RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6118
(660 letters)
>gnl|CDD|223733 COG0661, AarF, Predicted unusual protein kinase [General function
prediction only].
Length = 517
Score = 249 bits (637), Expect = 6e-75
Identities = 103/414 (24%), Positives = 191/414 (46%), Gaps = 18/414 (4%)
Query: 239 GVGTIAEVTRRTLGFGDSSLSVGTTLDSAF--INPANAERIVNTLCKVRGAALKIGQILS 296
+G + +T R +G + ++ + AER+ L ++ +K+GQILS
Sbjct: 21 LLGRLLRLTGRLALLLRLLSWLGKSKLASSEELREKRAERLRLALEELGPTFIKLGQILS 80
Query: 297 IQDSNVISPELQKAFERVRQSADFMPQWQVEKVLVTELGPDWKSKLSSLDLKPFAAASIG 356
+ +++ PE + +++ P + E+++ ELG + S + +P A+ASI
Sbjct: 81 TRP-DLVPPEYAEELAKLQDRVPPFPFEEAERIIEEELGRPIEELFSEFEPEPIASASIA 139
Query: 357 QVHAGLLKDGTEVAMKIQYPGVAKGIESDIDNLIGVMKIWNVFPEGM---FLDNLVEVAK 413
QVH +LK G EVA+K+Q PG+ + IE+D+ L + ++ P G L +V+ +
Sbjct: 140 QVHRAVLKSGEEVAVKVQRPGIRERIEADLKLLRRLARLIKRLPPGGRRLDLVEVVDEFE 199
Query: 414 KELGWEVDYKREAECTRKFKELVEPYPYYFVPTVIDELSTGQILTTELIEGVPVDQCVDL 473
K L E+DY+REA +F+E + P +VP V E +T ++LT E I+G+ + L
Sbjct: 200 KRLREELDYRREAANAERFRENFKDDPDVYVPKVYWEYTTRRVLTMEWIDGIKISDIAAL 259
Query: 474 DYE--SRKHICKLVMELCLRELFQFRYMQTDPNWSNFFYNKDTKQLILLDFGATRAYSKE 531
RK + +L++ LR+L + + DP+ N D +++LLDFG +
Sbjct: 260 KSAGIDRKELAELLVRAFLRQLLRDGFFHADPHPGNILVRSD-GRIVLLDFGIVGRLDPK 318
Query: 532 FMDQYIQVIKAGADGDKDKVLTISRKMGFLTGYESKIMEEAHVNTVMILSEVFSEKIGEF 591
F +++ A + D D+V + ++G++ + A + V L ++ + + E
Sbjct: 319 FRRYLAELLLAFLNRDYDRVAELHVELGYVPPDTDRDPLAAAIRAV--LEPIYGKPLEEI 376
Query: 592 DFGGQD------TTKRITELVPT-ILNHRLCPPPEEIYSLHRKLSGVFLLCSKL 638
FG + L P +L R E + ++ + L
Sbjct: 377 SFGEILDKLFEVARRFPMRLPPELVLLQRTLLLVEGVGRQLDPRFNLWAVAQPL 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 = 139 bits (352), Expect = 5e-39
Identities = 52/116 (44%), Positives = 67/116 (57%)
Query: 333 ELGPDWKSKLSSLDLKPFAAASIGQVHAGLLKDGTEVAMKIQYPGVAKGIESDIDNLIGV 392
ELG + + D +P AAASI QVH +LKDG EVA+K+Q PGV K I SD+ L +
Sbjct: 2 ELGAPVEEVFAEFDEEPIAAASIAQVHRAVLKDGEEVAVKVQRPGVKKRIRSDLKLLKFL 61
Query: 393 MKIWNVFPEGMFLDNLVEVAKKELGWEVDYKREAECTRKFKELVEPYPYYFVPTVI 448
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 = 127 bits (320), Expect = 2e-31
Identities = 77/289 (26%), Positives = 136/289 (47%), Gaps = 7/289 (2%)
Query: 271 PANAERIVNTLCKVRGAALKIGQILSIQDSNVISPELQKAFERVRQSADFMPQWQVEKVL 330
+ ER+ L ++ +K GQ LS + ++++ ++ + ++ KV+
Sbjct: 47 MSRGERLRLALEELGPTFIKFGQTLSTR-ADLLPADIAEELSLLQDRVPPFDFKVARKVI 105
