RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16211
(340 letters)
>gnl|CDD|223733 COG0661, AarF, Predicted unusual protein kinase [General function
prediction only].
Length = 517
Score = 209 bits (534), Expect = 2e-63
Identities = 87/330 (26%), Positives = 154/330 (46%), Gaps = 15/330 (4%)
Query: 1 MPQWQVEKVLVTELGPDWKSKLSSLDLKPFAAASIGQVHAGLLKDGTEVAMKIQYPGVAK 60
P + E+++ ELG + S + +P A+ASI QVH +LK G EVA+K+Q PG+ +
Sbjct: 104 FPFEEAERIIEEELGRPIEELFSEFEPEPIASASIAQVHRAVLKSGEEVAVKVQRPGIRE 163
Query: 61 GIESDIDNLIGVMKIWNVFPEGM---FLDNLVEVAKKELGWEVDYKREAECTRKFKELVE 117
IE+D+ L + ++ P G L +V+ +K L E+DY+REA +F+E +
Sbjct: 164 RIEADLKLLRRLARLIKRLPPGGRRLDLVEVVDEFEKRLREELDYRREAANAERFRENFK 223
Query: 118 PYPYYFVPTVIDELSTGQILTTELIEGVPVDQCVDLDYE--SRKHICKLVMELCLRELFQ 175
P +VP V E +T ++LT E I+G+ + L RK + +L++ LR+L +
Sbjct: 224 DDPDVYVPKVYWEYTTRRVLTMEWIDGIKISDIAALKSAGIDRKELAELLVRAFLRQLLR 283
Query: 176 FRYMQTDPNWSNFFYNKDTKQLILLDFGATRAYSKEFMDQYIQVIKAGADGDKDKVLTIS 235
+ DP+ N D +++LLDFG +F +++ A + D D+V +
Sbjct: 284 DGFFHADPHPGNILVRSD-GRIVLLDFGIVGRLDPKFRRYLAELLLAFLNRDYDRVAELH 342
Query: 236 RKMGFLTGYESKIMEEAHVNTVMILSEVFSEKIGEFDFGGQD------TTKRITELVPT- 288
++G++ + A + V L ++ + + E FG + L P
Sbjct: 343 VELGYVPPDTDRDPLAAAIRAV--LEPIYGKPLEEISFGEILDKLFEVARRFPMRLPPEL 400
Query: 289 ILNHRLCPPPEEIYSLHRKLSGVFLLCSKL 318
+L R E + ++ + L
Sbjct: 401 VLLQRTLLLVEGVGRQLDPRFNLWAVAQPL 430
>gnl|CDD|111949 pfam03109, ABC1, ABC1 family. This family includes ABC1 from yeast
and AarF from E. coli. These proteins have a nuclear or
mitochondrial subcellular location in eukaryotes. The
exact molecular functions of these proteins is not
clear, however yeast ABC1 suppresses a cytochrome b mRNA
translation defect and is essential for the electron
transfer in the bc 1 complex and E. coli AarF is
required for ubiquinone production. It has been
suggested that members of the ABC1 family are novel
chaperonins. These proteins are unrelated to the ABC
transporter proteins.
