RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032281
(144 letters)
>gnl|CDD|240326 PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional.
Length = 158
Score = 248 bits (636), Expect = 2e-86
Identities = 99/154 (64%), Positives = 109/154 (70%), Gaps = 13/154 (8%)
Query: 1 MAEQTEKAFLKQPG-------------KGGNRFWKSIGLGFKTPREAIEGTYIDKKCPFT 47
QTE+AF KQ G G R+WK +GLGFKTP+EAIEG YIDKKCPFT
Sbjct: 2 ADVQTERAFQKQEGVFQNSKRLLKKKTSKGVRYWKKVGLGFKTPKEAIEGKYIDKKCPFT 61
Query: 48 GTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGD 107
G VSIRGRIL G S KM RTII+RR+YLH+VKKY RYEKRH NIP H SPCF VKEGD
Sbjct: 62 GNVSIRGRILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFDVKEGD 121
Query: 108 HVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAF 141
V++GQCRPLSKTVRFNVLKV G +K F
Sbjct: 122 IVVVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQF 155
>gnl|CDD|236296 PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed.
Length = 108
Score = 137 bits (348), Expect = 4e-43
Identities = 54/108 (50%), Positives = 70/108 (64%), Gaps = 4/108 (3%)
Query: 22 KSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVK 81
++IGL K P E + D CPF GT+ +RG++L GT S KM++T++V R YLH+V
Sbjct: 1 RNIGLDVKPPEEECD----DPNCPFHGTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVP 56
Query: 82 KYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVI 129
KY+RYEKR S I AH PC K GD V I +CRPLSKT F V++
Sbjct: 57 KYERYEKRRSRIHAHNPPCIDAKVGDKVKIAECRPLSKTKSFVVVEKK 104
>gnl|CDD|132669 TIGR03630, arch_S17P, archaeal ribosomal protein S17P. This model
describes exclusively the archaeal ribosomal protein
S17P. It excludes the homologous ribosomal protein S17
from bacteria, and is not intended for use on eukaryotic
sequences, where some instances of ribosomal proteins
S11 score above the trusted cutoff [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 102
Score = 134 bits (339), Expect = 7e-42
Identities = 54/106 (50%), Positives = 68/106 (64%), Gaps = 4/106 (3%)
Query: 24 IGLGFKTPREAIEGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKY 83
IG+ K P D KCPF G + +RG+IL G S KMN+T++V R YL++ +KY
Sbjct: 1 IGIPVKPPERECN----DPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKY 56
Query: 84 QRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVI 129
+RYE+R S I AH PC VKEGD VIIG+ RPLSKT F VL +
Sbjct: 57 ERYERRRSKIHAHNPPCIDVKEGDIVIIGETRPLSKTKSFVVLGKV 102
>gnl|CDD|109426 pfam00366, Ribosomal_S17, Ribosomal protein S17.
Length = 69
Score = 109 bits (275), Expect = 1e-32
Identities = 39/70 (55%), Positives = 45/70 (64%), Gaps = 1/70 (1%)
Query: 59 GTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLS 118
G S KM +TI+VR L KY +YEKR PAH PCFR K GD V IG+CRPLS
Sbjct: 1 GVVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFR-KVGDVVKIGECRPLS 59
Query: 119 KTVRFNVLKV 128
KT RF V++V
Sbjct: 60 KTKRFRVVRV 69
>gnl|CDD|223264 COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 102 bits (257), Expect = 1e-29
Identities = 32/83 (38%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 47 TGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEG 106
G + +RGR+L G S KM++T++V + KY +Y +R AH C K G
Sbjct: 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAH-DECNEAKVG 59
Query: 107 DHVIIGQCRPLSKTVRFNVLKVI 129
D V I + RPLSKT RF V++++
Sbjct: 60 DIVRIAETRPLSKTKRFVVVEIV 82
>gnl|CDD|213841 TIGR03635, S17_bact, 30S ribosomal protein S17. This model
describes the bacterial ribosomal small subunit protein
S17, while excluding cytosolic eukaryotic homologs and
archaeal homologs. The model finds many, but not,
chloroplast and mitochondrial counterparts to bacterial
S17 [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 71
Score = 50.2 bits (121), Expect = 3e-09
Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 55 RILAGTCHSAKMNRTIIVR--RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112
+ L G S KM++TI+V R H Y + KR AH K GD V I
Sbjct: 2 KTLQGVVVSDKMDKTIVVLVERRVKH--PLYGKIVKRTKKYHAH-DENNECKVGDVVRII 58
Query: 113 QCRPLSKTVRFNV 125
+ RPLSKT R+ +
Sbjct: 59 ETRPLSKTKRWRL 71
>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed.
