RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7387
(196 letters)
>gnl|CDD|192445 pfam10018, Med4, Vitamin-D-receptor interacting Mediator subunit
4. Members of this family function as part of the
Mediator (Med) complex, which links DNA-bound
transcriptional regulators and the general
transcription machinery, particularly the RNA
polymerase II enzyme. They play a role in basal
transcription by mediating activation or repression
according to the specific complement of transcriptional
regulators bound to the promoter.
Length = 176
Score = 30.5 bits (69), Expect = 0.36
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 11/82 (13%)
Query: 20 VENDLSLKDHL--LGQLDQVEAHVEELRKMASQLENEKDQILTTI----HTLKNMDSLND 73
+ D LK L L + + + + ELR L+ + IL + L+ + L+
Sbjct: 8 ISADDELKSALKELEEHQENQQRILELRAEVESLDEKIKDILKELKEAEKELRTLPDLSS 67
Query: 74 IGDNDK-----DDILRYLDRIS 90
I +K +++L+Y RIS
Sbjct: 68 INKANKRKVSSEELLKYAHRIS 89
>gnl|CDD|238844 cd01709, RT_like_1, RT_like_1: A subfamily of reverse
transcriptases (RTs). An RT gene is usually indicative
of a mobile element such as a retrotransposon or
retrovirus. RTs occur in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 346
Score = 30.7 bits (70), Expect = 0.46
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 35 DQVEAHVEELRKMASQLENEKDQILTTIHT 64
QV+AH++ELRK QL + +L+ I
Sbjct: 198 SQVDAHIDELRK---QL-DACKSVLSWIQA 223
>gnl|CDD|133382 cd01107, HTH_BmrR, Helix-Turn-Helix DNA binding domain of the BmrR
transcription regulator. Helix-turn-helix (HTH)
multidrug-efflux transporter transcription regulator,
BmrR and YdfL of Bacillus subtilis, and related
proteins; N-terminal domain. Bmr is a membrane protein
which causes the efflux of a variety of toxic substances
and antibiotics. BmrR is comprised of two distinct
domains that harbor a regulatory (effector-binding) site
and an active (DNA-binding) site. The conserved
N-terminal domain contains a winged HTH motif that
mediates DNA binding, while the C-terminal domain binds
coactivating, toxic compounds. BmrR shares the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements.
Length = 108
Score = 29.0 bits (66), Expect = 0.60
Identities = 17/45 (37%), Positives = 28/45 (62%)
Query: 14 IEEPKDVENDLSLKDHLLGQLDQVEAHVEELRKMASQLENEKDQI 58
I+E D +ND L+ L +L ++EA +EEL+++ LE+ QI
Sbjct: 64 IKEILDADNDDELRKLLREKLAELEAEIEELQRILRLLEDRLKQI 108
>gnl|CDD|216160 pfam00864, P2X_receptor, ATP P2X receptor.
Length = 374
Score = 30.3 bits (69), Expect = 0.60
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 14/50 (28%)
Query: 117 CLIDNLIIGMRETPEQTQTKC--LSYVAACSS--------SSTVGNGDKT 156
++ NLI+ TP QTQ C + AAC+S + GNG KT
Sbjct: 88 FVMTNLIV----TPNQTQGTCPEVPDDAACTSDSDCTEGEAVRQGNGIKT 133
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 29.9 bits (68), Expect = 0.66
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 26 LKDHLLGQLDQVEAHVEELRKMASQ-LENEKDQILTTIHTLKNMDSLND 73
LK LL +LD +E VE++ + + LE +++++ + + D L++
Sbjct: 155 LKADLLQRLDAIEELVEKVESLMPEILEWYRERLVARL--NEAQDQLDE 201
>gnl|CDD|133398 cd04770, HTH_HMRTR, Helix-Turn-Helix DNA binding domain of Heavy
Metal Resistance transcription regulators.
