RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5048
(319 letters)
>gnl|CDD|215821 pfam00254, FKBP_C, FKBP-type peptidyl-prolyl cis-trans isomerase.
Length = 94
Score = 98.1 bits (245), Expect = 1e-25
Identities = 39/56 (69%), Positives = 42/56 (75%), Gaps = 1/56 (1%)
Query: 73 HDRDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYGDRG-AGNVIPGG 127
DR +PF FTLG GQVI GWD+GL M VGEKRKLTIPP LAYG+ G AG VIP
Sbjct: 29 KDRGKPFEFTLGSGQVIPGWDEGLLGMKVGEKRKLTIPPELAYGEEGLAGGVIPPN 84
>gnl|CDD|223619 COG0545, FkpA, FKBP-type peptidyl-prolyl cis-trans isomerases 1
[Posttranslational modification, protein turnover,
chaperones].
Length = 205
Score = 92.1 bits (229), Expect = 2e-22
Identities = 34/53 (64%), Positives = 37/53 (69%), Gaps = 2/53 (3%)
Query: 73 HDRDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYGDRGAGNVIP 125
+DR QP F LG VI GWD+GL M VG KRKLTIPP LAYG+RG VIP
Sbjct: 140 YDRGQPAEFPLG--GVIPGWDEGLQGMKVGGKRKLTIPPELAYGERGVPGVIP 190
>gnl|CDD|183207 PRK11570, PRK11570, peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 206
Score = 57.5 bits (139), Expect = 7e-10
Identities = 28/51 (54%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 75 RDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYGDRGAGNVIP 125
R +P F V VI GW + LT M VG K +LTIP LAYG+RGAG IP
Sbjct: 143 RGEPAEFP--VNGVIPGWIEALTLMPVGSKWELTIPHELAYGERGAGASIP 191
>gnl|CDD|223976 COG1047, SlpA, FKBP-type peptidyl-prolyl cis-trans isomerases 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 174
Score = 54.6 bits (132), Expect = 5e-09
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 73 HDRDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYGDR 118
+ P TF +G GQ+I G ++ L VGE+ + IPP A+G+
Sbjct: 27 DENYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEY 72
>gnl|CDD|236791 PRK10902, PRK10902, FKBP-type peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 269
Score = 49.4 bits (118), Expect = 7e-07
Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 6/54 (11%)
Query: 73 HDRDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYGDRGAGNVIPG 126
+ R +P +F L VI GW +GL + G K KL IPP LAYG G +PG
Sbjct: 185 YTRGEPLSFRLD--GVIPGWTEGLKNIKKGGKIKLVIPPELAYGKAG----VPG 232
>gnl|CDD|237908 PRK15095, PRK15095, FKBP-type peptidyl-prolyl cis-trans isomerase;
Provisional.
Length = 156
Score = 35.5 bits (82), Expect = 0.013
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 63 FKLTL----VAMRIHDRDQPFTFTLGVGQVIKGWDQGLTEMCVGEKRKLTIPPALAYG 116
F L L A + +P F LG G + +G +Q L + VG+K+ ++ P A+G
Sbjct: 15 FTLKLDDGSTAESTRNNGKPALFRLGDGSLSEGLEQQLLGLKVGDKKTFSLEPEAAFG 72
>gnl|CDD|181507 PRK08626, PRK08626, fumarate reductase flavoprotein subunit;
Provisional.
Length = 657
Score = 29.9 bits (68), Expect = 1.8
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 106 KLTIPPALAYGDRG--AGNVIPGGLSAVRQSE 135
K+ +PP G RG AGN+I + RQ+E
Sbjct: 588 KMELPP----GFRGYGAGNIIEHPDTEKRQAE 615
>gnl|CDD|212535 cd10011, HDAC2, Histone deacetylase 2 (HDAC2). Histone deacetylase
2 (HDAC2) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC2 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. It forms transcriptional repressor
complexes by associating with several proteins,
including the mammalian zinc-finger transcription factor
YY1, thus playing an important role in transcriptional
regulation, cell cycle progression and developmental
events. Additionally, a few non-histone HDAC2 substrates
have been found. HDAC2 plays a role in embryonic
development and cytokine signaling important for immune
response, and is over-expressed in several solid tumors
including oral, prostate, ovarian, endometrial and
gastric cancer. It participates in DNA-damage response,
along with HDAC1; together, they can promote DNA
non-homologous end-joining. HDAC2 is considered an
important cancer prognostic marker. Inhibitors
specifically targeting HDAC2 could be a therapeutic drug
option.
