RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14697
(175 letters)
>gnl|CDD|233221 TIGR00985, 3a0801s04tom, mitochondrial import receptor subunit
translocase of outer membrane 20 kDa subunit.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 148
Score = 137 bits (347), Expect = 3e-42
Identities = 60/140 (42%), Positives = 81/140 (57%), Gaps = 18/140 (12%)
Query: 49 VVTAVAVGAAVVVGYCLYFDKKRRSDPLFKEKLKERRRK-------NRELLQQKNKRGI- 100
VV A + AA +GY +YFD KRR+DP F++KL+ RR+K L ++K ++ I
Sbjct: 9 VVIAAGIAAAAFLGYAIYFDYKRRNDPDFRKKLRRRRKKQAGAEKQYGGLAKEKQRQRIR 68
Query: 101 ---------PDLKDHSAVQQYFLQEIQLGETLLAAGD-LDNGVEHLANALTVCGQPNQLL 150
PD D S + +FLQE+QLGE L+A G +D G H NAL V QP QLL
Sbjct: 69 PAAAGLAKAPDPTDPSEKEAFFLQEVQLGEELMAQGTNVDEGAVHFYNALKVYPQPQQLL 128
Query: 151 GVLQQTLPPNVFNALIEKLP 170
+ QQTLP +F +I +LP
Sbjct: 129 SIYQQTLPEPIFRLMIAQLP 148
>gnl|CDD|111006 pfam02064, MAS20, MAS20 protein import receptor.
Length = 184
Score = 70.5 bits (172), Expect = 1e-15
Identities = 42/153 (27%), Positives = 68/153 (44%), Gaps = 28/153 (18%)
Query: 46 GNKVVTAVAVGAAVVVGYCLYFDKKRRSDPLFKEKLKER-------------------RR 86
G A+A G+A+ Y +YFD KRR+DP F+++L++R +
Sbjct: 10 GLAATAAIAAGSAL--AYAIYFDYKRRNDPEFRKQLRQRAKEQAKMEEEAAEHAKEAKLQ 67
Query: 87 KNRELLQQKNKR-GIPDLKDHSAVQQYFLQEIQLGETL-LAAGDLDNGVEHLANALTVCG 144
K RE L + G P D + FL+ ++ GE L + G + AL V
Sbjct: 68 KIREFLDMEAAEDGFP--SDPDEKEATFLENVEAGEILGMDPGKAIDAALAFYKALKVYP 125
Query: 145 QPNQLLGVLQQTLPPNVFNALIEK---LPPAGI 174
QP L+G+ +++ + + + E PPA I
Sbjct: 126 QPADLIGIYDKSIAEAILDIIAEMIAIDPPAKI 158
>gnl|CDD|224569 COG1655, COG1655, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 267
Score = 33.0 bits (75), Expect = 0.061
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 59 VVVGYCLY--FDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGIPDLKDHS-AVQQYFL 114
VV C Y F ++EK +E R+KN EL + D++ + A+ +Y L
Sbjct: 63 VVCPICYYAAFKSDFEKIKSYQEKTEELRKKNIELK--WHSVKFSDIRTLNEAIARYKL 119
>gnl|CDD|216280 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain. This
domain belongs to a more diverse superfamily, including
pfam01331 and pfam01653.
Length = 195
Score = 30.8 bits (70), Expect = 0.29
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 64 CLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGI---PDLKDHSAVQQYFLQEIQLG 120
LY D + L E LKERR E + + I + D ++++ + I+ G
Sbjct: 114 VLYLD----GESLTDEPLKERRELLEEYFKIPVRIEIAETIETNDIEELKEFLEEAIKEG 169
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The
family functions as a highly conserved exonuclease that
is required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing
and export.