Helix-turn-helix (HTH) heavy metal resistance
transcription regulators (HMRTR): MerR1 (mercury), CueR
(copper), CadR (cadmium), PbrR (lead), ZntR (zinc),
and other related proteins. These transcription
regulators mediate responses to heavy metal stress in
eubacteria. They belong to the MerR superfamily of
transcription regulators that promote transcription of
various stress regulons by reconfiguring the operator
sequence located between the -35 and -10 promoter
elements. A typical MerR regulator is comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 123
Score = 29.1 bits (66), Expect = 0.72
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 27 KDHLLGQLDQVEAHVEELRKMASQLEN 53
+ L +L +VEA + EL+ + ++L
Sbjct: 81 RALLEEKLAEVEAKIAELQALRAELAG 107
>gnl|CDD|113471 pfam04703, FaeA, FaeA-like protein. This family represents a
number of fimbrial protein transcription regulators
found in Gram-negative bacteria. These proteins are
thought to facilitate binding of the leucine-rich
regulatory protein to regulatory elements, possibly by
inhibiting deoxyadenosine methylation of these elements
by deoxyadenosine methylase.
Length = 61
Score = 27.1 bits (60), Expect = 1.4
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 79 KDDILRYLDRISLRCTTIDVCVHTLRSDDQV 109
K+ IL +++ I C T ++ S Q
Sbjct: 2 KESILTFINSIGAPCKTREIADALGLSAYQA 32
>gnl|CDD|180700 PRK06800, fliH, flagellar assembly protein H; Validated.
Length = 228
Score = 28.7 bits (64), Expect = 1.6
Identities = 13/48 (27%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 12 VHIEEPKDVENDLSLKDHLLGQLDQVEAHVEELRKMASQLENEKDQIL 59
V +EE +++ LL Q + + +LR+ +LE E+ Q+L
Sbjct: 30 VEVEEEIQKDHE-----ELLAQQKSLHKELNQLRQEQQKLERERQQLL 72
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 28.4 bits (64), Expect = 2.0
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 11/58 (18%)
Query: 29 HLLGQLDQVEAHVEELRKMASQLENEKDQILTTIHTLKNMDSLNDIGDNDKDDILRYL 86
LG+ AH+ ELR+ + ++ +L + + D + +LR L
Sbjct: 157 RDLGEALGCGAHMSELRRTRV-----------GPFSEEDAVTLELLDELDAESLLRLL 203
>gnl|CDD|219791 pfam08317, Spc7, Spc7 kinetochore protein. This domain is found in
cell division proteins which are required for
kinetochore-spindle association.
Length = 321
Score = 28.5 bits (64), Expect = 2.6
Identities = 14/59 (23%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 14 IEEPKDVENDLSLKDHLL-----GQLDQVEAHVEELRKMASQLENEKDQILTTIHTLKN 67
I + + ++L+L D L +L + + E RK +L+ E ++ I L N
Sbjct: 191 IASLRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIAIEALTN 249
>gnl|CDD|236993 PRK11820, PRK11820, hypothetical protein; Provisional.
Length = 288
Score = 28.2 bits (64), Expect = 3.0
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 25 SLKDHLLGQLDQVEAHVEELRKMASQL 51
+LK LL +LD +EA V ++ +A ++
Sbjct: 152 ALKADLLQRLDAIEALVAKIEALAPEI 178
>gnl|CDD|222835 PHA01757, PHA01757, hypothetical protein.
Length = 98
Score = 26.9 bits (59), Expect = 3.0
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 51 LENEKDQILTTIHTLKNMDSLNDIGD 76
E+ KD +T I+ L NMD+L D+ D
Sbjct: 57 TESIKDTTVTGINALLNMDTLRDVND 82
>gnl|CDD|237398 PRK13489, PRK13489, chemoreceptor glutamine deamidase CheD;
Provisional.
Length = 233
Score = 27.5 bits (61), Expect = 4.4
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 38 EAHVEELRKMASQLENEKDQILTTIHTLKNMDSLNDIGDNDKDDILRYLDRISLRCTTID 97
E + EL K + E + ++ L M ++N IGD + D + RYL +R T D
Sbjct: 87 EVLINELIKAGGRRERFEAKVFGGAAVLAGMTTIN-IGDRNADFVRRYLALERIRITAED 145
>gnl|CDD|233791 TIGR02231, TIGR02231, conserved hypothetical protein. This family
consists of proteins over 500 amino acids long in
Caenorhabditis elegans and several bacteria (Pseudomonas
aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans,
etc.). The function is unknown.