Query: 331 VTELGPDWKSKLSSLDLKPFAAASIGQVHAGLLKDGTEVAMKIQYPGVAKGIESDIDNLI 390
LG + + + KP AAASI QVH L DG EVA+K+ PG+ K I +DI L
Sbjct: 106 EAALGGPLEELFAEFEEKPLAAASIAQVHRARLVDGKEVAVKVLRPGIEKTIAADIALLY 165
Query: 391 GVMKIWNVF-PEGMFLD--NLVEVAKKELGWEVDYKREAECTRKFKELVEPYPYYFVPTV 447
+ +I P+ L +V+ +K L E+D +REA + E + P +VP V
Sbjct: 166 RLARIVERLSPDSRRLRPTEVVKEFEKTLRRELDLRREAANASELGENFKNDPGVYVPEV 225
Query: 448 IDELSTGQILTTELIEGVPVD--QCVDLDYESRKHICKLVMELCLRELFQFRYMQTDPNW 505
+ ++ ++LT E I+G+P+ +D RK + + + L ++ + + D +
Sbjct: 226 YWDRTSERVLTMEWIDGIPLSDIAALDEAGLDRKALAENLARSFLNQVLRDGFFHADLHP 285
Query: 506 SNFFYNKDTKQLILLDFGATRAYSKEFMDQYIQVIKAGADGDKDKVLTI 554
N F KD K +I LDFG S+E +++ + D +V +
Sbjct: 286 GNIFVLKDGK-IIALDFGIVGRLSEEDRRYLAEILYGFLNRDYRRVAEV 333
>gnl|CDD|235310 PRK04750, ubiB, putative ubiquinone biosynthesis protein UbiB;
Reviewed.
Length = 537
Score = 70.7 bits (174), Expect = 1e-12
Identities = 58/196 (29%), Positives = 86/196 (43%), Gaps = 29/196 (14%)
Query: 290 KIGQILSI------QDSNVISPELQKAFERVRQSADFMPQWQVEKVLVTELGPDWKSKLS 343
K GQ+LS D I+ EL +RV F ++ LG +
Sbjct: 68 KFGQMLSTRRDLFPPD---IADELALLQDRV---PPFDGA-LARAIIEKALGGPVEEWFD 120
Query: 344 SLDLKPFAAASIGQVHAGLLKD-GTEVAMKIQYPGVAKGIESDIDNLIGVMKIW--NVFP 400
D+KP A+ASI QVH LKD G EV +K+ P + I++D+ L+ + W + P
Sbjct: 121 DFDIKPLASASIAQVHFARLKDNGREVVVKVLRPDILPVIDADL-ALMYRLARWVERLLP 179
Query: 401 EGMFLDNLVEVAK---KELGWEVDYKRE-AECT---RKFKELVEPYPYYFVPTVIDELST 453
+G L EV K L E+D RE A + R F++ Y VP V + +
Sbjct: 180 DGRRL-KPREVVAEFEKTLHDELDLMREAANASQLRRNFEDSDMLY----VPEVYWDYCS 234
Query: 454 GQILTTELIEGVPVDQ 469
++ E + G+PV
Sbjct: 235 ETVMVMERMYGIPVSD 250
>gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component.
Length = 463
Score = 35.9 bits (82), Expect = 0.063
Identities = 14/37 (37%), Positives = 25/37 (67%)
Query: 194 RAPGAPKPIPKAKNKPQLNPVAKQRKVPSSRLGRMVS 230
+AP +P P ++ +PQL P ++R+VP +RL + V+
Sbjct: 211 KAPSSPPPPKQSAKEPQLPPKERERRVPMTRLRKRVA 247
>gnl|CDD|177251 MTH00208, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 628
Score = 33.4 bits (77), Expect = 0.44
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 494 FQFRYMQTDPNWSNFF 509
F YM DPN + FF
Sbjct: 126 FSHYYMSNDPNKNAFF 141
>gnl|CDD|217197 pfam02711, Pap_E4, E4 protein. This is is a family of
Papillomavirus proteins, E4, coded for by ORF4. A splice
variant, E1--E4, exists but neither the function of E4
or E1--E4 is known.
