RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031813
(152 letters)
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 266 bits (682), Expect = 3e-93
Identities = 108/152 (71%), Positives = 133/152 (87%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
++L +DFQHILR+LNTNVDGK+K+ +ALT+IKGIGRR A +VCKKA +D+ KRAGEL+
Sbjct: 3 LTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELT 62
Query: 61 AAELDNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNH 120
A E++ ++ ++ANP QFKIPDWFLNRQ+D KDGK S + SN LD KLR+DLERLKKIR H
Sbjct: 63 AEEIEKIVEIIANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLH 122
Query: 121 RGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
RGLRH+WGLRVRGQHTKTTGRRG+TVGVS+K+
Sbjct: 123 RGLRHHWGLRVRGQHTKTTGRRGRTVGVSRKK 154
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 181 bits (463), Expect = 5e-60
Identities = 65/148 (43%), Positives = 104/148 (70%)
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 DNLMVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLR 124
+ + + +P + IP W LNR+KDY+ G+ ++ + L + +R+D+ R+KKIR++RG+R
Sbjct: 62 EKIEEALEDPAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIR 121
Query: 125 HYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
H GL+VRGQ T++TGR G TVGVS+K+
Sbjct: 122 HELGLKVRGQRTRSTGRTGGTVGVSRKK 149
>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 = 166 bits (422), Expect = 8e-54
Identities = 70/145 (48%), Positives = 106/145 (73%), Gaps = 1/145 (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 MVVVANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYW 127
V N ++ IP W LNR+KDY+ G+ ++ + LDM +R+D+ R+KKIR++RG+RH
Sbjct: 61 EEAVEN-YEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHEL 119
Query: 128 GLRVRGQHTKTTGRRGKTVGVSKKR 152
GL+VRGQ TK+TGRRG+TVGVS+K+
Sbjct: 120 GLKVRGQRTKSTGRRGRTVGVSRKK 144
>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 = 136 bits (344), Expect = 2e-42
Identities = 63/129 (48%), Positives = 78/129 (60%), Gaps = 23/129 (17%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+LNTN+DG +KI ALT IKGIGRR AN + KKA VD +KR GEL+ E+D + +++N
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 74 PRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 133
VV N L K+R+D+ERLKKIR +RGLRH GL VRG
Sbjct: 61 -----------------------YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVRG 97
Query: 134 QHTKTTGRR 142
Q TKT R
Sbjct: 98 QRTKTNART 106
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 129 bits (328), Expect = 7e-40
Identities = 52/143 (36%), Positives = 76/143 (53%), Gaps = 24/143 (16%)
Query: 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVV 71
+ R+ ++ G ++++ ALT I GIGRR A +CKKA +D +KR GEL+ E++ L +
Sbjct: 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60
Query: 72 ANPRQFKIPDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRV 131
N +V L ++R D++RL KI +RG+RH GL V
Sbjct: 61 QN----------------------KYLVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPV 98
Query: 132 RGQHTKTTGRR--GKTVGVSKKR 152
RGQ TKT R G GV+KK+
Sbjct: 99 RGQRTKTNARTRKGPRKGVAKKK 121
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 69.3 bits (171), Expect = 4e-16
Identities = 47/143 (32%), Positives = 70/143 (48%), Gaps = 28/143 (19%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ ++ ++++ ALT I GIGR A + A +D + R +L+ ELD + +
Sbjct: 3 RIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI-- 60
Query: 74 PRQFKIPDWFLNRQKDYK-DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
K+YK +G + VS +++K RL I +RGLRH GL VR
Sbjct: 61 -------------DKNYKVEGDLRREVS--MNIK------RLMDIGCYRGLRHRRGLPVR 99
Query: 133 GQHTKTTGR--RG--KTVGVSKK 151
GQ TKT R +G KT+ KK
Sbjct: 100 GQRTKTNARTRKGPRKTIAGKKK 122
>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 = 68.3 bits (168), Expect = 9e-16
Identities = 43/129 (33%), Positives = 64/129 (49%), Gaps = 24/129 (18%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVAN 73
R+ ++ +++ ALT I GIGR A + +KA +D +KR +L+ EL+ + +
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEI-- 58
Query: 74 PRQFKIPDWFLNRQKDYK-DGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVR 132
+ YK +G + VS L++K RL I +RGLRH GL VR
Sbjct: 59 -------------EAKYKVEGDLRREVS--LNIK------RLMDIGCYRGLRHRRGLPVR 97
Query: 133 GQHTKTTGR 141
GQ TKT R
Sbjct: 98 GQRTKTNAR 106