Length = 525
Score = 27.8 bits (62), Expect = 4.5
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 30 LLGQLDQVEAHVEELRKMASQLENEKDQILT 60
LL + + E + EL K S+L+NE + +LT
Sbjct: 143 LLTEDREAERRIRELEKQLSELQNELNALLT 173
>gnl|CDD|233242 TIGR01035, hemA, glutamyl-tRNA reductase. This enzyme, together
with glutamate-1-semialdehyde-2,1-aminomutase
(TIGR00713), leads to the production of
delta-amino-levulinic acid from Glu-tRNA [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 417
Score = 27.0 bits (60), Expect = 7.7
Identities = 18/102 (17%), Positives = 45/102 (44%), Gaps = 16/102 (15%)
Query: 39 AHVEELRKMASQLENEKDQILTTIHTLKNMDS-----------LNDIGDNDKD---DILR 84
A VE K++ E + + L T+ +++ + + DN + +L+
Sbjct: 11 APVEVREKLSID-EIKLKKALDTLKAEPSIEEAMVLSTCNRVEIYAVVDNLHEGKSALLQ 69
Query: 85 YL-DRISLRCTTIDVCVHTLRSDDQVESLHQVNCLIDNLIIG 125
L + ++ ++ ++ L + VE L +V +D++++G
Sbjct: 70 ILAENKNMSNEDLEKYLYILTGESAVEHLFRVASGLDSMVVG 111
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 27.2 bits (61), Expect = 8.0
Identities = 28/136 (20%), Positives = 56/136 (41%), Gaps = 23/136 (16%)
Query: 5 EAASSNDVHIEEPKDVENDLSLKDHLLGQLDQVEAHVEELRKMASQLENEKDQILTTIHT 64
+A + + E K V+ DL LL ++D+ + E+L++ +Q + Q +
Sbjct: 46 DALNKQKLLEAEDKLVQQDLEQTLALLDKIDRQKEETEQLKQQLAQAPAKLRQAQAELEA 105
Query: 65 LKNMDSLNDIGDNDKDDILRYLDRISLRCTTIDVCVHTL--RSDDQVESLHQV-NCL--I 119
LK D++ ++ L +SLR L R ++ L N L
Sbjct: 106 LK---------DDNDEETRETLSTLSLR---------QLESRLAQTLDQLQNAQNDLAEY 147
Query: 120 DNLIIGMRETPEQTQT 135
++ ++ ++ PE+ Q
Sbjct: 148 NSQLVSLQTQPERAQA 163
>gnl|CDD|110537 pfam01540, Lipoprotein_7, Adhesin lipoprotein. This family
consists of the p50 and variable adherence-associated
antigen (Vaa) adhesins from Mycoplasma hominis. M.
hominis is a mycoplasma associated with human urogenital
diseases, pneumonia, and septic arthritis. An adhesin is
a cell surface molecule that mediates adhesion to other
cells or to the surrounding surface or substrate. The
Vaa antigen is a 50-kDa surface lipoprotein that has
four tandem repetitive DNA sequences encoding a periodic
peptide structure, and is highly immunogenic in the
human host. p50 is also a 50-kDa lipoprotein, having
three repeats A,B and C, that may be a tetramer of
191-kDa in its native environment.
Length = 353
Score = 27.0 bits (59), Expect = 8.3
Identities = 21/96 (21%), Positives = 47/96 (48%), Gaps = 10/96 (10%)
Query: 31 LGQLDQVEAHVEELRKMASQLENEKDQILTTIHTLKNMDSLNDIGDND-----KDDILRY 85
L +++ + VEEL+K++ ++ + + TI L+ ++D + + K+++ +
Sbjct: 230 LTEINSIIKGVEELKKLSHEISEFSNSVKKTISELEKKFKIDDKTNKEEAKKFKNELENF 289
Query: 86 LDRISLRCTTID--VCVHTLRSD---DQVESLHQVN 116
D++ + ID V V + R D ++ES N
Sbjct: 290 ADQLLNKSHEIDKFVTVTSARGDFSLSELESFKSFN 325
>gnl|CDD|237407 PRK13516, PRK13516, gamma-glutamyl:cysteine ligase; Provisional.
Length = 373
Score = 26.8 bits (60), Expect = 9.3
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 24 LSLKDHLLGQLDQVEAHVEEL 44
L + +L LD++ H E L
Sbjct: 305 RPLAEDILRTLDRIAPHAEAL 325
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
0.315 0.131 0.371
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,618,964
Number of extensions: 864654
Number of successful extensions: 1421
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1413
Number of HSP's successfully gapped: 88
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.4 bits)