RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2461
(462 letters)
>gnl|CDD|240520 cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6. RPL6
contains KOW motif that has an extra ribosomal role as
an oncogenic. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. .
Length = 152
Score = 174 bits (444), Expect = 6e-53
Identities = 78/137 (56%), Positives = 100/137 (72%), Gaps = 5/137 (3%)
Query: 176 HARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVI 235
R+LRSS+ PGT++IL+AG +GKR VFLKQL+SGLLLVTGPF +N +PLRRV+Q YVI
Sbjct: 1 KPRKLRSSITPGTVLILLAGRFRGKRVVFLKQLDSGLLLVTGPFKINGVPLRRVNQRYVI 60
Query: 236 ATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQK 295
ATST++DISGVKVP+ ND +F+R KK K+ +K + F + KK+ Y VS+ RK QK
Sbjct: 61 ATSTKVDISGVKVPK-LNDAYFKRKKK--KKKKKKEGE--FFEEKKKKYVVSEERKEDQK 115
Query: 296 DMDEQLLKVIKVHPEKK 312
+D LL IK P K
Sbjct: 116 AVDAALLAAIKKVPLLK 132
Score = 76.8 bits (190), Expect = 9e-17
Identities = 32/65 (49%), Positives = 40/65 (61%), Gaps = 12/65 (18%)
Query: 60 HARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL-----KKNRVNFF-------L 107
R+LRSS+ PGT++IL+AG +GKR VFLKQL+SGLLL K N V +
Sbjct: 1 KPRKLRSSITPGTVLILLAGRFRGKRVVFLKQLDSGLLLVTGPFKINGVPLRRVNQRYVI 60
Query: 108 ATRTV 112
AT T
Sbjct: 61 ATSTK 65
>gnl|CDD|216337 pfam01159, Ribosomal_L6e, Ribosomal protein L6e.
Length = 108
Score = 95.8 bits (239), Expect = 6e-24
Identities = 48/92 (52%), Positives = 66/92 (71%), Gaps = 4/92 (4%)
Query: 221 LNAMPLRRVHQNYVIATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRSLFAKRK 280
+N +PLRRV+Q YVIATST++DISGVKVPE ND +F+R KK K+ +K + FA++K
Sbjct: 1 INGVPLRRVNQRYVIATSTKVDISGVKVPEKINDEYFKREKK--KKKKKS-EGEFFAEKK 57
Query: 281 KRAYKVSKARKVMQKDMDEQLLKVIKVHPEKK 312
++ +VS+ RK QK +D LL IK HP+ K
Sbjct: 58 EK-KEVSEQRKADQKAVDAALLAAIKKHPDLK 88
>gnl|CDD|225074 COG2163, RPL14A, Ribosomal protein L14E/L6E/L27E [Translation,
ribosomal structure and biogenesis].
Length = 125
Score = 59.3 bits (144), Expect = 7e-11
Identities = 30/128 (23%), Positives = 59/128 (46%), Gaps = 6/128 (4%)
Query: 180 LRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATST 239
+R+SL+ G +V++ AG GK+ V +K ++ +L+TGP + +P RR++ ++ T
Sbjct: 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVLITGPKKVKGVPRRRINIKHLEPTDK 60
Query: 240 QLDISGVKVPEAANDHFF-RRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKARKVMQKDMD 298
+D+ A+D + + + +K R R + K +
Sbjct: 61 VIDL-----VRGASDEKVKKANEAAGVLAKLDKSAKNLETKKVREPLTDAERFKVMKLVK 115
Query: 299 EQLLKVIK 306
E+ L+V K
Sbjct: 116 EERLQVGK 123
Score = 33.5 bits (77), Expect = 0.057
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 64 LRSSLKPGTIVILVAGVHKGKRGVFLKQLESGLLL 98
+R+SL+ G +V++ AG GK+ V +K ++ +L
Sbjct: 1 MRASLEVGRVVVVTAGRFAGKKVVIVKIIDDNFVL 35
>gnl|CDD|240504 cd00380, KOW, KOW: an acronym for the authors' surnames (Kyrpides,
Ouzounis and Woese). KOW domain is known as an
RNA-binding motif that is shared so far among some
families of ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. The KOW motif contains an
invariants glycine residue and comprises alternating
blocks of hydrophilic and hydrophobic residues.
