RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780367|ref|YP_003064780.1| ribonuclease protein
[Candidatus Liberibacter asiaticus str. psy62]
(281 letters)
>gnl|CDD|31486 COG1295, Rbn, Predicted membrane protein [Function unknown].
Length = 303
Score = 130 bits (327), Expect = 5e-31
Identities = 84/274 (30%), Positives = 147/274 (53%), Gaps = 4/274 (1%)
Query: 7 IVFDIIYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQ-FVPTVIDV 65
+ D++ A+E F E+DG +A+ ++ LLS+FP ++ +L GF AH + ++ +
Sbjct: 15 GILDLLRRALERFNEDDGSLLAAALAYYTLLSLFPLLLVVFSLLGFFLAHPILLEDLLFI 74
Query: 66 VFGAWPEVIAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEM 125
+ PE A I D + L+ L ++ + A + +SNG+ ALR +LN+ +RV
Sbjct: 75 IANLLPEQAADVIEDYLKNFLSQSRGSLLSLGLVVALWTASNGMSALRDALNKIWRVKPR 134
Query: 126 RSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFF--PALGNLLLIIWNGRIY 183
RS+ RL+S + L + L+ + V P+AL + F P L+LI+ R+
Sbjct: 135 RSFIRRRLLSLFWTLGTLLPLLFALLLSVVGPIALQALLLRFGLPFFDVLVLILLRLRLL 194
Query: 184 ATMLALFIGLIFVHLFLPAAKSKIMS-ILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMY 242
++L L +G ++ FLP + +LPG + I + +G LF +Y+ F+ YS+ Y
Sbjct: 195 VSLLLLTLGFFLLYRFLPNVRVLKWRDVLPGALLAAILFELGKYLFGYYLSNFANYSSTY 254
Query: 243 AGLASIMTCLVFLYMLGVFFILGAELNASMIIYY 276
L S++ L++LY+ + +LGAELNA++ Y
Sbjct: 255 GALGSVIILLLWLYISALIILLGAELNATLSEYK 288
>gnl|CDD|146329 pfam03631, Ribonuclease_BN, Ribonuclease BN-like family. This
family contains integral membrane proteins with 5 to 6
predicted transmembrane spans. The family include
ribonuclease BN that is involved in tRNA maturation.
This family of proteins does not seem to contain any
completely conserved polar residues that would be
expected in a nuclease enzyme, suggesting that many
members of this family may not have this catalytic
activity (Bateman A pers. obs.).
Length = 255
Score = 124 bits (313), Expect = 3e-29
Identities = 74/253 (29%), Positives = 133/253 (52%), Gaps = 4/253 (1%)
Query: 21 EEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAH-QFVPTVIDVVFGAWPEVIAKPIT 79
E+D +A+ ++ LLS+FP ++ L G G ++D++ PE A+ I
Sbjct: 2 EDDLSLLAAALAYYTLLSLFPLLLVLLALLGLFGGPPALQEQLLDLLAEVLPEEAAELIE 61
Query: 80 DEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSWYITRLISFGYV 139
D + ++L + GL + L + +S G ALR +LNR Y V E RS+ RL+S G
Sbjct: 62 DILQRLLTQASLGLLGLGVLL--WSASGGFAALRRALNRIYGVKEKRSFLRRRLLSLGLT 119
Query: 140 LLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIYATMLALFIGLIFVHLF 199
LL + L++ + V +P AL + LG +++ R ++L L + ++ F
Sbjct: 120 LLLGLLLLLSLLLSVFLP-ALLGILLLGLGLGLATVLLQLLRWLVSLLLLTLLFALLYRF 178
Query: 200 LPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCLVFLYMLG 259
LP K + + LPG + + W++ + F+ Y+ F+ Y++ Y L +++ L++LY+
Sbjct: 179 LPNRKVRWRAALPGALLAAVLWLLLSYGFSLYLSNFANYNSTYGSLGALIVLLLWLYLSA 238
Query: 260 VFFILGAELNASM 272
+ +LGAELNA++
Sbjct: 239 LILLLGAELNAAL 251
>gnl|CDD|30822 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 35.0 bits (80), Expect = 0.027
Identities = 37/225 (16%), Positives = 81/225 (36%), Gaps = 19/225 (8%)
Query: 12 IYDAIEHFVEEDGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAWP 71
+Y I+ F+ ++ +L++ + +F I+++ + P
