RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10530
(141 letters)
>gnl|CDD|185508 PTZ00194, PTZ00194, 60S ribosomal protein L26; Provisional.
Length = 143
Score = 164 bits (418), Expect = 2e-53
Identities = 84/122 (68%), Positives = 102/122 (83%), Gaps = 1/122 (0%)
Query: 16 LNKLVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHY 75
N +V+SSRRK RK HF APSH+RR++MSAPLSKELR KYNVRSMPVRKDDEV VVRGH+
Sbjct: 1 FNSIVSSSRRKARKAHFTAPSHLRRKLMSAPLSKELRAKYNVRSMPVRKDDEVMVVRGHH 60
Query: 76 KGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKMDKDRKKIIERR 135
KG++ GKV YRKK+VI+IEKI R+K NG V +GIHPS +I KLK++KDRK I+ER+
Sbjct: 61 KGRE-GKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITKLKLNKDRKAILERK 119
Query: 136 AK 137
A+
Sbjct: 120 AR 121
>gnl|CDD|130152 TIGR01080, rplX_A_E, ribosomal protein L24p/L26e,
archaeal/eukaryotic. This model represents the archaeal
and eukaryotic branch of the ribosomal protein L24p/L26e
family. Bacterial and organellar forms are represented
by related model TIGR01079 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 114
Score = 131 bits (331), Expect = 1e-40
Identities = 61/115 (53%), Positives = 84/115 (73%), Gaps = 2/115 (1%)
Query: 21 TSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQV 80
+ RK RK F AP H+RR++MSAPLSKELR+KY R++PVRK D+V+++RG +KG +
Sbjct: 1 SKQPRKQRKALFTAPLHVRRKLMSAPLSKELREKYGKRALPVRKGDKVRIMRGDFKGHE- 59
Query: 81 GKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKMDKD-RKKIIER 134
GKV + K++ IY+E + ++KVNG V V IHPS +I KL +D + RKKIIER
Sbjct: 60 GKVSKVDLKRYRIYVEGVTKEKVNGTEVPVPIHPSNVMITKLNLDDEKRKKIIER 114
>gnl|CDD|234915 PRK01191, rpl24p, 50S ribosomal protein L24P; Validated.
Length = 120
Score = 116 bits (292), Expect = 2e-34
Identities = 60/120 (50%), Positives = 85/120 (70%), Gaps = 2/120 (1%)
Query: 18 KLVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKG 77
++ RK RK +NAP H+R+++MSAPLSKELR+KY +RS+PVRK D V+V+RG +KG
Sbjct: 2 LTMSKQPRKQRKALYNAPLHLRQKLMSAPLSKELREKYGIRSLPVRKGDTVKVMRGDFKG 61
Query: 78 QQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKM-DKDRKKIIERRA 136
++ GKVV+ K+ IY+E + K +G V IHPS +I KL + D+ R+KI+ERRA
Sbjct: 62 EE-GKVVEVDLKRGRIYVEGVTVKKADGTEVPRPIHPSNVMITKLDLSDERREKILERRA 120
>gnl|CDD|240513 cd06089, KOW_RPL26, KOW motif of Ribosomal Protein L26. RPL26 and
its bacterial paralogs RPL24 have a KOW motif at their 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. RPL26 makes a very minor
contributions to the biogenesis, structure, and function
of 60s ribosomal subunits. However, RPL24 is essential
to generate the first intermediate during 50s ribosomal
subunits assembly. RPL26 have an extra-ribosomal
function to enhances p53 translation after DNA damage.
Length = 65
Score = 50.6 bits (122), Expect = 1e-09
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 12/66 (18%)
Query: 65 DDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVN-----------GATVYVGIH 113
DEVQV+RG KG+Q GKV++ RKK + +E + K + V IH
Sbjct: 1 GDEVQVIRGKDKGKQ-GKVLKVDRKKNRVIVEGVNVVKKHVKPSQENPQGGIIEVEAPIH 59
Query: 114 PSKCVI 119
S ++
Sbjct: 60 ISNVML 65
>gnl|CDD|223276 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
structure and biogenesis].
Length = 104
Score = 41.5 bits (98), Expect = 1e-05
Identities = 21/90 (23%), Positives = 33/90 (36%), Gaps = 16/90 (17%)
Query: 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGA----------- 106
M V+K D V+V+ G KG++ GKV++ KK + +E + K +
Sbjct: 1 MKMKVKKGDTVKVIAGKDKGKE-GKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGII 57
Query: 107 TVYVGIHPSKCVIVKLKM--DKDRKKIIER 134
IH S I+ R
Sbjct: 58 NKEAPIHISNVAIIDPNKTGKPTRVGYKVE 87
>gnl|CDD|144165 pfam00467, KOW, KOW motif. This family has been extended to
coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
motif is found in a variety of ribosomal proteins and
NusG.
Length = 32
Score = 30.1 bits (69), Expect = 0.037
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 64 KDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96
K D V+V+ G +KG++ GKVV+ K +++E
Sbjct: 1 KGDVVRVISGPFKGKK-GKVVEVDDSKARVHVE 32
>gnl|CDD|234566 PRK00004, rplX, 50S ribosomal protein L24; Reviewed.
