RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13
[Candidatus Liberibacter asiaticus str. psy62]
(122 letters)
>gnl|CDD|179955 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 197 bits (503), Expect = 7e-52
Identities = 74/111 (66%), Positives = 90/111 (81%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
MARIAGV+IPR KRVV AL YI+GIG +++I I P+ RV L + E+ +IR+ I
Sbjct: 1 MARIAGVDIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI 60
Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
+++Y+VEGDLRR V+MNIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 DKNYKVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 111
>gnl|CDD|163364 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.
Length = 113
Score = 178 bits (453), Expect = 4e-46
Identities = 72/109 (66%), Positives = 84/109 (77%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RIAGV+IP KRV AL YI+GIG ++ I K I P++RV L E E+ IR+ IE
Sbjct: 1 RIAGVDIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEIEA 60
Query: 63 DYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
Y+VEGDLRR V++NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK
Sbjct: 61 KYKVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQRTKTNARTRK 109
>gnl|CDD|179731 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 77.2 bits (191), Expect = 9e-16
Identities = 47/142 (33%), Positives = 70/142 (49%), Gaps = 25/142 (17%)
Query: 3 RIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
RIAG ++ K V AL I GIG ++++ I KL + P ++ L + E+ +I +A+E
Sbjct: 11 RIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALED 70
Query: 63 DYQ----------------------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRG 100
+ + DL TV +I R+ + YRG+RH GL VRG
Sbjct: 71 PAEEGIPSWMLNRRKDYETGEDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRG 130
Query: 101 QRTHTNARTRKKFGKGGVARKR 122
QRT + RT G GV+RK+
Sbjct: 131 QRTRSTGRTG---GTVGVSRKK 149
>gnl|CDD|132668 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.
Length = 144
Score = 76.5 bits (189), Expect = 2e-15
Identities = 45/143 (31%), Positives = 70/143 (48%), Gaps = 24/143 (16%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RIA ++ K V AL I GIG + ++ I KL + P ++ L + E+ ++ +A+
Sbjct: 5 IVRIADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAV 64
Query: 61 E--------------QDYQ-------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVR 99
E +DY+ + DL TV +I R+ + YRG+RH GL VR
Sbjct: 65 ENYEYGIPSWLLNRRKDYETGEDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVR 124
Query: 100 GQRTHTNARTRKKFGKGGVARKR 122
GQRT + R GV+RK+
Sbjct: 125 GQRTKSTGRRG---RTVGVSRKK 144
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 46.6 bits (111), Expect = 2e-06
Identities = 39/144 (27%), Positives = 63/144 (43%), Gaps = 25/144 (17%)
Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
+ RI N+ ++V AL I GIG + + +C K I +R +L E+ +I + I
Sbjct: 14 ILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEII 73
Query: 61 E---------------------QDYQV-EGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
++ + L + +++RL + +RGLRH GL V
Sbjct: 74 ANPLQFKIPDWFLNRQRDPKDGKNSHLTSNMLDTKLREDLERLKKIRLHRGLRHHWGLRV 133
Query: 99 RGQRTHTNARTRKKFGKGGVARKR 122
RGQ T T R + GV+RK+
Sbjct: 134 RGQHTKTTGRRGRTV---GVSRKK 154
>gnl|CDD|131167 TIGR02112, cyd_oper_ybgE, cyd operon protein YbgE. This model
describes a small protein of unknown function, about
100 amino acids in length, essentially always found in
an operon with CydAB, subunits of the cytochrome d
terminal oxidase. It appears to be an integral membrane
protein. It is found so far only in the Proteobacteria.
Length = 93
Score = 30.0 bits (68), Expect = 0.14
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 2 ARIAGVNIPRAKRVVRALC--YIHGIGFK 28
A I G N A ++ A+C +IHG+GF+
Sbjct: 37 AAIGGFNAVLALLMIWAVCILWIHGVGFR 65
>gnl|CDD|150308 pfam09600, Cyd_oper_YbgE, Cyd operon protein YbgE
(Cyd_oper_YbgE). This entry describes a small protein
of unknown function, about 100 amino acids in length,
essentially always found in an operon with CydAB,
subunits of the cytochrome d terminal oxidase. It
appears to be an integral membrane protein. It is found
so far only in the Proteobacteria.
