play roles in base excision repair, in
non-homologous end joining (NHEJ) which acts mainly to
repair damage due to ionizing radiation, and in V(D)J
recombination. This family includes eukaryotic Pol beta,
Pol lambda, Pol mu, and terminal deoxyribonucleotidyl
transferase (TdT). Pol beta and Pol lambda are primarily
DNA template-dependent polymerases. TdT is a DNA
template-independent polymerase. Pol mu has both
template dependent and template independent activities.
This subgroup belongs to the Pol beta-like NT
superfamily. In the majority of enzymes in this
superfamily, two carboxylates, Dx[D/E], together with a
third more distal carboxylate, coordinate two divalent
metal cations involved in a two-metal ion mechanism of
nucleotide addition. These three carboxylate residues
are fairly well conserved in this family.
Length = 307
Score = 29.5 bits (67), Expect = 1.7
Identities = 11/67 (16%), Positives = 27/67 (40%), Gaps = 8/67 (11%)
Query: 206 VGRWERKGYKGIDDVDQHITEKM-KGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEV 264
+ G + ++D+ + K+ + LE +++++ IP EE I +
Sbjct: 98 ARKLYELGIRTLEDLRKAAGAKLEQNILIGLE-------YYEDFQQRIPREEALAIAEII 150
Query: 265 FSELHQL 271
L ++
Sbjct: 151 KEALREV 157
>gnl|CDD|184468 PRK14035, PRK14035, citrate synthase; Provisional.
Length = 371
Score = 29.7 bits (67), Expect = 1.9
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 215 KGIDDVDQHITEKMKGQKK---------KLEEPWEKYDLMKEYRRTIPEE-EQEEIF 261
+ I DVD ++ EK ++K K +P KY ++E R I + +EE+F
Sbjct: 233 RSIGDVDAYLDEKFANKEKIMGFGHRVYKDGDPRAKY--LREMSRKITKGTGREELF 287
>gnl|CDD|176468 cd01596, Aspartase_like, aspartase (L-aspartate ammonia-lyase) and
fumarase class II enzymes. This group contains
aspartase (L-aspartate ammonia-lyase), fumarase class II
enzymes, and related proteins. It is a member of the
Lyase class I family. Members of this family for the
most part catalyze similar beta-elimination reactions in
which a C-N or C-O bond is cleaved with the release of
fumarate as one of the products. These proteins are
active as tetramers. The four active sites of the
homotetrameric enzyme are each formed by residues from
three different subunits. Aspartase catalyzes the
reversible deamination of aspartic acid. Fumarase
catalyzes the reversible hydration/dehydration of
fumarate to L-malate during the Krebs cycle.
Length = 450
Score = 29.3 bits (67), Expect = 2.8
Identities = 11/26 (42%), Positives = 13/26 (50%)
Query: 145 PTIHNITVLRLEKRLDDDLLYLRDAL 170
P H L L +RL L L+DAL
Sbjct: 141 PAAHIAAALALLERLLPALEQLQDAL 166
>gnl|CDD|220350 pfam09700, Cas_Cmr3, CRISPR-associated protein (Cas_Cmr3). CRISPR
is a term for Clustered Regularly Interspaced Short
Palindromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. This highly
divergent family, found in at least ten different
archaeal and bacterial species, is represented by TM1793
from Thermotoga maritima.