Length = 105
Score = 29.3 bits (67), Expect = 0.30
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKI 98
M ++K D V V+ G KG++ GKV++ KK + +E +
Sbjct: 3 MKIKKGDTVIVIAGKDKGKR-GKVLKVLPKKNKVIVEGV 40
>gnl|CDD|237233 PRK12853, PRK12853, glucose-6-phosphate 1-dehydrogenase;
Provisional.
Length = 482
Score = 29.9 bits (68), Expect = 0.47
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 57 VRSMPVRKDDEVQVVRGHYK-GQQVGKVVQSYR 88
+R++ D+V VRG Y G G+ V YR
Sbjct: 266 LRAIRPLDPDDVHTVRGQYTAGTVGGEPVPGYR 298
>gnl|CDD|233412 TIGR01438, TGR, thioredoxin and glutathione reductase
selenoprotein. This homodimeric, FAD-containing member
of the pyridine nucleotide disulfide oxidoreductase
family contains a C-terminal motif Cys-SeCys-Gly, where
SeCys is selenocysteine encoded by TGA (in some sequence
reports interpreted as a stop codon). In some members of
this subfamily, Cys-SeCys-Gly is replaced by
Cys-Cys-Gly. The reach of the selenium atom at the
C-term arm of the protein is proposed to allow broad
substrate specificity.
Length = 484
Score = 28.7 bits (64), Expect = 1.2
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 10/66 (15%)
Query: 52 RQKYN---VRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATV 108
R +N + + +K++E +VV H G G+V Q + + K D
Sbjct: 400 RDNHNKCYAKLVCNKKENE-RVVGFHVVGPNAGEVTQGFAAALRCGLTKKDLDNT----- 453
Query: 109 YVGIHP 114
+GIHP
Sbjct: 454 -IGIHP 458
>gnl|CDD|128978 smart00739, KOW, KOW (Kyprides, Ouzounis, Woese) motif. Motif in
ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Length = 28
Score = 26.1 bits (59), Expect = 1.2
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89
D V+V+ G +KG+ GKV++ +
Sbjct: 1 KFEVGDTVRVIAGPFKGKV-GKVLEVDGE 28
>gnl|CDD|131943 TIGR02897, QoxC, cytochrome aa3 quinol oxidase, subunit III. This
family (QoxC) encodes subunit III of the aa3-type
quinone oxidase, one of several bacterial terminal
oxidases. This complex couples oxidation of reduced
quinones with the reduction of molecular oxygen to water
and the pumping of protons to form a proton gradient
utilized for ATP production. aa3-type oxidases contain
two heme a cofactors as well as copper atoms in the
active site [Energy metabolism, Electron transport].
Length = 190
Score = 28.3 bits (63), Expect = 1.3
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 74 HYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKM 124
HY + V + SY F + + +G V +GI + C++++++
Sbjct: 108 HYASEGVTPQIGSYWSSFFVLL------GTHGCHVTLGIVWAICLLIQIQR 152
>gnl|CDD|199841 cd03856, M14_Nna1_like, Peptidase M14-like domain of ATP/GTP
binding proteins, cytosolic carboxypeptidases and
related proteins. Peptidase M14-like domain of Nna-1
(Nervous system Nuclear protein induced by Axotomy),
also known as ATP/GTP binding protein (AGTPBP-1) and
cytosolic carboxypeptidase (CCP), and related proteins.
The Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This subfamily includes the human AGTPBP-1
and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1
and CCP -2 through -6. Nna1-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Nna1 is widely expressed in the developing and
adult nervous systems, including cerebellar Purkinje and
granule neurons, miral cells of the olfactory bulb and
retinal photoreceptors. Nna1 is also induced in
axotomized motor neurons. Mutations in Nna1 cause
Purkinje cell degeneration (pcd). The Nna1 CP domain is
required to prevent the retinal photoreceptor loss and
cerebellar ataxia phenotypes of pcd mice, and a
functional zinc-binding domain is needed for Nna-1 to
support neuron survival in these mice. Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a characteristic N-terminal
conserved domain right before the CP domain. It has been
suggested that this N-terminal domain might act as a
folding domain.
Length = 258
Score = 28.4 bits (63), Expect = 1.3
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 42 IMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVG 81
++ LS L +++N +P D V G+++ G
Sbjct: 81 LLDEALSTPLFERFNFLIVPDLNPD--GVETGNWRHNANG 118
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 28.3 bits (63), Expect = 1.6
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 78 QQVGKVVQSYRKKFVIYIEKIQRDKVNGA 106
QVGK + S ++ + + E VNG
Sbjct: 470 TQVGKTLASKGRRLIGWDEGAHGGDVNGT 498
>gnl|CDD|233263 TIGR01079, rplX_bact, ribosomal protein L24, bacterial/organelle.
