RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10196
(354 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 73.3 bits (181), Expect = 8e-17
Identities = 26/45 (57%), Positives = 31/45 (68%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RR RTTFT QL ELE+ FEK+ YP REELA K+ L E +V+
Sbjct: 1 RRKRTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVK 45
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 63.0 bits (154), Expect = 4e-13
Identities = 24/45 (53%), Positives = 31/45 (68%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RR RT+FT QL ELE+ F+K+ YP REELA K+ L E +V+
Sbjct: 2 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVK 46
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 62.6 bits (153), Expect = 6e-13
Identities = 24/45 (53%), Positives = 30/45 (66%)
Query: 72 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
RR RT FT QL ELE+ FEK+ YP REELA ++ L E +V+
Sbjct: 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 40.9 bits (96), Expect = 2e-04
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 58 SLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 116
L K +R RTT QL LER FE + YP +R +L++ +N+P VQ
Sbjct: 40 KLERKQDGSSPPKSKRRRTT--DEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 32.3 bits (74), Expect = 0.32
Identities = 13/51 (25%), Positives = 19/51 (37%)
Query: 266 DDLDSEDSDQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKP 316
D DS+ S + PP S AA P +K + ++ KK
Sbjct: 323 DTSDSDPSTETPPPASLSHSPPAAFERPLALSPKRKREGDKKQKKKKSKKL 373
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.8 bits (72), Expect = 0.63
Identities = 24/107 (22%), Positives = 37/107 (34%), Gaps = 7/107 (6%)
Query: 219 PSPPVLTPFSPLDETESSRPPTLVAHKRHCVGPTNTGGGFYKRRTVHDDLDSEDSDQQEP 278
P+ P+ P S T PP G GG +R + + P
Sbjct: 2824 PAGPLPPPTSAQ-PTAPPPPPGPPPPSLPLGGSVAPGGDVRRRPPSRSPAAKPAAPARPP 2882
Query: 279 ------PQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPTKP 319
P +S +++ A + RPP+ P PP +P P +P
Sbjct: 2883 VRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQP 2929
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 30.2 bits (68), Expect = 1.8
Identities = 16/61 (26%), Positives = 24/61 (39%)
Query: 10 QLSQRASIAENSGNSSSDEQAVSDLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKK 69
SQ + +S + E+A S + + +SD + SR S S SP KK
Sbjct: 203 DYSQYDGMLVDSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSEESSPPSKK 262
Query: 70 K 70
Sbjct: 263 P 263
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 30.0 bits (68), Expect = 1.9
Identities = 21/112 (18%), Positives = 32/112 (28%), Gaps = 9/112 (8%)
Query: 216 KVQPSPPVLTPFSPLDETESSRPPTLVAHKRHCVGPTNTGGGFYKRRTVHDDLDSEDSDQ 275
QP PV P + + P A + ++ V +
Sbjct: 98 SAQPRQPVQQPPEAQVPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVAPAPQPV 157
Query: 276 QEPPQLSPESQAAATTCRKRGRPPKKHP-PEPPIQEPPVKKPTKPNFVSIVL 326
PQ + ++ A P P PEP + PV K IV+
Sbjct: 158 HSAPQPAQQAFQPA--------EPVAAPQPEPVAEPAPVMDKPKRKEAVIVM 201
Score = 29.6 bits (67), Expect = 2.2
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 11/56 (19%)
Query: 264 VHDDLDSEDSDQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPTKP 319
H+ Q +PP S + R P + PPE + +P +P
Sbjct: 80 EHEAARPSPQHQYQPPYASAQP-----------RQPVQQPPEAQVPPQHAPRPAQP 124
>gnl|CDD|222581 pfam14181, YqfQ, YqfQ-like protein. The YqfQ-like protein family
includes the B. subtilis YqfQ protein, also known as
VrrA, which is functionally uncharacterized. This family
of proteins is found in bacteria. Proteins in this
family are typically between 146 and 237 amino acids in
length. There are two conserved sequence motifs: QYGP
and PKLY.
