RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15035
(816 letters)
>gnl|CDD|176393 cd01798, parkin_N, amino-terminal ubiquitin-like of parkin protein.
parkin_N parkin protein is a RING-type E3 ubiquitin
ligase with an amino-terminal ubiquitin-like (Ubl)
domain and an RBR signature consisting of two RING
finger domains separated by an IBR/DRIL domain.
Naturally occurring mutations in parkin are thought to
cause the disease AR_JP (autosomal-recessive juvenile
parkinsonism). Parkin binds the Rpn10 subunit of 26S
proteasomes through its Ubl domain.
Length = 70
Score = 100 bits (251), Expect = 8e-26
Identities = 36/70 (51%), Positives = 56/70 (80%)
Query: 607 INIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLG 666
+ +++NTG+T V +DP +DI+ +KE++A + G+ +++++IFAGKEL +TT I ECDLG
Sbjct: 1 VYVRTNTGHTFPVEVDPDTDIKQLKEVVAKRQGVPPDQLRVIFAGKELRNTTTIQECDLG 60
Query: 667 QQSILHAVKS 676
QQSILHAV+
Sbjct: 61 QQSILHAVRR 70
>gnl|CDD|149284 pfam08144, CPL, CPL (NUC119) domain. This C terminal domain is
fund in Penguin-like proteins associated with Pumilio
like repeats.
Length = 148
Score = 93.7 bits (233), Expect = 2e-22
Identities = 53/155 (34%), Positives = 78/155 (50%), Gaps = 14/155 (9%)
Query: 266 ANHEYGRKVIAHLVSWCDPGFFHPTCIAHVKSGDEFSTSKKDRDIRNKEILEAVSEPLLS 325
N +YGRKV+ +L+S DP FHP I +K GD + SKKD ++R KE+LEA+S PLL
Sbjct: 1 INDKYGRKVLLYLLSPRDPTHFHPEIIRLLKKGDGNAHSKKDTELRRKELLEAISPPLLE 60
Query: 326 SIAKDADFWLSTGSVAMVTAVILKNALGPGLKEAFDSVANVIVDLERRVPLELKKDFASG 385
IA+ A +S ++ + + IL +A G + A ++A V ++ G
Sbjct: 61 YIAEHAAELVSDKAICQLVSDILLSATGD-SQPAMAALAQVAA-----------QELVPG 108
Query: 386 NKNKQKKAAQQNKGGE--KNQTAQGKKGTEGKKEA 418
K+ + A+ G K Q KK E KE
Sbjct: 109 GKDGELHIAEHPAGHLVLKWLIEQDKKKKENGKEG 143
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which also
coordinate the ubls with their downstream pathways.
Length = 69
Score = 56.9 bits (138), Expect = 2e-10
Identities = 22/68 (32%), Positives = 37/68 (54%)
Query: 609 IKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLGQQ 668
+K+ TG T + + P + +K IA K G+ E+ ++I+AGK L+D +S+ +
Sbjct: 2 VKTLTGKTFELEVSPDDTVAELKAKIAAKEGVPPEQQRLIYAGKILKDDKTLSDYGIQDG 61
Query: 669 SILHAVKS 676
S LH V
Sbjct: 62 STLHLVLR 69
>gnl|CDD|176398 cd01803, Ubiquitin, Ubiquitin. Ubiquitin (includes Ubq/RPL40e and
Ubq/RPS27a fusions as well as homopolymeric
multiubiquitin protein chains).
Length = 76
Score = 52.6 bits (126), Expect = 7e-09
Identities = 26/70 (37%), Positives = 46/70 (65%)
Query: 605 LMINIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECD 664
+ I +K+ TG T+ + ++P+ I NVK I K G+ ++ ++IFAGK+LED +S+ +
Sbjct: 1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN 60
Query: 665 LGQQSILHAV 674
+ ++S LH V
Sbjct: 61 IQKESTLHLV 70
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 51.5 bits (124), Expect = 2e-08
Identities = 19/72 (26%), Positives = 39/72 (54%)
Query: 605 LMINIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECD 664
+ + +K+ G T+ + + P+ + +KE IA G+ E+ ++I+ GK LED +++
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYG 60
Query: 665 LGQQSILHAVKS 676
+ S +H V
Sbjct: 61 IQDGSTIHLVLR 72
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A number
of them are thought to carry a distinctive five-residue
motif termed the proteasome-interacting motif (PIM),
which may have a biologically significant role in
protein delivery to proteasomes and recruitment of
proteasomes to transcription sites.