Length = 134
Score = 30.0 bits (68), Expect = 0.38
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 67 FDKKRRSDPL--F-KEKLKERRRKNRELLQQKNKR 98
FDK+ R + L F K K +RR+K +E ++K +
Sbjct: 15 FDKEARKEYLTGFHKRKQ-QRRKKAQEEAKEKERE 48
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
eukaryotic DNA Ligase I. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriophages, eukarya, archaea and
bacteria. Some organisms express a variety of different
ligases which appear to be targeted to specific
functions. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
I is required for the ligation of Okazaki fragments
during lagging-strand DNA synthesis and for base
excision repair (BER). DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
adenylation domain binds ATP and contains many of the
active-site residues. DNA ligase I is the main
replicative ligase in eukaryotes. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases.
Length = 219
Score = 30.2 bits (69), Expect = 0.44
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 18/64 (28%)
Query: 64 CLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGIP---------DLKDHSAVQQYFL 114
LY + + L K+ L+ERR L ++ +P D +D +Q++
Sbjct: 132 LLYLNGE----SLLKKPLRERRELLHSLFKE-----VPGRFQFATSKDSEDTEEIQEFLE 182
Query: 115 QEIQ 118
+ ++
Sbjct: 183 EAVK 186
>gnl|CDD|205286 pfam13105, DUF3959, Protein of unknown function (DUF3959). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 260 amino acids in length.
Length = 242
Score = 29.5 bits (66), Expect = 0.71
Identities = 20/107 (18%), Positives = 34/107 (31%), Gaps = 23/107 (21%)
Query: 9 VLPSSFCWF--GDWCGYFGLWSG---------RIGPSGRLMSPMELISGNKVVTAVAVGA 57
++P + G G LW + R+ S L++ V + +G
Sbjct: 83 LIPCILRFRTYGITFGLLALWGALLWDMKEVQSLVILERMTS---LMTSEYVYLLLLIGG 139
Query: 58 AVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGIPDLK 104
+ G K K+ ++N L +QK KR K
Sbjct: 140 LIFGGLLANL---------IHRKEKDDNKENINLFKQKKKRKKLSFK 177
>gnl|CDD|200454 cd11315, AmyAc_bac1_AmyA, Alpha amylase catalytic domain found in
bacterial Alpha-amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes Firmicutes, Proteobacteria, Actinobacteria, and
Cyanobacteria. The Alpha-amylase family comprises the
largest family of glycoside hydrolases (GH), with the
majority of enzymes acting on starch, glycogen, and
related oligo- and polysaccharides. These proteins
catalyze the transformation of alpha-1,4 and alpha-1,6
glucosidic linkages with retention of the anomeric
center. The protein is described as having 3 domains: A,
B, C. A is a (beta/alpha) 8-barrel; B is a loop between
the beta 3 strand and alpha 3 helix of A; C is the
C-terminal extension characterized by a Greek key. The
majority of the enzymes have an active site cleft found
between domains A and B where a triad of catalytic
residues (Asp, Glu and Asp) performs catalysis. Other
members of this family have lost the catalytic activity
as in the case of the human 4F2hc, or only have 2
residues that serve as the catalytic nucleophile and the
acid/base, such as Thermus A4 beta-galactosidase with 2
Glu residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 352
Score = 29.6 bits (67), Expect = 0.74
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 87 KNRELLQQKNKRGIPDLKDHS-AVQQYFLQEIQLGETLLAAG 127
+R + Q G+PDL + AVQQ ++ L+A G
Sbjct: 128 NDRWQVTQGRLGGLPDLNTENPAVQQQQKAYLK---ALVALG 166
>gnl|CDD|219882 pfam08524, rRNA_processing, rRNA processing. This is a family of
proteins that are involved in rRNA processing. In a
localisation study they were found to localise to the
nucleus and nucleolus. The family also includes other
metazoa members from plants to mammals where the protein
has been named BR22 and is associated with TTF-1,
thyroid transcription factor 1. In the lungs, the family
binds TTF-1 to form a complex which influences the
expression of the key lung surfactant protein-B (SP-B)
and -C (SP-C), the small hydrophobic surfactant proteins
that maintain surface tension in alveoli.