Length = 49
Score = 34.5 bits (80), Expect = 0.007
Identities = 12/50 (24%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 187 GTIVILVAGVHKGKRGVFLKQLES-GLLLVTGPFALNAMPLRRVHQNYVI 235
G +V ++ G +KG+ GV + G++ V G +V + V
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSK-GAELKVRFDDVD 49
Score = 27.6 bits (62), Expect = 1.6
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 71 GTIVILVAGVHKGKRGVFLKQLESG 95
G +V ++ G +KG+ GV +
Sbjct: 1 GDVVRVLRGPYKGREGVVVDIDPRF 25
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 35.0 bits (80), Expect = 0.093
Identities = 36/142 (25%), Positives = 51/142 (35%), Gaps = 10/142 (7%)
Query: 49 KKVRGRRPFR-----KHARRLRSSLKPGTIVILVAGVHKGKRGVFLKQLES--GLLLKKN 101
+K RGR P R RLRS VA H G+ GV L GL K+
Sbjct: 284 RKARGRSPRRLIRSPPPPGRLRSPPPLHASDSPVASPHVGELGVNFSPLAFRPGLTRTKS 343
Query: 102 RVNFFLATRTVEKHSPHPNAHPKSPKPKKPIYKIKPIGGEKNGKERKVLIRKPKAY--YP 159
+E P + + ++ I K G E+K RK K + +
Sbjct: 344 LPRTPNPFHRLEYILPFNERDERESSTTRDVHVRGAIDIVK-GLEQKRQRRKEKFWRQHC 402
Query: 160 TKDKIKKVRGRRPFRKHARRLR 181
K + ++ R K A R+R
Sbjct: 403 RKARKEQAERRPIPGKGAERMR 424
>gnl|CDD|240514 cd06090, KOW_RPL27, KOW motif of eukaryotic Ribosomal Protein L27.
RPL27e has a KOW motif at its N terminal. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the essential
bacterial transcriptional elongation factor NusG, the
eukaryotic chromatin elongation factor Spt5, the higher
eukaryotic KIN17 proteins and Mtr4. .
Length = 83
Score = 30.6 bits (70), Expect = 0.31
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 185 KPGTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFAL 221
KPG +VI+++G + GK+ V +K + G AL
Sbjct: 1 KPGKVVIVLSGRYAGKKAVIVKNNDEGTKDRPYGHAL 37
Score = 29.8 bits (68), Expect = 0.51
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 69 KPGTIVILVAGVHKGKRGVFLKQLESG 95
KPG +VI+++G + GK+ V +K + G
Sbjct: 1 KPGKVVIVLSGRYAGKKAVIVKNNDEG 27
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 31.6 bits (72), Expect = 0.95
Identities = 15/74 (20%), Positives = 26/74 (35%), Gaps = 14/74 (18%)
Query: 274 SLFAKRKKRAYKVSKARKVMQKDMDEQLLKVIKVHPEKKI-----LLSYPPWGWINTRDF 328
+ FA +K + + AR +M D+ + V P+ K+ S +
Sbjct: 377 THFANKKCQDV-LVTARNLMTSDLH----NTVLVTPDSKVVKPKLPSSKAETKAQAKSER 431
Query: 329 ----NQKKLSVSPL 338
N+K LS
Sbjct: 432 LWLENEKHLSCLSF 445
>gnl|CDD|187705 cd09767, Csx17_I-U, CRISPR/Cas system-associated protein Csx17.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins; Predicted subunit of the Cascade
complex;.
Length = 652
Score = 31.2 bits (71), Expect = 1.3
Identities = 17/67 (25%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 3 AWTSAPVVY--LVIFQHLRPGHAKRTDQNLRQHYQEVESHLPPFLHRIKKVRGRRPFRKH 60
A TS P Y L + P R + +P L ++ R R
Sbjct: 584 ANTSLPRAYALLKLLFV--PDELLREALEVEIDRSLPRPPVPEVLALLQAQRVDRACELA 641
Query: 61 ARRLRSS 67
RRLR+S
Sbjct: 642 TRRLRAS 648
>gnl|CDD|206774 cd11369, RNase_PH_RRP43, RRP43 subunit of eukaryotic exosome. The
RRP43 subunit of eukaryotic exosome is a member of the
RNase_PH family, named after the bacterial Ribonuclease
PH, a 3'-5' exoribonuclease. Structurally all members of
this family form hexameric rings (trimers of
Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The
eukaryotic exosome core is composed of six individually
encoded RNase PH-like subunits and three additional
proteins (Rrp4, Csl4 and Rrp40) that form a stable cap
and contain RNA-binding domains. The RNase PH-like
subunits are no longer phosphorolytic enzymes, the
exosome directly associates with Rrp44 and Rrp6,
hydrolytic exoribonucleases related to bacterial RNase
II/R and RNase D. The exosome plays an important role in
RNA turnover. It plays a crucial role in the maturation
of stable RNA species such as rRNA, snRNA and snoRNA,
quality control of mRNA, and the degradation of RNA
processing by-products and non-coding transcripts.
