RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4772
(235 letters)
>gnl|CDD|215423 PLN02789, PLN02789, farnesyltranstransferase.
Length = 320
Score = 152 bits (385), Expect = 7e-45
Identities = 61/129 (47%), Positives = 82/129 (63%), Gaps = 3/129 (2%)
Query: 99 IQIAPKNESPWNYLRGAVVNAGEKSERALALTADAITMNPANYTVWQYRREILKALNKDL 158
I P+ +Y R AV + E+S RAL LTAD I +NP NYTVW +RR L+AL+ DL
Sbjct: 30 IAYTPEFREAMDYFR-AVYASDERSPRALDLTADVIRLNPGNYTVWHFRRLCLEALDADL 88
Query: 159 HQELKYIGEKIKENSKNYQVWRHRQIIVEWMGE--PDEELALTAAILAQDAKNYHAWQHR 216
+EL + + ++N KNYQ+W HR+ + E +G ++EL T IL+ DAKNYHAW HR
Sbjct: 89 EEELDFAEDVAEDNPKNYQIWHHRRWLAEKLGPDAANKELEFTRKILSLDAKNYHAWSHR 148
Query: 217 QWVINLLDD 225
QWV+ L
Sbjct: 149 QWVLRTLGG 157
Score = 83.6 bits (207), Expect = 4e-19
Identities = 34/73 (46%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 44 QKCNLFSDELSYIEGLISHDVRNNSAWTQRYFVINHTTQFTPEVIQR--EIDYCRDKIQI 101
+ + DEL Y L+ DVRNNSAW QRYFVI + R E+ Y D I
Sbjct: 153 RTLGGWEDELEYCHQLLEEDVRNNSAWNQRYFVITRSPLLGGLEAMRDSELKYTIDAILA 212
Query: 102 APKNESPWNYLRG 114
P+NESPW YLRG
Sbjct: 213 NPRNESPWRYLRG 225
Score = 40.5 bits (95), Expect = 3e-04
Identities = 30/130 (23%), Positives = 49/130 (37%), Gaps = 34/130 (26%)
Query: 52 ELSYIEGLISHDVRNNSAWTQRYFVINHTTQFTPEVIQREIDYCRDKIQIAPKNESPWNY 111
EL + ++S D +N AW+ R +V+ + E++YC ++ +N S WN
Sbjct: 127 ELEFTRKILSLDAKNYHAWSHRQWVLRTLGGWE-----DELEYCHQLLEEDVRNNSAWN- 180
Query: 112 LRGAVVNAGEKSERALALTADAITMNPANYTVWQYRREILKALNKDLHQELKYIGEKIKE 171
+R +T R +L L ELKY + I
Sbjct: 181 ------------QRYFVIT----------------RSPLLGGLEAMRDSELKYTIDAILA 212
Query: 172 NSKNYQVWRH 181
N +N WR+
Sbjct: 213 NPRNESPWRY 222
>gnl|CDD|227823 COG5536, BET4, Protein prenyltransferase, alpha subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 328
Score = 86.5 bits (214), Expect = 6e-20
Identities = 52/129 (40%), Positives = 73/129 (56%), Gaps = 14/129 (10%)
Query: 121 EKSERALALTADAITMNPANYTVWQYRREILKALNKD-------LHQELKYIGEKIKENS 173
E S RAL LT + I NP YT+W YR ILK + L EL ++ E +K+N
Sbjct: 46 EYSVRALKLTQELIDKNPEFYTIWNYRFSILKHVQMVSEDKEHLLDNELDFLDEALKDNP 105
Query: 174 KNYQVWRHRQIIVEWMGEP--DEELALTAAILAQDAKNYHAWQHRQWVINLLDD-----D 226
KNYQ+W HRQ ++E +P EL +T +L D++NYH W +R+WV+ ++D D
Sbjct: 106 KNYQIWHHRQWMLELFPKPSWGRELFITKKLLDSDSRNYHVWSYRRWVLRTIEDLFNFSD 165
Query: 227 DRGVLEYET 235
+ LEY T
Sbjct: 166 LKHELEYTT 174
Score = 66.0 bits (161), Expect = 1e-12
Identities = 41/174 (23%), Positives = 75/174 (43%), Gaps = 18/174 (10%)
Query: 67 NSAWTQRYFVINH---TTQFTPEVIQREIDYCRDKIQIAPKNESPWNYLRGAVVNAGEKS 123
+ W R+ ++ H ++ ++ E+D+ + ++ PKN W++ + + + S
Sbjct: 66 YTIWNYRFSILKHVQMVSEDKEHLLDNELDFLDEALKDNPKNYQIWHHRQWMLELFPKPS 125
Query: 124 -ERALALTADAITMNPANYTVWQYRREILK----ALNK-DLHQELKYIGEKIKENSKNYQ 177
R L +T + + NY VW YRR +L+ N DL EL+Y I+ + N
Sbjct: 126 WGRELFITKKLLDSDSRNYHVWSYRRWVLRTIEDLFNFSDLKHELEYTTSLIETDIYNNS 185
Query: 178 VWRHRQIIVEWM---GEP------DEELALTAAILAQDAKNYHAWQHRQWVINL 222
W HR I +E G+ ++EL + D N W + + V +
Sbjct: 186 AWHHRYIWIERRFNRGDVISQKYLEKELEYIFDKIFTDPDNQSVWGYLRGVSSE 239
Score = 54.5 bits (131), Expect = 9e-09
Identities = 30/83 (36%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 37 VVAIAYSQKCNLFSDELSYIEGLISHDVRNNSAWTQRYFVINHTTQFTPEVIQR-----E 91
