RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3837
(93 letters)
>gnl|CDD|201664 pfam01210, NAD_Gly3P_dh_N, NAD-dependent glycerol-3-phosphate
dehydrogenase N-terminus. NAD-dependent
glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the
interconversion of dihydroxyacetone phosphate and
L-glycerol-3-phosphate. This family represents the
N-terminal NAD-binding domain.
Length = 157
Score = 33.0 bits (76), Expect = 0.009
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 22 WAFSE--RDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNI 65
W E ++I RE+++ L + RA +DL EA++ +D I
Sbjct: 28 WGRDEELIEEINTTRENVKYLPGIKLPDNLRATTDLEEAIKGADII 73
>gnl|CDD|191187 pfam05087, Rota_VP2, Rotavirus VP2 protein. Rotavirus particles
consist of three concentric proteinaceous capsid
layers. The innermost capsid (core) is made of VP2. The
genomic RNA and the two minor proteins VP1 and VP3 are
encapsidated within this layer. The N-terminus of
rotavirus VP2 is necessary for the encapsidation of VP1
and VP3.
Length = 887
Score = 29.1 bits (65), Expect = 0.25
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 11/79 (13%)
Query: 23 AFSERDKIVLERESIRTLCDKLRKERDRAVSDLA----------EALRDSDNIKKQKNET 72
E+D ++++ L +K+ +++ V+D E L+ +D +KK E
Sbjct: 16 RMQEKDDEKQDQKNRMELKEKVLDKKEEVVTDNVDSPVKEQSSQENLKIADEVKKSTKEE 75
Query: 73 SKEL-KVLKEKMEAQVELE 90
SK+L +VLK K E Q E++
Sbjct: 76 SKQLLEVLKTKEEHQKEIQ 94
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 28.5 bits (65), Expect = 0.35
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 32 LERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNETSKELKVLKEK 82
LE IR D+LRKE +L EA+ S+ +K + KELK +K
Sbjct: 437 LEEIEIRKEQDELRKEIA----EL-EAILASE--RKLRKLIKKELKADAKK 480
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 28.3 bits (63), Expect = 0.45
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 16/89 (17%)
Query: 21 DWAFSERDKIVLERESIRTLCDKLRKERDRAVSDLAEALR------------DS---DNI 65
D E K +LE E++R DK+ +++ R ++ E LR D +
Sbjct: 160 DPLERELQKRLLEVETLRDQVDKMVEQQVRVINSQLERLRLEKRRLQLNGQLDDEFQQHY 219
Query: 66 KKQKNETSKELKVLKEKMEA-QVELERYT 93
+K+E K L L+ +++A + ELER
Sbjct: 220 VAEKSELQKRLAQLQTELDALRAELERQF 248
>gnl|CDD|223318 COG0240, GpsA, Glycerol-3-phosphate dehydrogenase [Energy
production and conversion].
Length = 329
Score = 28.3 bits (64), Expect = 0.45
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 22 WAFSER--DKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNI 65
W E +I RE+ + L L +A +DLAEAL +D I
Sbjct: 30 WGRDEEIVAEINETRENPKYLPGILLPPNLKATTDLAEALDGADII 75
>gnl|CDD|237702 PRK14399, PRK14399, membrane protein; Provisional.
