RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1871
(139 letters)
>gnl|CDD|217479 pfam03297, Ribosomal_S25, S25 ribosomal protein.
Length = 105
Score = 147 bits (372), Expect = 5e-47
Identities = 78/112 (69%), Positives = 87/112 (77%), Gaps = 8/112 (7%)
Query: 21 PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
PPKK K K K +GGKAKKKKWSKGKV+DKLNN VLFDKA+YDKLLKE
Sbjct: 2 PPKKQQK--------KAAKAAAASAGGKAKKKKWSKGKVKDKLNNAVLFDKATYDKLLKE 53
Query: 81 VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132
VP YKLITPSV+S+RLK+ GSLAR+AL EL +KGLIK VVKH AQ+IYTR T
Sbjct: 54 VPTYKLITPSVLSDRLKINGSLARRALRELEEKGLIKPVVKHSAQLIYTRAT 105
>gnl|CDD|227238 COG4901, COG4901, Ribosomal protein S25 [Translation, ribosomal
structure and biogenesis].
Length = 107
Score = 70.7 bits (173), Expect = 7e-17
Identities = 37/101 (36%), Positives = 59/101 (58%)
Query: 33 QPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVV 92
Q K +K ++ +G KKKWSK K +++ V D+ DK+ KEVP +++TP V+
Sbjct: 6 QLSKEKKAEKAKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVL 65
Query: 93 SERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133
+ R + GS+AR L L ++G+++ V K+ Q IYTR
Sbjct: 66 ASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYTRAKA 106
>gnl|CDD|181784 PRK09334, PRK09334, 30S ribosomal protein S25e; Provisional.
Length = 86
Score = 40.8 bits (96), Expect = 1e-05
Identities = 22/82 (26%), Positives = 43/82 (52%)
Query: 48 KAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKAL 107
K KKKK ++ + + D+ ++ KEV K++TP ++ + ++ S+A+K L
Sbjct: 3 KKKKKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVL 62
Query: 108 EELLQKGLIKQVVKHHAQVIYT 129
EL ++G++ K+ IY
Sbjct: 63 RELEKRGVLVLYSKNRRTPIYV 84
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 31.8 bits (73), Expect = 0.093
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 5/47 (10%)
Query: 18 YKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLN 64
K P +K T S K K +KKE K K+K K + RD N
Sbjct: 380 TKAPSEKKTGKPSKKVLAKRAEKKE-----KEKEKPKVKKRHRDTKN 421
>gnl|CDD|235144 PRK03635, PRK03635, chromosome replication initiation inhibitor
protein; Validated.
Length = 294
Score = 29.7 bits (68), Expect = 0.36
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 19/44 (43%)
Query: 69 FDKASYDKLLKEVPAYKL-ITPSVVSERLKVRGSLARKALEELL 111
F++A A KL IT S VS+R+ KALEE +
Sbjct: 19 FERA----------AQKLHITQSAVSQRI--------KALEERV 44
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 29.9 bits (68), Expect = 0.42
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 16 KSYKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKK 53
+ Y PPKK + K+PQK +KKK+ GK +KKK
Sbjct: 377 EKYPKPPKKKRE---EKKPQKRKKKKKRKKKGKKRKKK 411
>gnl|CDD|221778 pfam12802, MarR_2, MarR family. The Mar proteins are involved in
the multiple antibiotic resistance, a non-specific
resistance system. The expression of the mar operon is
controlled by a repressor, MarR. A large number of
compounds induce transcription of the mar operon. This
is thought to be due to the compound binding to MarR,
and the resulting complex stops MarR binding to the DNA.
With the MarR repression lost, transcription of the
operon proceeds. The structure of MarR is known and
shows MarR as a dimer with each subunit containing a
winged-helix DNA binding motif.
Length = 60
Score = 26.8 bits (60), Expect = 1.2
Identities = 7/33 (21%), Positives = 19/33 (57%)
Query: 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119
+T + ++ RL + + ++ L +KGL+++
Sbjct: 20 LTVAELARRLGLSKQTVSRLVKRLEEKGLVERE 52
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 28.2 bits (63), Expect = 1.8
Identities = 12/38 (31%), Positives = 14/38 (36%)
Query: 16 KSYKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKK 53
K K K + K KTQK +A KKK
Sbjct: 773 KKAKPKAAKKDARKAKKPSAKTQKIAAATKAKRAAKKK 810
>gnl|CDD|197774 smart00529, HTH_DTXR, Helix-turn-helix diphteria tox regulatory
element. iron dependent repressor.