+ I + EL Y LI D+ NNSAW RY I +VI + E
Sbjct: 154 LRTIEDLFNFSDLKHELEYTTSLIETDIYNNSAWHHRYIWIERRFN-RGDVISQKYLEKE 212
Query: 92 IDYCRDKIQIAPKNESPWNYLRG 114
++Y DKI P N+S W YLRG
Sbjct: 213 LEYIFDKIFTDPDNQSVWGYLRG 235
Score = 36.8 bits (85), Expect = 0.007
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 13/136 (9%)
Query: 49 FSDELSYIEGLISHDVRNNSAWTQR-YFVINHTTQFTPEVIQREIDYCRDKIQIAPKNES 107
+ EL + L+ D RN W+ R + + F ++ E++Y I+ N S
Sbjct: 126 WGRELFITKKLLDSDSRNYHVWSYRRWVLRTIEDLFNFSDLKHELEYTTSLIETDIYNNS 185
Query: 108 PWNY---LRGAVVNAGE-----KSERALALTADAITMNPANYTVWQYRREILKALNKDLH 159
W++ N G+ E+ L D I +P N +VW Y R + D+
Sbjct: 186 AWHHRYIWIERRFNRGDVISQKYLEKELEYIFDKIFTDPDNQSVWGYLRGVSSEFATDIV 245
Query: 160 QELKYIGEKIKENSKN 175
IGEK+++ K
Sbjct: 246 M----IGEKVEDLGKY 257
>gnl|CDD|201678 pfam01239, PPTA, Protein prenyltransferase alpha subunit repeat.
Both farnesyltransferase (FT) and
geranylgeranyltransferase 1 (GGT1) recognise a CaaX
motif on their substrates where 'a' stands for
preferably aliphatic residues, whereas GGT2 recognises a
completely different motif. Important substrates for FT
include, amongst others, many members of the Ras
superfamily. GGT1 substrates include some of the other
small GTPases and GGT2 substrates include the Rab
family.
Length = 30
Score = 43.3 bits (103), Expect = 2e-06
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 194 EELALTAAILAQDAKNYHAWQHRQWVINLL 223
EEL LT +L D KNY AW +R+W++ L
Sbjct: 1 EELELTEKLLELDPKNYSAWNYRRWLLEKL 30
Score = 41.7 bits (99), Expect = 5e-06
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 125 RALALTADAITMNPANYTVWQYRREILKAL 154
L LT + ++P NY+ W YRR +L+ L
Sbjct: 1 EELELTEKLLELDPKNYSAWNYRRWLLEKL 30
Score = 38.3 bits (90), Expect = 1e-04
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 160 QELKYIGEKIKENSKNYQVWRHRQIIVEWM 189
+EL+ + ++ + KNY W +R+ ++E +
Sbjct: 1 EELELTEKLLELDPKNYSAWNYRRWLLEKL 30
Score = 34.8 bits (81), Expect = 0.001
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 51 DELSYIEGLISHDVRNNSAWTQRYFVINH 79
+EL E L+ D +N SAW R +++
Sbjct: 1 EELELTEKLLELDPKNYSAWNYRRWLLEK 29
Score = 34.8 bits (81), Expect = 0.002
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 90 REIDYCRDKIQIAPKNESPWNYLRG 114
E++ +++ PKN S WNY R
Sbjct: 1 EELELTEKLLELDPKNYSAWNYRRW 25
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 31.2 bits (71), Expect = 0.13
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 1/65 (1%)
Query: 92 IDYCRDKIQIAPKNESPWNYLRGAVVNAGEKSERALALTADAITMNPANYTVWQYRREIL 151
++Y +++ P N + Y A K E AL A+ ++P N +
Sbjct: 20 LEYYEKALELDPDNADAY-YNLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNLGLAY 78
Query: 152 KALNK 156
L K
Sbjct: 79 YKLGK 83
Score = 27.3 bits (61), Expect = 2.9
Identities = 14/98 (14%), Positives = 33/98 (33%), Gaps = 1/98 (1%)
Query: 111 YLRGAVVNAGEKSERALALTADAITMNPANYTVWQYRREILKALNKDLHQELKYIGEKIK 170
G + + AL A+ ++P N + Y + L+ + ++
Sbjct: 4 LNLGNLYYKLGDYDEALEYYEKALELDPDNADAY-YNLAAAYYKLGKYEEALEDYEKALE 62
Query: 171 ENSKNYQVWRHRQIIVEWMGEPDEELALTAAILAQDAK 208
+ N + + + + +G+ +E L L D
Sbjct: 63 LDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
>gnl|CDD|227608 COG5283, COG5283, Phage-related tail protein [Function unknown].