Length = 82
Score = 27.6 bits (62), Expect = 0.92
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 2 ARIAGVNIPRAKRVVRALC--YIHGIGFK 28
A I G N A ++ A+C IHG+GF+
Sbjct: 26 AAIGGFNPLLAPLLIWAVCAGMIHGVGFR 54
>gnl|CDD|179652 PRK03815, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 401
Score = 26.9 bits (60), Expect = 1.5
Identities = 5/19 (26%), Positives = 10/19 (52%)
Query: 25 IGFKSSQDICNKLAIPPER 43
I ++ +D+ K I E+
Sbjct: 208 IFYEDEEDLAEKFGIDSEK 226
>gnl|CDD|162152 TIGR00998, 8a0101, efflux pump membrane protein (multidrug
resistance protein A).
Length = 334
Score = 26.7 bits (59), Expect = 1.5
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 42 ERRVHQL---VESEVIQIRQAIEQDYQVEGDLRRTVAM 76
E V QL VES I++ QA E+ Q E DLRR V +
Sbjct: 100 EITVQQLQAKVESLKIKLEQAREKLLQAELDLRRRVPL 137
>gnl|CDD|140257 PTZ00230, PTZ00230, variable surface protein Vir7; Provisional.
Length = 364
Score = 26.4 bits (58), Expect = 1.8
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 14 RVVRALCYIHGIGFKSSQD--ICNKL 37
++++ALCY++ SS D ICN L
Sbjct: 54 KILKALCYVYRESSSSSFDSNICNFL 79
>gnl|CDD|161725 TIGR00129, fdhD_narQ, formate dehydrogenase family accessory
protein FdhD. FdhD in E. coli and NarQ in B. subtilis
are required for the activity of formate dehydrogenase.
The gene name in B. subtilis reflects the requirement
of the neighboring gene narA for nitrate assimilation,
for which NarQ is not required. In some species, the
gene is associated not with a known formate
dehydrogenase but with a related putative
molybdopterin-binding oxidoreductase. A reasonable
hypothesis is that this protein helps prepare a
required cofactor for assembly into the holoenzyme.
Length = 237
Score = 26.3 bits (58), Expect = 2.3
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 11/74 (14%)
Query: 25 IGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDL 84
+GF S+ I N + E I+I I + Q++ RR + + R
Sbjct: 35 VGFLLSEGIINSPD-----------DIEGIEIDDNINIEVQIDLSSRRFMILKENRTGCS 83
Query: 85 GCYRGLRHRRGLPV 98
GC R +R V
Sbjct: 84 GCGRERLNRIPKMV 97
>gnl|CDD|179773 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 25.2 bits (56), Expect = 3.9
Identities = 8/39 (20%), Positives = 22/39 (56%)
Query: 24 GIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62
+G K++ +I K + P ++ +L E+ ++ +A ++
Sbjct: 268 RVGDKTADEILEKAGLDPNKKPKELTREELERLVEAFKK 306
>gnl|CDD|179062 PRK00553, PRK00553, ribose-phosphate pyrophosphokinase;
Provisional.
Length = 332
Score = 25.3 bits (55), Expect = 4.2
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 7 VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIR 57
++I ++ V+ +L K IC KL++ P V Q IR
Sbjct: 3 LSIDKSNHVIFSLSKAK----KLVDSICRKLSMKPGEIVIQKFADGETYIR 49
>gnl|CDD|183384 PRK11924, PRK11924, RNA polymerase sigma factor; Provisional.
Length = 179
Score = 24.9 bits (55), Expect = 5.1
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 10 PRAKRVVRALCYIHGIGFKSSQDICNKLAIP 40
P +R V L Y+ G S ++I L +P
Sbjct: 127 PVKQREVFLLRYVEG---LSYREIAEILGVP 154
>gnl|CDD|132354 TIGR03311, Se_dep_Molyb_1, selenium-dependent molybdenum
hydroxylase 1. Members of this protein family show full
length homology to the molybdenum-containing aldehyde
oxido-reductase of Desulfovibrio gigas. Members,
however, are found only within species that have, and
near those genes that encode, a set of predicted
accessory proteins for selenium-dependent molybdenum
hydroxylases. The best known examples of such enzymes
are forms of xanthine dehydrogenase and purine
hydroxylase; this family appears to be another such
enzyme.