Length = 69
Score = 51.1 bits (123), Expect = 2e-08
Identities = 24/67 (35%), Positives = 39/67 (58%)
Query: 610 KSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLGQQS 669
K+ G T+ + +DP+ + +KE I K G+ ++ ++IF+GK LED T +SE + S
Sbjct: 1 KTLDGKTITLEVDPSDTVSELKEKIEDKEGIPVDQQRLIFSGKVLEDDTTLSEYGIQDGS 60
Query: 670 ILHAVKS 676
LH V
Sbjct: 61 TLHLVLR 67
>gnl|CDD|153420 cd07920, Pumilio, Pumilio-family RNA binding domain. Puf repeats
(also labelled PUM-HD or Pumilio homology domain)
mediate sequence specific RNA binding in fly Pumilio,
worm FBF-1 and FBF-2, and many other proteins such as
vertebrate Pumilio. These proteins function as
translational repressors in early embryonic development
by binding to sequences in the 3' UTR of target mRNAs,
such as the nanos response element (NRE) in fly
Hunchback mRNA, or the point mutation element (PME) in
worm fem-3 mRNA. Other proteins that contain Puf domains
are also plausible RNA binding proteins. Yeast PUF1
(JSN1), for instance, appears to contain a single
RNA-recognition motif (RRM) domain. Puf repeat proteins
have been observed to function asymmetrically and may be
responsible for creating protein gradients involved in
the specification of cell fate and differentiation. Puf
domains usually occur as a tandem repeat of 8 domains.
This model encompasses all 8 tandem repeats. Some
proteins may have fewer (canonical) repeats.
Length = 322
Score = 48.4 bits (116), Expect = 8e-06
Identities = 57/287 (19%), Positives = 112/287 (39%), Gaps = 29/287 (10%)
Query: 11 SRIIQWLLKLSSPQMKKDIVKELLPFTVAMIKSKYSNALVKHMLKSGDENTKNEIIKALQ 70
SR +Q L+ ++P+ K+ I E+LP V ++ + N +++ + + G E + ++++ +
Sbjct: 22 SRFLQQKLEEATPEEKELIFDEILPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKIL 81
Query: 71 PHVVTLLSHTTASPVLMYAHDQVASPAQKLAMRQELYGGLYESTGD--------KKINCL 122
HVV L V+ + S Q + +EL G + E D K I
Sbjct: 82 GHVVRLSLDMYGCRVIQKLLE-SISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKF 140
Query: 123 GDIFEQSPEMKTAIL-SVTKKTILKSLQKTQVTGSALLHAVLLDFISHSSDSPDLMEVLE 181
PE I+ + + S G ++ L + S P L E+LE
Sbjct: 141 ------PPEDLQFIIDAFKGNCVALSTHPY---GCRVIQRCL-EHCSEEQREPLLEEILE 190
Query: 182 MLAPLPLLPFVHSKAGASVAMHIIWNATNKLKKKIVKELKGHLREVATSEFG-HLV--LV 238
L F G V H++ +I+++L G++ +++ +F ++V +
Sbjct: 191 HALELVQDQF-----GNYVVQHVLELGDPDDTSRIIEKLLGNIVQLSCHKFASNVVEKCL 245
Query: 239 TLLDNVDDTLLLKKALLPELLAEVVP-LANHEYGRKVIAHLVSWCDP 284
+ L++ + L + L +YG VI +
Sbjct: 246 KHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKE 292
Score = 41.4 bits (98), Expect = 0.001
Identities = 17/83 (20%), Positives = 41/83 (49%), Gaps = 6/83 (7%)
Query: 11 SRIIQWLLKLSSPQMKKDIVKELLPFTVA------MIKSKYSNALVKHMLKSGDENTKNE 64
S +++ LK +S + ++ I+ E+L ++K +Y N +++ L E +
Sbjct: 238 SNVVEKCLKHASKEERELIIDEILASGNETSALDTLMKDQYGNYVIQTALDVAKEEQREL 297
Query: 65 IIKALQPHVVTLLSHTTASPVLM 87
+++A++PH+ +L +L
Sbjct: 298 LVEAIRPHLPSLRKSPYGKHILA 320
Score = 32.9 bits (76), Expect = 0.64
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 2 GQIV-FSHDM--SRIIQWLLKLSSPQMKKDIVKELLPFTVAMIKSKYSNALVKHMLKSGD 58
G +V S DM R+IQ LL+ S + +VKEL V ++K + N +++ ++
Sbjct: 82 GHVVRLSLDMYGCRVIQKLLESISEEQISLLVKELRGHVVELVKDQNGNHVIQKCIEKFP 141
Query: 59 ENTKNEIIKALQPHVVTLLSH 79
II A + + V L +H
Sbjct: 142 PEDLQFIIDAFKGNCVALSTH 162
>gnl|CDD|185411 PTZ00044, PTZ00044, ubiquitin; Provisional.