Length = 95
Score = 29.6 bits (67), Expect = 1.6
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 99 EQDSQYSEPVDSTPIPQVQTSTPITATTTAT 129
+ DS + S P PQ T P T TTT +
Sbjct: 45 DSDSSSTTSPSSPPTPQPTTECPWTVTTTGS 75
>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 = 28.3 bits (64), Expect = 1.7
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 493 LFQFRYMQTDPNWSNFFY 510
L+ YM DPN + FF
Sbjct: 41 LYSIWYMSHDPNINRFFS 58
>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 = 31.0 bits (70), Expect = 1.8
Identities = 20/91 (21%), Positives = 27/91 (29%), Gaps = 20/91 (21%)
Query: 547 DKDKVLTISRKMGFLTGYESKIMEEAHVNTVMILSEV----------FSEKIGEFDFGG- 595
+K+ I K + +E V V L F++ D GG
Sbjct: 154 PNEKLRQIGEKASLEGAF--DHADEVLVRAVGGLFGAIEIEGEINVDFADVKNVMDGGGV 211
Query: 596 -------QDTTKRITELVPTILNHRLCPPPE 619
+D T R TE V L P E
Sbjct: 212 AMVGYGSEDVTNRATEAVRKAALGPLLLPCE 242
>gnl|CDD|173690 cd05599, STKc_NDR_like, Catalytic domain of Nuclear Dbf2-Related
kinase-like Protein Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), Nuclear Dbf2-Related
(NDR) kinase subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The NDR subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. NDR kinase contains an N-terminal regulatory
(NTR) domain and an insert within the catalytic domain
that contains an auto-inhibitory sequence. Like many
other AGC kinases, NDR kinase requires phosphorylation
at two sites, the activation loop (A-loop) and the
hydrophobic motif (HM), for activity. NDR kinases
regulate mitosis, cell growth, embryonic development,
and neurological processes. They are also required for
proper centrosome duplication. Higher eukaryotes contain
two NDR isoforms, NDR1 and NDR2. This subfamily also
contains fungal NDR-like kinases.
Length = 364
Score = 29.6 bits (67), Expect = 5.3
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 142 IDSESLERIKQIPFMKGVDPKTNLEKS-----KLGYKKAMELTKKKDAFAVVDEDVARAP 196
+ + + IK PF KGVD + E+ +L K++ T D F +D DV +P
Sbjct: 285 LGNNGVNEIKSHPFFKGVDWEHIRERPAPIIPEL---KSITDTSNFDDFEEIDLDVPTSP 341
Query: 197 GAPKPIPKAKN 207
G P+ K+K+
Sbjct: 342 GPPRGKIKSKD 352
>gnl|CDD|233050 TIGR00609, recB, exodeoxyribonuclease V, beta subunit. The RecBCD
holoenzyme is a multifunctional nuclease with potent
ATP-dependent exodeoxyribonuclease activity. Ejection of
RecD, as occurs at chi recombinational hotspots,
cripples exonuclease activity in favor of recombinagenic
helicase activity. All proteins in this family for which
functions are known are DNA-DNA helicases that are used
as part of an exonuclease-helicase complex (made up of
RecBCD homologs) that function to generate substrates
for the initiation of recombination and recombinational
repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1087
Score = 29.7 bits (67), Expect = 6.3
Identities = 11/50 (22%), Positives = 20/50 (40%)
Query: 9 LKGVLKGLQLVANAGIKHQTLEIQQKWTNSSFKSLASNLDQSLKSTSTTP 58
L +L+ L A ++ Q I +K + + L + L+ TP
Sbjct: 867 LHAILESLIFSQAADLEKQRNLIAEKLKKTGLEGWEPELQEWLEKMLNTP 916
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 29.6 bits (67), Expect = 6.8
Identities = 19/80 (23%), Positives = 38/80 (47%), Gaps = 6/80 (7%)
Query: 505 WSNFFYNKDTKQLILLDFGAT-----RAYSKEFMDQYIQVIKAGADGDKDKVLTISRKMG 559
W + F++ TK+ I + A RA+ + +D Q+ A + DK+K + + +
Sbjct: 239 WGDNFFDAKTKKWIKDETNAQGKKLKRAFCQFILDPICQLFDAVMNEDKEKYDKMLKSLN 298
Query: 560 F-LTGYESKIMEEAHVNTVM 578
LTG + ++ + + VM