Length = 848
Score = 24.8 bits (54), Expect = 5.3
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 12/55 (21%)
Query: 6 GVNIP---RAKRVVR---------ALCYIHGIGFKSSQDICNKLAIPPERRVHQL 48
GV IP R V A C G+G +Q +C +PPE V +L
Sbjct: 588 GVGIPDTGRCNLAVEDGKVHIRTSAACIGQGLGTVLTQIVCETTGLPPEVIVCEL 642
>gnl|CDD|129401 TIGR00300, TIGR00300, conserved hypothetical protein TIGR00300.
All members of the family come from genome projects. A
partial length search brings in two plant
lysine-ketoglutarate reductase/saccharopine
dehydrogenase bifunctional enzymes hitting the
N-terminal region of the family.
Length = 407
Score = 24.4 bits (53), Expect = 7.2
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 32 DICNKLAIPPERRVHQLVESEVIQ---IRQAIEQDYQVEGDLRRTVAMNI 78
DI + +P R H + V + IR A+EQ +G + V NI
Sbjct: 256 DIQRGIPVPGGHRHHLKAINSVRRAGGIRDAVEQGIIKKGVMYECVKNNI 305
>gnl|CDD|162378 TIGR01472, gmd, GDP-mannose 4,6-dehydratase. Excluded from this
model are members of the clade that score poorly
because of highly dervied (phylogenetically
long-branch) sequences, e.g. Aneurinibacillus
thermoaerophilus Gmd, described as a bifunctional
GDP-mannose
4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase
(PUBMED:11096116).
Length = 343
Score = 24.4 bits (53), Expect = 7.3
Identities = 8/25 (32%), Positives = 17/25 (68%)
Query: 60 IEQDYQVEGDLRRTVAMNIKRLMDL 84
+E+ Y+V G +RR+ + N +R+ +
Sbjct: 21 LEKGYEVHGLIRRSSSFNTQRIEHI 45
>gnl|CDD|178551 PLN02967, PLN02967, kinase.
Length = 581
Score = 24.6 bits (53), Expect = 7.4
Identities = 8/33 (24%), Positives = 15/33 (45%)
Query: 33 ICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQ 65
+ PP+ + VE + IR E++Y+
Sbjct: 529 LARTRGFPPKEDMEDEVEPDPNGIRSITEKEYR 561
>gnl|CDD|171521 PRK12467, PRK12467, peptide synthase; Provisional.
Length = 3956
Score = 24.4 bits (53), Expect = 7.8
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 31 QDICNKLAIPP-ERRVHQLVESEVIQIRQAI 60
A P ER VHQL+E++V + +A
Sbjct: 3082 HAWNATAAAYPSERLVHQLIEAQVARTPEAP 3112
Score = 24.0 bits (52), Expect = 9.4
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 40 PPERRVHQLVESEVIQIRQAI 60
P R VHQL+E + +A+
Sbjct: 1571 PLARLVHQLIEDQAAATPEAV 1591
>gnl|CDD|178741 PLN03200, PLN03200, cellulose synthase-interactive protein;
Provisional.
Length = 2102
Score = 24.3 bits (53), Expect = 8.6
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 97 PVRGQRTHTNARTRKKFGKGGVAR 120
P +GQ+ H + +++ FGK + +
Sbjct: 2037 PPKGQKLHISCKSKNTFGKSSLGK 2060
>gnl|CDD|181885 PRK09470, cpxA, two-component sensor protein; Provisional.
Length = 461
Score = 24.1 bits (53), Expect = 9.4
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 43 RRVHQLVESEVIQ---IRQAIEQDYQVEGDLRRTVAMNIKRL 81
R++ +L++SE Q I Q IE + + M +RL
Sbjct: 37 RQMTELLDSEQRQGLMIEQHIEAELANDPPNDL---MWWRRL 75
>gnl|CDD|182616 PRK10647, PRK10647, ferric iron reductase involved in ferric
hydroximate transport; Provisional.
Length = 262
Score = 23.9 bits (52), Expect = 9.7
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 35 NKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDL 70
N + P+ R+ L+ +I + QA+E ++ G L
Sbjct: 147 NATPLSPQERMETLISQALIPVVQALEATGEINGKL 182
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.326 0.141 0.416
Gapped
Lambda K H
0.267 0.0836 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,044,759
Number of extensions: 119827
Number of successful extensions: 365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 32
Length of query: 122
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 40
Effective length of database: 4,222,617
Effective search space: 168904680
Effective search space used: 168904680
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: 51 (23.2 bits)