Length = 76
Score = 44.0 bits (104), Expect = 9e-06
Identities = 19/70 (27%), Positives = 40/70 (57%)
Query: 605 LMINIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECD 664
+ I IK+ TG N +P + ++ VK + K G+ +++++I++GK++ D +S+
Sbjct: 1 MQILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYK 60
Query: 665 LGQQSILHAV 674
+ S +H V
Sbjct: 61 VVPGSTIHMV 70
>gnl|CDD|176401 cd01806, Nedd8, Nebb8-like ubiquitin protein. Nedd8 (also known
as Rub1) has a single conserved ubiquitin-like domain
that is part of a protein modification pathway similar
to that of ubiquitin. Nedd8 modifies a family of
molecular scaffold proteins called cullins that are
responsible for assembling the ROC1/Rbx1 RING-based E3
ubiquitin ligases, of which several play a direct role
in tumorigenesis.
Length = 76
Score = 44.0 bits (104), Expect = 9e-06
Identities = 18/70 (25%), Positives = 42/70 (60%)
Query: 605 LMINIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECD 664
++I +K+ TG + ++++P + +KE + K G+ ++ ++I++GK++ D ++
Sbjct: 1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDDKTAADYK 60
Query: 665 LGQQSILHAV 674
L S+LH V
Sbjct: 61 LEGGSVLHLV 70
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell cycle
progression. Other family members are protein modifiers
that perform a wide range of functions. Ubiquitination
usually results in a covalent bond between the
C-terminus of ubiquitin and the epsilon-amino group of a
substrate lysine. The three-step mechanism requires an
activating enzyme (E1) that forms a thiol ester with the
C-terminal carboxy group, a conjugating enzyme (E2) that
transiently carries the activated ubiquitin molecule as
a thiol ester, and a ligase (E3) that transfers the
activated ubiquitin from the E2 to the substrate lysine
residue. In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 43.3 bits (102), Expect = 1e-05
Identities = 20/67 (29%), Positives = 35/67 (52%)
Query: 609 IKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLGQQ 668
+K N G TV + + + + ++KE +A KLGL E+ +++ GK L D+ + + L
Sbjct: 2 VKLNDGKTVELLVPSGTTVADLKEKLAKKLGLPPEQQRLLVNGKILPDSLTLEDYGLQDG 61
Query: 669 SILHAVK 675
L V
Sbjct: 62 DELVLVP 68
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs to
a family of adaptor molecules having affinity for both
the proteasome and ubiquitinylated proteins and thought
to shuttle these ubiquitinylated proteins to the
proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 42.3 bits (100), Expect = 3e-05
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 607 INIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEE--VKIIFAGKELEDTTIISECD 664
I K+ T + +DP + +KE I + G Y K+I++GK L+D T + E
Sbjct: 3 ITFKTLKQQTFPIEVDPDDTVAELKEKIEEEKGCDYPPEQQKLIYSGKILKDDTTLEEYK 62
Query: 665 L 665
+
Sbjct: 63 I 63
>gnl|CDD|227410 COG5078, COG5078, Ubiquitin-protein ligase [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 41.1 bits (97), Expect = 5e-04
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 524 PRNFRLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRTSTTGHI 576
RLL+EL+ Q+ G IS G +DD++ HW I GPP T G I
Sbjct: 5 SALKRLLKELKKLQKDPPPG-ISAGPVDDDNLF--HWEATITGPPDTPYEGGI 54
>gnl|CDD|214562 smart00212, UBCc, Ubiquitin-conjugating enzyme E2, catalytic domain
homologues. Proteins destined for proteasome-mediated
degradation may be ubiquitinated. Ubiquitination follows
conjugation of ubiquitin to a conserved cysteine residue
of UBC homologues. This pathway functions in regulating
many fundamental processes required for cell
viability.TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 145
Score = 40.4 bits (95), Expect = 7e-04
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 3/43 (6%)
Query: 528 RLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRT 570
RLL+EL+ ++ G ++ +++++ L WTG I+GPP T
Sbjct: 1 RLLKELKELRKDPPPGFTAYPVDDEN---LLEWTGTIVGPPGT 40
>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein. Scythe
protein (also known as Bat3) is an apoptotic regulator
that is highly conserved in eukaryotes and contains a
ubiquitin-like domain near its N-terminus. Scythe binds
reaper, a potent apoptotic inducer, and Scythe/Reaper
are thought to signal apoptosis, in part through
regulating the folding and activity of apoptotic
signaling molecules.