Length = 366
Score = 28.9 bits (64), Expect = 3.7
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 161 FTQKGPMAKNREHIAHRARRDRG-KRRIQSFKPHRAESEKLYAHCSSAY 208
+ Q PM +R + H + G R+++ ++PH+A +E++ + S Y
Sbjct: 17 YGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEY 65
>gnl|CDD|232831 TIGR00115, tig, trigger factor. Trigger factor is a
ribosome-associated molecular chaperone and is the first
chaperone to interact with nascent polypeptide. Trigger
factor can bind at the same time as the signal
recognition particle (SRP), but is excluded by the SRP
receptor (FtsY). The central domain of trigger factor
has peptidyl-prolyl cis/trans isomerase activity. This
protein is found in a single copy in virtually every
bacterial genome [Protein fate, Protein folding and
stabilization].
Length = 408
Score = 29.0 bits (66), Expect = 3.7
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 79 FTFTLGVGQVIKGWDQGLTEMCVGEKR--KLTIP 110
F+ LG GQ I G+++ L M GE++ K+T P
Sbjct: 174 FSLELGSGQFIPGFEEQLVGMKAGEEKEIKVTFP 207
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 28.9 bits (65), Expect = 4.0
Identities = 32/114 (28%), Positives = 43/114 (37%), Gaps = 24/114 (21%)
Query: 205 SSAYALLVKKT---PSIHNCFLLST---KSMLTFARNQSTIPAWTHDYTRLALLLPFLQY 258
++A ALL KT P + FLL ++L S W L +LQ
Sbjct: 122 AAANALL--KTLEEPRPNTYFLLQADLSAALL--PTIYSRCQTWLIHPPEEQQALDWLQA 177
Query: 259 EFPPEQSQCLPLLGIRAQHQRG----HMITQGSL--------YFFLFYNMSSPL 300
+ E S+ L L R + R + QG L F+LFY SPL
Sbjct: 178 QSSAEISEILTAL--RINYGRPLLALTFLEQGLLEQRKTFLRQFWLFYRRRSPL 229
>gnl|CDD|212534 cd10010, HDAC1, Histone deacetylase 1 (HDAC1). Histone deacetylase
1 (HDAC1) is a Zn-dependent class I enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDAC1 is involved in regulation through
association with DNA binding proteins to target specific
chromatin regions. In particular, HDAC1 appears to play
a major role in pre-implantation embryogenesis in
establishing a repressive chromatin state. Its
interaction with retinoblastoma tumor-suppressor protein
is essential in the control of cell proliferation and
differentiation. Together with metastasis-associated
protein-2 (MTA2), it deacetylates p53, thereby
modulating its effect on cell growth and apoptosis. It
participates in DNA-damage response, along with HDAC2;
together, they promote DNA non-homologous end-joining.
HDAC1 is also involved in tumorogenesis; its
overexpression modulates cancer progression. Specific
inhibitors of HDAC1 are currently used in cancer
therapy.
Length = 371
Score = 28.9 bits (64), Expect = 4.4
Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 161 FTQKGPMAKNREHIAHRARRDRG-KRRIQSFKPHRAESEKLYAHCSSAY 208
+ Q PM +R + H + G R+++ ++PH+A +E++ + S Y
Sbjct: 21 YGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDY 69
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 28.8 bits (65), Expect = 4.8
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 79 FTFTLGVGQVIKGWDQGLTEMCVGEKR--KLTIP 110
F+ LG G+ I G++ L M GE++ K+T P
Sbjct: 185 FSLELGSGRFIPGFEDQLVGMKAGEEKDIKVTFP 218
>gnl|CDD|235891 PRK06933, PRK06933, type III secretion system protein; Validated.
Length = 308
Score = 27.4 bits (61), Expect = 9.4
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 229 MLTFARNQSTIPAWTHDYTRLALLLPFLQYEFPPEQSQCLPLL 271
L +R+ +++ W L LLP P + +PLL
Sbjct: 120 SLRLSRDNASLSLWLTSPEALLALLP----PRPSSERLPIPLL 158
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
0.323 0.136 0.419
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,867,117
Number of extensions: 1481317
Number of successful extensions: 966
Number of sequences better than 10.0: 1
Number of HSP's gapped: 965
Number of HSP's successfully gapped: 16
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
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 (22.0 bits)
S2: 59 (26.4 bits)