Sbjct: 697 VYVNIKKFI-----LYLLSKNVGEVLTLLIYSLFNLFFLPLTPLQL---LWINLLTDSLP 748
Query: 72 EV---IAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRSW 128
+ + P +D + + P +GLF + A I + + +
Sbjct: 749 ALALGVEDPESDVMKRPPRGPEEGLFNRKIFWRFILIIGLLSA--ILFILTFLLYLLGFI 806
Query: 129 YITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIYATMLA 188
T + LL + ++ + + + LA+ + F L ++++ + L
Sbjct: 807 ANTLGLDLFQALLQTTAFTVLVLIQLLLTLAVRSRGRPF-----LSSLLFSNKYLWLALL 861
Query: 189 LFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIV 233
+ I L + +FLP KI P +F W+ + L YIV
Sbjct: 862 VIIILQLLIIFLPPLNLKIFQPTPLSLFEWL-IAIAVALLLLYIV 905
>gnl|CDD|32387 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 32.1 bits (73), Expect = 0.18
Identities = 28/131 (21%), Positives = 50/131 (38%), Gaps = 25/131 (19%)
Query: 120 YRVVEMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWN 179
+R SW L++ LA+ + + F + + ++ LG L++ +
Sbjct: 387 WRPKIQGSWSRDYLVAILICALATAIAIQLDKFFDLANIVMLFL------LGVLVVAVLT 440
Query: 180 GRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYS 239
GR A + AL L+F + F +T+ AV Y+VTF+
Sbjct: 441 GRWPAVLAALLSVLVFNYFFTEP------------RYTF------AVSDPQYLVTFAVML 482
Query: 240 TMYAGLASIMT 250
+ A L +T
Sbjct: 483 AV-ALLTGNLT 492
>gnl|CDD|39049 KOG3845, KOG3845, KOG3845, MLN, STAR and related lipid-binding
proteins [Lipid transport and metabolism].
Length = 241
Score = 29.6 bits (66), Expect = 0.91
Identities = 19/132 (14%), Positives = 30/132 (22%), Gaps = 10/132 (7%)
Query: 12 IYDAIEHFVEE-DGWAMASHISLSALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAW 70
+Y+ +E + D W + FI G+ + V T +
Sbjct: 83 VYNMLEKIQKNTDIWTSEFDSFNVDIFRPRVFIDSGSVFRLEHMINIPVTTCVS-----R 137
Query: 71 PEVIAKPITDE----ILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMR 126
+ AK I V VP I A +F R +
Sbjct: 138 AFLSAKVILVRGYNHPCGVFCVPLPIEPFILAWLREWFLDLRGLPQENVGERPEARTLVN 197
Query: 127 SWYITRLISFGY 138
Sbjct: 198 FELAPLKAPKAL 209
>gnl|CDD|145481 pfam02357, NusG, Transcription termination factor nusG.
Length = 90
Score = 28.8 bits (65), Expect = 1.8
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 176 IIWNGRIYATMLALFIGLIFVHLFLPAAKSKIMSILPGVI 215
+ NG+ LF G +FV + L KI S PGV
Sbjct: 37 VRKNGKKKKVERPLFPGYVFVRMDLNDETWKIRST-PGVS 75
>gnl|CDD|35409 KOG0188, KOG0188, KOG0188, Alanyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 895
Score = 28.0 bits (62), Expect = 3.1
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 8/63 (12%)
Query: 51 GFLGAHQFVPTVIDVVFGAWPEVIAKP------ITDEILQVLAVPAKGLFTISALAAAYF 104
GF VP V++ + A+PE+ P I +E Q L +G +A
Sbjct: 330 GFFS--TLVPVVVETLGDAFPELKRDPQHVIDIINEEEAQFLKTLDRGRKLFDRVARELG 387
Query: 105 SSN 107
SS
Sbjct: 388 SSK 390
>gnl|CDD|177097 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 28.0 bits (62), Expect = 3.3
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 193 LIFVHLFLPAAKSKIMSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASIMTCL 252
LI+ HL P + + SIL ++ V G ++ TH + S + I + +
Sbjct: 1329 LIWTHLRSPNVREFLYSIL------FLLLVAGYLVRTHLLFVSRASSELQTEFEKIKSLM 1382
Query: 253 VFLYML 258
+ YM+
Sbjct: 1383 IPSYMI 1388
>gnl|CDD|31348 COG1154, Dxs, Deoxyxylulose-5-phosphate synthase [Coenzyme
metabolism / Lipid metabolism].