Length = 258
Score = 27.9 bits (62), Expect = 0.62
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 58 ALRDSDNIKKQKNETSKELKVLKEK 82
+R S NIK+ KN+T + KEK
Sbjct: 231 VVRHSQNIKRIKNKTEPDTFPKKEK 255
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 28.0 bits (63), Expect = 0.67
Identities = 19/70 (27%), Positives = 29/70 (41%), Gaps = 10/70 (14%)
Query: 34 RESIRTLCDKLRKERDR------AVSDLAEALRDSDNIKKQKNETS---KELKVLKEKM- 83
++ D L K++ DL + L D I +QK ET ++L K+
Sbjct: 38 EADVQAQLDALNKQKLLEAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLR 97
Query: 84 EAQVELERYT 93
+AQ ELE
Sbjct: 98 QAQAELEALK 107
>gnl|CDD|233379 TIGR01369, CPSaseII_lrg, carbamoyl-phosphate synthase, large
subunit. Carbamoyl-phosphate synthase (CPSase)
catalyzes the first committed step in pyrimidine,
arginine, and urea biosynthesis. In general, it is a
glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II
in eukaryotes. An exception is the mammalian
mitochondrial urea-cycle form, CPSase I, in which the
glutamine amidotransferase domain active site Cys on the
small subunit has been lost, and the enzyme is
ammonia-dependent. In both CPSase I and the closely
related, glutamine-dependent CPSase III (allosterically
activated by acetyl-glutamate) demonstrated in some
other vertebrates, the small and large chain regions are
fused in a single polypeptide chain. This model
represents the large chain of glutamine-hydrolysing
carbamoyl-phosphate synthases, or the corresponding
regions of larger, multifunctional proteins, as found in
all domains of life, and CPSase I forms are considered
exceptions within the family. In several thermophilic
species (Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, Aquifex aeolicus), the large
subunit appears split, at different points, into two
separate genes [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 1050
Score = 28.0 bits (63), Expect = 0.73
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 4/85 (4%)
Query: 7 EESIQEAEVSKRRRDWAFSERDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIK 66
EE++Q+A S F D+ V E L L+K DR + +AEALR ++
Sbjct: 389 EEALQKALRSLEIGATGFDLPDREV---EPDEDLWRALKKPTDRRIFAIAEALRRGVSV- 444
Query: 67 KQKNETSKELKVLKEKMEAQVELER 91
+ +E +K + K++ V+LE
Sbjct: 445 DEIHELTKIDRWFLHKIKNIVDLEE 469
>gnl|CDD|234629 PRK00094, gpsA, NAD(P)H-dependent glycerol-3-phosphate
dehydrogenase; Validated.
Length = 325
Score = 27.3 bits (62), Expect = 0.85
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 22 WAFSER--DKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNI 65
WA +I +RE+ R L + RA +DLAEAL D+D I
Sbjct: 30 WARDPEQAAEINADRENPRYLPGIKLPDNLRATTDLAEALADADLI 75
>gnl|CDD|221710 pfam12685, SpoIIIAH, SpoIIIAH-like protein. Stage III
sporulation protein AH (SpoIIIAH) is a protein that is
involved in forespore engulfment. It forms a channel
with SpoIIIAH that is open on the forespore end and
closed (or gated) on the mother cell end. This allows
sigma-E-directed gene expression in the mother-cell
compartment of the sporangium to trigger the activation
of sigma-G forespore-specific gene expression by a
pathway of intercellular signaling. This family of
proteins is found in bacteria, archaea and eukaryotes
and so must have a wider function that in sporulation.
Proteins in this family are typically between 174 and
223 amino acids in length.
Length = 141
Score = 26.8 bits (60), Expect = 1.1
Identities = 10/45 (22%), Positives = 23/45 (51%)
Query: 46 KERDRAVSDLAEALRDSDNIKKQKNETSKELKVLKEKMEAQVELE 90
++R + + L E + + + ++K E +L L E E ++ +E
Sbjct: 42 QKRSKQIETLKEIIANENASAEEKKEAQDKLLELTELAEKEMAIE 86
>gnl|CDD|240580 cd12945, NOPS_NONA_like, NOPS domain, including C-terminal
coiled-coil region, in p54nrb/PSF/PSP1 homologs from
invertebrate species. The family contains a DBHS
domain (for Drosophila behavior, human splicing), which
comprises two conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1)
domain. This model corresponds to the NOPS domain, with
a long helical C-terminal extension , found in
Drosophila melanogaster gene no-ontransient A (nonA)
encoding puff-specific protein Bj6 (also termed NONA),
Chironomus tentans hrp65 gene encoding protein Hrp65
and similar proteins. D. melanogaster NONA is involved
in eye development and behavior, and may play a role in
circadian rhythm maintenance, similar to vertebrate
p54nrb. C. tentans hrp65 is a component of nuclear
fibers associated with ribonucleoprotein particles in
transit from the gene to the nuclear pore. The NOPS
domain specifically binds to the second RNA recognition
motif (RRM2) domain of the partner DBHS protein via a
substantial interaction surface. Its highly conserved
C-terminal residues are critical for functional DBHS
dimerization while the highly conserved C-terminal
helical extension, forming a right-handed antiparallel
heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies.