This model recognizes bacterial and organellar forms
of ribosomal protein L24. It excludes eukaryotic and
archaeal forms, designated L26 in eukaryotes [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 104
Score = 26.9 bits (60), Expect = 1.9
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90
M ++K D V+V+ G KG++ GKV++ K
Sbjct: 2 MKIKKGDTVKVISGKDKGKR-GKVLKVLPKT 31
>gnl|CDD|226116 COG3588, COG3588, Fructose-1,6-bisphosphate aldolase
[Carbohydrate transport and metabolism].
Length = 332
Score = 27.5 bits (61), Expect = 2.8
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 3 AATRSSGTEVKMKLNKL----VTSSRRKNRKRHFNAPSHIRRRIMSAPLSKE-LRQK 54
AA S GT + + SRR R+R F +P + I+ A L +E + QK
Sbjct: 21 AADESGGT-TPKRFDSYGIEETEYSRRDMRERLFTSPDFMEDYILGAILFEETMDQK 76
>gnl|CDD|239869 cd04404, RhoGAP-p50rhoGAP, RhoGAP-p50rhoGAP: RhoGAP
(GTPase-activator protein [GAP] for Rho-like small
GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP,
also known as RhoGAP-1, contains a C-terminal RhoGAP
domain and an N-terminal Sec14 domain which binds
phosphatidylinositol 3,4,5-trisphosphate
(PtdIns(3,4,5)P3). It is ubiquitously expressed and
preferentially active on Cdc42. This subgroup also
contains closely related ARHGAP8. Small GTPases cluster
into distinct families, and all act as molecular
switches, active in their GTP-bound form but inactive
when GDP-bound. The Rho family of GTPases activates
effectors involved in a wide variety of developmental
processes, including regulation of cytoskeleton
formation, cell proliferation and the JNK signaling
pathway. GTPases generally have a low intrinsic GTPase
hydrolytic activity but there are family-specific
groups of GAPs that enhance the rate of GTP hydrolysis
by several orders of magnitude.
Length = 195
Score = 26.9 bits (60), Expect = 3.8
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 38 IRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQV 70
I RR + + KE++QKYN PV D V
Sbjct: 44 IFRRSANTQVVKEVQQKYN-MGEPVDFDQYEDV 75
>gnl|CDD|201202 pfam00392, GntR, Bacterial regulatory proteins, gntR family.
This family of regulatory proteins consists of the
N-terminal HTH region of GntR-like bacterial
transcription factors. At the C-terminus there is
usually an effector-binding/oligomerisation domain. The
GntR-like proteins include the following sub-families:
MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many
of these proteins have been shown experimentally to be
autoregulatory, enabling the prediction of operator
sites and the discovery of cis/trans relationships. The
DasR regulator has been shown to be a global regulator
of primary metabolism and development in Streptomyces
coelicolor.
Length = 64
Score = 24.9 bits (55), Expect = 6.1
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 8/36 (22%)
Query: 37 HIRRRIMSAPLS--------KELRQKYNVRSMPVRK 64
+R I+S L +EL ++ V VR+
Sbjct: 8 RLREDILSGRLRPGDKLPSERELAAEFGVSRTTVRE 43
>gnl|CDD|220943 pfam11017, DUF2855, Protein of unknown function (DUF2855). This
family of proteins has no known function.
Length = 314
Score = 26.4 bits (59), Expect = 6.2
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 26 KNRKRHFNAPSHIRRRI 42
+ F AP I++RI
Sbjct: 246 GPKPEFFFAPDQIQKRI 262
>gnl|CDD|217888 pfam04091, Sec15, Exocyst complex subunit Sec15-like.
Length = 311
Score = 26.1 bits (58), Expect = 6.6
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 32 FNAPSHIRRRIMSAPLSKELRQ 53
F A HI I+ LS E+++
Sbjct: 209 FRAFDHISESILDLLLSDEVKR 230
>gnl|CDD|199861 cd06237, M14_Nna1_like_3, Peptidase M14-like domain of ATP/GTP
binding proteins and cytosolic carboxypeptidases;
uncharacterized bacterial subgroup. A bacterial
subgroup of the Peptidase M14-like domain of Nna-1
(Nervous system Nuclear protein induced by Axotomy),
also known as ATP/GTP binding protein (AGTPBP-1) and
cytosolic carboxypeptidase (CCP),-like proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Nna1-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins (such as alpha-tubulin in eukaryotes) to remove
a C-terminal tyrosine. Nna1-like proteins from the
different phyla are highly diverse, but they all contain
a unique N-terminal conserved domain right before the CP
domain. It has been suggested that this N-terminal
domain might act as a folding domain.
Length = 245
Score = 25.9 bits (57), Expect = 7.8
Identities = 13/31 (41%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 46 PLSKELRQKYNVRSMPVRKDDEVQVVRGHYK 76
LSKE R+KYNV ++P D V++ G+++
Sbjct: 84 ALSKEFREKYNVLAIPNMNPDGVEL--GNWR 112
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
0.319 0.132 0.362
Gapped
Lambda K H
0.267 0.0941 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,997,853
Number of extensions: 626708
Number of successful extensions: 603
Number of sequences better than 10.0: 1
Number of HSP's gapped: 595
Number of HSP's successfully gapped: 41
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.2 bits)