Length = 261
Score = 30.2 bits (69), Expect = 1.9
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 13/58 (22%)
Query: 337 PLDTSANGKISPASSLPPSLMSRGGKLCSPDAKQGPGGPPG--MMSINEQIESMISRS 392
DT G + P LPP LCS + P GPP ++ + ++ S
Sbjct: 65 AADTPDEGYLVPNVDLPP--------LCSSKFR--P-GPPSEEAQVLSSFLADILLNS 111
>gnl|CDD|235283 PRK04333, PRK04333, 50S ribosomal protein L14e; Validated.
Length = 84
Score = 27.7 bits (62), Expect = 3.0
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 187 GTIVILVAGVHKGKRGVFLKQLESGLLLVTGPFALNAMPLRRVHQNYVIATSTQLDIS 244
G + + AG G++ V + ++ +LVTGP +L + RR + ++ T ++DI
Sbjct: 7 GRVCVKTAGREAGRKCVIVDIIDKNFVLVTGP-SLTGVKRRRCNIKHLEPTDKKVDIE 63
>gnl|CDD|234100 TIGR03067, Planc_TIGR03067, Planctomycetes uncharacterized domain
TIGR03067. This domain occurs in several species,
mostly from the Planctomycetes division of the bacteria.
It is expanded into a paralogous family of at least
twenty-five members in Gemmata obscuriglobus UQM 2246.
This family appears related to TIGR03066, which also is
expanded into a large paralogous family in Gemmata
obscuriglobus [Unknown function, General].
Length = 107
Score = 28.1 bits (63), Expect = 3.4
Identities = 20/81 (24%), Positives = 29/81 (35%), Gaps = 1/81 (1%)
Query: 136 KPIGGEKNGKERKVLIRKPKAYYPTKDKIKKVRGRRPFRKHARRLRSSLKPGTI-VILVA 194
K + EK GK + DK+ G K +L + P TI +
Sbjct: 12 KVVAAEKGGKAVPADKGDRLVWTFKGDKLTVKDGEGDQGKGTFKLDPAANPKTIDLTSPD 71
Query: 195 GVHKGKRGVFLKQLESGLLLV 215
G KGK + +L+ L V
Sbjct: 72 GPDKGKTIKGIYKLDGDTLTV 92
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 29.6 bits (67), Expect = 3.5
Identities = 14/75 (18%), Positives = 28/75 (37%), Gaps = 9/75 (12%)
Query: 378 MMSINEQIESMISRSTPNMYEQQAWKLRRALQQKEEEAHRKQSSPGAGGRYYGDPVPISP 437
++I+ +S S +++ ALQ A + S Y P +
Sbjct: 26 WIAIDPDSYLRLSASP-----AGRRQIKNALQM----AIIRMFSTKTALDYLAKPEVTAN 76
Query: 438 LDYVKNRIAEVMRTS 452
D +NRI +++ +
Sbjct: 77 FDIEENRIYQLLSLN 91
>gnl|CDD|200507 cd11246, Sema_plexin_C1, The Sema domain, a protein interacting
module, of Plexin C1. Plexins serve as semaphorin
receptors. Plexin C1 has been identified as the receptor
of semaphorin 7A, which plays regulation roles in both
the immune and nervous systems. Unlike other semaphorins
which act as repulsive guidance cues, Sema7A enhances
central and peripheral axon growth and is required for
proper axon tract formation during embryonic
development. Plexin C1 is a potential tumor suppressor
for melanoma progression. The expression of Plexin C1 is
diminished or absent in human melanoma cell lines.
Cofilin, an actin-binding protein involved in cell
migration, is a downstream target of Sema7A-Plexin C1
signaling. Cofilin is not phosphorylated when Plexin C1
expression is silenced. Thus, melanoma invasion and
metastasis may be promoted through the loss of Plexin C1
inhibitory signaling on cofilin activation. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a ligand-recognition and -binding
module.
Length = 401
Score = 29.5 bits (66), Expect = 3.6
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 4/53 (7%)
Query: 332 KLSVSPLDTSANGK----ISPASSLPPSLMSRGGKLCSPDAKQGPGGPPGMMS 380
+L+++ L G +S A P S+ +L P ++G GG G++
Sbjct: 30 ELALARLYRDQAGNCTEPVSLAPPARPRPGSQFSRLLLPYLREGAGGLSGLLL 82
>gnl|CDD|212674 cd10232, ScSsz1p_like_NBD, Nucleotide-binding domain of
Saccharmomyces cerevisiae Ssz1pp and similar proteins.
Saccharomyces cerevisiae Ssz1p (also known as
/Pdr13p/YHR064C) belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly and can direct incompetent "client"
proteins towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). Some
family members are not chaperones but rather, function
as NEFs for their Hsp70 partners, while other family
members function as both chaperones and NEFs. Ssz1 does
not function as a chaperone; it facilitates the
interaction between the HSP70 Ssb protein and its
partner J-domain protein Zuo1 (also known as zuotin) on
the ribosome. Ssz1 is found in a stable heterodimer
(called RAC, ribosome associated complex) with Zuo1.