Length = 117
Score = 138 bits (350), Expect = 9e-41
Identities = 52/116 (44%), Positives = 67/116 (57%)
Query: 13 ELGPDWKSKLSSLDLKPFAAASIGQVHAGLLKDGTEVAMKIQYPGVAKGIESDIDNLIGV 72
ELG + + D +P AAASI QVH +LKDG EVA+K+Q PGV K I SD+ L +
Sbjct: 2 ELGAPVEEVFAEFDEEPIAAASIAQVHRAVLKDGEEVAVKVQRPGVKKRIRSDLKLLKFL 61
Query: 73 MKIWNVFPEGMFLDNLVEVAKKELGWEVDYKREAECTRKFKELVEPYPYYFVPTVI 128
KI F G LD LV+ +K L E+D+ REA KF+E P+ +VP V
Sbjct: 62 AKILKKFFPGFDLDWLVDEFRKSLPQELDFLREAANAEKFRENFADLPWVYVPKVY 117
>gnl|CDD|233667 TIGR01982, UbiB, 2-polyprenylphenol 6-hydroxylase. This model
represents the enzyme (UbiB) which catalyzes the first
hydroxylation step in the ubiquinone biosynthetic
pathway in bacteria. It is believed that the reaction is
2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This
model finds hits primarily in the proteobacteria. The
gene is also known as AarF in certain species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 437
Score = 114 bits (287), Expect = 1e-28
Identities = 69/235 (29%), Positives = 113/235 (48%), Gaps = 6/235 (2%)
Query: 5 QVEKVLVTELGPDWKSKLSSLDLKPFAAASIGQVHAGLLKDGTEVAMKIQYPGVAKGIES 64
KV+ LG + + + KP AAASI QVH L DG EVA+K+ PG+ K I +
Sbjct: 100 VARKVIEAALGGPLEELFAEFEEKPLAAASIAQVHRARLVDGKEVAVKVLRPGIEKTIAA 159
Query: 65 DIDNLIGVMKIWNVF-PEGMFLD--NLVEVAKKELGWEVDYKREAECTRKFKELVEPYPY 121
DI L + +I P+ L +V+ +K L E+D +REA + E + P
Sbjct: 160 DIALLYRLARIVERLSPDSRRLRPTEVVKEFEKTLRRELDLRREAANASELGENFKNDPG 219
Query: 122 YFVPTVIDELSTGQILTTELIEGVPVD--QCVDLDYESRKHICKLVMELCLRELFQFRYM 179
+VP V + ++ ++LT E I+G+P+ +D RK + + + L ++ + +
Sbjct: 220 VYVPEVYWDRTSERVLTMEWIDGIPLSDIAALDEAGLDRKALAENLARSFLNQVLRDGFF 279
Query: 180 QTDPNWSNFFYNKDTKQLILLDFGATRAYSKEFMDQYIQVIKAGADGDKDKVLTI 234
D + N F KD K +I LDFG S+E +++ + D +V +
Sbjct: 280 HADLHPGNIFVLKDGK-IIALDFGIVGRLSEEDRRYLAEILYGFLNRDYRRVAEV 333
>gnl|CDD|235310 PRK04750, ubiB, putative ubiquinone biosynthesis protein UbiB;
Reviewed.
Length = 537
Score = 68.4 bits (168), Expect = 9e-13
Identities = 44/137 (32%), Positives = 66/137 (48%), Gaps = 16/137 (11%)
Query: 23 SSLDLKPFAAASIGQVHAGLLKD-GTEVAMKIQYPGVAKGIESDIDNLIGVMKIW--NVF 79
D+KP A+ASI QVH LKD G EV +K+ P + I++D+ L+ + W +
Sbjct: 120 DDFDIKPLASASIAQVHFARLKDNGREVVVKVLRPDILPVIDADL-ALMYRLARWVERLL 178
Query: 80 PEGMFLDNLVEVAK---KELGWEVDYKRE-AECT---RKFKELVEPYPYYFVPTVIDELS 132
P+G L EV K L E+D RE A + R F++ Y VP V +
Sbjct: 179 PDGRRL-KPREVVAEFEKTLHDELDLMREAANASQLRRNFEDSDMLY----VPEVYWDYC 233
Query: 133 TGQILTTELIEGVPVDQ 149
+ ++ E + G+PV
Sbjct: 234 SETVMVMERMYGIPVSD 250
>gnl|CDD|177251 MTH00208, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 628
Score = 33.4 bits (77), Expect = 0.16
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 174 FQFRYMQTDPNWSNFF 189
F YM DPN + FF
Sbjct: 126 FSHYYMSNDPNKNAFF 141
>gnl|CDD|100020 cd02191, FtsZ, FtsZ is a GTPase that is similar to the eukaryotic
tubulins and is essential for cell division in
prokaryotes. FtsZ is capable of polymerizing in a
GTP-driven process into structures similar to those
formed by tubulin. FtsZ forms a ring-shaped septum at
the site of bacterial cell division, which is required
for constriction of cell membrane and cell envelope to
yield two daughter cells.
