RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy146
(253 letters)
>gnl|CDD|220534 pfam10036, RLL, Putative carnitine deficiency-associated protein.
This family of proteins conserved from nematodes to
humans is of approximately 250 amino acids. It is
purported to be carnitine deficiency-associated protein
but this could not be confirmed. It carries a
characteristic RLL sequence-motif. The function is
unknown.
Length = 245
Score = 240 bits (615), Expect = 4e-80
Identities = 119/251 (47%), Positives = 154/251 (61%), Gaps = 12/251 (4%)
Query: 7 IRKLKTLGYASPESFNPIREKEFRNMVVWLEDQKIRIYKIEDRAELRKLESPHWMNSFHQ 66
RKL LGY +P+ N KEFR++++WLEDQKIR+YKIEDR +LR ++S W + +
Sbjct: 3 RRKLAALGYPNPDLLNIDDPKEFRSLILWLEDQKIRLYKIEDREKLRNVDSADWTEALEK 62
Query: 67 YCTDVGLPITLLSTPLEQIEWLLGHASRLEYADNVDQYKSQTAEFVSSNQSSA-PKVVST 125
Y D+ +PI L T EQ++WLL A RLEY DN S + + S
Sbjct: 63 YLKDLEIPIDL-KTRQEQLDWLLSLAIRLEYKDNTQYDLSGARDLPEEESKRTKLQDDSA 121
Query: 126 NPLDNLNFDSPEFKKGVNSLAEKLKIRPHPNHLTTLEACCKLISARLNEDALA---HPEF 182
N L+F SPEF++GV +LA+ L I HP+HL L A CK+I RL+ +A A
Sbjct: 122 NDN--LDFTSPEFEEGVRALAKLLGIAHHPDHLVLLLAACKVIQERLSTEAKAENPIEGK 179
Query: 183 VIPKGKPFPFLEIDNGFTLPDPVLNKAAKILNLLYIHDLRDLQTKINEAIVAVQTVTANP 242
P+ K FP GF + D LN+AA+IL LL+I LR+LQTKINE +VAVQ +TANP
Sbjct: 180 PFPEDKLFPL-----GFDVGDAELNEAARILRLLHIEQLRELQTKINETLVAVQNLTANP 234
Query: 243 KTDTKLGKVGF 253
KTDTKLGKVG
Sbjct: 235 KTDTKLGKVGR 245
>gnl|CDD|179420 PRK02399, PRK02399, hypothetical protein; Provisional.
Length = 406
Score = 29.8 bits (68), Expect = 1.4
Identities = 30/111 (27%), Positives = 45/111 (40%), Gaps = 32/111 (28%)
Query: 120 PKVVSTNPLDNLNFDSPEFKKGVNSLAEKLKIRPHPNH-------LTTLEACCKL---IS 169
P+VVS LD +NF +P+ ++ EK + R H TT E ++ I+
Sbjct: 273 PQVVSPGALDMVNFGAPD------TVPEKFRGRLLYKHNPQVTLMRTTPEENRQIGRWIA 326
Query: 170 ARLNEDALAHPEFVIP---------KGKPFPFLEIDNGF------TLPDPV 205
+LN A F+IP G+PF E D F T+ +
Sbjct: 327 EKLNR-AKGPVAFLIPLGGVSALDRPGQPFHDPEADAAFFDALEETVTETR 376
>gnl|CDD|224484 COG1568, COG1568, Predicted methyltransferases [General function
prediction only].
Length = 354
Score = 29.4 bits (66), Expect = 2.0
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 10/86 (11%)
Query: 143 NSLAEKLKIRPHPNHLTTLEACCKLISARLNEDALAHPEF-VIPKGKPFPFLEIDNGFTL 201
LAE+L I+ ++ T E CC+ L +F I K +P P + D GF
Sbjct: 78 EELAEELGIKKKYDY--TCE-CCEGRGISLQAFKDLLEKFREIAKDRPEPLHQYDQGFVT 134
Query: 202 PDPVLNKAAKILNLLYIHDLRDLQTK 227
P+ +++ A ++ DL+ K
Sbjct: 135 PETTVSRVA------LMYSRGDLEGK 154
>gnl|CDD|234003 TIGR02768, TraA_Ti, Ti-type conjugative transfer relaxase TraA.
This protein contains domains distinctive of a single
strand exonuclease (N-terminus, MobA/MobL, pfam03389) as
well as a helicase domain (central region, homologous to
the corresponding region of the F-type relaxase TraI,
TIGR02760). This protein likely fills the same role as
TraI(F), nicking (at the oriT site) and unwinding the
coiled plasmid prior to conjugative transfer.
