RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033487
(118 letters)
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 204 bits (522), Expect = 2e-69
Identities = 79/118 (66%), Positives = 100/118 (84%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
++L +DFQHILR+LNTNVDGK+K+ +ALT+IKGIGRR A +VCKKA +D+ KRAGEL+
Sbjct: 3 LTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELT 62
Query: 61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
A E++ ++ ++ANP QFKIPDWFLNRQ+D KDGK S + SN LD KLR+DLERLKKIR
Sbjct: 63 AEEIEKIVEIIANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIR 120
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 134 bits (340), Expect = 7e-42
Identities = 44/114 (38%), Positives = 75/114 (65%)
Query: 5 ANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAEL 64
E+F++I+R+ T++DG + + +ALT IKGIGRR A + +K +D N + G LS E+
Sbjct: 2 MEEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEI 61
Query: 65 DNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
+ + + +P + IP W LNR+KDY+ G+ ++ + L + +R+D+ R+KKIR
Sbjct: 62 EKIEEALEDPAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIR 115
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 121 bits (306), Expect = 1e-36
Identities = 47/111 (42%), Positives = 75/111 (67%), Gaps = 1/111 (0%)
Query: 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
+F++I+R+ +T++DG + + +ALT IKGIGRR A + +K VD N + G L E++ L
Sbjct: 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKL 60
Query: 68 MVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
V N ++ IP W LNR+KDY+ G+ ++ + LDM +R+D+ R+KKIR
Sbjct: 61 EEAVEN-YEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIR 110
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 94.6 bits (236), Expect = 1e-26
Identities = 48/105 (45%), Positives = 62/105 (59%), Gaps = 23/105 (21%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+LNTN+DG +KI ALT IKGIGRR AN + KKA VD +KR GEL+ E+D + +++N
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 74 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
VV N L K+R+D+ERLKKIR
Sbjct: 61 -----------------------YVVENDLRRKIRNDIERLKKIR 82
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 83.7 bits (208), Expect = 3e-22
Identities = 35/107 (32%), Positives = 55/107 (51%), Gaps = 22/107 (20%)
Query: 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71
+ R+ ++ G ++++ ALT I GIGRR A +CKKA +D +KR GEL+ E++ L
Sbjct: 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL---- 56
Query: 72 ANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIR 118
+D KY +V L ++R D++RL KI
Sbjct: 57 ----------------RDAIQNKY--LVEGDLRREVRMDIKRLMKIG 85
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13. This model
describes bacterial ribosomal protein S13, to the
exclusion of the homologous archaeal S13P and
eukaryotic ribosomal protein S18. This model identifies
some (but not all) instances of chloroplast and
mitochondrial S13, which is of bacterial type [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 50.6 bits (122), Expect = 2e-09
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ ++ +++ ALT I GIGR A + +KA +D +KR +L+ EL+ + +
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 48.2 bits (116), Expect = 3e-08
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ ++ ++++ ALT I GIGR A + A +D + R +L+ ELD + +
Sbjct: 3 RIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEIDK 62
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 32.7 bits (75), Expect = 0.016
Identities = 15/44 (34%), Positives = 27/44 (61%)
Query: 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
++I +ALT I GIG A + +KA++D + R +L+ ++ L
Sbjct: 13 KRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL 56
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 29.9 bits (68), Expect = 0.25
Identities = 15/62 (24%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65
E Q + R+ +N K+ + L + + +RLA ++ ++ +D + A +LS E+
Sbjct: 268 EELEQRLKRLRKSN--PKKTVKNILKGL--LPKRLAELLLEQLGIDPDLPAAQLSKKEIK 323
Query: 66 NL 67
L
Sbjct: 324 KL 325
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 28.7 bits (65), Expect = 0.61
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLM 68
F + +G + A+ + +KA +D NK+ EL+ EL+ L+
Sbjct: 261 FLVEEFSRVGDKTADEILEKAGLDPNKKPKELTREELERLV 301
>gnl|CDD|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 28.7 bits (65), Expect = 0.61
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
K+ + AL + + +RLA + ++A +D +K+ +LS +L L
Sbjct: 288 KKSLKNALAGL--LPKRLALFLLEQAGIDPDKKLAQLSKKDLAAL 330
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 28.4 bits (64), Expect = 0.86
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNL 67
+ + +G+ LA +C +A +D ELS + + L
Sbjct: 192 VQAFQGLSPLLAEELCYRAGLDKETPVEELSDEDWERL 229
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 27.6 bits (62), Expect = 1.2
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 10 QHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVC 45
+ I+ V L ++ G+GR+ AN+V
Sbjct: 65 RAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVL 100
>gnl|CDD|217966 pfam04209, HgmA, homogentisate 1,2-dioxygenase. Homogentisate
dioxygenase cleaves the aromatic ring during the
metabolic degradation of Phe and Tyr. Homogentisate
dioxygenase deficiency causes alkaptonuria. The
structure of homogentisate dioxygenase shows that the
enzyme forms a hexamer arrangement comprised of a dimer
of trimers. The active site iron ion is coordinated near
the interface between the trimers.
