RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11162
(91 letters)
>gnl|CDD|132902 cd06926, RNAP_II_RPB11, RPB11 subunit of Eukaryotic RNA
polymerase II. The eukaryotic RPB11 subunit of RNA
polymerase (RNAP) II is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP II is responsible
for the synthesis of mRNA precursor. The RPB11 subunit
heterodimerizes with the RPB3 subunit, and together
with RPB10 and RPB12, anchors the two largest subunits,
RPB1 and RPB2, and stabilizes their association.
Length = 93
Score = 150 bits (382), Expect = 2e-49
Identities = 63/89 (70%), Positives = 74/89 (83%)
Query: 3 RKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ 62
+KI ++ DTKVPNAA FT+NKEDHTLGN++R QLLKDP+VLFAGYK PHPLEHK LRIQ
Sbjct: 5 KKITEKKDTKVPNAATFTINKEDHTLGNLLRMQLLKDPNVLFAGYKVPHPLEHKIELRIQ 64
Query: 63 TTAESTPHDALMNAITDLLAELSLFEERF 91
T TP +AL NAITDL++ELSL +E F
Sbjct: 65 TDGSITPKEALKNAITDLISELSLLKEEF 93
>gnl|CDD|222292 pfam13656, RNA_pol_L_2, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp. Many of the members of this family carry
only the N-terminal region of Rpb11.
Length = 77
Score = 92.2 bits (230), Expect = 2e-26
Identities = 40/77 (51%), Positives = 49/77 (63%)
Query: 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALM 74
N A F + EDHTLGN++R +LLKDP V FAGY PHPLE K LRIQT + P D L
Sbjct: 1 NEATFEIEGEDHTLGNLLREELLKDPDVEFAGYSVPHPLEDKINLRIQTKSGKDPLDVLK 60
Query: 75 NAITDLLAELSLFEERF 91
A+ DL++ E+ F
Sbjct: 61 EALEDLISICDELEKEF 77
>gnl|CDD|224675 COG1761, RPB11, DNA-directed RNA polymerase, subunit L
[Transcription].
Length = 99
Score = 87.8 bits (218), Expect = 2e-24
Identities = 32/84 (38%), Positives = 45/84 (53%)
Query: 8 ELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAES 67
+ K N+ + EDHTLGN++R +LLKD V FA Y PHPL +RI+T
Sbjct: 8 RIIKKDDNSLELEIEGEDHTLGNLLREELLKDEDVEFAAYSIPHPLIDNPKIRIKTKGGV 67
Query: 68 TPHDALMNAITDLLAELSLFEERF 91
P +AL A +L +L ++F
Sbjct: 68 DPKEALKRAARKILKDLEELLDQF 91
>gnl|CDD|132905 cd07027, RNAP_RPB11_like, RPB11 subunit of RNA polymerase. The
eukaryotic RPB11 subunit of RNA polymerase (RNAP), as
well as its archaeal (L subunit) and bacterial (alpha
subunit) counterparts, is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III, for the synthesis of
ribosomal RNA precursor, mRNA precursor, and 5S and
tRNA, respectively. A single distinct RNAP complex is
found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. The assembly
of the two largest eukaryotic RNAP subunits that
provide most of the enzyme's catalytic functions
depends on the presence of RPB3/RPB11 heterodimer
subunits. This is also true for the archaeal (D/L
subunits) and bacterial (alpha subunit) counterparts.
