RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3867
(521 letters)
>gnl|CDD|220676 pfam10288, DUF2392, Protein of unknown function (DUF2392). This is
a family of proteins conserved from plants to humans.
The function is not known. It carries a characteristic
GRG sequence motif.
Length = 104
Score = 109 bits (276), Expect = 4e-29
Identities = 44/104 (42%), Positives = 61/104 (58%), Gaps = 3/104 (2%)
Query: 258 LATKIIANISLGKGAHVPLDVGFSDDRTGDIITLRPLRDFSSKEVIYYNIFNDLSPVHVP 317
LA K+++ + G+G+ +P DV D R DI LRPLRD KE+ Y +L P+ +
Sbjct: 1 LAAKLLSLTAKGRGSSIPWDVSDGDSRGNDIKILRPLRDLLLKEIEAYCSLKNLPPLLIN 60
Query: 318 SLATLADPL---ASLQKAAESFVTDLQTNFPSTVSTVFRTADKL 358
SL +A L S+ + E + +LQ N+PSTVSTV RT DKL
Sbjct: 61 SLIQIASKLSKNMSINELTEQYFDNLQENYPSTVSTVVRTGDKL 104
>gnl|CDD|223115 COG0037, MesJ, tRNA(Ile)-lysidine synthase MesJ [Cell cycle
control, cell division, chromosome partitioning].
Length = 298
Score = 67.2 bits (164), Expect = 2e-12
Identities = 54/226 (23%), Positives = 85/226 (37%), Gaps = 40/226 (17%)
Query: 86 CLLQYLNHKFRAALGKSKMMRPQDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVC 145
CL + L K + A+ + + + K+LVA SG S+ALLHLL+E V
Sbjct: 1 CLREKLERKVKRAIREFNL--IEYKILVAVSGGKDSLALLHLLKE-------LGRRIEVE 51
Query: 146 AIYIDDGSISQVSISERKANNAQIATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQ 205
A+++D G S+++A + L + L L +E+
Sbjct: 52 AVHVDHG---LRGYSDQEAELVE-------------KLCEKLGI----------PLIVER 85
Query: 206 FAKDSEINKMFQTVTTLSSRQYLLQTLRQNLLLQAAKKLNCTKIFTAETQTDLATKIIAN 265
D + S + LR+ LL + AK+L KI T D A + N
Sbjct: 86 VTDDLGRETL-----DGKSICAACRRLRRGLLYKIAKELGADKIATGHHLDDQAETFLMN 140
Query: 266 ISLGKGAHVPLDVGFSDDRTGDIITLRPLRDFSSKEVIYYNIFNDL 311
+ G G + G ++ +RPL KE+ Y L
Sbjct: 141 LLRGSGLRGLRGMPPKRPFEGGLLIIRPLLYVREKEIELYAKEKGL 186
>gnl|CDD|233864 TIGR02432, lysidine_TilS_N, tRNA(Ile)-lysidine synthetase,
N-terminal domain. The only examples in which the
wobble position of a tRNA must discriminate between G
and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop)
vs. UGG (Trp). In all bacteria, the wobble position of
the tRNA(Ile) recognizing AUA is lysidine, a lysine
derivative of cytidine. This family describes a protein
domain found, apparently, in all bacteria in a single
copy. Eukaryotic sequences appear to be organellar. The
domain archictecture of this protein family is variable;
some, including characterized proteins of E. coli and B.
subtilis known to be tRNA(Ile)-lysidine synthetase,
include a conserved 50-residue domain that many other
members lack. This protein belongs to the ATP-binding
PP-loop family ( pfam01171). It appears in the
literature and protein databases as TilS, YacA, and
putative cell cycle protein MesJ (a misnomer) [Protein
synthesis, tRNA and rRNA base modification].
