RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 032855
(132 letters)
>gnl|CDD|240326 PTZ00241, PTZ00241, 40S ribosomal protein S11; Provisional.
Length = 158
Score = 202 bits (516), Expect = 2e-68
Identities = 76/105 (72%), Positives = 82/105 (78%)
Query: 25 GTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAH 84
G YIDKKCPFTG VSIRGRIL G S KM RTII+RR+YLH+VKKY RYEKRH NIP H
Sbjct: 51 GKYIDKKCPFTGNVSIRGRILRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVH 110
Query: 85 ISPCFRVKEGDHVIIGQCRPLSKTVRFNVLKVIPAGSSGGAKKAF 129
SPCF VKEGD V++GQCRPLSKTVRFNVLKV G +K F
Sbjct: 111 CSPCFDVKEGDIVVVGQCRPLSKTVRFNVLKVEKNEIIGNVRKQF 155
>gnl|CDD|236296 PRK08572, rps17p, 30S ribosomal protein S17P; Reviewed.
Length = 108
Score = 131 bits (333), Expect = 4e-41
Identities = 48/89 (53%), Positives = 61/89 (68%)
Query: 29 DKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPC 88
D CPF GT+ +RG++L GT S KM++T++V R YLH+V KY+RYEKR S I AH PC
Sbjct: 16 DPNCPFHGTLPVRGQVLEGTVVSDKMHKTVVVEREYLHYVPKYERYEKRRSRIHAHNPPC 75
Query: 89 FRVKEGDHVIIGQCRPLSKTVRFNVLKVI 117
K GD V I +CRPLSKT F V++
Sbjct: 76 IDAKVGDKVKIAECRPLSKTKSFVVVEKK 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 = 130 bits (329), Expect = 1e-40
Identities = 50/89 (56%), Positives = 63/89 (70%)
Query: 29 DKKCPFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPC 88
D KCPF G + +RG+IL G S KMN+T++V R YL++ +KY+RYE+R S I AH PC
Sbjct: 14 DPKCPFHGHLKVRGQILEGVVVSDKMNKTVVVEREYLYYDRKYERYERRRSKIHAHNPPC 73
Query: 89 FRVKEGDHVIIGQCRPLSKTVRFNVLKVI 117
VKEGD VIIG+ RPLSKT F VL +
Sbjct: 74 IDVKEGDIVIIGETRPLSKTKSFVVLGKV 102
>gnl|CDD|109426 pfam00366, Ribosomal_S17, Ribosomal protein S17.
Length = 69
Score = 107 bits (268), Expect = 1e-31
Identities = 39/70 (55%), Positives = 45/70 (64%), Gaps = 1/70 (1%)
Query: 47 GTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQCRPLS 106
G S KM +TI+VR L KY +YEKR PAH PCFR K GD V IG+CRPLS
Sbjct: 1 GVVVSDKMEKTIVVRVERLVPHPKYGKYEKRTKKYPAHDPPCFR-KVGDVVKIGECRPLS 59
Query: 107 KTVRFNVLKV 116
KT RF V++V
Sbjct: 60 KTKRFRVVRV 69
>gnl|CDD|223264 COG0186, RpsQ, Ribosomal protein S17 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 101 bits (253), Expect = 3e-29
Identities = 32/83 (38%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 35 TGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEG 94
G + +RGR+L G S KM++T++V + KY +Y +R AH C K G
Sbjct: 1 HGKLRVRGRVLEGVVVSDKMDKTVVVEVERKVYHPKYGKYVRRSKKYHAH-DECNEAKVG 59
Query: 95 DHVIIGQCRPLSKTVRFNVLKVI 117
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 = 49.1 bits (118), Expect = 5e-09
Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 43 RILAGTCHSAKMNRTIIVR--RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 100
+ L G S KM++TI+V R H Y + KR AH K GD V I
Sbjct: 2 KTLQGVVVSDKMDKTIVVLVERRVKH--PLYGKIVKRTKKYHAH-DENNECKVGDVVRII 58
Query: 101 QCRPLSKTVRFNV 113
+ RPLSKT R+ +
Sbjct: 59 ETRPLSKTKRWRL 71
>gnl|CDD|235532 PRK05610, rpsQ, 30S ribosomal protein S17; Reviewed.