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 49.3 bits (118), Expect = 2e-08
Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 26/132 (19%)
Query: 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDNLMVVVANPRQFKIPDWF 83
++I +ALT I GIG A + +KA++D + R +L+ ++ L ++
Sbjct: 13 KRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII------------ 60
Query: 84 LNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGR-- 141
+++Y+ V L +++RL +I +RG RH GL VRGQ T+T R
Sbjct: 61 ---EENYQ-------VEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRTRTNARTR 110
Query: 142 RG--KTVGVSKK 151
RG KTV KK
Sbjct: 111 RGAKKTVAGKKK 122
>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 = 0.53
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 = 1.1
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|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 = 28.7 bits (65), Expect = 1.2
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|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 28.3 bits (64), Expect = 1.5
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|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 = 1.8
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|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 27.0 bits (60), Expect = 2.7
Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 6/87 (6%)
Query: 36 IGRRLANIVCKKADV---DMNKRAGELSAAELDNLMVVVANPRQFKIPDWFLNRQKDYKD 92
+ LA + A+V D+++ A E + L +F D Q +D
Sbjct: 17 LTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENV---EFIQGDIEELPQLQLED 73
Query: 93 GKYSQVVSNALDMKLRDDLERLKKIRN 119
+ V+SN + L D + L++I
Sbjct: 74 NSFDVVISNEVLNHLPDPDKVLEEIIR 100
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 27.5 bits (61), Expect = 3.2
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 62 AELDNLMVVVANPRQFKI-PDWFLNRQKDYKDGKYSQVVSNALDMKLRDDLERLKKIRN 119
+LDNL++V+ NP ++ + + + +YK+ K + N L K D +++KKI N
Sbjct: 167 NDLDNLIIVLENPEKYNVRKTLYDEKFNEYKNKKEA--FYNCLKNKKEDYDKKIKKINN 223
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 27.5 bits (61), Expect = 3.9
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 23 KQKIMFALTSIKGIGRRLAN 42
KQ I F +IKG G L
Sbjct: 747 KQIIRFGFNTIKGFGDELLK 766
>gnl|CDD|237068 PRK12344, PRK12344, putative alpha-isopropylmalate/homocitrate
synthase family transferase; Provisional.
Length = 524
Score = 27.0 bits (61), Expect = 5.3
Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 25/67 (37%)
Query: 101 NALDMKLRDDLER----LKKIRNHRGLRHYWGLRVR----GQHT--KT--------TGRR 142
NALD LR LE+ L ++ L Y +VR G+ T RR
Sbjct: 438 NALDNALRKALEKFYPELAEVE----LVDY---KVRILDGGKGTAAVVRVLIESTDGKRR 490
Query: 143 GKTVGVS 149
TVGVS
Sbjct: 491 WTTVGVS 497
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 26.6 bits (59), Expect = 6.3
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|185489 PTZ00160, PTZ00160, 60S ribosomal protein L27a; Provisional.
Length = 147
Score = 25.8 bits (57), Expect = 7.5
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 113 RLKKIRNHRGLRHYWGLRVRGQHTKTTGRRGKTVGVSKKR 152
R KK R RG + RV G+H K G RG G R
Sbjct: 4 RFKKCRKMRGHVSHGYGRV-GKHRKHPGGRGNAGGQHHHR 42
>gnl|CDD|130153 TIGR01081, mpl,
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-
diaminopimelate ligase. Alternate name: murein
tripeptide ligase [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 448
Score = 26.3 bits (58), Expect = 8.1
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 123 LRHYWGLRVRGQHTKTT 139
L W L V G H KTT
Sbjct: 99 LHDRWVLAVAGTHGKTT 115
>gnl|CDD|225695 COG3153, COG3153, Predicted acetyltransferase [General function
prediction only].
Length = 171
Score = 25.7 bits (57), Expect = 8.8
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
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 0.395
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: 7,665,754
Number of extensions: 694328
Number of successful extensions: 736
Number of sequences better than 10.0: 1
Number of HSP's gapped: 730
Number of HSP's successfully gapped: 39
Length of query: 152
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 64
Effective length of database: 7,034,450
Effective search space: 450204800
Effective search space used: 450204800
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: 55 (24.7 bits)