RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy836
(122 letters)
>gnl|CDD|216695 pfam01780, Ribosomal_L37ae, Ribosomal L37ae protein family. This
ribosomal protein is found in archaebacteria and
eukaryotes. It contains four conserved cysteine residues
that may bind to zinc.
Length = 90
Score = 124 bits (313), Expect = 2e-38
Identities = 60/115 (52%), Positives = 72/115 (62%), Gaps = 25/115 (21%)
Query: 7 AKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCK 66
AKRTKKVGI G++GTRYGASLRK VKK+EI+QHAKYTC FCGK
Sbjct: 1 AKRTKKVGIAGRFGTRYGASLRKRVKKIEISQHAKYTCPFCGK----------------- 43
Query: 67 RIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVNE 121
D++KR VGIW C++C + AGGA+ T A +VR IRRLRE+ E
Sbjct: 44 --------DAVKRKAVGIWKCRKCGKTFAGGAYTPETPAGKTVRRTIRRLRELKE 90
>gnl|CDD|240332 PTZ00255, PTZ00255, 60S ribosomal protein L37a; Provisional.
Length = 90
Score = 121 bits (306), Expect = 2e-37
Identities = 64/114 (56%), Positives = 75/114 (65%), Gaps = 25/114 (21%)
Query: 7 AKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCK 66
AKRTKKVGITGKYGTRYGASLRK +KK+EI+QHAKY C FCGK ++KR VGIW C
Sbjct: 2 AKRTKKVGITGKYGTRYGASLRKQIKKIEISQHAKYFCPFCGKHAVKRQAVGIWRC---- 57
Query: 67 RIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVN 120
K CK+ VAGGAW +T AA++VRS IRRLR++
Sbjct: 58 ---------------------KGCKKTVAGGAWTLSTPAASTVRSTIRRLRKLK 90
>gnl|CDD|232904 TIGR00280, L37a, ribosomal protein L37a. This model finds
eukaryotic ribosomal protein L37a and its archaeal
orthologs. The nomeclature is tricky because eukaryotes
have proteins called both L37 and L37a [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 92
Score = 80.7 bits (199), Expect = 3e-21
Identities = 41/68 (60%), Positives = 51/68 (75%)
Query: 7 AKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCK 66
KRTKKVGITG++G RYG LR+ VKK+EI Q AKY C FCGK ++KR GIW+C++C
Sbjct: 2 MKRTKKVGITGRFGPRYGLKLRRQVKKIEIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCG 61
Query: 67 RIVAGGAW 74
AGGA+
Sbjct: 62 AKFAGGAY 69
>gnl|CDD|235183 PRK03976, rpl37ae, 50S ribosomal protein L37Ae; Reviewed.
Length = 90
Score = 80.4 bits (199), Expect = 4e-21
Identities = 31/69 (44%), Positives = 41/69 (59%)
Query: 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRC 65
RTKKVG G++G RYG +RK V +E AK+ C CG+ +KR GIW C++C
Sbjct: 1 MMSRTKKVGSAGRFGARYGRKIRKRVADIEEKMRAKHVCPVCGRPKVKRVGTGIWECRKC 60
Query: 66 KRIVAGGAW 74
AGGA+
Sbjct: 61 GAKFAGGAY 69
>gnl|CDD|224908 COG1997, RPL43A, Ribosomal protein L37AE/L43A [Translation,
ribosomal structure and biogenesis].
Length = 89
Score = 77.0 bits (190), Expect = 8e-20
Identities = 42/110 (38%), Positives = 56/110 (50%), Gaps = 25/110 (22%)
Query: 9 RTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68
+TKKVGI G++G RYG+ LR+ VK++E Q AK+ C FCG+
Sbjct: 3 KTKKVGIAGRFGPRYGSKLRRRVKEIEAQQRAKHVCPFCGR-----------------TT 45
Query: 69 VAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRSAIRRLRE 118
V KR GIW C++C AGGA+ T A +V+ IRR E
Sbjct: 46 V--------KRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVKRTIRREVE 87
>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 34.8 bits (81), Expect = 0.006
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 11/53 (20%)
Query: 27 LRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKR 79
LR +V + + + +Y C CG + R+ W C CK AW+++K
Sbjct: 341 LRDLVGEQ-LKRKPRYRCRNCGFTA--RTL--YWHCPSCK------AWETIKP 382
>gnl|CDD|224487 COG1571, COG1571, Predicted DNA-binding protein containing a
Zn-ribbon domain [General function prediction only].