Length = 72
Score = 36.4 bits (85), Expect = 0.003
Identities = 18/70 (25%), Positives = 38/70 (54%)
Query: 607 INIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLG 666
I +K+ T ++ + ++KE IA ++G+ E+ ++I++G+ L+D +SE +
Sbjct: 3 IKVKTLDSQTHTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYSGRVLKDDETLSEYKVE 62
Query: 667 QQSILHAVKS 676
+H VK
Sbjct: 63 DGHTIHLVKR 72
>gnl|CDD|227430 COG5099, COG5099, RNA-binding protein of the Puf family,
translational repressor [Translation, ribosomal
structure and biogenesis].
Length = 777
Score = 38.2 bits (89), Expect = 0.019
Identities = 28/90 (31%), Positives = 50/90 (55%), Gaps = 5/90 (5%)
Query: 11 SRIIQWLLKLSSPQMKKDIVKELLPFTVAMIKSKYSNALVKHMLKSGDE-NTKNEIIKAL 69
SR++Q L+ + + K+++V+E++ + + + +Y N +V+H+L +G E N + IIK L
Sbjct: 598 SRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDNGAEPNKERIIIKLL 657
Query: 70 QPHVVTLLSHTTAS----PVLMYAHDQVAS 95
VV L +H AS + YA D
Sbjct: 658 SKRVVELSTHKFASNVVEKCIKYASDSFKR 687
Score = 31.6 bits (72), Expect = 1.9
Identities = 59/278 (21%), Positives = 116/278 (41%), Gaps = 45/278 (16%)
Query: 11 SRIIQWLLKLSSPQMKKDIVKELLPFTVAMIKSKYSNALVKHMLKSGDENTKNEIIKALQ 70
SR +Q LL +S + I E+L V + + N L++ + + G E K+ ++
Sbjct: 453 SRFLQKLLDSNSSPEIEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSS 512
Query: 71 PHVVTLLSHTTASPVLMYAHDQVASPAQKLAMRQELYGGLYESTGDKKINCLGDIFEQSP 130
H+V+L H + VL A D V++ Q + +EL CL I +Q+
Sbjct: 513 KHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEELRP-----------YCLQLIKDQNG 561
Query: 131 EMKTAILSVTKKTILKSLQKTQVTGSALLHAVLLDFISHSSDSPDLMEVLEMLAPLPLLP 190
V +K I K + FI S + +L ++
Sbjct: 562 N------HVIQKCIEK------------FNKEKNQFIFDSI-NENLYDL----------- 591
Query: 191 FVHSKAGASVAMHIIWNATNKLKKKIVKELKGHLREVATSEFGHLVLVTLLDNVDDTLLL 250
+ G+ V + N ++ K+ +V+E+ + + ++ ++G+ V+ +LDN
Sbjct: 592 -STHRYGSRVVQRCLENCNSEDKENLVEEIISNSKYLSQDQYGNYVVQHILDN--GAEPN 648
Query: 251 KKALLPELLA-EVVPLANHEYGRKVIAHLVSWCDPGFF 287
K+ ++ +LL+ VV L+ H++ V+ + + F
Sbjct: 649 KERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFK 686
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N N-terminal
ubiquitin-like (Ubl) domain of the BAG1 protein. This
domain occurs together with the BAG domain and is
closely related to the Ubl domain of a family of
deubiquitinases that includes Rpn11, UBP6 (USP14), USP7
(HAUSP).