Length = 189
Score = 57.6 bits (140), Expect = 1e-09
Identities = 47/211 (22%), Positives = 79/211 (37%), Gaps = 41/211 (19%)
Query: 110 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSISERKANNAQI 169
++LVA SG SMALLHLL L ++ + A ++D G + A+
Sbjct: 1 RILVAVSGGVDSMALLHLL-----LKLQPKLKIRLIAAHVDHG------LRPESDEEAEF 49
Query: 170 ATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQFAKDSEINKMFQTVTTLSSRQYLL 229
++Q + N+ L + ++ ++ AK + N + +R+
Sbjct: 50 -------------VQQFCKKLNIPLE--IKKVDVKALAKGKKKN--LEEA----ARE--- 85
Query: 230 QTLRQNLLLQAAKKLNCTKIFTAETQTDLATKIIANISLGKGAHVPLDVGFSDDRT--GD 287
R + + AKK I TA D A I+ + L +G+ + G R
Sbjct: 86 --ARYDFFEEIAKKHGADYILTAHHADDQAETIL--LRLLRGSGLRGLSGMKPIRILGNG 141
Query: 288 IITLRPLRDFSSKEVIYYNIFNDLSPVHVPS 318
+RPL S E+ Y N L +
Sbjct: 142 GQIIRPLLGISKSEIEEYLKENGLPWFEDET 172
>gnl|CDD|238951 cd01993, Alpha_ANH_like_II, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily.Adeninosine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins is predicted to bind ATP.
This domainhas a strongly conserved motif SGGKD at the
N terminus.
Length = 185
Score = 51.5 bits (124), Expect = 1e-07
Identities = 49/211 (23%), Positives = 78/211 (36%), Gaps = 36/211 (17%)
Query: 110 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSISERKANNAQI 169
++LVA SG S+ LLH+L++ L F + A+ +D+G S
Sbjct: 1 RILVALSGGKDSLVLLHVLKK---LQRRYPYGFELEALTVDEGIPGYRDESLEVVERLAE 57
Query: 170 ATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQFAKDSEINKMFQTVTTLSSRQYLL 229
++ F YTD E + + +L
Sbjct: 58 ELGIELEIVSFKEE-----------YTDDIE--------VKKRGGK--SPCSLCGV---- 92
Query: 230 QTLRQNLLLQAAKKLNCTKIFTAETQTDLATKIIANISLGKGAH---VPLDVGFSDDRTG 286
LR+ LL + AK+L K+ T D A ++ N+ L G P + + D+ G
Sbjct: 93 --LRRGLLNKIAKELGADKLATGHNLDDEAETLLMNL-LRGGILRLMRPGPILYLDE--G 147
Query: 287 DIITLRPLRDFSSKEVIYYNIFNDLSPVHVP 317
D+ +RPL KE++ Y N L V
Sbjct: 148 DVTRIRPLVYVREKEIVLYAELNGLPFVEEE 178
>gnl|CDD|238950 cd01992, PP-ATPase, N-terminal domain of predicted ATPase of the
PP-loop faimly implicated in cell cycle control [Cell
division and chromosome partitioning]. This is a
subfamily of Adenine nucleotide alpha hydrolases
superfamily.Adeninosine nucleotide alpha hydrolases
superfamily includes N type ATP PPases and ATP
sulphurylases. It forms a apha/beta/apha fold which
binds to Adenosine group. This domain has a strongly
conserved motif SGGXD at the N terminus.
Length = 185
Score = 45.6 bits (109), Expect = 1e-05
Identities = 41/216 (18%), Positives = 66/216 (30%), Gaps = 55/216 (25%)
Query: 110 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSISERKANNAQI 169
K+LVA SG SMALLHLL E R+ + A+++D G + A
Sbjct: 1 KILVAVSGGPDSMALLHLLSE-----LKPRLGLRLVAVHVDHG------LRPESDEEAAF 49
Query: 170 ATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQFAKDSEINKMFQTVTTLSSRQYLL 229
+ I + + +
Sbjct: 50 ---------------------------------VADLCAKLGIP--LYILVVALAPKPGG 74
Query: 230 Q------TLRQNLLLQAAKKLNCTKIFTAETQTDLATKIIANISLGKGAHV-PLDVGFSD 282
R + + AK+ + TA D A ++ + L +G+ + L +
Sbjct: 75 NLEAAAREARYDFFAEIAKEHGADVLLTAHHADDQAETVL--MRLLRGSGLRGLAGMPAR 132
Query: 283 DRTGDIITLRPLRDFSSKEVIYYNIFNDLSPVHVPS 318
G +RPL + E+ Y N L PS
Sbjct: 133 IPFGGGRLIRPLLGITRAEIEAYLRENGLPWWEDPS 168
>gnl|CDD|216343 pfam01171, ATP_bind_3, PP-loop family. This family of proteins
belongs to the PP-loop superfamily.