Length = 83
Score = 80.2 bits (198), Expect = 1e-21
Identities = 30/66 (45%), Positives = 39/66 (59%)
Query: 15 NAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAESTPHDALM 74
N+ + EDHTLGN++R +LLKD V FA Y HP+ K +RIQT + P DAL
Sbjct: 9 NSVTVEMENEDHTLGNLLREELLKDDQVDFARYYIKHPVIDKIQIRIQTKSGIKPKDALK 68
Query: 75 NAITDL 80
A+ L
Sbjct: 69 RAVNKL 74
>gnl|CDD|132907 cd07029, RNAP_I_III_AC19, AC19 subunit of Eukaryotic RNA
polymerase (RNAP) I and RNAP III. The eukaryotic AC19
subunit of RNA polymerase (RNAP) I and RNAP III is
involved in the assembly of RNAP subunits. RNAP is a
large multi-subunit complex responsible for the
synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes
are found in eukaryotic nuclei: RNAP I, RNAP II, and
RNAP III. RNAP I is responsible for the synthesis of
ribosomal RNA precursor, while RNAP III functions in
the synthesis of 5S and tRNA. The AC19 subunit is the
equivalent of the RPB11 subunit of RNAP II. The RPB11
subunit heterodimerizes with the RPB3 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC19 to RPB11 suggests a
similar function. The AC19 subunit is likely to
associate with the RPB3 counterpart, AC40, to form a
heterodimer, which stabilizes the association of the
two largest subunits of RNAP I and RNAP III.
Length = 85
Score = 73.4 bits (181), Expect = 5e-19
Identities = 31/74 (41%), Positives = 39/74 (52%)
Query: 7 KELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTAE 66
E + + A F EDHTLGN +R ++K+P V F GY PHP E+K LRIQT
Sbjct: 1 VEGEGTDESCATFVFYGEDHTLGNSLRYVIMKNPEVEFCGYSIPHPSENKINLRIQTKGG 60
Query: 67 STPHDALMNAITDL 80
D L + DL
Sbjct: 61 EPAVDVLKKGLEDL 74
>gnl|CDD|234909 PRK01146, PRK01146, DNA-directed RNA polymerase subunit L;
Provisional.
Length = 85
Score = 63.3 bits (155), Expect = 6e-15
Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 4/89 (4%)
Query: 1 MIRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILR 60
M K++++ D ++ + EDHTL N+++ +LL+DP V A Y HPL +L+
Sbjct: 1 MEIKVLEKEDNEL----ELEIEGEDHTLMNLLKEELLEDPGVEAASYDIDHPLISNPVLK 56
Query: 61 IQTTAESTPHDALMNAITDLLAELSLFEE 89
I+T P +AL A ++ F +
Sbjct: 57 IKTDGGIDPLEALKEAAKRIIDLCDEFLD 85
>gnl|CDD|132903 cd06927, RNAP_L, L subunit of Archaeal RNA polymerase. The
archaeal L subunit of RNA polymerase (RNAP) is involved
in the assembly of RNAP subunits. RNAP is a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. A single distinct RNAP complex is found in
archaea, which may be responsible for the synthesis of
all RNAs. The archaeal RNAP harbors homologues of all
eukaryotic RNAP II subunits with two exceptions (RPB8
and RPB9). The 12 archaeal subunits are designated by
letters and can be divided into three functional groups
that are engaged in: (I) catalysis (A'/A", B'/B" or B);
(II) assembly (L, N, D and P); and (III) auxiliary
functions (F, E, H and K). The assembly of the two
largest archaeal RNAP subunits that provide most of the
enzyme's catalytic functions depends on the presence of
the archaeal D/L heterodimer.
Length = 83
Score = 61.4 bits (150), Expect = 3e-14
Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 4/86 (4%)
Query: 4 KIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQT 63
K+I++ D ++ + EDHTL N+++ +LL+DP V A Y HPL +L+I+T
Sbjct: 2 KVIEKEDNEL----ELEIEGEDHTLLNLLKEELLRDPGVKVASYDIEHPLLSNPVLKIKT 57
Query: 64 TAESTPHDALMNAITDLLAELSLFEE 89
P +AL A L+ F +
Sbjct: 58 DGGVDPLEALKEAAKRLIDLCEEFLD 83
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp.