Length = 71
Score = 33.4 bits (77), Expect = 0.037
Identities = 13/51 (25%), Positives = 28/51 (54%)
Query: 619 VNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISECDLGQQS 669
+++ + ++K+M+AP G++ + K+IF GKE +D + + S
Sbjct: 14 LSISSQATFGDLKKMLAPVTGVEPRDQKLIFKGKERDDAETLDMSGVKDGS 64
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
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 = 378
Score = 36.8 bits (85), Expect = 0.043
Identities = 21/121 (17%), Positives = 44/121 (36%), Gaps = 15/121 (12%)
Query: 607 INIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGLKYEEV---KIIFAGKELEDTTIISEC 663
+ K+ ++++P ++ +KE I + G V K+I++GK L D + E
Sbjct: 3 LTFKTLQQQKFKIDMEPDETVKELKEKIEAEQGKDAYPVAQQKLIYSGKILSDDKTVKEY 62
Query: 664 DLGQQSILHAVKSSPENNKIQKSKPMNSTLTDFHIQELDEESARSSSPDITQEPVTPSKA 723
+ ++ + + S K K + SA + +P P +
Sbjct: 63 KIKEKDFVVVMVS--------KPKTGTGKVAPPAAT---PTSAPTPTPSPPASP-ASGMS 110
Query: 724 H 724
Sbjct: 111 A 111
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The small
ubiquitin-related modifier SUMO-1 is a Ub/Ubl family
member, and although SUMO-1 shares structural similarity
to Ub, SUMO's cellular functions remain distinct
insomuch as SUMO modification alters protein function
through changes in activity, cellular localisation, or
by protecting substrates from ubiquitination. Rad60
family members contain functionally enigmatic, integral
SUMO-like domains (SLDs). Despite their divergence from
SUMO, each Rad60 SLD interacts with a subset of SUMO
pathway enzymes: SLD2 specifically binds the SUMO E2
conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO
E1 (Fub2, also called Uba2) activating and E3 (Pli1,
also called Siz1 and Siz2) specificity enzymes.
Structural analysis of PDB:2uyz reveals a mechanistic
basis for the near-synonymous roles of Rad60 and SUMO in
survival of genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 32.9 bits (76), Expect = 0.075
Identities = 14/69 (20%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 607 INIKSNTGNTVCVNLDPASDIRNVKEMIAPKLGL-KYEEVKIIFAGKELEDTTIISECDL 665
I +K G V + + P + + + K G+ ++V++IF G+ L+ +++ D+
Sbjct: 3 IKLKGKDGKEVFIKVKPTTTLSKLINAYRKKRGIPADQQVRLIFDGERLDPNDTVADYDI 62
Query: 666 GQQSILHAV 674
+ V
Sbjct: 63 EDGDTIDVV 71
>gnl|CDD|179217 PRK01076, PRK01076, L-rhamnose isomerase; Provisional.
Length = 419
Score = 34.9 bits (81), Expect = 0.18
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 287 FHPTCIAHVKSGDEFSTSKKDRDIRN 312
F+PTC +H S D F+ S D +IR
Sbjct: 131 FNPTCFSHPLSADGFTLSHPDPEIRQ 156
>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like
domain. DDI1_N DDI1 (DNA damage inducible protein 1)
has an amino-terminal ubiquitin-like domain, an
retroviral protease-like (RVP-like) domain, and a UBA
(ubiquitin-associated) domain. This CD represents the
amino-terminal ubiquitin-like domain of DDI1.
Length = 71
Score = 31.6 bits (72), Expect = 0.21
Identities = 11/49 (22%), Positives = 25/49 (51%)
Query: 614 GNTVCVNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDTTIISE 662
T +++DP ++ N K + + G+ + ++I+ G+EL D +
Sbjct: 9 ETTFSLDVDPDLELENFKALCEAESGIPASQQQLIYNGRELVDNKRLLA 57
>gnl|CDD|214475 smart00025, Pumilio, Pumilio-like repeats. Pumilio-like repeats
that bind RNA.
Length = 36
Score = 29.7 bits (68), Expect = 0.34
Identities = 8/36 (22%), Positives = 19/36 (52%)
Query: 32 ELLPFTVAMIKSKYSNALVKHMLKSGDENTKNEIIK 67
+ + + K +Y N +V+ +L+ E+ + +II
Sbjct: 1 LIKGHLLELSKDQYGNRVVQKLLEHASESQREQIID 36
>gnl|CDD|133159 cd06095, RP_RTVL_H_like, Retropepsin of the RTVL_H family of human
endogenous retrovirus-like elements. This family
includes aspartate proteases from retroelements with LTR
(long terminal repeats) including the RTVL_H family of
human endogenous retrovirus-like elements. While fungal
and mammalian pepsins are bilobal proteins with
structurally related N- and C-termini, retropepsins are
half as long as their fungal and mammalian counterparts.
The monomers are structurally related to one lobe of the
pepsin molecule and retropepsins function as homodimers.