Length = 95
Score = 26.8 bits (60), Expect = 1.9
Identities = 8/26 (30%), Positives = 16/26 (61%)
Query: 92 VSERLKVRGSLARKALEELLQKGLIK 117
++ERL V + L++L + GL++
Sbjct: 4 IAERLNVSPPTVTEMLKKLEKMGLVE 29
>gnl|CDD|211803 TIGR03298, argP, transcriptional regulator, ArgP family. ArgP used
to be known as IciA. ArgP is a positive regulator of
argK. It is a negative autoregulator in presence of
arginine. It competes with DnaA for oriC iteron (13-mer)
binding. It activates dnaA and nrd transcription. It has
been demonstrated to be part of the pho regulon
(PMID:10589831). ArgP mutants convey canavanine (an
L-arginine structural homolog) sensitivity (PMID:
15150242) [Cellular processes, Toxin production and
resistance, DNA metabolism, DNA replication,
recombination, and repair, Regulatory functions, DNA
interactions].
Length = 278
Score = 27.6 bits (62), Expect = 2.1
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 31/71 (43%)
Query: 69 FDKASYDKLLKEVPAYKL-ITPSVVSERLKVRGSLARKALEELLQKGLI----------- 116
F++A A L +TPS VS+R+ KALEE L + L+
Sbjct: 18 FERA----------AAALSVTPSAVSQRI--------KALEERLGQPLLVRTQPCRATEA 59
Query: 117 -KQVVKHHAQV 126
+++++H QV
Sbjct: 60 GQRLLRHARQV 70
>gnl|CDD|222538 pfam14094, DUF4272, Domain of unknown function (DUF4272). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 221 and
399 amino acids in length.
Length = 209
Score = 27.3 bits (61), Expect = 2.5
Identities = 12/43 (27%), Positives = 15/43 (34%), Gaps = 8/43 (18%)
Query: 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKG 114
A D + PA + VV ER AL L+ G
Sbjct: 167 ACVDARINGRPAPAGLDEGVVYER--------HYALNWLVGYG 201
>gnl|CDD|239896 cd04449, DEP_DEPDC5-like, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in DEPDC5-like proteins. DEPDC5, in human
also known as KIAA0645, is a DEP domain containing
protein of unknown function.
Length = 83
Score = 26.1 bits (58), Expect = 2.7
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 103 ARKALEELLQKGLIKQVVKHHAQVIY 128
A + +EL+ +GLI+ V H +
Sbjct: 52 AVELGQELMNEGLIEHVSGRH-PFLD 76
>gnl|CDD|197669 smart00345, HTH_GNTR, helix_turn_helix gluconate operon
transcriptional repressor.
Length = 60
Score = 25.6 bits (57), Expect = 3.1
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116
P KL + ++ +L V + R+AL L +GL+
Sbjct: 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAEGLV 50
>gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). The major groups
in this CD correspond to DOPA/tyrosine decarboxylase
(DDC), histidine decarboxylase (HDC), and glutamate
decarboxylase (GDC). DDC is active as a dimer and
catalyzes the decarboxylation of tyrosine. GDC catalyzes
the decarboxylation of glutamate and HDC catalyzes the
decarboxylation of histidine.
Length = 345
Score = 27.2 bits (61), Expect = 3.5
Identities = 21/93 (22%), Positives = 33/93 (35%), Gaps = 28/93 (30%)
Query: 43 GGS-----GGKAKKKKWSK------GKVRDKLN------NQVLFDKASY--DKLLKEVPA 83
GGS A + + K G+ DKL V +KA+ D ++ VP
Sbjct: 65 GGSESNLLALLAARDRARKRLKAGGGRGIDKLVIVCSDQAHVSVEKAAAYLDVKVRLVP- 123
Query: 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLI 116
V E ++ A++E +GL
Sbjct: 124 --------VDEDGRMDPEALEAAIDEDKAEGLN 148
>gnl|CDD|224240 COG1321, TroR, Mn-dependent transcriptional regulator
[Transcription].