Length = 84
Score = 49.4 bits (119), Expect = 6e-09
Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 43 RILAGTCHSAKMNRTIIVR--RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIG 100
+ L G S KM++TI+V R H Y + KR AH K GD V I
Sbjct: 7 KTLQGRVVSDKMDKTIVVLVERRVKH--PLYGKIVKRSKKYHAH-DENNEAKIGDVVRIM 63
Query: 101 QCRPLSKTVRFNVLKVI 117
+ RPLSKT R+ +++++
Sbjct: 64 ETRPLSKTKRWRLVEIV 80
>gnl|CDD|177064 CHL00142, rps17, ribosomal protein S17; Validated.
Length = 84
Score = 36.9 bits (86), Expect = 2e-04
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 15/83 (18%)
Query: 47 GTCHSAKMNRTIIVR-------RNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVII 99
G S KMN+TI+V Y + K ++Y H + C GD V+I
Sbjct: 8 GIVVSNKMNKTIVVAVENRYKHPIYGKIITKTKKY-LVHD----EENEC---NIGDQVLI 59
Query: 100 GQCRPLSKTVRFNVLKVIPAGSS 122
+ RPLSKT R+ + +++ S
Sbjct: 60 EETRPLSKTKRWILKEILSKSSL 82
>gnl|CDD|221570 pfam12421, DUF3672, Fibronectin type III protein. This domain
family is found in bacteria and viruses, and is
typically between 126 and 146 amino acids in length.
The family is found in association with pfam09327,
pfam00041. There are two completely conserved G
residues that may be functionally important. Many of
the proteins in this family are annotated as
fibronectin type III however there is little
accompanying literature to confirm this.
Length = 130
Score = 28.2 bits (63), Expect = 0.79
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 3/45 (6%)
Query: 23 FSGTYIDKKCPFTGTV---SIRGRILAGTCHSAKMNRTIIVRRNY 64
F+ I + C GTV I G I+ S N T+I
Sbjct: 25 FNNVTIAENCTILGTVYAEKIEGDIVKAVGKSFSGNVTVIYIDPQ 69
>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 = 0.88
Identities = 10/40 (25%), Positives = 18/40 (45%)
Query: 33 PFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQ 72
PF G+ R ++ G R + +R++ +KYQ
Sbjct: 172 PFEGSAYFRKKLRGGVVCKEYKERVFLTKRDFEFLAEKYQ 211
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 28.1 bits (64), Expect = 1.5
Identities = 19/71 (26%), Positives = 26/71 (36%), Gaps = 23/71 (32%)
Query: 33 PFTGTVSIRGRILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIP--AHISPCFR 90
GTVS G+ G R I++ ++Y IP H+
Sbjct: 933 EIDGTVSF-GKETKG-------KRRIVIT-PDDGEEREYL--------IPKGKHL----L 971
Query: 91 VKEGDHVIIGQ 101
V+EGDHV G
Sbjct: 972 VQEGDHVEAGD 982
>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 = 26.9 bits (60), Expect = 3.6
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 6/24 (25%)
Query: 90 RVKEGDHVII------GQCRPLSK 107
VK GDHV++ G+CR S
Sbjct: 76 GVKPGDHVVLSFIPACGRCRWCST 99
>gnl|CDD|177014 CHL00075, rpl21, ribosomal protein L21.
Length = 108
Score = 25.2 bits (56), Expect = 6.4
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 16 RVLMSLCFSGTYIDKKCPFTGTVSIRGRILAGTCHSAKMNRTII 59
RVL+ S I K P+ +++GRIL H + + +
Sbjct: 39 RVLLIRNESEILIGK--PWLENATVKGRIL----HHFRGKKITV 76
>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 = 25.2 bits (55), Expect = 7.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 35 TGTVSIRGRILAGTCHSAKMN 55
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 = 25.4 bits (56), Expect = 7.9
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 6/59 (10%)
Query: 43 RILAGTCHSAKMNRTIIVRRNYLHFVKKYQRYEKRHSNIPAHISPCFRVKEGDHVIIGQ 101
R+ T S + VRR Y F+ Q+ E+ H P HI P K H + G
Sbjct: 22 RVTTKTTRSEFDSSEYSVRRRYQDFLWLRQKLEESH---PTHIIPPLPEK---HSVKGL 74
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 26.0 bits (58), Expect = 8.3
Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 6/21 (28%)
Query: 90 RVKEGDHVII------GQCRP 104
VK GDHV++ G CR
Sbjct: 74 GVKPGDHVVLSWIPACGTCRY 94
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
0.327 0.138 0.427
Gapped
Lambda K H
0.267 0.0637 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,578,514
Number of extensions: 564943
Number of successful extensions: 663
Number of sequences better than 10.0: 1
Number of HSP's gapped: 658
Number of HSP's successfully gapped: 22
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.4 bits)