Length = 88
Score = 59.6 bits (145), Expect = 2e-13
Identities = 33/88 (37%), Positives = 41/88 (46%), Gaps = 19/88 (21%)
Query: 17 AIFTVNKEDHTLGNMIRNQLLKD-PHVLFAGYKQPHPLEH------------------KF 57
F + EDHTLGN +R LL D P V AG K PHP + K
Sbjct: 1 IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIPHPAKFSPVKKVNYRVVGVGTDYDKL 60
Query: 58 ILRIQTTAESTPHDALMNAITDLLAELS 85
ILRI+T TP +AL A+ L+ +L
Sbjct: 61 ILRIETDGSITPEEALKEALKILIEKLD 88
>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA
polymerase. The eukaryotic RPB11 and RPB3 subunits of
RNA polymerase (RNAP), as well as their archaeal (L and
D subunits) and bacterial (alpha subunit) counterparts,
are involved in the assembly of RNAP, a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. At least three distinct RNAP complexes are found
in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III,
for the synthesis of ribosomal RNA precursor, mRNA
precursor, and 5S and tRNA, respectively. A single
distinct RNAP complex is found in prokaryotes and
archaea, which may be responsible for the synthesis of
all RNAs. The assembly of the two largest eukaryotic
RNAP subunits that provide most of the enzyme's
catalytic functions depends on the presence of
RPB3/RPB11 heterodimer subunits. This is also true for
the archaeal (D/L subunits) and bacterial (alpha
subunit) counterparts.
Length = 86
Score = 59.4 bits (144), Expect = 2e-13
Identities = 33/75 (44%), Positives = 40/75 (53%), Gaps = 7/75 (9%)
Query: 12 KVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEH------KFILRIQTTA 65
K N F + EDHTLGN +R LLK P V FA Y HP++ KFILRI+T
Sbjct: 6 KEKNYVDFVLENEDHTLGNSLRRILLKSP-VEFAAYYVEHPVKLQRTDEDKFILRIETVG 64
Query: 66 ESTPHDALMNAITDL 80
P +AL A+ L
Sbjct: 65 SIPPEEALRRAVEIL 79
>gnl|CDD|212523 cd09999, Arginase-like_1, Arginase-like amidino hydrolase family.
This family includes arginase, also known as
arginase-like amidino hydrolase family, as well as
arginase-like proteins and are found in bacteria,
archaea and eykaryotes, but does not include metazoan
arginases. Arginase is a binuclear Mn-dependent
metalloenzyme and catalyzes hydrolysis of L-arginine to
L-ornithine and urea (Arg, EC 3.5.3.1), the reaction
being the fifth and final step in the urea cycle,
providing the path for the disposal of nitrogenous
compounds. Arginase controls cellular levels of arginine
and ornithine which are involved in protein
biosynthesis, and in production of creatine, polyamines,
proline and nitric acid.
Length = 272
Score = 28.4 bits (64), Expect = 0.45
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 25 DHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQ-TTAESTPHDALMNAITDLLAE 83
D L +++ L V+ AG + P E +FI R+ A A+ D L E
Sbjct: 138 DPELTAIVKP-PLSPERVVLAGLRDPDDEEEEFIARLGIRVLRPEGLAASAQAVLDWLKE 196
>gnl|CDD|233026 TIGR00564, trpE_most, anthranilate synthase component I,
non-proteobacterial lineages. This enzyme resembles
some other chorismate-binding enzymes, including
para-aminobenzoate synthase (pabB) and isochorismate
synthase. There is a fairly deep split between two sets,
seen in the pattern of gaps as well as in amino acid
sequence differences. Archaeal enzymes have been
excluded from this model (and are now found in
TIGR01820) as have a clade of enzymes which constitute a
TrpE paralog which may have PabB activity (TIGR01824).
This allows the B. subtilus paralog which has been shown
to have PabB activity to score below trusted to this
model. This model contains sequences from gram-positive
bacteria, certain proteobacteria, cyanobacteria, plants,
fungi and assorted other bacteria.A second family of
TrpE enzymes is modelled by TIGR00565. The breaking of
the TrpE family into these diverse models allows for the
separation of the models for the related enzyme, PabB
[Amino acid biosynthesis, Aromatic amino acid family].