Length = 155
Score = 29.0 bits (65), Expect = 2.1
Identities = 16/51 (31%), Positives = 24/51 (47%)
Query: 269 DSEDSDQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPTKP 319
E+S + + PE++ + +KR P K E P EP KP+KP
Sbjct: 101 TEEESTDETEQEDPPETKTESKEKKKREVPKPKTEKEKPKTEPKKPKPSKP 151
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 29.6 bits (66), Expect = 2.3
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 276 QEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPP 312
Q+P +P Q ++ +P ++ P+ P Q+PP
Sbjct: 214 QQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPP 250
>gnl|CDD|236214 PRK08274, PRK08274, tricarballylate dehydrogenase; Validated.
Length = 466
Score = 29.5 bits (67), Expect = 2.7
Identities = 19/51 (37%), Positives = 25/51 (49%), Gaps = 12/51 (23%)
Query: 177 PAE--LVDILRVTGGQEDRD-----VEVSLDVRMWSPEMKKNENEVKVQPS 220
P E D+LRVTGG+ D + S D R W M+K + V+ QP
Sbjct: 67 PEEEFWQDLLRVTGGRTDEALARLLIRESSDCRDW---MRK--HGVRFQPP 112
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 29.4 bits (66), Expect = 3.5
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 101 REELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEAESTSQHFLFL 147
ELA ++ L V+ Q AL ++ + +A A G TS H LF
Sbjct: 272 EAELAEQIGLERVKRQVAALKSSTAMALARAERGLPVAQTSNHMLFA 318
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.2 bits (66), Expect = 3.8
Identities = 16/61 (26%), Positives = 21/61 (34%), Gaps = 1/61 (1%)
Query: 278 PPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPTKPNFVSIVLANKNKQLKSLF 337
P P A + + P P PPI E P PTK + + K L F
Sbjct: 550 PTPPPPPPTATQASSNAPAQIPADSSPPPPIPEEPTPSPTKDSSPE-EIDKAAKNLADFF 608
Query: 338 D 338
+
Sbjct: 609 N 609
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 29.1 bits (65), Expect = 4.5
Identities = 10/46 (21%), Positives = 13/46 (28%), Gaps = 1/46 (2%)
Query: 275 QQEPPQLSPESQAAATTCR-KRGRPPKKHPPEPPIQEPPVKKPTKP 319
+ E P +P S AAA P P + K
Sbjct: 13 EAEQPAPAPPSPAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKPKK 58
>gnl|CDD|234797 PRK00575, tatA, twin arginine translocase protein A; Provisional.
Length = 92
Score = 27.0 bits (60), Expect = 4.7
Identities = 8/50 (16%), Positives = 15/50 (30%), Gaps = 3/50 (6%)
Query: 268 LDSEDSDQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPT 317
+ S++ + Q A T + R P Q+ +P
Sbjct: 46 MQSDNKAEASAAAAQAPYQVATPTPVQSQRVD---PAAASGQDSTEARPA 92
>gnl|CDD|187654 cd08951, DR_C-13_KR_SDR_c_like, daunorubicin C-13 ketoreductase
(KR), classical (c)-like SDRs. Daunorubicin is a
clinically important therapeutic compound used in some
cancer treatments. Daunorubicin C-13 ketoreductase is
member of the classical SDR family with a canonical
glycine-rich NAD(P)-binding motif, but lacking a
complete match to the active site tetrad characteristic
of this group. The critical Tyr, plus the Lys and
upstream Asn are present, but the catalytic Ser is
replaced, generally by Gln. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes 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 prostaglandin dehydrogenase
(PGDH) numbering). In addition to the Tyr and Lys, there
is often an upstream Ser (Ser-138, PGDH numbering)
and/or an Asn (Asn-107, PGDH numbering) 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. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. 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 KRs have a TGXXXGX(1-2)G
NAD(P)-binding motif. Some atypical SDRs have lost
catalytic activity and/or have an unusual NAD(P)-binding
motif and missing or unusual active site residues.