Length = 100
Score = 26.6 bits (59), Expect = 1.3
Identities = 16/30 (53%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 64 NIKKQKNETSK-ELKVLKEKMEAQVELERY 92
+ KQK E K ELK+ +EK+EAQ+E RY
Sbjct: 59 ELYKQKEEALKRELKMEEEKLEAQMEYARY 88
>gnl|CDD|130164 TIGR01092, P5CS, delta l-pyrroline-5-carboxylate synthetase. This
protein contains a glutamate 5-kinase (ProB, EC
2.7.2.11) region followed by a gamma-glutamyl phosphate
reductase (ProA, EC 1.2.1.41) region [Amino acid
biosynthesis, Glutamate family].
Length = 715
Score = 26.8 bits (59), Expect = 1.5
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 26 ERDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNE 71
ERD V RES R L ++R + D+A+AL D+++ +N+
Sbjct: 288 ERDMAVAARESSRMLQALSSEQRKEILHDIADALEDNEDEILAENK 333
>gnl|CDD|226809 COG4372, COG4372, Uncharacterized protein conserved in bacteria
with the myosin-like domain [Function unknown].
Length = 499
Score = 26.9 bits (59), Expect = 1.5
Identities = 18/71 (25%), Positives = 34/71 (47%)
Query: 12 EAEVSKRRRDWAFSERDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNE 71
E ++ + A +ER+ E + R + +R+E A +LA+A ++ + KQ +
Sbjct: 89 ELGTAQGEKRAAETEREAARSELQKARQEREAVRQELAAARQNLAKAQQELARLTKQAQD 148
Query: 72 TSKELKVLKEK 82
LK L E+
Sbjct: 149 LQTRLKTLAEQ 159
>gnl|CDD|185766 cd09243, BRO1_Brox_like, Protein-interacting Bro1-like domain of
human Brox1 and related proteins. This family contains
the Bro1-like domain of a single-domain protein, human
Brox, and related domains. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1
and Rim20 (also known as PalA) from Saccharomyces
cerevisiae, Ustilago maydis Rim23 (also known as PalC),
and related domains. Alix, HD-PTP, Brox, Bro1, Rim20,
and Rim23, interact with the ESCRT (Endosomal Sorting
Complexes Required for Transport) system. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: CHMP4 in the case of Brox. Human Brox can bind
to human immunodeficiency virus type 1 (HIV-1)
nucleocapsid. In addition to a Bro1-like domain, Brox
also has a C-terminal thioester-linkage site for
isoprenoid lipids (CaaX motif). This family lacks the
V-shaped (V) domain found in many members of the
BRO1_Alix_like superfamily.