Length = 421
Score = 29.2 bits (66), Expect = 0.54
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 31 VKKMEITQHAKYT-----CSFCGKDSMKRSCVGIWSCKRCKRI 68
++K ++ + A+Y C CG MK + + CK+C
Sbjct: 335 LEKFQVLKLARYERVNPVCPRCGG-RMKSAGRNGFRCKKCGTR 376
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 28.3 bits (64), Expect = 0.90
Identities = 17/82 (20%), Positives = 27/82 (32%), Gaps = 25/82 (30%)
Query: 23 YGASLRKMVKKMEI-----TQHAKYTCSFCGKDSMKRSC-------VGIWSCKRCKRIVA 70
G S R + K + + + C CGK++ R C ++ C RC
Sbjct: 603 AGGSTRDINKAAKYKGTIEVEIGRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRC----- 657
Query: 71 GGAWDSMKRSCVGIWSCKRCKR 92
V C++C R
Sbjct: 658 --------GIEVEEDECEKCGR 671
>gnl|CDD|216284 pfam01074, Glyco_hydro_38, Glycosyl hydrolases family 38 N-terminal
domain. Glycosyl hydrolases are key enzymes of
carbohydrate metabolism.
Length = 269
Score = 27.2 bits (61), Expect = 1.9
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 93 IVAGGAWVYNTTAATSVRSAIRRL 116
GG WV S S IR+L
Sbjct: 76 EPVGGGWVEPDENLPSGESLIRQL 99
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 27.4 bits (62), Expect = 2.2
Identities = 15/50 (30%), Positives = 19/50 (38%), Gaps = 19/50 (38%)
Query: 30 MVKKMEITQHAKYTCSFCGKDSMKRSCVGIWS--CKRCKRIVAGGAWDSM 77
M KK Y C CG +S K W C C GAW+++
Sbjct: 1 MAKKKTA-----YVCQECGAESPK------WLGRCPEC------GAWNTL 33
>gnl|CDD|185681 cd09286, NMNAT_Eukarya, Nicotinamide/nicotinate mononucleotide
adenylyltransferase, Eukaryotic.
Nicotinamide/nicotinate mononucleotide (NMN/
NaMN)adenylyltransferase (NMNAT). NMNAT represents the
primary bacterial and eukaryotic adenylyltransferases
for nicotinamide-nucleotide and for the deamido form,
nicotinate nucleotide. It is an indispensable enzyme in
the biosynthesis of NAD(+) and NADP(+).
Nicotinamide-nucleotide adenylyltransferase synthesizes
NAD via the salvage pathway, while nicotinate-nucleotide
adenylyltransferase synthesizes the immediate precursor
of NAD via the de novo pathway. Human NMNAT displays
unique dual substrate specificity toward both NMN and
NaMN, and can participate in both de novo and salvage
pathways of NAD synthesis. This subfamily consists
strictly of eukaryotic members and includes secondary
structural elements not found in all NMNATs.
Length = 225
Score = 26.5 bits (59), Expect = 3.3
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 88 KRCKRIVAGGAWVYNTTAATSVRSAIRR 115
K I W+ N ++T VR A+RR
Sbjct: 176 KYQDNIHLVKDWIPNDISSTKVRRALRR 203
>gnl|CDD|216588 pfam01586, Basic, Myogenic Basic domain. This basic domain is
found in the MyoD family of muscle specific proteins
that control muscle development. The bHLH region of the
MyoD family includes the basic domain and the
Helix-loop-helix (HLH) motif. The bHLH region mediates
specific DNA binding. With 12 residues of the basic
domain involved in DNA binding. The basic domain forms
an extended alpha helix in the structure.
Length = 84
Score = 25.1 bits (55), Expect = 5.1
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 59 IWSCKRCKR 67
+W+CK CKR
Sbjct: 70 MWACKACKR 78
Score = 25.1 bits (55), Expect = 5.1
Identities = 6/9 (66%), Positives = 8/9 (88%)
Query: 84 IWSCKRCKR 92
+W+CK CKR
Sbjct: 70 MWACKACKR 78
>gnl|CDD|188630 cd00408, DHDPS-like, Dihydrodipicolinate synthase family.