Length = 454
Score = 26.1 bits (58), Expect = 2.9
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 57 FILRIQTTAESTPHDALMNAITDLLAELS 85
I +TTA + A + L+A+L
Sbjct: 141 LIHNNRTTASRSAKAAADARLEALVADLQ 169
>gnl|CDD|236784 PRK10876, recB, exonuclease V subunit beta; Provisional.
Length = 1181
Score = 25.7 bits (57), Expect = 3.9
Identities = 20/45 (44%), Positives = 22/45 (48%), Gaps = 5/45 (11%)
Query: 46 GYKQPHPLEHKF---ILRIQTTAESTPHDALMNAITDLLAE-LSL 86
Y+ P LE KF L +T TP L AI LLAE LSL
Sbjct: 280 SYQLPKELE-KFSQRFLLEKTKKGETPQHPLFEAIDQLLAEPLSL 323
>gnl|CDD|204898 pfam12390, Se-cys_synth_N, Selenocysteine synthase N terminal.
This domain family is found in bacteria, and is
approximately 40 amino acids in length. The family is
found in association with pfam03841. There is a single
completely conserved residue P that may be functionally
important. This family is the N terminal region of
selenocysteine synthase which catalyzes the conversion
of seryl-tRNA(Sec) into selenocysteyl-tRNA(Sec).
Length = 40
Score = 23.9 bits (53), Expect = 3.9
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 59 LRIQTTAESTPHDALMNAITDLLAEL 84
I E ++ A+ + L E
Sbjct: 14 PAIAPLLEEYGRTLVVEAVREALDEA 39
>gnl|CDD|215577 PLN03103, PLN03103, GDP-L-galactose-hexose-1-phosphate
guanyltransferase; Provisional.
Length = 403
Score = 25.4 bits (56), Expect = 4.2
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 75 NAITDLLAELSLFEERF 91
LLAE+SL EERF
Sbjct: 368 EYAWRLLAEVSLSEERF 384
>gnl|CDD|176552 cd08610, GDPD_GDE6, Glycerophosphodiester phosphodiesterase domain
of mammalian glycerophosphodiester phosphodiesterase
GDE6 and similar proteins. This subfamily corresponds
to the glycerophosphodiester phosphodiesterase domain
(GDPD) present in mammalian GDE6 (also known as
glycerophosphodiester phosphodiesterase
domain-containing protein 4 (GDPD4)) and their metazoan
homologs. Mammalian GDE6 is a transmembrane protein
predominantly expressed in the spermatocytes of testis.
Although the specific physiological function of
mammalian GDE6 has not been elucidated, its different
pattern of tissue distribution suggests it might play a
critical role in the completion of meiosis during male
germ cell differentiation.
Length = 316
Score = 25.2 bits (55), Expect = 5.0
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 22 NKEDHTLGNMIRNQLLKDPHVLFAGYKQP--HPLEHKFILRI 61
N+ L N +R ++ V+F Y+ P HP H +I R+
Sbjct: 131 NQSIPKLSNFLRLAEKENKLVIFDLYRPPPKHPYRHTWIRRV 172
>gnl|CDD|224702 COG1788, AtoD, Acyl CoA:acetate/3-ketoacid CoA transferase, alpha
subunit [Lipid metabolism].
Length = 220
Score = 25.3 bits (56), Expect = 5.4
Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 8/76 (10%)
Query: 2 IRKIIKELDTKVPNAAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRI 61
IR+ +K+L T + N A F D LG +I N +K + A Y +P + +L
Sbjct: 40 IRQGVKDL-TVISNNAGF----PDLGLGKLIGNGQVKK---MIASYIGSNPEFGRQMLAG 91
Query: 62 QTTAESTPHDALMNAI 77
+ E P L I
Sbjct: 92 ELEVELVPQGTLAERI 107
>gnl|CDD|235656 PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate
transaminase; Provisional.