Length = 84
Score = 49.8 bits (120), Expect = 5e-09
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 55 RILAGTCHSAKMNRTIIVR--RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 112
+ L G S KM++TI+V R H Y + KR AH K GD V I
Sbjct: 7 KTLQGRVVSDKMDKTIVVLVERRVKH--PLYGKIVKRSKKYHAH-DENNEAKIGDVVRIM 63
Query: 113 QCRPLSKTVRFNVLKVI 129
+ RPLSKT R+ +++++
Sbjct: 64 ETRPLSKTKRWRLVEIV 80
>gnl|CDD|177064 CHL00142, rps17, ribosomal protein S17; Validated.
Length = 84
Score = 38.1 bits (89), Expect = 1e-04
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 59 GTCHSAKMNRTIIVR-------RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVII 111
G S KMN+TI+V Y + K ++Y H + C GD V+I
Sbjct: 8 GIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKY-LVHD----EENEC---NIGDQVLI 59
Query: 112 GQCRPLSKTVRFNVLKVIPAGSS 134
+ RPLSKT R+ + +++ S
Sbjct: 60 EETRPLSKTKRWILKEILSKSSL 82
>gnl|CDD|115526 pfam06875, PRF, Plethodontid receptivity factor PRF. This family
consists of several plethodontid receptivity factor
(PRF) proteins which seem to be specific to Plethodon
jordani (Jordan's salamander). PRF is a courtship
pheromone produced by males increase female receptivity.
Length = 214
Score = 28.6 bits (63), Expect = 0.97
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 45 PFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQ 84
PF G+ R ++ G R + +R++ +KYQ
Sbjct: 172 PFEGSAYFRKKLRGGVVCKEYKERVFLTKRDFEFLAEKYQ 211
>gnl|CDD|226189 COG3663, Mug, G:T/U mismatch-specific DNA glycosylase [DNA
replication, recombination, and repair].
Length = 169
Score = 27.8 bits (62), Expect = 1.7
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 17 GNRFWKSIGLGFKTPREAIEGTYIDKKCPFTGTVSIRGR 55
NRFW+ +GL F T + Y G + +RG
Sbjct: 34 RNRFWRVLGLVFFTDAQLEPQEYEKLLDYAKGFLKLRGI 72
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 27.7 bits (63), Expect = 2.9
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 23/71 (32%)
Query: 45 PFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIP--AHISPCFR 102
GTVS G+ G R I++ ++Y IP H+
Sbjct: 933 EIDGTVSF-GKETKG-------KRRIVIT-PDDGEEREYL--------IPKGKHL----L 971
Query: 103 VKEGDHVIIGQ 113
V+EGDHV G
Sbjct: 972 VQEGDHVEAGD 982
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 27.3 bits (61), Expect = 3.4
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 34 AIEGTYIDKKCPFTGTVSIRGRIL 57
A+E +D+ TG++S+RG +L
Sbjct: 523 ALENIPVDQSVAMTGSLSVRGDVL 546
>gnl|CDD|151285 pfam10836, DUF2574, Protein of unknown function (DUF2574). This
family of proteins appears to be restricted to
Enterobacteriaceae. Members of the family are annotated
as yehE however currently no function is known.