The active site aspartate occurs within a motif
(Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral
aspartyl protease is synthesized as part of the POL
polyprotein that contains an aspartyl protease, a
reverse transcriptase, RNase H, and an integrase. The
POL polyprotein undergoes specific enzymatic cleavage to
yield the mature proteins. In aspartate peptidases, Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 86
Score = 31.1 bits (71), Expect = 0.40
Identities = 14/62 (22%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 621 LDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELED--TTIISECDLGQQSILHAVKSSP 678
+D + +K + PK L V I + + TT + DLG ++ H+ P
Sbjct: 14 VDTGATHSVLKSDLGPKQELSTTSVLIRGVSGQSQQPVTTYRTLVDLGGHTVSHSFLVVP 73
Query: 679 EN 680
Sbjct: 74 NC 75
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 31.2 bits (71), Expect = 0.88
Identities = 12/55 (21%), Positives = 23/55 (41%)
Query: 371 ERRVPLELKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGKKEAGNEKEEE 425
+R + KK K KK ++ + + + ++G E K+E E E+
Sbjct: 88 AKRQKKKQKKKKKKKAKKGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIMEK 142
Score = 29.6 bits (67), Expect = 2.8
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 386 NKNKQKKAAQQNKGGEKNQTAQGKKGTEGKKEAGNEKEEET 426
K ++KK ++ K K + +K E +++EEE
Sbjct: 88 AKRQKKKQKKKKKKKAKKGNKKEEKEGSKSSEESSDEEEEG 128
>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2.
hPLIC-1 and hPLIC-2 (human homologs of the yeast
ubiquitin-like Dsk2 protein) are type2 UBL's
(ubiquitin-like) proteins that are thought to serve as
adaptors that link the ubiquitination machinery to the
proteasome. The hPLIC's have an N-terminal UBL domain
that binds the S5a subunit of the proteasome and a
C-terminal UBA (ubiquitin-associated) domain that binds
a ubiquitylated protein.
Length = 71
Score = 29.0 bits (65), Expect = 1.5
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 619 VNLDPASDIRNVKEMIAPKLGLKYEEVKIIFAGKELEDT 657
+ + + +++ KE ++ K E++ +IFAGK L+DT
Sbjct: 14 IEIAEDASVKDFKEAVSKKFKANQEQLVLIFAGKILKDT 52
>gnl|CDD|176409 cd01814, NTGP5, Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4
are plant-specific isoprenylated GTP-binding proteins
with a single fold that resembles ubiquitin. The
function of these proteins is unknown.
Length = 113
Score = 30.2 bits (68), Expect = 1.6
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 644 EVKIIFAGKELEDTTIISECDL------GQQSILHAVKSSP----ENNKIQKSKP 688
EVK+I AGK LE++ + EC G +H V P + K P
Sbjct: 52 EVKLISAGKILENSKTVGECRSPVGDIAGGVITMHVVVQPPLADKKTEKKVDKAP 106
>gnl|CDD|227143 COG4806, RhaA, L-rhamnose isomerase [Carbohydrate transport and
metabolism].
Length = 419
Score = 31.0 bits (70), Expect = 2.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 287 FHPTCIAHVKSGDEFSTSKKDRDIR 311
F+PTC +H S D F+ S D +IR
Sbjct: 131 FNPTCFSHPLSADGFTLSHPDDEIR 155
>gnl|CDD|130809 TIGR01748, rhaA, L-rhamnose isomerase. This enzyme interconverts
L-rhamnose and L-rhamnulose. In some species, including
E. coli, this is the first step in rhamnose catabolism.
Sequential steps are catalyzed by rhamnulose kinase
(rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to
yield glycerone phosphate and (S)-lactaldehyde.
Characterization of this family is based on members in
E. coli and Salmonella [Energy metabolism, Sugars].
Length = 414
Score = 31.0 bits (70), Expect = 2.6
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 287 FHPTCIAHVKSGDEFSTSKKDRDIRN 312
F+PTC +H S D F+ S D IR
Sbjct: 127 FNPTCFSHPLSADGFTLSHPDDSIRQ 152
>gnl|CDD|114011 pfam05262, Borrelia_P83, Borrelia P83/100 protein. This family
consists of several Borrelia P83/P100 antigen proteins.