Length = 1213
Score = 30.3 bits (68), Expect = 0.94
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 110 NYLRGAVV---NAGEKSERALALTADAITMNPANYTVWQYRREILKALNKDLHQELKYIG 166
N L+ ++ + E+ LT D ++ + Y E K +DL QE+K +
Sbjct: 25 NVLKSSIKDSTQFWKMLEKQQKLTKDGLSASKGKYEGLSEAMEKQKKAYEDLKQEVKEVN 84
Query: 167 EKIKENSKNYQ 177
+ + K YQ
Sbjct: 85 RATQASKKAYQ 95
>gnl|CDD|240016 cd04658, Piwi_piwi-like_Euk, Piwi_piwi-like_Euk: PIWI domain,
Piwi-like subfamily found in eukaryotes. This domain is
found in Piwi and closely related proteins, where it is
believed to perform a crucial role in germline cells,
via RNA silencing. RNA silencing refers to a group of
related gene-silencing mechanisms mediated by short RNA
molecules, including siRNAs, miRNAs, and
heterochromatin-related guide RNAs. The mechanism in
Piwi is believed to be similar to that in Argonaute, the
central component of the RNA-induced silencing complex
(RISC). The PIWI domain is the C-terminal portion of
Argonaute and consists of two subdomains, one of which
provides the 5' anchoring of the guide RNA and the
other, the catalytic site for slicing.
Length = 448
Score = 29.5 bits (67), Expect = 1.4
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 59 LISHDVRNNSAWTQRYFVINHTTQFTPEVIQR 90
L+S VR + Y V+ TT P+ +QR
Sbjct: 383 LVSQSVRQGTVTPTHYNVLYDTTGLKPDHLQR 414
>gnl|CDD|233354 TIGR01312, XylB, D-xylulose kinase. This model describes
D-xylulose kinases, a subfamily of the FGGY family of
carbohydrate kinases. The member from Klebsiella
pneumoniae, designated DalK (see PMID:9324246), was
annotated erroneously in GenBank as D-arabinitol kinase
but is authentic D-xylulose kinase. D-xylulose kinase
(XylB) generally is found with xylose isomerase (XylA)
and acts in xylose utilization [Energy metabolism,
Sugars].
Length = 481
Score = 27.7 bits (62), Expect = 5.6
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 13/63 (20%)
Query: 149 EILKALNKDLHQELKYIGEKIKENSKNYQVWRHRQIIVEWMG------EPDEELALTAAI 202
+IL+ Q ++ IG +K+ WR Q++ + G E +E AL AAI
Sbjct: 381 DILREAGGIPIQSIRLIGG----GAKS-PAWR--QMLADIFGTPVDVPEGEEGPALGAAI 433
Query: 203 LAQ 205
LA
Sbjct: 434 LAA 436
>gnl|CDD|211799 TIGR03247, glucar-dehydr, glucarate dehydratase. Glucarate
dehydratase converts D-glucarate (and L-idarate, a
stereoisomer) to 5-dehydro-4-deoxyglucarate which is
subsequently acted on by GarL, tartronate semialdehyde
reductase and glycerate kinase (, GenProp0716). The E.
coli enzyme has been well-characterized.