Length = 347
Score = 28.9 bits (65), Expect = 3.2
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 8/79 (10%)
Query: 190 PVPINDIKVKLKPR---PWVGRWERKGYKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMK 246
P P+ D+ VK++ + R E G + D D ++ G+K+ L K
Sbjct: 86 PAPL-DLLVKVEKEDGLVNLLRLEPLGPLPLPDRDPLEEPRIGGKKEPAPGYLSLEGLEK 144
Query: 247 EYRRTIPE----EEQEEIF 261
R +PE E+EEIF
Sbjct: 145 WLRGELPEDSELVEEEEIF 163
>gnl|CDD|239871 cd04406, RhoGAP_myosin_IXA, RhoGAP_myosin_IXA: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain present in myosins IXA. Class IX myosins
contain a characteristic head domain, a neck domain and
a tail domain which contains a C6H2-zinc binding motif
and a Rho-GAP domain. Class IX myosins are
single-headed, processive myosins that are partly
cytoplasmic, and partly associated with membranes and
the actin cytoskeleton. Class IX myosins are implicated
in the regulation of neuronal morphogenesis and function
of sensory systems, like the inner ear. There are two
major isoforms, myosin IXA and IXB with several splice
variants, which are both expressed in developing
neurons. Small GTPases cluster into distinct families,
and all act as molecular switches, active in their
GTP-bound form but inactive when GDP-bound. The Rho
family of GTPases activates effectors involved in a wide
variety of developmental processes, including regulation
of cytoskeleton formation, cell proliferation and the
JNK signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 186
Score = 28.0 bits (62), Expect = 3.8
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 217 IDDVDQH-ITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFSELHQLS 272
+DD + H I K + L P ++L +E+ R + +E+ E V+S + QLS
Sbjct: 62 LDDYNIHVIASVFKQWLRDLPNPLMTFELYEEFLRAMGLQERRETVRGVYSVIDQLS 118
>gnl|CDD|215091 PLN00179, PLN00179, acyl- [acyl-carrier protein] desaturase.
Length = 390
Score = 28.5 bits (64), Expect = 4.0
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 44 PQENRFMYQEFLPDPE-LKFRNQVREKLERS 73
P E + Q+FLPDP F +QV+E ER+
Sbjct: 82 PVEKSWQPQDFLPDPASEGFYDQVKELRERA 112
>gnl|CDD|181439 PRK08472, fliI, flagellum-specific ATP synthase; Validated.
Length = 434
Score = 28.5 bits (64), Expect = 4.7
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 229 KGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFSELHQL 271
KG K+L+E K + M+++ + P E F + F +L ++
Sbjct: 392 KGNDKELDEAISKKEFMEQFLKQNPNELFP--FEQTFEQLEEI 432
>gnl|CDD|225661 COG3119, AslA, Arylsulfatase A and related enzymes [Inorganic ion
transport and metabolism].
Length = 475
Score = 28.6 bits (64), Expect = 5.0
Identities = 25/123 (20%), Positives = 37/123 (30%), Gaps = 32/123 (26%)
Query: 147 IHNITVLRLEKRLDDDLLYLRDALPQYSTFP--FDMEPEYLLDGAPVPINDIKVKLKPRP 204
I ++ R+ D L+ L D LP T + P LDG +P K L P
Sbjct: 326 IRWPGGIKPGGRVVDALVSLIDLLP---TLLDAAGVPPPKDLDGQSLPPKLQKPGLDGVP 382
Query: 205 WVGR-----------------------WERKGYKGIDDVDQHITEKMKGQKKKLEEPWEK 241
+ R +K I + T + +PWE
Sbjct: 383 LLEWLAGGKAAVREEYGYFGELFGLRAIRRDDWKYIVFLPADPTLLYDVR----NDPWEL 438
Query: 242 YDL 244
+L
Sbjct: 439 TNL 441
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 28.3 bits (64), Expect = 5.7
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 226 EKMKGQKKKLEEPWEKYDLMKEYRRTI-----PEEEQEEIFSEV--FSELHQLS 272
E++K +K+L E + D ++E R I P+E +E+ E+ + +S
Sbjct: 233 EQLKAIQKELGEDDDDKDEVEELREKIEKLKLPKEAKEKAEKELKKLETMSPMS 286
>gnl|CDD|173865 cd08500, PBP2_NikA_DppA_OppA_like_4, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 499
Score = 28.0 bits (63), Expect = 6.7
Identities = 8/44 (18%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 229 KGQKKKLEEPWEK--YDLMKEYRRTIPEEEQEEIFSEVFSELHQ 270
PWEK DL + + +E+++ +++E+ ++
Sbjct: 433 GPPGGPEPPPWEKKIDDLYDKGAVELDQEKRKALYAEIQ-KIAA 475
>gnl|CDD|227669 COG5378, COG5378, Predicted nucleotide-binding protein [General
function prediction only].
