RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 031812
(152 letters)
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 263 bits (674), Expect = 4e-92
Identities = 107/152 (70%), Positives = 134/152 (88%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
++L +DFQHILR+LNTNVDGK+K+ +ALT+IKGIGRR A +VCKKA +D+ KRAGEL+
Sbjct: 3 LTLEKADDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELT 62
Query: 61 AAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNH 120
A E+++++ ++ANP QFKIPDWFLNRQ+D KDG+ 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 = 7e-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 DQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLR 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 (423), Expect = 5e-54
Identities = 70/145 (48%), Positives = 106/145 (73%), Gaps = 1/145 (0%)
Query: 8 DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67
+F++I+R+ +T++DG + + +ALT IKGIGRR A + +K VD N + G L E+++L
Sbjct: 1 EFKYIVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKL 60
Query: 68 MVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYW 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 = 79/129 (61%), Gaps = 23/129 (17%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
R+LNTN+DG +KI ALT IKGIGRR AN + KKA VD +KR GEL+ E+D++ +++N
Sbjct: 1 RILNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN 60
Query: 74 PRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRG 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 = 131 bits (331), Expect = 3e-40
Identities = 52/143 (36%), Positives = 77/143 (53%), Gaps = 24/143 (16%)
Query: 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71
+ R+ ++ G ++++ ALT I GIGRR A +CKKA +D +KR GEL+ E+++L +
Sbjct: 1 MARIAGVDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERLRDAI 60
Query: 72 ANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRV 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 = 72.4 bits (179), Expect = 3e-17
Identities = 47/145 (32%), Positives = 71/145 (48%), Gaps = 32/145 (22%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
R+ ++ ++++ ALT I GIGR A + A +D + R +L+ ELD++ +
Sbjct: 3 RIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI-- 60
Query: 74 PRQFKIPDWFLNRQKDYK---DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLR 130
K+YK D R +V ++++K RL I +RGLRH GL
Sbjct: 61 -------------DKNYKVEGDLR-REV---SMNIK------RLMDIGCYRGLRHRRGLP 97
Query: 131 VRGQHTKTTGR--RG--KTVGVSKK 151
VRGQ TKT R +G KT+ KK
Sbjct: 98 VRGQRTKTNARTRKGPRKTIAGKKK 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 = 69.1 bits (170), Expect = 5e-16
Identities = 43/131 (32%), Positives = 64/131 (48%), Gaps = 28/131 (21%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
R+ ++ +++ ALT I GIGR A + +KA +D +KR +L+ EL+ + +
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEI-- 58
Query: 74 PRQFKIPDWFLNRQKDYK---DGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLR 130
+ YK D R +V +L++K RL I +RGLRH GL
Sbjct: 59 -------------EAKYKVEGDLR-REV---SLNIK------RLMDIGCYRGLRHRRGLP 95
Query: 131 VRGQHTKTTGR 141
VRGQ TKT R
Sbjct: 96 VRGQRTKTNAR 106
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 48.5 bits (116), Expect = 4e-08
Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 26/132 (19%)
Query: 24 QKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWF 83
++I +ALT I GIG A + +KA++D + R +L+ ++ L ++
Sbjct: 13 KRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII------------ 60
Query: 84 LNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIRNHRGLRHYWGLRVRGQHTKTTGR-- 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|217590 pfam03486, HI0933_like, HI0933-like protein.