Length = 182
Score = 44.1 bits (105), Expect = 4e-05
Identities = 41/212 (19%), Positives = 72/212 (33%), Gaps = 47/212 (22%)
Query: 110 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSISERKANNAQI 169
K+LVA SG SMALL+LL + + A ++D G + + S E + ++
Sbjct: 1 KILVAVSGGPDSMALLYLL-----KKLKPKFGIDLTAAHVDHG-LREESDREAQF-VKEL 53
Query: 170 ATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQFAKDSEINKMFQTVTTLSSRQYLL 229
+ N+ L ++ + + ++R+
Sbjct: 54 CRQL-----------------NIPLEVLRVDV-------AKKSGLNLEE----AARE--- 82
Query: 230 QTLRQNLLLQAAKKLNCTKIFTAETQTDLATKIIANISLGKGAHVPLDV--GFSDDRT-G 286
R + + AKK + TA D A + + G G L G + R
Sbjct: 83 --ARYDFFEEIAKKNGAEVLLTAHHADDQAETFLMRLLRGSG----LAGLAGIAPVRPLA 136
Query: 287 DIITLRPLRDFSSKEVIYYNIFNDLSPVHVPS 318
+RPL + E+ Y + + V S
Sbjct: 137 GGRIVRPLLKVTKSEIEEYLKEHGIPWVEDES 168
>gnl|CDD|236737 PRK10696, PRK10696, tRNA 2-thiocytidine biosynthesis protein TtcA;
Provisional.
Length = 258
Score = 37.5 bits (88), Expect = 0.009
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 91 LNHKFRAALGKSKMMRPQDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 150
L + A+ M+ D+V+V SG S LL +L + L I F + A+ +D
Sbjct: 12 LRRQVGQAIADFNMIEEGDRVMVCLSGGKDSYTLLDIL---LNLQKRAPINFELVAVNLD 68
Query: 151 DG 152
Sbjct: 69 QK 70
>gnl|CDD|129370 TIGR00269, TIGR00269, TIGR00269 family protein. [Hypothetical
proteins, Conserved].
Length = 104
Score = 33.2 bits (76), Expect = 0.073
Identities = 26/95 (27%), Positives = 40/95 (42%), Gaps = 11/95 (11%)
Query: 288 IITLRPLRDFSSKEVIYYNIFNDLSPVHVPSLATLADPLASL--QKAAESFVTDLQTNFP 345
+ ++PLR KEV+ Y N+L VH+ P +SL + F+ DL+ P
Sbjct: 1 VPRIKPLRYIPEKEVVLYAFLNEL-KVHLDEC-----PYSSLSVRARIRDFLYDLENKKP 54
Query: 346 STVSTVFRTADKLSLDLTSMNVN---NTCLLCKAP 377
+V R +KL L ++ C C P
Sbjct: 55 GVKFSVLRGFEKLIPLLKELSEQEDLRRCERCGEP 89
>gnl|CDD|215526 PLN02974, PLN02974, adenosylmethionine-8-amino-7-oxononanoate
transaminase.