Length = 175
Score = 27.6 bits (61), Expect = 6.8
Identities = 10/50 (20%), Positives = 25/50 (50%)
Query: 217 IDDVDQHITEKMKGQKKKLEEPWEKYDLMKEYRRTIPEEEQEEIFSEVFS 266
+D++ +HI +K K + + +L+ + IP+E+ + E ++
Sbjct: 55 LDELKEHIEKKCKKANVDESKFIKIANLILSNVKIIPKEKYNDKSKEAYN 104
>gnl|CDD|188618 cd09898, H3TH_53EXO, H3TH domain of the 5'-3' exonuclease of Taq
DNA polymerase I and homologs. H3TH
(helix-3-turn-helix) domains of the 5'-3' exonuclease
(53EXO) of mutli-domain DNA polymerase I and single
domain protein homologs are included in this family. Taq
DNA polymerase I contains a polymerase domain for
synthesizing a new DNA strand and a 53EXO domain for
cleaving RNA primers or damaged DNA strands. Taq's 53EXO
recognizes and endonucleolytically cleaves a
structure-specific DNA substrate that has a bifurcated
downstream duplex and an upstream template-primer duplex
that overlaps the downstream duplex by 1 bp. The 53EXO
cleaves the unpaired 5'-arm of the overlap flap DNA
substrate. 5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region/I
domain (not included here) and inserted within the PIN
domain is an atypical helix-hairpin-helix-2 (HhH2)-like
region. This atypical HhH2 region, the H3TH domain, has
an extended loop with at least three turns between the
first two helices, and only three of the four helices
appear to be conserved. Both the H3TH domain and the
helical arch/clamp region are involved in DNA binding.
Studies suggest that a glycine-rich loop in the H3TH
domain contacts the phosphate backbone of the template
strand in the downstream DNA duplex. The nucleases
within this family have a carboxylate rich active site
that is involved in binding essential divalent metal ion
cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for
nuclease activity. The first metal binding site is
composed entirely of Asp/Glu residues from the PIN
domain, whereas, the second metal binding site is
composed generally of two Asp residues from the PIN
domain and two Asp residues from the H3TH domain.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 73
Score = 25.4 bits (57), Expect = 8.9
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 214 YKGIDDVDQHITEKMKGQKKKLEEPWEKYDLMKE 247
Y ++++ ++ E ++KLEE E+ L ++
Sbjct: 36 YGSLENILANLDELKGKLREKLEENKEQALLSRK 69
>gnl|CDD|179392 PRK02249, PRK02249, DNA primase large subunit; Validated.
Length = 343
Score = 27.2 bits (61), Expect = 9.3
Identities = 12/41 (29%), Positives = 17/41 (41%)
Query: 122 RHEFVLRNVVDNLGIEIAYDMYDPTIHNITVLRLEKRLDDD 162
+ LR + +LGI + +H LRL RL D
Sbjct: 105 EPDDDLRELARDLGIPARVEGDGFAVHVTDYLRLAARLKDP 145
>gnl|CDD|182473 PRK10455, PRK10455, periplasmic protein; Reviewed.
Length = 161
Score = 26.7 bits (59), Expect = 9.8
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 187 DGAPVPINDIKVKLKPRPWVGRWERKGYKGIDDVD---QHITEKMKGQKKKLEEPWEKYD 243
D P D K + + G +KG++ D Q I + MK Q+ +++ P
Sbjct: 25 DTTTAPPADAKPMMHHKGKFGPHHDMMFKGLNLTDAQKQQIRDIMKAQRDQMKRP----- 79
Query: 244 LMKEYRRTI 252
E RR +
Sbjct: 80 -PLEERRAM 87
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 0.137 0.402
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: 15,366,099
Number of extensions: 1546350
Number of successful extensions: 1703
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1699
Number of HSP's successfully gapped: 61
Length of query: 291
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 195
Effective length of database: 6,679,618
Effective search space: 1302525510
Effective search space used: 1302525510
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 (21.7 bits)
S2: 59 (26.4 bits)