Reactions catalyzed within the SDR family include
isomerization, decarboxylation, epimerization, C=N bond
reduction, dehydratase activity, dehalogenation,
Enoyl-CoA reduction, and carbonyl-alcohol
oxidoreduction.
Length = 260
Score = 28.6 bits (64), Expect = 4.9
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 254 TGGGFYKRRTVHDDLDSEDSDQQE 277
+GG FY RR SEDS QE
Sbjct: 223 SGGYFYHRRLQEPHPASEDSRLQE 246
>gnl|CDD|238251 cd00445, Uricase, Urate oxidase (UO, uricase) is a peroxisomal
enzyme that catalyzes the oxidation of uric acid to
allantoin in most fish, amphibian, and mammalian
species. The enzymatic process involves catalyzing the
oxidative opening of the purine ring during the purine
degradation pathway. In humans and certain other
primates, however, the enzyme has been lost by some
unknown mechanism. Each monomer contains two instances
of this domain. Its functional form is a homotetramer
for most species, though there are reports that some may
form heterotetramers based on a few biochemical studies.
Length = 286
Score = 28.5 bits (64), Expect = 5.4
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 9/63 (14%)
Query: 98 VYSREELAMKVNLPEVRVQFTALAAALRVGVAIATFGPEA---ESTS-QHFLFLLSSRIL 153
YS E + P F A +R + GP S S QH L+L++ +IL
Sbjct: 181 RYSNTEDS-----PAKSPDFDAAWEQVRDILLDTFAGPPDVGVYSPSVQHTLYLMAKQIL 235
Query: 154 DRF 156
DRF
Sbjct: 236 DRF 238
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 28.7 bits (64), Expect = 6.0
Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 6/48 (12%)
Query: 273 SDQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPPVKKPTKPN 320
+ PQ +P AAA P + PEP P +PN
Sbjct: 390 NLLHNAPQAAPAPSAAAP------EPKHQPAPEPRPVLAPTPASGEPN 431
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 28.6 bits (64), Expect = 6.9
Identities = 9/39 (23%), Positives = 10/39 (25%)
Query: 274 DQQEPPQLSPESQAAATTCRKRGRPPKKHPPEPPIQEPP 312
PP + A R P P P PP
Sbjct: 396 APAAPPPAAAPPVPPAAPARPAAARPAPAPAPPAAAAPP 434
>gnl|CDD|202139 pfam02178, AT_hook, AT hook motif. At hooks are DNA binding motifs
with a preference for A/T rich regions.
Length = 13
Score = 24.9 bits (56), Expect = 7.3
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 293 RKRGRPPKKHPP 304
RKRGRP K
Sbjct: 2 RKRGRPRKAPKD 13
>gnl|CDD|197691 smart00384, AT_hook, DNA binding domain with preference for A/T
rich regions. Small DNA-binding motif first described
in the high mobility group non-histone chromosomal
protein HMG-I(Y).
Length = 13
Score = 24.5 bits (55), Expect = 7.8
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 293 RKRGRPPKKHPP 304
RKRGRP K
Sbjct: 2 RKRGRPRKAPKD 13
>gnl|CDD|220496 pfam09972, DUF2207, Predicted membrane protein (DUF2207). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 503
Score = 28.1 bits (63), Expect = 8.1
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 293 RKRGRPPKKHPPEPPIQEPPVKKPTKPNFVSIV 325
K GR PK EPP + P V+++
Sbjct: 250 LKYGREPKYTKDIIYSFEPP--EDLSPALVNLI 280
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 0.130 0.375
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,181,096
Number of extensions: 1759051
Number of successful extensions: 1605
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1545
Number of HSP's successfully gapped: 73
Length of query: 354
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 256
Effective length of database: 6,590,910
Effective search space: 1687272960
Effective search space used: 1687272960
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: 59 (26.4 bits)