Length = 817
Score = 35.5 bits (82), Expect = 0.087
Identities = 24/67 (35%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 327 ASLQKAAESFVTDLQTNFP--STVSTVFRTADKLSLDLTSMNVNNTCLLCKAPLDTRADL 384
A+ +++ +V +QT FP S VFR AD LS S+ +N L P A
Sbjct: 52 AASRRSPVLYVKPVQTGFPDDSDARFVFRKADSLSRRSESLFASNRTLFLSPPAAKSALG 111
Query: 385 ASSSMGA 391
SSMGA
Sbjct: 112 GVSSMGA 118
>gnl|CDD|182626 PRK10660, tilS, tRNA(Ile)-lysidine synthetase; Provisional.
Length = 436
Score = 33.8 bits (78), Expect = 0.23
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 107 PQDKVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDG 152
++LVAFSG S LLHLL +Q + + ++ AI++ G
Sbjct: 14 TSRQILVAFSGGLDSTVLLHLL---VQWRTENPGV-TLRAIHVHHG 55
>gnl|CDD|238944 cd01986, Alpha_ANH_like, Adenine nucleotide alpha hydrolases
superfamily including N type ATP PPases and ATP
sulphurylases. The domain forms a apha/beta/apha fold
which binds to Adenosine group..
Length = 103
Score = 30.9 bits (70), Expect = 0.37
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 9/65 (13%)
Query: 111 VLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYIDDGSISQVSISERKANNAQIA 170
VLVAFSG S LL K++ + V A+ +D G ++ ++ A A+
Sbjct: 1 VLVAFSGGKDSSVAAALL---------KKLGYQVIAVTVDHGISPRLEDAKEIAKEAREE 51
Query: 171 TAMKY 175
A +
Sbjct: 52 AAKRI 56
>gnl|CDD|184771 PRK14623, PRK14623, hypothetical protein; Provisional.
Length = 106
Score = 29.4 bits (66), Expect = 1.7
Identities = 17/63 (26%), Positives = 33/63 (52%)
Query: 389 MGATRFSRYVSNATREQLSHVIISSESPDHASKVTTDVNQTVGSQDIPEKSVNGSEDIPN 448
MG + ++ AT+++L V+I +S D KVT N+ + S I ++ + E + +
Sbjct: 7 MGKLKEAQQKVEATKKRLDTVLIDEQSSDGLLKVTVTANREIKSISIDDELLEDKEQLED 66
Query: 449 QIV 451
+V
Sbjct: 67 YLV 69
>gnl|CDD|240463 cd12883, SPRY_RING, SPRY domain at N-terminus of Really Interesting
New Gene (RING) finger domain. This SPRY domain is
found at the N-terminus of RING finger domains which are
present in a variety of functionally distinct proteins
and known to be involved in protein-protein and
protein-DNA interactions. RING-finger domain is a type
of Zn-finger that binds two Zn atoms and is identified
in proteins with a wide range of functions such as viral
replication, signal transduction, and development.
Length = 121
Score = 29.2 bits (66), Expect = 2.2
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 284 RTGDIITLRPLRDFSSKEVIYYNIFNDLSPVHVPSLATLADPLASLQKAAESFVTDLQTN 343
+ GD++ L D K++I+ L+ +P +S AA SF++ Q
Sbjct: 65 KPGDVVGC--LLDLDKKQMIFS-----LNGNRLPPERLPFTSASSGFFAAASFMSFQQCE 117
Query: 344 F 344
F
Sbjct: 118 F 118
>gnl|CDD|238846 cd01713, PAPS_reductase, This domain is found in phosphoadenosine
phosphosulphate (PAPS) reductase enzymes or PAPS
sulphotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including N
type ATP PPases and ATP sulphurylases. A highly modified
version of the P loop, the fingerprint peptide of
mononucleotide-binding proteins, is present in the
active site of the protein, which appears to be a
positively charged cleft containing a number of
conserved arginine and lysine residues. Although PAPS
reductase has no ATPase activity, it shows a striking
similarity to the structure of the ATP pyrophosphatase
(ATP PPase) domain of GMP synthetase, indicating that
both enzyme families have evolved from a common
ancestral nucleotide-binding fold. The enzyme uses
thioredoxin as an electron donor for the reduction of
PAPS to phospho-adenosine-phosphate (PAP) . It is also
found in NodP nodulation protein P from Rhizobium
meliloti which has ATP sulphurylase activity (sulphate
adenylate transferase) .