Length = 744
Score = 29.4 bits (66), Expect = 2.1
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 163 ACCKLISARL-------NEDALAHPEFVIPKGKPFPFLE 194
+ +L+ R+ +D +AH E V+P G P FLE
Sbjct: 27 SAARLVDERIGRVFDFTRKDGVAHSEIVLPDGAPDSFLE 65
>gnl|CDD|109609 pfam00559, Vif, Retroviral Vif (Viral infectivity) protein.
Human immunodeficiency virus type 1 (HIV-1) Vif is
required for productive infection of T lymphocytes and
macrophages. Virions produced in the absence of Vif
have abnormal core morphology and those produced in
primary T cells carry immature core proteins and low
levels of mature capsid.
Length = 192
Score = 28.5 bits (64), Expect = 2.3
Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 19/90 (21%)
Query: 25 REKEFRNMVVWLED-------QKIRIYKIEDRAELRKLESPHWMNSFHQY-CTDVGLPIT 76
EK + W + Y + +L+K H + C+ V +P+
Sbjct: 1 EEKRWIVRPTWRVPEMRIERWHSLVKYLMYRTKKLQKWFYRHHYQITWAWTCSRVIIPLG 60
Query: 77 LLS---------TPLEQIEWLLGHASRLEY 97
TP E+ WL +A +++
Sbjct: 61 KGKLEVQGYWHLTP-ER-GWLSTYAVGIQW 88
>gnl|CDD|113132 pfam04349, MdoG, Periplasmic glucan biosynthesis protein, MdoG.
This family represents MdoG, a protein that is
necessary for the synthesis of periplasmic glucans. The
function of MdoG remains unknown. It has been suggested
that it may catalyze the addition of branches to a
linear glucan backbone.
Length = 484
Score = 28.7 bits (64), Expect = 3.3
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 14/90 (15%)
Query: 8 RKLKTLGYASPESFNPIREKEFRNMVVWLEDQKIRIYKIEDRAELRKLESPHWMNSFHQY 67
R L Y +P+S P + + + Q+IR +D A L++P + FHQ
Sbjct: 11 RALAGKPYHAPKSNLP---SPLERLS-YDDYQQIRF--RQDHAYWADLKTPFQLKFFHQ- 63
Query: 68 CTDVGLPITLLSTPLEQIEWLLGHASRLEY 97
GL TP++ E A L+Y
Sbjct: 64 ----GL---YFDTPVKINEVTATMAKELKY 86
>gnl|CDD|223040 PHA03311, PHA03311, helicase-primase subunit BBLF4; Provisional.
Length = 782
Score = 28.3 bits (64), Expect = 4.2
Identities = 15/57 (26%), Positives = 19/57 (33%), Gaps = 7/57 (12%)
Query: 64 FHQYCTDVGLPITLLSTPLEQIEWLLGHASRL-EYADNVDQYKSQTAEFVSSNQSSA 119
F +Y G P L +WL + RL Y+ DQ S S Q
Sbjct: 398 FEEYKELTGQP------SLTPEKWLRANLGRLSNYSQFRDQDMSAVRTEEHSAQGLT 448
>gnl|CDD|233048 TIGR00605, rad4, DNA repair protein rad4. All proteins in this
family for which functions are known are involved in
targeting nucleotide excision repair to specific regions
of the genome.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 = 713
Score = 27.5 bits (61), Expect = 8.1
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 14 GYASPESFNPIREKEFRNMV--VWLEDQKIRIYKIEDRAELRKLES 57
GY+ P I +EFR + W E ++I+ K +++ R L +
Sbjct: 648 GYSKPVLDGIIVCEEFREAIETAWEEIEQIQEEKEQEKHRKRALGN 693
>gnl|CDD|130290 TIGR01223, Pmev_kin_anim, phosphomevalonate kinase, animal type.
This enzyme is part of the mevalonate pathway, one of
two alternative pathways for the biosynthesis of IPP.
In an example of nonorthologous gene displacement, two
different types of phosphomevalonate kinase are found.
One is this type, found in animals. The other is the
ERG8 type, found in plants and fungi (TIGR01219) and in
Gram-positive bacteria (TIGR01220) [Central
intermediary metabolism, Other].
Length = 182
Score = 27.0 bits (59), Expect = 8.4
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 23 PIREKEFRNMVVWLEDQKIRIYKIEDRAELRKLESPHWMNS 63
+E ++M+ W E+++ R + + P W+ S
Sbjct: 57 TYKEAFRKDMIRWGEEKRQADPGFFCRKIVEGISQPIWLVS 97
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 0.134 0.395
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,873,476
Number of extensions: 1204799
Number of successful extensions: 1170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1167
Number of HSP's successfully gapped: 15
Length of query: 253
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 158
Effective length of database: 6,723,972
Effective search space: 1062387576
Effective search space used: 1062387576
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: 58 (26.4 bits)