Length = 489
Score = 31.1 bits (70), Expect = 2.6
Identities = 22/87 (25%), Positives = 31/87 (35%), Gaps = 6/87 (6%)
Query: 371 ERRVPLELKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGKKE----AGNEKEEET 426
+ K DFA N +KQ+ +Q + KN T KE A N+K E
Sbjct: 227 IDADKAQQKADFAQDNADKQRDEVRQKQQEAKN--LPKPADTSSPKEDKQVAENQKREIE 284
Query: 427 TPFIEHPGFHTVLKKLLQHDRDNVAKE 453
IE K H ++ +E
Sbjct: 285 KAQIEIKKNDEEALKAKDHKAFDLKQE 311
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.0 bits (71), Expect = 2.8
Identities = 26/130 (20%), Positives = 47/130 (36%), Gaps = 25/130 (19%)
Query: 302 STSKKDRDIRNKEILEAVSEPLLSSIAKDADFWLSTGSVAMVTAVILKNALGPGLKEAFD 361
S +K+ R+ R+ I + ++E L +S K ++ + P L F
Sbjct: 339 SKTKEKRETRDS-IAKKIAEKLHTSKRK------------------VRREVLPFLSIIFK 379
Query: 362 SVANVIVDLERRVPLE------LKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGK 415
+ L + L L + K K+ + K E+ + + K K
Sbjct: 380 HNPELAARLAAFLELTEEEIEFLTGSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKK 439
Query: 416 KEAGNEKEEE 425
KE E+E+E
Sbjct: 440 KEEEEEEEKE 449
>gnl|CDD|240415 PTZ00429, PTZ00429, beta-adaptin; Provisional.
Length = 746
Score = 31.1 bits (70), Expect = 2.9
Identities = 44/182 (24%), Positives = 74/182 (40%), Gaps = 27/182 (14%)
Query: 17 LLKLSSPQMKKDIVKEL--------LPFTVAMIKSKYSNALVKHMLKSGDENTKNEIIK- 67
LLKL +P + +I+KEL + F V ++++ S A+ + N +I+
Sbjct: 357 LLKLVTPSVAPEILKELAEYASGVDMVFVVEVVRAIASLAIKVDSVAPDCANLLLQIVDR 416
Query: 68 --ALQPHVVTLLSHTTAS-PVLM--------YAHDQVASPAQKLAMRQEL--YGGLYEST 114
L P VVT P L+ Y D+V K+++ L Y E+
Sbjct: 417 RPELLPQVVTAAKDIVRKYPELLMLDTLVTDYGADEVVEEEAKVSLLWMLGEYCDFIENG 476
Query: 115 GDKKINCLGDIFEQSPEMKTAILSVTKKTILKSLQKTQVTGSALLHAVLLDFISHSSDSP 174
D + I E ++ AILS K L+ Q + + +L+ ++ SD P
Sbjct: 477 KDIIQRFIDTIMEHEQRVQLAILSAAVKMFLRDPQGMEPQLN-----RVLETVTTHSDDP 531
Query: 175 DL 176
D+
Sbjct: 532 DV 533
>gnl|CDD|185035 PRK15076, PRK15076, alpha-galactosidase; Provisional.
Length = 431
Score = 30.6 bits (70), Expect = 3.8
Identities = 27/94 (28%), Positives = 38/94 (40%), Gaps = 23/94 (24%)
Query: 576 IMDTI-IGYIMSVLNEILHLFWISRK-----PDNTLMINIKSNTGNTVCVN---LDPASD 626
I DT+ IG IM L I L I PD L+ N N + +N ++
Sbjct: 108 IGDTLGIGGIMRALRTIPVLLDICEDMEEVCPDALLL-----NYVNPMAMNTWAMNRYPG 162
Query: 627 IRNV---------KEMIAPKLGLKYEEVKIIFAG 651
I+ V E +A LG+ EE++ AG
Sbjct: 163 IKTVGLCHSVQGTAEQLARDLGVPPEELRYRCAG 196
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.5 bits (68), Expect = 4.8
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 377 ELKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGKK--EAGNEKEEE 425
E K A K + + AA + + E+ A KK E KK +A +K EE
Sbjct: 1339 EEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEE 1389
Score = 29.7 bits (66), Expect = 7.9
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 371 ERRVPLELKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGKKEAGNEKEEE 425
E + E K A ++ + A ++ + EK + KK KK+A +K+ +
Sbjct: 1340 EAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKAD 1394
>gnl|CDD|191458 pfam06134, RhaA, L-rhamnose isomerase (RhaA). This family consists
of several bacterial L-rhamnose isomerase proteins
(EC:5.3.1.14).
Length = 417
Score = 29.8 bits (67), Expect = 5.8
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 287 FHPTCIAHVKSGDEFSTSKKDRDIRN 312
F+PT +H K+ D + + D++IR
Sbjct: 130 FNPTLFSHPKAADGLTLAHPDKEIRQ 155
>gnl|CDD|219025 pfam06430, L_lactis_RepB_C, Lactococcus lactis RepB C-terminus.