Length = 150
Score = 29.1 bits (65), Expect = 0.76
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 76 LFKEKLKERRRKNRELLQQKNKRGIP 101
L K+K KER R+ R+ L +K K G P
Sbjct: 105 LSKKKQKERERR-RKKLTKKTKSGQP 129
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 29.3 bits (65), Expect = 0.99
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 125 AAGDLDNGVEHLANALTVCG------QPNQLLGVLQQTLPPNVFNALIEKLPPA 172
A G L + + L A++ CG Q Q+LG++ ++ NA+I+ P A
Sbjct: 210 AKGSLRDALSLLDQAISFCGGELKQAQIKQMLGIIDSEEVYSIINAIIDNDPKA 263
>gnl|CDD|236685 PRK10414, PRK10414, biopolymer transport protein ExbB; Provisional.
Length = 244
Score = 29.1 bits (65), Expect = 1.1
Identities = 24/91 (26%), Positives = 35/91 (38%), Gaps = 16/91 (17%)
Query: 49 VVTAVAVGA--AVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGIPDLKD- 105
VV V +G A VV + ++F K E ++RR RE R + D
Sbjct: 22 VVKCVMIGLILASVVTWAIFFSKS-------VEFFNQKRRLKREQQLLAEARSLDQANDI 74
Query: 106 -----HSAVQQYFLQEIQLGETLLAAGDLDN 131
++ + L E Q E L+ G DN
Sbjct: 75 AADFGSKSLSLHLLNEAQ-NELELSEGSDDN 104
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 28.9 bits (65), Expect = 1.5
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 89 RELLQQ-KNKRGIPDLKDHSAVQQY-FLQE--IQLGETLLAAGDLDNGVEHLANALTVCG 144
+ LQ+ K K I LK +A+Q+ E LG+ LA GD + L AL++
Sbjct: 30 KSYLQKNKYKAAIIQLK--NALQKDPNDAEARFLLGKIYLALGDYAAAEKELRKALSLGY 87
Query: 145 QPNQLL 150
NQ+L
Sbjct: 88 PKNQVL 93
Score = 27.0 bits (60), Expect = 6.2
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 119 LGETLLAAGDLDNGVEHLANA 139
LGE LA GD + E+LA A
Sbjct: 369 LGEAYLALGDFEKAAEYLAKA 389
>gnl|CDD|106979 PHA00671, PHA00671, hypothetical protein.
Length = 135
Score = 28.1 bits (61), Expect = 1.7
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 50 VTAVAVGAAVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRG 99
VTAVAVGAAV VG +Y K+ K +R ++ QQ ++
Sbjct: 5 VTAVAVGAAVGVGASMYMSNKQE---------KAQRSAQQQAQQQAQQQA 45
>gnl|CDD|218835 pfam05975, EcsB, Bacterial ABC transporter protein EcsB. This
family consists of several bacterial ABC transporter
proteins which are homologous to the EcsB protein of
Bacillus subtilis. EcsB is thought to encode a
hydrophobic protein with six membrane-spanning helices
in a pattern found in other hydrophobic components of
ABC transporters.
Length = 385
Score = 28.7 bits (65), Expect = 1.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 52 AVAVGAAVVVGYCLYFDKKRRSDPLFKEKL--KERRRKNR 89
A + ++V L K ++ L EKL E+RRK R
Sbjct: 188 AAILFLILLVVLLLLLRKLKKKKLLDWEKLIELEQRRKQR 227
>gnl|CDD|203848 pfam08079, Ribosomal_L30_N, Ribosomal L30 N-terminal domain.
This presumed domain is found at the N-terminus of
Ribosomal L30 proteins and has been termed RL30NT or
NUC018.