Length = 154
Score = 26.5 bits (59), Expect = 4.3
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 92 VSERLKVRGSLARKALEELLQKGLIKQV 119
++ERLKV + L+ L + GL++
Sbjct: 30 IAERLKVSPPSVTEMLKRLERLGLVEYE 57
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 26.7 bits (59), Expect = 4.5
Identities = 13/41 (31%), Positives = 17/41 (41%)
Query: 19 KHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKV 59
K P +K TK K + K KAK KK +K +
Sbjct: 744 KTPYEKKTKAKKKSASTKGKAAKTVKKKSKAKSKKTTKKRA 784
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 26.5 bits (59), Expect = 4.9
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 89 PSVVSERLKVRGSLARKALE----ELLQKGLIKQ-VVKHHAQVIYTRTTKGD 135
P V+ ERLK RG K LE E+L +I V+ VI TT
Sbjct: 93 PEVLYERLKGRGYSEEKILENVEAEIL--DVILIEAVERFEAVIEVDTTNRS 142
>gnl|CDD|224759 COG1846, MarR, Transcriptional regulators [Transcription].
Length = 126
Score = 26.0 bits (57), Expect = 5.0
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH--AQVIYTRTTKG 134
IT ++ERL + S + L+ L KGLI+++ V+ T KG
Sbjct: 37 ITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKG 86
>gnl|CDD|215836 pfam00282, Pyridoxal_deC, Pyridoxal-dependent decarboxylase
conserved domain.
Length = 373
Score = 26.6 bits (59), Expect = 5.8
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 9/39 (23%)
Query: 78 LKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116
L+E+P E K+RG KA+EE + GLI
Sbjct: 165 LREIPT---------DENGKMRGMDLEKAIEEDKENGLI 194
>gnl|CDD|216824 pfam01978, TrmB, Sugar-specific transcriptional regulator TrmB.
One member of this family, TrmB, has been shown to be a
sugar-specific transcriptional regulator of the
trehalose/maltose ABC transporter in Thermococcus
litoralis.
Length = 68
Score = 24.8 bits (55), Expect = 6.0
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117
Y LLK PA T ++E V S + L L +KGL++
Sbjct: 14 YLALLKLGPA----TADEIAEESGVPRSKVYEVLRSLEKKGLVE 53
>gnl|CDD|225420 COG2865, COG2865, Predicted transcriptional regulator containing an
HTH domain and an uncharacterized domain shared with the
mammalian protein Schlafen [Transcription].
Length = 467
Score = 26.5 bits (59), Expect = 6.2
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119
+L+KE +T + E L + R+ + L+++GL+KQ+
Sbjct: 409 ELIKENGK---VTARELREILGISSETIRRRIANLVKRGLLKQL 449
>gnl|CDD|202159 pfam02212, GED, Dynamin GTPase effector domain.
Length = 90
Score = 25.1 bits (56), Expect = 6.6
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 12/58 (20%)
Query: 58 KVRDKLNN---QVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLAR--KALEEL 110
+ ++ L Q+L+ K D+LLKE P + +R +++ L R KA E L
Sbjct: 37 ESKESLQKELLQLLYKKEDLDELLKE-------DPEIAQKRKELKKRLERLKKAREIL 87
>gnl|CDD|153418 cd07377, WHTH_GntR, Winged helix-turn-helix (WHTH) DNA-binding
domain of the GntR family of transcriptional regulators.
This CD represents the winged HTH DNA-binding domain of
the GntR (named after the gluconate operon repressor in
Bacillus subtilis) family of bacterial transcriptional
regulators and their putative homologs found in
eukaryota and archaea. The GntR family has over 6000
members distributed among almost all bacterial species,
which is comprised of FadR, HutC, MocR, YtrA, AraR,
PlmA, and other subfamilies for the regulation of the
most varied biological process. The monomeric proteins
of the GntR family are characterized by two function
domains: a small highly conserved winged
helix-turn-helix prokaryotic DNA binding domain in the
N-terminus, and a very diverse regulatory ligand-binding
domain in the C-terminus for
effector-binding/oligomerization, which provides the
basis for the subfamily classifications. Binding of the
effector to GntR-like transcriptional regulators is
presumed to result in a conformational change that
regulates the DNA-binding affinity of the repressor. The
GntR-like proteins bind as dimers, where each monomer
recognizes a half-site of 2-fold symmetric DNA
sequences.