Length = 441
Score = 27.5 bits (61), Expect = 6.3
Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 14/106 (13%)
Query: 63 DVRNNSAWTQRYFVINHTTQFTPEVIQREIDYCRDKIQIAPKNESPWNYLRGAVVNAGEK 122
R+ +F + H TPE + R + D+ L+G V+ E+
Sbjct: 159 PYRSGPQDDDDWFRLRHEEALTPEAVVRLAEAAYDRYGFRDFK------LKGGVLRGEEE 212
Query: 123 SERALALTA---DA-ITMNPANYTVWQYRREILKALNKDLHQELKY 164
E AL A IT++P W I AL KDL L Y
Sbjct: 213 IEAVTALAKRFPQARITLDPNG--AWSLDEAI--ALCKDLKGVLAY 254
>gnl|CDD|181704 PRK09218, PRK09218, peptide deformylase; Validated.
Length = 136
Score = 26.8 bits (60), Expect = 6.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 81 TQFTPEVIQREIDYCRDKI 99
T FT ++IQ E+D+C +
Sbjct: 117 TGFTAQIIQHELDHCEGIL 135
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 27.2 bits (61), Expect = 7.8
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 7/40 (17%)
Query: 156 KDLHQELKYIGEKIKENSKNYQVWRHRQIIVEWMGEPDEE 195
+ L L+ I +K + + R +I M E +EE
Sbjct: 81 RPLEVNLREIRR-VKRD------YPDRALIASIMVECNEE 113
>gnl|CDD|181285 PRK08199, PRK08199, thiamine pyrophosphate protein; Validated.
Length = 557
Score = 27.5 bits (62), Expect = 7.9
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 8/36 (22%)
Query: 185 IVEWMGE--PDEELALTAAILAQDAKNYHAWQHRQW 218
++ W+ E P + AI+ A NY W HR +
Sbjct: 372 VMAWLRERLPAD------AIITNGAGNYATWLHRFF 401
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 27.5 bits (61), Expect = 7.9
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 151 LKALNKDLHQELKYIGEKIKENSKNYQVWRHRQIIVEWMGEPDEEL 196
+KA + + K I ++I + Q R+ +VE + E DEEL
Sbjct: 181 MKAYFFNGDKGTKAIEKEIPSDLLE-QAKELRENLVEAVAEFDEEL 225
>gnl|CDD|238577 cd01172, RfaE_like, RfaE encodes a bifunctional ADP-heptose
synthase involved in the biosynthesis of the
lipopolysaccharide (LPS) core precursor
ADP-L-glycero-D-manno-heptose. LPS plays an important
role in maintaining the structural integrity of the
bacterial outer membrane of gram-negative bacteria. RfaE
consists of two domains, a sugar kinase domain,
represented here, and a domain belonging to the
cytidylyltransferase superfamily.
Length = 304
Score = 27.1 bits (61), Expect = 8.9
Identities = 20/94 (21%), Positives = 33/94 (35%), Gaps = 31/94 (32%)
Query: 83 FTPEVIQREIDYCRDK---IQIAPKNESPWNYLRGAVVNAGEKSERALALTADAITMNPA 139
TP VI+ I R+ + + PK Y A +T N
Sbjct: 148 LTPRVIEALIAAARELGIPVLVDPKGRDYSKYRG-----------------ATLLTPN-- 188
Query: 140 NYTVWQYRREILKALNKDLHQE--LKYIGEKIKE 171
+E +AL +++ + L+ GEK+ E
Sbjct: 189 -------EKEAREALGDEINDDDELEAAGEKLLE 215
>gnl|CDD|233082 TIGR00668, apaH, bis(5'-nucleosyl)-tetraphosphatase (symmetrical).
Diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) is a
regulatory metabolite of stress conditions. It is
hydrolyzed to two ADP by this enzyme. Alternate names
include diadenosine-tetraphosphatase and Ap4A hydrolase
[Cellular processes, Adaptations to atypical
conditions].
Length = 279
Score = 26.8 bits (59), Expect = 9.8
Identities = 17/79 (21%), Positives = 24/79 (30%), Gaps = 13/79 (16%)
Query: 42 YSQKCNLFSDELSYIEGLISHDVRNNSAWTQRYFVINHTTQFTPEVIQREIDYCRDKIQI 101
Y N +S EL GL N+ R+ N Y ++ +
Sbjct: 156 YGDMPNRWSPELQ---GLARLRFIINAFTRMRFCFPNGQLDM----------YSKESPED 202
Query: 102 APKNESPWNYLRGAVVNAG 120
AP PW + G V
Sbjct: 203 APAPLKPWFAIPGPVYEEY 221
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
0.316 0.132 0.408
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,484,063
Number of extensions: 1179950
Number of successful extensions: 1344
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1321
Number of HSP's successfully gapped: 43
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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: 57 (25.6 bits)