Length = 93
Score = 25.6 bits (56), Expect = 4.7
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 47 TGTVSIRGRILAGTCHSAKMN 67
T T++I GR+ A TC +N
Sbjct: 25 TATLTISGRVTAPTCSMDVVN 45
>gnl|CDD|132770 cd06860, PX_SNX7_30_like, The phosphoinositide binding Phox
Homology domain of Sorting Nexins 7 and 30. The PX
domain is a phosphoinositide (PI) binding module present
in many proteins with diverse functions. Sorting nexins
(SNXs) make up the largest group among PX domain
containing proteins. They are involved in regulating
membrane traffic and protein sorting in the endosomal
system. The PX domain of SNXs binds PIs and targets the
protein to PI-enriched membranes. SNXs differ from each
other in PI-binding specificity and affinity, and the
presence of other protein-protein interaction domains,
which help determine subcellular localization and
specific function in the endocytic pathway. Some SNXs
are localized in early endosome structures such as
clathrin-coated pits, while others are located in late
structures of the endocytic pathway. This subfamily
consists of SNX7, SNX30, and similar proteins. They
harbor a Bin/Amphiphysin/Rvs (BAR) domain, which detects
membrane curvature, C-terminal to the PX domain, similar
to the sorting nexins SNX1-2, SNX4-6, SNX8, and SNX32.
Both domains have been shown to determine the specific
membrane-targeting of SNX1. The specific function of the
sorting nexins in this subfamily has yet to be
elucidated.
Length = 116
Score = 25.8 bits (57), Expect = 5.7
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 55 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQ 113
R+ T S + VRR Y F+ Q+ E+ H P HI P K H + G
Sbjct: 22 RVTTKTTRSEFDSSEYSVRRRYQDFLWLRQKLEESH---PTHIIPPLPEK---HSVKGL 74
>gnl|CDD|188504 TIGR03989, Rxyl_3153, oxidoreductase, Rxyl_3153 family. This model
describes a clade within the family pfam00107 of
zinc-binding dehydrogenases. The family pfam00107
contains class III alcohol dehydrogenases, including
enzymes designated S-(hydroxymethyl)glutathione
dehydrogenase and NAD/mycothiol-dependent formaldehyde
dehydrogenase. Members of the current family occur only
in species that contain the very small protein
mycofactocin (TIGR03969), a possible cofactor precursor,
and radical SAM protein TIGR03962. We name this family
for Rxyl_3153, where the lone member of the family
co-clusters with these markers in Rubrobacter
xylanophilus [Unknown function, Enzymes of unknown
specificity].
Length = 369
Score = 26.5 bits (59), Expect = 6.0
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 6/24 (25%)
Query: 102 RVKEGDHVII------GQCRPLSK 119
VK GDHV++ G+CR S
Sbjct: 76 GVKPGDHVVLSFIPACGRCRWCST 99
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 26.5 bits (59), Expect = 6.6
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 20 FWKSIGLGFKTPREAIEG-----TYIDKKCPFTGT-VSIRGRILAGTCHSAKMNRTI 70
F K+IG+ K +E EG + + P +G +I+ + T + KM +T+
Sbjct: 103 FRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSGYGKTIKHGKI--TLKTTKMEKTL 157
>gnl|CDD|180789 PRK06997, PRK06997, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 260
Score = 26.3 bits (58), Expect = 6.6
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 3 EQTEKAF--LKQPGKGGNRFWKSIGLGFKTPREAIEGTYID 41
EQ + F L Q G + SIG PREAI G ++D
Sbjct: 69 EQIDALFASLGQHWDGLDGLVHSIGFA---PREAIAGDFLD 106
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
0.323 0.138 0.423
Gapped
Lambda K H
0.267 0.0606 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,355,101
Number of extensions: 648072
Number of successful extensions: 549
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 26
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.8 bits)