Length = 71
Score = 26.8 bits (60), Expect = 1.8
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 69 KKRRSDPLFKEKLKERRRKNRELLQQKNK 97
KKR+ + EKL+ +R K R + K
Sbjct: 4 KKRKRN----EKLRAKRAKKRAAKKAARK 28
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 27.7 bits (62), Expect = 2.0
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 7/37 (18%)
Query: 69 KKRRSDPLFKEKLKERRR-------KNRELLQQKNKR 98
KK D F++K +E++R K R Q+K ++
Sbjct: 60 KKETEDEEFQQKREEKKRKDEEKTAKKRAKRQKKKQK 96
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 28.2 bits (62), Expect = 2.9
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 33 PSGRLMSPMELISGNKVVTAVAVGAAVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELL 92
P+G + + SG + + A+ +V VG Y D P+F+ +LK+R + ELL
Sbjct: 1471 PTGSVSMIADTSSGIEPIFALVYKKSVTVGEFYYVD------PVFEAELKKRGLYSEELL 1524
Query: 93 QQ 94
++
Sbjct: 1525 KK 1526
>gnl|CDD|220178 pfam09321, DUF1978, Domain of unknown function (DUF1978). Members
of this family are found in various hypothetical
proteins produced by the bacterium Chlamydia pneumoniae.
Their exact function has not, as yet, been identified.
Length = 241
Score = 27.5 bits (61), Expect = 3.1
Identities = 10/45 (22%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 82 KERRRKNRELLQQKNKRGIPDLKDHSAVQQYFLQEIQLGETLLAA 126
K+ ++N+++LQ + Q ++ +EI+ E L A
Sbjct: 86 KQSSKENKKVLQDAQREFE------RQSQDFYDKEIEEVEERLEA 124
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 28.2 bits (62), Expect = 3.1
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 65 LYFDKKRRSDPLFKEKLKERRRKNRELLQQ 94
LY + +S P +K K++E RR +E+
Sbjct: 171 LYTEVIDKSSPSYKSKVQEARRIAKEIELS 200
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 27.6 bits (62), Expect = 3.4
Identities = 20/84 (23%), Positives = 24/84 (28%), Gaps = 11/84 (13%)
Query: 15 CWFGDWCGYFGLWSGRIGPSGRLM------SPMELISGNKVVTAV-AVGAAVVVGYCLYF 67
G G L G G L+ EL S + V A+ G +Y
Sbjct: 253 SLPGIRLGSGLLIEALRGEGGILVNDDGRRFMNELASRDVVSRAITRNEIDEGRGAHVYL 312
Query: 68 DKKRRSDPLFKEKLKERRRK-NRE 90
D L E LK N E
Sbjct: 313 DADGS---LDAEGLKATLPAFNEE 333
>gnl|CDD|226014 COG3483, TDO2, Tryptophan 2,3-dioxygenase (vermilion) [Amino acid
transport and metabolism].
Length = 262
Score = 27.5 bits (61), Expect = 3.4
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 114 LQEIQLGETLLAAGDLDNGVEHLANALTVCGQPNQLLGVLQQTLPPNVFNALIEKLPPA 172
L E++ LL A DL ++ LA + Q NQ VL T+ P + + L +
Sbjct: 46 LHELRAARDLLRADDLPPALKMLARVSRIFEQLNQAWDVL-ATMTPADYLDFRDALGQS 103
>gnl|CDD|216728 pfam01828, Peptidase_A4, Peptidase A4 family.
Length = 208
Score = 26.9 bits (60), Expect = 5.0
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 32 GPSGRLMSPMELISGNKVVTAVAV--GAAVVVGY 63
G SG + +++ KV+T V+V + V V Y
Sbjct: 176 GLSGATI--IDIKQNGKVLTDVSVTGDSEVTVKY 207
>gnl|CDD|234958 PRK01544, PRK01544, bifunctional N5-glutamine
S-adenosyl-L-methionine-dependent methyltransferase/tRNA
(m7G46) methyltransferase; Reviewed.