Length = 353
Score = 26.1 bits (58), Expect = 2.5
Identities = 13/43 (30%), Positives = 18/43 (41%)
Query: 29 KIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNE 71
K V + LC LR R R + L++ D D +K N
Sbjct: 18 KGVATTPAASKLCSDLRTARARLLELLSDPSNDVDTVKTAFNA 60
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 26.2 bits (58), Expect = 2.9
Identities = 20/88 (22%), Positives = 44/88 (50%), Gaps = 1/88 (1%)
Query: 7 EESIQEAEVSKRRRDWAFSERDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIK 66
E +E E ++ R +E DK++ E E + ++ RK RD+ + AE + ++++
Sbjct: 311 AEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLR 370
Query: 67 KQKNETSKELKVLKEK-MEAQVELERYT 93
+ E KE +++ + + +LE+
Sbjct: 371 AELEEVDKEFAETRDELKDYREKLEKLK 398
>gnl|CDD|187539 cd05228, AR_FR_like_1_SDR_e, uncharacterized subgroup of aldehyde
reductase and flavonoid reductase related proteins,
extended (e) SDRs. This subgroup contains proteins of
unknown function related to aldehyde reductase and
flavonoid reductase of the extended SDR-type. Aldehyde
reductase I (aka carbonyl reductase) is an NADP-binding
SDR; it has an NADP-binding motif consensus that is
slightly different from the canonical SDR form and lacks
the Asn of the extended SDR active site tetrad. Aldehyde
reductase I catalyzes the NADP-dependent reduction of
ethyl 4-chloro-3-oxobutanoate to ethyl
(R)-4-chloro-3-hydroxybutanoate. The related flavonoid
reductases act in the NADP-dependent reduction of
flavonoids, ketone-containing plant secondary
metabolites. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 318
Score = 26.1 bits (58), Expect = 3.1
Identities = 12/47 (25%), Positives = 16/47 (34%), Gaps = 7/47 (14%)
Query: 22 WAFSERDKIVLERESIRTLCDKLRKERDRAVSDL-------AEALRD 61
A +L + R L D+A +L EALRD
Sbjct: 267 KARLTGKPPLLTPRTARVLRRNYLYSSDKARRELGYSPRPLEEALRD 313
>gnl|CDD|218124 pfam04518, Effector_1, Effector from type III secretion system.
This is a family of effector proteins which are secreted
by the type III secretion system. The precise function
of this family is unknown.
Length = 380
Score = 25.7 bits (57), Expect = 4.2
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 4/52 (7%)
Query: 35 ESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNETSKELKVLKEKMEAQ 86
S KL KE+++ D+ R K N+ +K + Q
Sbjct: 197 GSYDEALAKLEKEKEQIRRDIKRCER----AKAVLNKLLARIKADAKLTSEQ 244
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 25.4 bits (57), Expect = 4.4
Identities = 16/62 (25%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 33 ERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNET---SKELKVLKEKM-EAQVE 88
ER ++T ++L+ ER+ ++ +A R ++ + E +E+K L+ ++ E + E
Sbjct: 36 ERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAE 95
Query: 89 LE 90
LE
Sbjct: 96 LE 97
>gnl|CDD|235040 PRK02463, PRK02463, OxaA-like protein precursor; Provisional.
Length = 307
Score = 25.5 bits (56), Expect = 4.9
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 70 NETSKELKVLKEKMEAQVEL 89
NE K +EKM AQ EL
Sbjct: 104 NERLKNATTQEEKMAAQTEL 123
>gnl|CDD|237272 PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
Length = 596
Score = 25.3 bits (56), Expect = 5.3
Identities = 3/15 (20%), Positives = 8/15 (53%)
Query: 10 IQEAEVSKRRRDWAF 24
+ + E+++RR
Sbjct: 536 VSDEELARRRAALKP 550
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 25.3 bits (56), Expect = 6.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 74 KELKVLKEKMEAQVELER 91
K L ++EKMEAQ+EL R
Sbjct: 986 KTLGSMEEKMEAQLELAR 1003
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 25.3 bits (56), Expect = 6.3
Identities = 14/82 (17%), Positives = 34/82 (41%), Gaps = 12/82 (14%)
Query: 15 VSKRRRDWAFSER-DKIVLERESIRTLCDKLRKERDRAVSDLAEAL-----------RDS 62
+ KR D ++ ++ ER + ++L+ ER+ ++ AL +
Sbjct: 18 LKKRGGDALDVDKLLELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEV 77
Query: 63 DNIKKQKNETSKELKVLKEKME 84
+K++ E L L+ +++
Sbjct: 78 KELKEKLKELEAALDELEAELD 99
>gnl|CDD|225280 COG2423, COG2423, Predicted ornithine cyclodeaminase, mu-crystallin
homolog [Amino acid transport and metabolism].