Sbjct: 299 ISLTGEDKELTGKPLLKAVM 318
>gnl|CDD|193577 cd09888, NGN_Euk, Eukaryotic N-Utilization Substance G (NusG)
N-terminal (NGN) domain, including plant KTF1 (KOW
domain-containing Transcription Factor 1). The
N-Utilization Substance G (NusG) protein and its
eukaryotic homolog, Spt5, are involved in transcription
elongation and termination. NusG contains an NGN domain
at its N-terminus and Kyrpides Ouzounis and Woese (KOW)
repeats at its C-terminus. Spt5 forms an Spt4-Spt5
complex that is an essential RNA polymerase II
elongation factor. NusG was originally discovered as an
N-dependent antitermination enhancing activity in
Escherichia coli, and has a variety of functions such
as its involvement in RNA polymerase elongation and
Rho-termination in bacteria. Orthologs of the NusG gene
exist in all bacteria, but their functions and
requirements are different. Spt5-like is homologous to
the Spt5 proteins present in all eukaryotes, which is
unique as it encodes a protein with an additional long
carboxy-terminal extension that contains WG/GW motifs.
Spt5-like, or KTF1 (KOW domain-containing Transcription
Factor 1), is a RNA-directed DNA methylation (RdDM)
pathway effector in plants.
Length = 86
Score = 27.5 bits (62), Expect = 6.8
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 74 SSVVLDGVKAFVFKEAGSERDVSEF 98
S DG+K +++ EA E V +
Sbjct: 37 SVFARDGLKGYIYIEARKEAHVKDA 61
>gnl|CDD|182128 PRK09875, PRK09875, putative hydrolase; Provisional.
Length = 292
Score = 29.0 bits (65), Expect = 7.5
Identities = 24/97 (24%), Positives = 35/97 (36%), Gaps = 22/97 (22%)
Query: 237 GLGVGTIAEVTRRTLG---------FGDSSLSVGTT---LDSAFINPANAERIVNTLCK- 283
GV + E+T R +G ++ ++V AF A R V L +
Sbjct: 45 TRGVRNVIEMTNRYMGRNAQFMLDVMRETGINVVACTGYYQDAFFPEHVATRSVQELAQE 104
Query: 284 --------VRGAALKIGQILSIQDSN-VISPELQKAF 311
+ G LK G I I S I+P +K F
Sbjct: 105 MVDEIEQGIDGTELKAGIIAEIGSSEGKITPLEEKVF 141
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 29.3 bits (65), Expect = 8.5
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 616 PPPEEIYSLHRKLSGVFLLCSKL 638
PPP YS+H S F LC +L
Sbjct: 262 PPPRRNYSVHSGYSAAFHLCGRL 284
>gnl|CDD|235322 PRK04950, PRK04950, ProP expression regulator; Provisional.
Length = 213
Score = 28.4 bits (64), Expect = 9.7
Identities = 14/59 (23%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 167 KSKLGYKKAMELTKKKDAFAVVDEDVARAPGAPKPIPKAKNKPQLNPVAKQRKVPSSRL 225
K+K+ ++A + KK++A E R PKP K + + + P S +
Sbjct: 107 KAKVQAQRAEQQAKKREAAGE-KEKAPRRERKPKPKAPRKKRKPRAQKPEPQHTPVSDI 164
>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 = 27.9 bits (63), Expect = 10.0
Identities = 15/42 (35%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 402 GMFLD--NLVEVAKKELGWEVDYKREAECTRKFKELVEPYPY 441
+F+D NL A+ LGW++DY++ E + +ELV + Y
Sbjct: 4 AVFVDGANLYYAAR-NLGWKIDYEKLLEFAVRGRELVRAFAY 44
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 0.133 0.379
Gapped
Lambda K H
0.267 0.0595 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,989,414
Number of extensions: 3247165
Number of successful extensions: 3037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3025
Number of HSP's successfully gapped: 27
Length of query: 660
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 557
Effective length of database: 6,369,140
Effective search space: 3547610980
Effective search space used: 3547610980
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: 62 (28.0 bits)