Length = 405
Score = 29.1 bits (66), Expect = 0.78
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 23 KQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67
K+ + AL + + +RLA + ++A +D +K+ +LS +L L
Sbjct: 288 KKSLKNALAGL--LPKRLALFLLEQAGIDPDKKLAQLSKKDLAAL 330
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 29.1 bits (66), Expect = 0.82
Identities = 13/41 (31%), Positives = 25/41 (60%)
Query: 28 FALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLM 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 = 29.1 bits (66), Expect = 0.91
Identities = 10/38 (26%), Positives = 20/38 (52%)
Query: 30 LTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67
+ + +G+ LA +C +A +D ELS + ++L
Sbjct: 192 VQAFQGLSPLLAEELCYRAGLDKETPVEELSDEDWERL 229
>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 = 28.7 bits (65), Expect = 1.2
Identities = 15/62 (24%), Positives = 32/62 (51%), 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 QL 67
+L
Sbjct: 324 KL 325
>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 = 1.9
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|235868 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1151
Score = 27.9 bits (63), Expect = 2.5
Identities = 28/103 (27%), Positives = 43/103 (41%), Gaps = 32/103 (31%)
Query: 20 VDGKQKIMFALTSIKGIGRR-LANIV---------------CKKADV-DMNKRAGE--LS 60
V+G KI F L ++K +G + +IV C++ D +NKRA E +
Sbjct: 817 VEGD-KIRFGLAAVKNVGENAIDSIVEEREKKGKFKSLVDFCERVDTSQINKRAVESLIK 875
Query: 61 AAELD-------QLMVVVANPRQFKIPDWFLNRQKDYKDGRYS 96
A D QL+ V KI D ++K +G+ S
Sbjct: 876 AGAFDSLGVYRSQLLAVYE-----KILDSISKQRKKNIEGQIS 913
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 27.5 bits (61), Expect = 3.3
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 = 5.2
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|237432 PRK13572, PRK13572, anthranilate synthase component I; Provisional.
Length = 435
Score = 26.6 bits (59), Expect = 6.2
Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 6/67 (8%)
Query: 75 RQFKIPDWFLNRQKDYKDGRYSQVVSNALDM-----KLRDDLERLKKIRN-HRGLRHYWG 128
R P + +K + RY+ + +N M K + D E + K N + L+ +
Sbjct: 19 RDEGYPFILESAEKGQRKARYTYISANPEFMVRIGNKTKVDGETISKESNPFKALKENFK 78
Query: 129 LRVRGQH 135
+ G
Sbjct: 79 ITQSGDR 85
>gnl|CDD|185489 PTZ00160, PTZ00160, 60S ribosomal protein L27a; Provisional.
Length = 147
Score = 25.8 bits (57), Expect = 7.1
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|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 25.9 bits (57), Expect = 7.3
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 6/87 (6%)
Query: 36 IGRRLANIVCKKADV---DMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKD 92
+ LA + A+V D+++ A E + +L +F D Q +D
Sbjct: 17 LTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENV---EFIQGDIEELPQLQLED 73
Query: 93 GRYSQVVSNALDMKLRDDLERLKKIRN 119
+ V+SN + L D + L++I
Sbjct: 74 NSFDVVISNEVLNHLPDPDKVLEEIIR 100
>gnl|CDD|236130 PRK07914, PRK07914, hypothetical protein; Reviewed.
Length = 320
Score = 26.3 bits (58), Expect = 7.9
Identities = 13/41 (31%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 29 ALTSIKGIGRRLANIVCKKADVDMNK-RAGELSAAELDQLM 68
A+ ++ R+ A ADV +++ RAG++S EL +L+
Sbjct: 21 AVAAVLRSARQRAGT----ADVPVSRMRAGDVSTYELAELL 57
>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|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 26.2 bits (58), Expect = 9.9
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 10/86 (11%)
Query: 29 ALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQK 88
L G+G LA + +A +D A +L E+ ++ + P
Sbjct: 191 LLARFLGLGGLLAEELLSRAGLDKKVPAKDLFEEEIKKVREALEELLNPLKP------NY 244
Query: 89 DYKDGRYSQVVSNALDMKLRDDLERL 114
YKD +Y VV +K DLE+L
Sbjct: 245 YYKDEKYLDVVP----LKAYADLEKL 266
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
0.322 0.136 0.397
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: 7,702,597
Number of extensions: 701961
Number of successful extensions: 747
Number of sequences better than 10.0: 1
Number of HSP's gapped: 741
Number of HSP's successfully gapped: 41
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)