Length = 330
Score = 25.0 bits (55), Expect = 6.3
Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 34 RESIRTLCDKLRKERD---RAVSDLAEALRDSDNI 65
E+ +LRK A EA+ +D +
Sbjct: 165 PEAAEAFAARLRKRGGEAVGAADSAEEAVEGADIV 199
>gnl|CDD|215643 PLN03241, PLN03241, magnesium chelatase subunit H; Provisional.
Length = 1315
Score = 25.2 bits (55), Expect = 6.8
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 28 DKIVLERESIRTLCDKLRKERD 49
D I L E +R L ++L+
Sbjct: 482 DDIYLVPERVRKLANRLKSWVS 503
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 24.9 bits (55), Expect = 7.2
Identities = 12/50 (24%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 43 KLRKERDRAVSDLAEALRDSDNIKKQK-NETSKELKVLKEKMEAQVELER 91
KL + A + EA ++++ +KK+ E +E+ L+ ++E +++ R
Sbjct: 26 KLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERR 75
>gnl|CDD|235115 PRK03317, PRK03317, histidinol-phosphate aminotransferase;
Provisional.
Length = 368
Score = 24.8 bits (55), Expect = 7.3
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 42 DKLRKERDRAVSDLAE 57
LR ERDR V+ L E
Sbjct: 282 AALRAERDRVVAWLRE 297
>gnl|CDD|148721 pfam07278, DUF1441, Protein of unknown function (DUF1441). This
family consists of several hypothetical Enterobacterial
proteins of around 160 residues in length. The function
of this family is unknown. However, it appears to be
distantly related to other HTH families so may act as a
transcriptional regulator.
Length = 152
Score = 24.7 bits (54), Expect = 7.4
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 17 KRRRDWAFSERDKIVLERE 35
K R+ W SE +++ LE+E
Sbjct: 67 KERKAWFQSENERLKLEKE 85
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 24.8 bits (54), Expect = 8.1
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 41 CDKLRKERDRAVSDLAEALRDSDNIKKQKNETSKELKVLKEKMEAQV 87
K + +RD + S A + SD K + SKEL LK+ ++ V
Sbjct: 218 SKKAKTDRDVSTSTAASQKKSSDLESKLE-AQSKELWSLKDDLKKHV 263
>gnl|CDD|219215 pfam06881, Elongin_A, RNA polymerase II transcription factor SIII
(Elongin) subunit A. This family represents a
conserved region within RNA polymerase II transcription
factor SIII (Elongin) subunit A. In mammals, the
Elongin complex activates elongation by RNA polymerase
II by suppressing transient pausing of the polymerase
at many sites within transcription units. Elongin is a
heterotrimer composed of A, B, and C subunits of 110,
18, and 15 kilodaltons, respectively. Subunit A has
been shown to function as the transcriptionally active
component of Elongin.
Length = 108
Score = 24.2 bits (53), Expect = 8.3
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 19 RRDWAFSERDKIVLERESIRTLCDKLRKERDRAVSDLAEALRDSDNIKKQKNETSK 74
+RD+ S+ E ES R L +L +ER++ + + L NIK+ K
Sbjct: 47 KRDFPESKEPL-PEEPESWRELYLRLVEEREQKLKESGRRLT--KNIKRANANKPK 99
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 24.7 bits (55), Expect = 9.3
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 51 AVSDLAEALR--DSDNIKKQKNETSKELKVLKEKMEAQ 86
A+ +L EAL+ D + IK + E ++ + L E M Q
Sbjct: 561 AIKELKEALKGEDKEAIKAKTEELTQASQKLGEAMYQQ 598
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
0.312 0.126 0.334
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,520,185
Number of extensions: 380577
Number of successful extensions: 913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 876
Number of HSP's successfully gapped: 229
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.3 bits)