Length = 506
Score = 27.1 bits (60), Expect = 5.4
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 16/55 (29%)
Query: 74 DPLFKEKLKERRRKNRE---LLQQKNKRGIPDLKDH------SAVQQYFLQEIQL 119
DP K K K++R N+E +LQ K LKD+ S ++ YF + I+L
Sbjct: 427 DPWIKNKQKKKRIFNKERLKILQDK-------LKDNGNLVFASDIENYFYEAIEL 474
>gnl|CDD|239984 cd04611, CBS_pair_PAS_GGDEF_DUF1_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains in association with a PAS domain, a GGDEF
(DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain
downstream. PAS domains have been found to bind ligands,
and to act as sensors for light and oxygen in signal
transduction. The GGDEF domain has been suggested to be
homologous to the adenylyl cyclase catalytic domain and
is thought to be involved in regulating cell surface
adhesiveness in bacteria. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 111
Score = 26.0 bits (58), Expect = 5.7
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 114 LQEIQLGETLLAAGDL--DNGVEHLANALTVCGQPNQLLGVLQQT 156
L + +L A L ++G+ HL V +LLG+L QT
Sbjct: 66 LLTVPADTSLYDARQLMREHGIRHLV----VVDDDGELLGLLSQT 106
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited to
promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 26.5 bits (59), Expect = 5.9
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 69 KKRRSDPLFKEKLKERRRKNREL--LQQKNKRGIPDLKD 105
+K R E + +R++KN E L + LK+
Sbjct: 136 RKLRRRVNSPELVAKRKKKNNESSDLSGLAPYILYMLKE 174
>gnl|CDD|227881 COG5594, COG5594, Uncharacterized integral membrane protein
[Function unknown].
Length = 827
Score = 27.0 bits (60), Expect = 6.2
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 145 QPNQLLGVLQQTLPPNVFNALIEKLPP 171
P L G+L LP + L+ +P
Sbjct: 456 DPPFLAGILTGLLPTVALSLLMSIVPY 482
>gnl|CDD|217376 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This
family represents the major capsid protein (MCP) of
herpes viruses. The capsid shell consists of 150 MCP
hexamers and 12 MCP pentamers. One pentamer is found at
each of the 12 apices of the icosahedral shell, and the
hexamers form the edges and 20 faces.
Length = 1352
Score = 27.2 bits (61), Expect = 6.7
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 44 ISGNKVVTAVAVGAAV 59
ISG +VTA+A G A+
Sbjct: 297 ISGENLVTAIAYGKAM 312
>gnl|CDD|233819 TIGR02307, RNA_lig_RNL2, RNA ligase, Rnl2 family. Members of this
family ligate (seal breaks in) RNA. Members so far
include phage proteins that can counteract a host
defense of cleavage of specific tRNA molecules,
trypanosome ligases involved in RNA editing, but no
prokaryotic host proteins [Mobile and extrachromosomal
element functions, Prophage functions, Transcription,
RNA processing].
Length = 325
Score = 26.7 bits (59), Expect = 7.1
Identities = 14/63 (22%), Positives = 20/63 (31%), Gaps = 6/63 (9%)
Query: 43 LISGNKVVTAVAVGAAVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELLQQKNKRGIPD 102
L+ VV +C R L + KN + ++KNK G P
Sbjct: 177 LVDAGNYPLEGNTAEGYVVKHC------RPGKWLRNGNRTIIKCKNSKFSEKKNKAGKPI 230
Query: 103 LKD 105
L
Sbjct: 231 LAK 233
>gnl|CDD|213836 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
HK022 subfamily. Members of this family are phage (or
prophage-region) homologs of the bacterial homohexameric
replicative helicase DnaB. Some phage may rely on host
DnaB, while others encode their own verions. This model
describes the largest phage-specific clade among the
close homologs of DnaB, but there are, or course, other
DnaB homologs from phage that fall outside the scope of
this model [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 420
Score = 26.6 bits (59), Expect = 7.3
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 88 NRELLQQKNKRGIP-DLKDHSAVQQ 111
NR ++ +KR I DL+D A++Q
Sbjct: 353 NRGSEKRTDKRPIMSDLRDSGAIEQ 377
>gnl|CDD|235221 PRK04123, PRK04123, ribulokinase; Provisional.