Zuo1 can only stimulate the ATPase activity of Ssb, when
it is in complex with Ssz1. Ssz1 binds ATP but neither
nucleotide-binding, hydrolysis, or its SBD, is needed
for its in vivo function.
Length = 386
Score = 29.7 bits (67), Expect = 4.0
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 233 YVIATSTQLDISGVKVPEAANDHFFRRIKKHNKQPRKGDKRSLFAKRKKRAYKVSKA 289
++AT+ + G + +A HF + K K + + R+L AK + + K
Sbjct: 219 TILATAHDPGLGGDTLDDALVKHFAKEFTKKTKTDPRTNARAL-AKLRAESEITKKT 274
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 25.4 bits (57), Expect = 6.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 68 LKPGTIVILVAGVHKGKRGVFLK 90
+ G V ++AG KGK G L+
Sbjct: 2 FEVGDTVRVIAGPFKGKVGKVLE 24
Score = 25.4 bits (57), Expect = 6.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 184 LKPGTIVILVAGVHKGKRGVFLK 206
+ G V ++AG KGK G L+
Sbjct: 2 FEVGDTVRVIAGPFKGKVGKVLE 24
>gnl|CDD|239164 cd02763, MopB_2, The MopB_2 CD includes a group of related
uncharacterized bacterial molybdopterin-binding
oxidoreductase-like domains with a putative N-terminal
iron-sulfur [4Fe-4S] cluster binding site and
molybdopterin cofactor binding site. These members
belong to the molybdopterin_binding (MopB) superfamily
of proteins.
Length = 679
Score = 29.0 bits (65), Expect = 6.6
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 116 SPHPNAHPKSPKPKKPIYKIKPIG 139
P+P P PKP K KP
Sbjct: 341 PPYPRHIPPLPKPPKIPSADKPFT 364
>gnl|CDD|198079 smart01011, AMP_N, Aminopeptidase P, N-terminal domain. This
domain is structurally very similar to the creatinase
N-terminal domain. However, little or no sequence
similarity exists between the two families.
Length = 135
Score = 27.6 bits (62), Expect = 7.5
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 56 PFRKHARRLRSSLKPGTIVILVAG 79
+ RRL + L PG++ +L AG
Sbjct: 5 EYAARRRRLAAKLFPGSVAVLPAG 28
Score = 27.6 bits (62), Expect = 7.5
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 172 PFRKHARRLRSSLKPGTIVILVAG 195
+ RRL + L PG++ +L AG
Sbjct: 5 EYAARRRRLAAKLFPGSVAVLPAG 28
>gnl|CDD|233034 TIGR00584, mug, mismatch-specific thymine-DNA glycosylate (mug).
All proteins in this family for whcih functions are
known are G-T or G-U mismatch glycosylases that function
in base excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). Used 2pf model [DNA metabolism,
DNA replication, recombination, and repair].
Length = 328
Score = 28.5 bits (63), Expect = 7.7
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 121 AHPKSPKPKKPIYKIKPIGGEKNGKERKVLIRKPKAY--YPTKDKIKKVRGRR 171
P+S +P +P+ KP +K+GK K ++ K + K K+ + G
Sbjct: 62 RKPRSNEPYRPVEPKKPSDSKKSGKSTKSKEKQEKITDKFKVKRKVDRFNGVS 114
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 26.9 bits (60), Expect = 8.4
Identities = 30/108 (27%), Positives = 47/108 (43%), Gaps = 19/108 (17%)
Query: 68 LKPGTIVILVAGVHKGKRGVFLKQLESGLLLKKNRVNFFLATRTVEKHSPHPNAHPKSPK 127
+K G V ++AG KGK G LK L ++++ VN V+KH +P+
Sbjct: 5 VKKGDTVKVIAGKDKGKEGKVLKVLPKKVVVEG--VN------VVKKHIKPSQENPEGGI 56
Query: 128 PKK--PIY--KIKPIGGEKNGKERKVLIRKPKAYYPTKDKIKKVRGRR 171
K PI+ + I K GK +V + ++ KKVR +
Sbjct: 57 INKEAPIHISNVAIIDPNKTGKPTRVGYKV-------EEDGKKVRVAK 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
0.318 0.135 0.400
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,313,471
Number of extensions: 2411344
Number of successful extensions: 2644
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2634
Number of HSP's successfully gapped: 54
Length of query: 462
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 362
Effective length of database: 6,502,202
Effective search space: 2353797124
Effective search space used: 2353797124
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: 61 (27.2 bits)