Length = 173
Score = 29.3 bits (66), Expect = 3.1
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 110 KVLVAFSGSHSSMALLHLLQEGMQLSSHKRILFSVCAIYID 150
V+V+FSG S LLHL + L V I++D
Sbjct: 1 NVVVSFSGGKDSTVLLHLALK------ALPELKPVPVIFLD 35
>gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt).
This entry represents 77 residues of an 80 amino acid
(240 nucleotide) tandem repeat, found in a variable
number of copies in an immunodominant outer membrane
protein of Ehrlichia chaffeensis, a tick-borne obligate
intracellular pathogen.
Length = 707
Score = 29.2 bits (64), Expect = 6.1
Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 1/96 (1%)
Query: 418 HASKVTTDVNQTVGSQDIPEKSVNGSEDIPNQIVNGMQYTPNEKVSRTEDNEG-PDNLQR 476
H S+V +T ++ PE + + V E TE EG P++
Sbjct: 234 HESEVGDKPAETSKEEETPEVKAEDLQPAVDGSVEHSSSEIEEHQGETEKEEGIPESHAE 293
Query: 477 SLCYACQYVVKDMTSDKDIGEGILKKCLQEKSLNEM 512
L A +V+ +S+ + E + + +E++ E+
Sbjct: 294 DLQPAVDDIVEHPSSEPFVAEEEVSETEKEENNPEV 329
>gnl|CDD|217816 pfam03959, FSH1, Serine hydrolase (FSH1). This is a family of
serine hydrolases.
Length = 209
Score = 28.4 bits (64), Expect = 6.7
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 112 LVAFS-GSHSSMALLHLLQEGMQLSSHKRILFSVCA 146
++ FS G+ + L LL+EG+ L SH + F++
Sbjct: 104 ILGFSQGAALAAILASLLEEGLPLESHPPLKFAILI 139
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein
1 (CRP1). The first LIM domain of Cysteine Rich
Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 26.5 bits (58), Expect = 6.9
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 56 SFSRADKLCPRC--NTNNGEVVLRLKDIYCKAC 86
SF ++ LC C N ++ V + ++IYCK+C
Sbjct: 22 SFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSC 54
>gnl|CDD|237215 PRK12815, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1068
Score = 28.8 bits (65), Expect = 8.8
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 328 SLQKAAESFVTDLQTNFPSTVSTVFRTADKL 358
+L+K E + T + N P TVST + TAD+L
Sbjct: 584 ALKK--EGYETIMINNNPETVSTDYDTADRL 612
>gnl|CDD|223059 PHA03367, PHA03367, single-stranded DNA binding protein;
Provisional.
Length = 1115
Score = 28.8 bits (65), Expect = 9.9
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 10/76 (13%)
Query: 158 SISERKANNAQIATAMKYFDSYFTCLEQALEPDNMKLYTDVAELPLEQFAKDSEINKMFQ 217
+ R N ++ + F S +T QAL ++K ++ E +QF +D +
Sbjct: 195 FVQLRGFYNPAVSEYL--FYSLYTSWAQALRVRDVK---ELIEALEKQFVQDQY-----K 244
Query: 218 TVTTLSSRQYLLQTLR 233
T ++Y Q L
Sbjct: 245 TAKLAPLKEYPAQKLS 260
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
0.317 0.130 0.367
Gapped
Lambda K H
0.267 0.0608 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,866,074
Number of extensions: 2331152
Number of successful extensions: 1970
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1964
Number of HSP's successfully gapped: 28
Length of query: 521
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 420
Effective length of database: 6,457,848
Effective search space: 2712296160
Effective search space used: 2712296160
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 (21.7 bits)
S2: 61 (27.5 bits)