Length = 422
Score = 26.6 bits (59), Expect = 3.1
Identities = 8/22 (36%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 71 VANPRQFKIP-DWFLNRQKDYK 91
+ANPR FK P + + + Y
Sbjct: 213 LANPRDFKAPVAAYEDEETPYT 234
>gnl|CDD|225695 COG3153, COG3153, Predicted acetyltransferase [General function
prediction only].
Length = 171
Score = 26.1 bits (58), Expect = 3.9
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 10/57 (17%)
Query: 2 SLVANEDFQHILRVLNTNVD--GKQKIMFALTSI--------KGIGRRLANIVCKKA 48
SLVA +D + + +L + V G++ L + +GIG L +
Sbjct: 48 SLVAEDDGEVVGHILFSPVTVGGEELGWLGLAPLAVDPEYQGQGIGSALVREGLEAL 104
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 26.3 bits (58), Expect = 5.4
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 23 KQKIMFALTSIKGIGRRLAN 42
KQ I F +IKG G L
Sbjct: 747 KQIIRFGFNTIKGFGDELLK 766
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 25.8 bits (57), Expect = 7.9
Identities = 23/86 (26%), Positives = 33/86 (38%), Gaps = 10/86 (11%)
Query: 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQK 88
L G+G LA + +A +D A +L E+ + + P
Sbjct: 191 LLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEELLNPLKP------NY 244
Query: 89 DYKDGKYSQVVSNALDMKLRDDLERL 114
YKD KY VV +K DLE+L
Sbjct: 245 YYKDEKYLDVVP----LKAYADLEKL 266
>gnl|CDD|236130 PRK07914, PRK07914, hypothetical protein; Reviewed.
Length = 320
Score = 25.5 bits (56), Expect = 8.0
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 5/41 (12%)
Query: 29 ALTSIKGIGRRLANIVCKKADVDMNK-RAGELSAAELDNLM 68
A+ ++ R+ A ADV +++ RAG++S EL L+
Sbjct: 21 AVAAVLRSARQRAGT----ADVPVSRMRAGDVSTYELAELL 57
>gnl|CDD|133216 cd05085, PTKc_Fer, Catalytic domain of the Protein Tyrosine Kinase,
Fer. Protein Tyrosine Kinase (PTK) family; Fer kinase;
catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Fer kinase is a member
of the Fes subfamily of proteins which are cytoplasmic
(or nonreceptor) tyr kinases containing an N-terminal
region with FCH (Fes/Fer/CIP4 homology) and coiled-coil
domains, followed by a SH2 domain, and a C-terminal
catalytic domain. Fer kinase is expressed in a wide
variety of tissues, and is found to reside in both the
cytoplasm and the nucleus. It plays important roles in
neuronal polarization and neurite development,
cytoskeletal reorganization, cell migration, growth
factor signaling, and the regulation of cell-cell
interactions mediated by adherens junctions and focal
adhesions. Fer kinase also regulates cell cycle
progression in malignant cells.
Length = 250
Score = 25.3 bits (55), Expect = 8.2
Identities = 29/96 (30%), Positives = 40/96 (41%), Gaps = 17/96 (17%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
M LV DF LR + KQ + FAL + G+ L + C D L+
Sbjct: 71 MELVPGGDFLSFLRKKKDELKTKQLVKFALDAAAGMA-YLESKNCIHRD---------LA 120
Query: 61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYS 96
A +V KI D+ ++RQ+D DG YS
Sbjct: 121 ARN-----CLVGENNVLKISDFGMSRQED--DGIYS 149
>gnl|CDD|235564 PRK05691, PRK05691, peptide synthase; Validated.
Length = 4334
Score = 25.5 bits (56), Expect = 8.9
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 36 IGRRLANIVCKKADVDMNKR----AGEL 59
IGR L N++C+ D ++N AGEL
Sbjct: 1445 IGRPLGNVLCRVLDAELNLLPPGVAGEL 1472
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 25.1 bits (55), Expect = 10.0
Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 6/86 (6%)
Query: 36 IGRRLANIVCKKADV---DMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKD 92
+ LA + A+V D+++ A E + L +F D Q +D
Sbjct: 17 LTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENV---EFIQGDIEELPQLQLED 73
Query: 93 GKYSQVVSNALDMKLRDDLERLKKIR 118
+ V+SN + L D + L++I
Sbjct: 74 NSFDVVISNEVLNHLPDPDKVLEEII 99
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
0.321 0.136 0.381
Gapped
Lambda K H
0.267 0.0851 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,951,128
Number of extensions: 515210
Number of successful extensions: 521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 41
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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 (21.9 bits)
S2: 53 (24.0 bits)