Length = 548
Score = 26.7 bits (60), Expect = 7.7
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 14/81 (17%)
Query: 89 RELLQQKNKRGIPDLKDHSAVQQYFLQEIQLGETLLAAGDLDNGVEH-LANA-LTVCGQP 146
++ + + K+ + L + +A + GE L A D NG LA+ L
Sbjct: 351 KDEAEARGKQLLELLTEAAA-------KQPPGEHGLVALDWFNGRRTPLADQRLKGV--- 400
Query: 147 NQLLGVLQQTLPPNVFNALIE 167
+ G+ T P+++ ALIE
Sbjct: 401 --ITGLTLGTDAPDIYRALIE 419
>gnl|CDD|216431 pfam01321, Creatinase_N, Creatinase/Prolidase N-terminal domain.
This family includes the N-terminal non-catalytic
domains from creatinase and prolidase. The exact
function of this domain is uncertain.
Length = 128
Score = 25.7 bits (57), Expect = 8.4
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 131 NGVEHLANALTVCGQPNQLLGVLQQTLPPNVFNALIEKLPPAGIV 175
+ E LA+ L G + LG L + L E LP A +V
Sbjct: 72 DDAEALADLLKELGLELKRLGFEGDHLTVAEYERLKEALPDAELV 116
>gnl|CDD|185711 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of
archaeal and bacterial LigB-like DNA ligases.
ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA ligases
play a vital role in the diverse processes of DNA
replication, recombination and repair. ATP-dependent
ligases are present in many organisms such as viruses,
bacteriophages, eukarya, archaea and bacteria. Bacterial
DNA ligases are divided into two broad classes:
NAD-dependent and ATP-dependent. All bacterial species
have a NAD-dependent DNA ligase (LigA). Some bacterial
genomes contain multiple genes for DNA ligases that are
predicted to use ATP as their cofactor, including
Mycobacterium tuberculosis LigB, LigC, and LigD. This
group is composed of archaeal DNA ligases and bacterial
proteins similar to Mycobacterium tuberculosis LigB.
Members of this group contain adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains, comprising a catalytic core unit that is common
to most members of the ATP-dependent DNA ligase family.
The adenylation domain binds ATP and contains many of
the active-site residues. The common catalytic core unit
comprises six conserved sequence motifs (I, III, IIIa,
IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 207
Score = 26.3 bits (59), Expect = 8.4
Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 12/98 (12%)
Query: 31 IGPSGRLMSPMELIS--GNKVVTAVAVGAAVVVGY---CLYFDKKRRSDPLFKEKLKERR 85
P GR + E + K A + + LY D + L L ERR
Sbjct: 86 YDPDGRPLPFQETLRRFRRKYDVEEAAEEIPLTLFLFDILYLDGE----DLLDLPLSERR 141
Query: 86 RKNRELLQQKNKRGIPDLK---DHSAVQQYFLQEIQLG 120
+ E++ + + D +++F + ++ G
Sbjct: 142 KILEEIVPETEAILLAPRIVTDDPEEAEEFFEEALEAG 179
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 26.6 bits (59), Expect = 9.4
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 10/37 (27%)
Query: 58 AVVVGYCLYFDKKRRSDPLFKEKLKERRRKNRELLQQ 94
VV+G D KR + PL + R+R ++ELLQQ
Sbjct: 866 EVVIGV----DPKRET-PL-----ELRKRFHQELLQQ 892
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 0.140 0.442
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,350,325
Number of extensions: 876932
Number of successful extensions: 1295
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1288
Number of HSP's successfully gapped: 51
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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 (25.6 bits)