Dihydrodipicolinate synthase family. A member of the
class I aldolases, which use an active-site lysine which
stabilizes a reaction intermediate via Schiff base
formation, and have TIM beta/alpha barrel fold. The
dihydrodipicolinate synthase family comprises several
pyruvate-dependent class I aldolases that use the same
catalytic step to catalyze different reactions in
different pathways and includes such proteins as
N-acetylneuraminate lyase, MosA protein,
5-keto-4-deoxy-glucarate dehydratase,
trans-o-hydroxybenzylidenepyruvate hydratase-aldolase,
trans-2'-carboxybenzalpyruvate hydratase-aldolase, and
2-keto-3-deoxy- gluconate aldolase. The family is also
referred to as the N-acetylneuraminate lyase (NAL)
family.
Length = 281
Score = 26.0 bits (58), Expect = 5.7
Identities = 11/35 (31%), Positives = 12/35 (34%)
Query: 88 KRCKRIVAGGAWVYNTTAATSVRSAIRRLREVNEL 122
+ VAG V A S R AI R E
Sbjct: 57 EAVVEAVAGRVPVIAGVGANSTREAIELARHAEEA 91
>gnl|CDD|239124 cd02659, peptidase_C19C, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 334
Score = 26.1 bits (58), Expect = 5.8
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 26 SLRKMVKKMEITQHAKYTCSFCGK--DSMKRSC 56
SL V+ + KY C CGK D+ K C
Sbjct: 156 SLDAYVQGETLEGDNKYFCEKCGKKVDAEKGVC 188
>gnl|CDD|184563 PRK14195, PRK14195, camphor resistance protein CrcB; Provisional.
Length = 125
Score = 25.4 bits (56), Expect = 6.6
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 70 AGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRS 111
AGGA S+ R VG+ + + + G A+ + T A S
Sbjct: 9 AGGALGSVARYLVGVGALR-----LMGPAFPWGTLAVNVTGS 45
>gnl|CDD|219926 pfam08600, Rsm1, Rsm1-like. Rsm1 is a protein involved in mRNA
export from the nucleus.
Length = 91
Score = 25.1 bits (55), Expect = 7.2
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 74 WDSMKRSCVGIWSCKRCKRIVAGGAWVY 101
WD + +G+ SC C R + G W++
Sbjct: 9 WDGLPDGRLGLASCGTCFRRL--GLWMF 34
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This
protein is not related to archael radA any more than is
to other RecA-like NTPases. Sms has a role in
recombination and recombinational repair and is
responsible for the stabilization or processing of
branched DNA molecules.
Length = 372
Score = 25.7 bits (57), Expect = 7.4
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 14/40 (35%)
Query: 42 YTCSFCGKDSMKRSCVGIW--SCKRCKRIVAGGAWDSMKR 79
Y CS CG S K W C C G W+++
Sbjct: 1 YVCSECGYVSPK------WLGKCPEC------GEWNTLVE 28
>gnl|CDD|226175 COG3649, COG3649, CRISPR system related protein [Defense
mechanisms].
Length = 283
Score = 25.3 bits (55), Expect = 8.7
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRS 55
Q+K+ G+ G RY SL +K M I + T SF ++S +RS
Sbjct: 113 QSKKGMSSGVRGPVSIRYATSLHP-IKIMSI----QITASFNTENSKQRS 157
>gnl|CDD|214675 smart00462, PTB, Phosphotyrosine-binding domain,
phosphotyrosine-interaction (PI) domain. PTB/PI domain
structure similar to those of pleckstrin homology (PH)
and IRS-1-like PTB domains.
Length = 134
Score = 25.0 bits (55), Expect = 9.1
Identities = 10/64 (15%), Positives = 16/64 (25%), Gaps = 10/64 (15%)
Query: 32 KKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCK 91
K + +H SFC G + S + +C K +
Sbjct: 62 TKAVLHEHPLRRISFCAVGPDDLDVFGYI-ARDP---------GSSRFACHVFRCEKAAE 111
Query: 92 RIVA 95
I
Sbjct: 112 DIAL 115
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
0.324 0.132 0.430
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,855,981
Number of extensions: 453305
Number of successful extensions: 668
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 46
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)