Length = 303
Score = 32.5 bits (74), Expect = 0.28
Identities = 20/91 (21%), Positives = 27/91 (29%), Gaps = 20/91 (21%)
Query: 227 DKDKVLTISRKMGFLTGYESKIMEEAHVNTVMILSEV----------FSEKIGEFDFGG- 275
+K+ I K + +E V V L F++ D GG
Sbjct: 154 PNEKLRQIGEKASLEGAF--DHADEVLVRAVGGLFGAIEIEGEINVDFADVKNVMDGGGV 211
Query: 276 -------QDTTKRITELVPTILNHRLCPPPE 299
+D T R TE V L P E
Sbjct: 212 AMVGYGSEDVTNRATEAVRKAALGPLLLPCE 242
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 30.1 bits (67), Expect = 2.0
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 296 PPPEEIYSLHRKLSGVFLLCSKL 318
PPP YS+H S F LC +L
Sbjct: 262 PPPRRNYSVHSGYSAAFHLCGRL 284
>gnl|CDD|109709 pfam00662, Oxidored_q1_N, NADH-Ubiquinone oxidoreductase (complex
I), chain 5 N-terminus. This sub-family represents an
amino terminal extension of pfam00361. Only
NADH-Ubiquinone chain 5 and eubacterial chain L are in
this family. This sub-family is part of complex I which
catalyzes the transfer of two electrons from NADH to
ubiquinone in a reaction that is associated with proton
translocation across the membrane.
Length = 62
Score = 27.2 bits (61), Expect = 2.6
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 173 LFQFRYMQTDPNWSNFFY 190
L+ YM DPN + FF
Sbjct: 41 LYSIWYMSHDPNINRFFS 58
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 29.6 bits (67), Expect = 3.0
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 185 WSNFFYNKDTKQLILLDFGAT-----RAYSKEFMDQYIQVIKAGADGDKDKVLTISRKMG 239
W + F++ TK+ I + A RA+ + +D Q+ A + DK+K + + +
Sbjct: 239 WGDNFFDAKTKKWIKDETNAQGKKLKRAFCQFILDPICQLFDAVMNEDKEKYDKMLKSLN 298
Query: 240 F-LTGYESKIMEEAHVNTVM 258
LTG + ++ + + VM
Sbjct: 299 ISLTGEDKELTGKPLLKAVM 318
>gnl|CDD|199897 cd10911, LabA, LabA_like proteins. A well conserved group of
bacterial and archaeal proteins with no defined
function. LabA, a member from Synechococcus elongatus
PCC 7942, has been shown to play a role in
cyanobacterial circadian timing. It is required for
negative feedback regulation of the
autokinase/autophosphatase KaiC, a central component of
the circadian clock system. In particular, LabA seems
necessary for KaiC-dependent repression of gene
expression. LabA_like domains exhibit some similarity to
the NYN domain, a distant relative of the PIN-domain
nucleases.
Length = 155
Score = 27.5 bits (62), Expect = 6.5
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 82 GMFLD--NLVEVAKKELGWEVDYKREAECTRKFKELVEPYPY 121
+F+D NL A+ LGW++DY++ E + +ELV + Y
Sbjct: 4 AVFVDGANLYYAAR-NLGWKIDYEKLLEFAVRGRELVRAFAY 44
>gnl|CDD|227824 COG5537, IRR1, Cohesin [Cell division and chromosome partitioning].
Length = 740
Score = 28.3 bits (63), Expect = 6.8
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 203 GATRAYSKEFMDQYIQVIKAGAD---GDKDKVLTISRKMGFLTGYESKIME--------- 250
A R + + F D+ ++ ++ +D K L R +G L+ E I+
Sbjct: 349 DAIRRFVERFKDRILEFLRTDSDCVRICSIKSLCYLRILGVLSSSEILIVSSCMLDIIPD 408
Query: 251 ------EAHVNTVMILSEVFSEKIGEF 271
E+ + I +EV EKI
Sbjct: 409 SRENIVESVESICKIDAEVIKEKIPLA 435
>gnl|CDD|166230 PLN02589, PLN02589, caffeoyl-CoA O-methyltransferase.
Length = 247
Score = 27.7 bits (61), Expect = 9.9
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 102 YKREAECTRKFKELVEPYPYYFVPTVIDELSTGQIL 137
Y RE E ++ +EL +P+ + T DE GQ L
Sbjct: 39 YPREPESMKELRELTAKHPWNIMTTSADE---GQFL 71
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
0.321 0.139 0.416
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,541,600
Number of extensions: 1714251
Number of successful extensions: 1296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1289
Number of HSP's successfully gapped: 19
Length of query: 340
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 242
Effective length of database: 6,590,910
Effective search space: 1595000220
Effective search space used: 1595000220
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 (21.8 bits)
S2: 59 (26.4 bits)