Length = 66
Score = 24.7 bits (55), Expect = 6.6
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116
P +L + ++E L V + R+AL EL +GL+
Sbjct: 21 PGDRLPSERELAEELGVSRTTVREALRELEAEGLV 55
>gnl|CDD|225099 COG2188, PhnF, Transcriptional regulators [Transcription].
Length = 236
Score = 26.1 bits (58), Expect = 6.6
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 103 ARKALEELLQKGLIKQV 119
RKAL+EL+++GLI +
Sbjct: 48 VRKALDELVEEGLIVRR 64
>gnl|CDD|205590 pfam13412, HTH_24, Winged helix-turn-helix DNA-binding.
Length = 48
Score = 24.3 bits (54), Expect = 7.1
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 87 ITPSVVSERLKVRGSLARKALEELLQKGLIK 117
I+ ++ERL + + L+ L ++GLIK
Sbjct: 18 ISQRELAERLGLSLGTVNRRLKRLEEEGLIK 48
>gnl|CDD|234657 PRK00135, scpB, segregation and condensation protein B; Reviewed.
Length = 188
Score = 25.6 bits (57), Expect = 8.8
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 4/38 (10%)
Query: 83 AYKL-ITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119
AYK IT + E +RG + AL+ LL KGLIK+V
Sbjct: 100 AYKQPITRIEIDE---IRGVNSDGALQTLLAKGLIKEV 134
>gnl|CDD|220663 pfam10266, Strumpellin, Hereditary spastic paraplegia protein
strumpellin. This is a family of proteins conserved
from plants to humans, in which two closely situated
point mutations in the human protein lead to the
condition of hereditary spastic paraplegia. Strumpellin
contains one known domain called a spectrin repeat that
consists of three alpha-helices of a characteristic
length wrapped in a left-handed coiled coil. The
spectrin proteins have multiple copies of this repeat,
which can then form multimers in the cell. Spectrin
associates with the cell membrane via spectrin repeats
in the ankyrin protein. The spectrin repeat is a
structural platform for cytoskeletal protein assemblies.
Length = 1077
Score = 26.1 bits (58), Expect = 9.0
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 5/32 (15%)
Query: 109 ELLQKGLIKQVVKH-----HAQVIYTRTTKGD 135
+LL+ G+ K++VK H+Q+I+ K
Sbjct: 675 QLLEDGIRKELVKQITKALHSQLIFDNKKKSK 706
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 25.9 bits (58), Expect = 9.6
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGD 135
K+LK + K T ++E+L + +A E L +KGL+K V+ + +Y T +G
Sbjct: 10 KVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVK--VEERVEEVYVLTEEGK 67
Query: 136 D 136
Sbjct: 68 K 68
>gnl|CDD|221671 pfam12623, Hen1_L, RNA repair, ligase-Pnkp-associating, region of
Hen1. This domain is the N-terminal region of the
bacterial Hen1 protein. This protein forms stable
heterotetramer with Pnkp. The heterotetramer was able to
repair transfer RNAs cleaved by ribotoxins in vitro.
This domain provides the ligase activity of the
heterotetramer.
Length = 245
Score = 25.7 bits (57), Expect = 9.8
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 11/45 (24%)
Query: 75 DKLLK-------EVPAYKLITPSVVSERLKVRGSLARKALEELLQ 112
DKLL+ E P +LIT L R SL R+AL L +
Sbjct: 204 DKLLRAGEGWLAEHPERELIT----RRYLAHRRSLTREALARLAE 244
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
0.309 0.128 0.353
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,807,039
Number of extensions: 586716
Number of successful extensions: 723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 707
Number of HSP's successfully gapped: 75
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 54 (24.5 bits)