Length = 423
Score = 25.2 bits (56), Expect = 5.6
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 32 IRNQLLKDPHVLFAGY 47
IR QL + HV+FAG+
Sbjct: 67 IREQLDRLDHVIFAGF 82
>gnl|CDD|233000 TIGR00508, bioA, adenosylmethionine-8-amino-7-oxononanoate
transaminase. All members of the seed alignment have
been demonstrated experimentally to act as EC 2.6.1.62,
an enzyme in the biotin biosynthetic pathway. Alternate
names include 7,8-diaminopelargonic acid
aminotransferase, DAPA aminotransferase, and
adenosylmethionine-8-amino-7-oxononanoate
aminotransferase. The gene symbol is bioA in E. coli
and BIO3 in S. cerevisiae [Biosynthesis of cofactors,
prosthetic groups, and carriers, Biotin].
Length = 417
Score = 25.1 bits (56), Expect = 5.8
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 32 IRNQLLKDPHVLFAG 46
I+ QL K HV+F G
Sbjct: 56 IKEQLDKLEHVMFGG 70
>gnl|CDD|233982 TIGR02715, amido_AtzE, amidohydrolase, AtzE family. Members of
this protein family are aminohydrolases related to, but
distinct from, glutamyl-tRNA(Gln) amidotransferase
subunit A. The best characterized member is the biuret
hydrolase of Pseudomonas sp. ADP, which hydrolyzes
ammonia from the three-nitrogen compound biuret to
yield allophanate. Allophanate is also an intermediate
in urea degradation by the urea carboxylase/allophanate
hydrolase pathway, an alternative to urease [Unknown
function, Enzymes of unknown specificity].
Length = 452
Score = 25.1 bits (55), Expect = 6.8
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 62 QTTAESTPHDALMNAITDLLAELSLFEER 90
T A D +NA T + AE +L +
Sbjct: 22 ATLARINQADGGLNAFTAVTAERALADAA 50
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 24.9 bits (55), Expect = 7.3
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 49 QPHPLEHKFILRIQTTAESTPHDALMNAITDLLAELSLFE 88
K I ++T P +A++ A L +L F
Sbjct: 185 DEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAFV 224
>gnl|CDD|220375 pfam09742, Dymeclin, Dyggve-Melchior-Clausen syndrome protein.
Dymeclin (Dyggve-Melchior-Clausen syndrome protein)
contains a large number of leucine and isoleucine
residues and a total of 17 repeated dileucine motifs. It
is characteristically about 700 residues long and
present in plants and animals. Mutations in the gene
coding for this protein in humans give rise to the
disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM
223800) which is an autosomal-recessive disorder
characterized by the association of a
spondylo-epi-metaphyseal dysplasia and mental
retardation. DYM transcripts are widely expressed
throughout human development and Dymeclin is not an
integral membrane protein of the ER, but rather a
peripheral membrane protein dynamically associated with
the Golgi apparatus.
Length = 659
Score = 24.7 bits (54), Expect = 8.3
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 11/47 (23%)
Query: 28 LGNMIRNQLLKDPHV---------LFAGYKQPHPLEHKFILRIQTTA 65
L +++ QL +P + LF ++ HP + L +Q
Sbjct: 548 LNSILTYQLDSNPELVYALLRKRELFEQFRNDHPAFQE--LPLQNID 592
>gnl|CDD|235010 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
Length = 887
Score = 24.8 bits (54), Expect = 8.9
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 16 AAIFTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQPHPLEHKFILRIQTTA 65
TV + LG + R L PH + G+ P PL RI T
Sbjct: 195 VETLTVARGHQVLG-ITRKHLGPPPHFVEIGHDFPAPLSAPQRERIVRTV 243
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 24.7 bits (54), Expect = 9.0
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 9 LDTKVPNAAI--FTVNKEDHTLGNMIRNQLLKDPHVLFAGYKQP 50
L K PN I T +++R LK+P + + +P
Sbjct: 156 LKQKFPNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFDRP 199
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
0.322 0.137 0.390
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,683,022
Number of extensions: 385531
Number of successful extensions: 361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 357
Number of HSP's successfully gapped: 30
Length of query: 91
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 33
Effective length of database: 8,365,070
Effective search space: 276047310
Effective search space used: 276047310
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 (21.9 bits)
S2: 53 (24.1 bits)