This family consists of the C-terminal region of RepB
proteins from Lactococcus lactis (See pfam01051).
Length = 122
Score = 28.6 bits (64), Expect = 5.9
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 30 VKELLPFTVAMIKSKYSNALVKHMLKSGDENTKNEIIKALQPHVVTL 76
E + AM KS Y+ L++H L S + T I+ LQ +V L
Sbjct: 25 ETEKDLYAEAM-KSPYTKLLMEHFLLSPYDMTDTAIMAGLQKNVYPL 70
>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein
complex aNOP56 subunit; Provisional.
Length = 414
Score = 29.9 bits (68), Expect = 5.9
Identities = 13/51 (25%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 369 DLERRVPLELKKDFASGNKNKQKKAAQQNKGGEKNQTAQGKKGTEGKKEAG 419
+L +R+ E+K+ + K K+++ Q + +K + KKG + KK+
Sbjct: 367 ELNKRIE-EIKEKYPKPPKKKREEKKPQKRKKKK---KRKKKGKKRKKKGR 413
>gnl|CDD|216298 pfam01101, HMG14_17, HMG14 and HMG17.
Length = 93
Score = 27.9 bits (62), Expect = 6.8
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 389 KQKKAAQQNKGGEKNQTAQGKKGTEGKKEAGNEKEEETTP 428
K KKAA +K +GKKG +GKKE E+ +E P
Sbjct: 37 KPKKAA----AKKKKPAVKGKKGAKGKKETKQEEAKEENP 72
>gnl|CDD|215772 pfam00179, UQ_con, Ubiquitin-conjugating enzyme. Proteins destined
for proteasome-mediated degradation may be
ubiquitinated. Ubiquitination follows conjugation of
ubiquitin to a conserved cysteine residue of UBC
homologues. TSG101 is one of several UBC homologues that
lacks this active site cysteine.
Length = 139
Score = 28.3 bits (64), Expect = 7.9
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 528 RLLEELEHGQRGVGDGTISWGLENDDDMTLTHWTGMIIGPPRT 570
RL +EL+ + G IS +D+ L W IIGP T
Sbjct: 1 RLQKELKELLKDPPPG-ISAFPVDDN---LFEWEVTIIGPEGT 39
>gnl|CDD|237349 PRK13321, PRK13321, pantothenate kinase; Reviewed.
Length = 256
Score = 29.1 bits (66), Expect = 8.6
Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 215 KIVKELKGHLREVATSEFGHLV--LVTLLDNVDDTLLLK 251
+I EL G R +AT F L+ D+VD LLL+
Sbjct: 207 RIKAELGGPPRVIATGGFASLIAKESRCFDHVDPDLLLE 245
>gnl|CDD|218228 pfam04720, DUF506, Protein of unknown function (DUF506). Family of
uncharacterized plant proteins.
Length = 218
Score = 29.0 bits (65), Expect = 8.8
Identities = 24/108 (22%), Positives = 50/108 (46%), Gaps = 15/108 (13%)
Query: 401 EKNQTAQGKKGTEGKKEAGNEKEEETTPFIEHPGFHTVLKKLLQ----HDRDNVAKELPT 456
+ N+T + + + ++ +E++EE + ++ LK LL+ +R
Sbjct: 11 DGNETVEDESFSGSGDDSSDEEDEEDSSSEDNGDVSDELKSLLECTLYRERYRR------ 64
Query: 457 LSESIVAKASKEVLDFWTKCNRACF---ILVLILESGMESCVSELKSK 501
E+ VA+A +E + NR+C ++ L+ E G ++ + KSK
Sbjct: 65 SLEAKVARAVEEASKHVSSGNRSCLRRKVMSLLRELGYDAAIC--KSK 110
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 29.5 bits (66), Expect = 9.4
Identities = 8/42 (19%), Positives = 18/42 (42%)
Query: 387 KNKQKKAAQQNKGGEKNQTAQGKKGTEGKKEAGNEKEEETTP 428
+ K A++ K + + K+ + +K+ EK +E
Sbjct: 88 PAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPK 129
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 0.383
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,465,030
Number of extensions: 3959949
Number of successful extensions: 3631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3617
Number of HSP's successfully gapped: 62
Length of query: 816
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 711
Effective length of database: 6,280,432
Effective search space: 4465387152
Effective search space used: 4465387152
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: 63 (28.0 bits)