Length = 627
Score = 27.8 bits (62), Expect = 3.8
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 35 ALLSVFPFIVFGANLAGFLGAHQFVPTVIDVVFGAWPEVIAKPITDEILQVLAVPAKGLF 94
A+L+ + +A L A+ TV+D F KP+ + +L LA +
Sbjct: 505 AILAFGTMLPEALKVAEKLNAYGISVTVVDPRF-------VKPLDEALLLELAKSHDLVV 557
Query: 95 TIS 97
T+
Sbjct: 558 TLE 560
>gnl|CDD|38926 KOG3722, KOG3722, KOG3722, Lipocalin-interacting membrane receptor
(LIMR) [Defense mechanisms].
Length = 538
Score = 27.6 bits (61), Expect = 3.9
Identities = 27/127 (21%), Positives = 52/127 (40%), Gaps = 16/127 (12%)
Query: 145 TLVIMSFVFVAIPLALAYVRKFFPALGNLLLI--IWNGRIYATMLALFIGLIFVHLFLPA 202
++++ F ++ + L Y ++ N LI +WN + L+LF+ L F + F+ +
Sbjct: 80 AVLLLPFSIISNEVLLLYPGNYYIQWLNGSLIHGLWNLVFLFSNLSLFVLLPFAYFFIES 139
Query: 203 ---AKSKI-----------MSILPGVIFTWISWVVGAVLFTHYIVTFSTYSTMYAGLASI 248
A SK + +L ++ + WV A+L S L +
Sbjct: 140 EGFAGSKKGILQRIYETMVILMLLALLVLGLVWVASAILDYPKAQFESFLDLWSVYLPYL 199
Query: 249 MTCLVFL 255
+C+ FL
Sbjct: 200 YSCVSFL 206
>gnl|CDD|144001 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 27.1 bits (61), Expect = 5.9
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 90 AKGLFTISALAAAYFSSNGVEALRISLNR 118
A G + + AL ++ +EA RI++NR
Sbjct: 26 AFGDYGLKALEPGRITARQIEAARIAINR 54
>gnl|CDD|176177 cd08488, PBP2_AmpR, The C-terminal substrate domain of LysR-type
transcriptional regulator AmpR that involved in control
of the expression of beta-lactamase gene ampC, contains
the type 2 periplasmic binding fold. AmpR acts as a
transcriptional activator by binding to a DNA region
immediately upstream of the ampC promoter. In the
absence of a beta-lactam inducer, AmpR represses the
synthesis of beta-lactamase, whereas expression is
induced in the presence of a beta-lactam inducer. The
AmpD, AmpG, and AmpR proteins are involved in the
induction of AmpC-type beta-lactamase (class C) which
produced by enterobacterial strains and many other
gram-negative bacilli. The activation of ampC by AmpR
requires ampG for induction or high-level expression of
AmpC. It is probable that the AmpD and AmpG work
together to modulate the ability of AmpR to activate
ampC expression. This substrate-binding domain shows
significant homology to the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 191
Score = 26.7 bits (59), Expect = 6.6
Identities = 15/62 (24%), Positives = 22/62 (35%), Gaps = 10/62 (16%)
Query: 68 GAWPEVIAKPITDEILQVLAVPAKGLFTISALAAAYFSSNGVEALRISLNRAYRVVEMRS 127
GAW + A + + L L P A + R +L R+YR E
Sbjct: 56 GAWHGIDATRLFEAPLSPLCTPE----------LARQLREPADLARHTLLRSYRADEWPQ 105
Query: 128 WY 129
W+
Sbjct: 106 WF 107
>gnl|CDD|32008 COG1823, COG1823, Predicted Na+/dicarboxylate symporter [General
function prediction only].
Length = 458
Score = 26.4 bits (58), Expect = 9.4
Identities = 21/76 (27%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 124 EMRSWYITRLISFGYVLLASVTLVIMSFVFVAIPLALAYVRKFFPALGNLLLIIWNGRIY 183
E W+ ++ GYV L + +++M VF++I A+A + LG + L+ ++
Sbjct: 61 ETIDWF--NIVGNGYVRL--LQMIVMPLVFISILSAIAKLDNA-SKLGKISLLTIGTLLF 115
Query: 184 ATMLALFIGLIFVHLF 199
T +A IG++ LF
Sbjct: 116 TTAIAALIGILVALLF 131
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.333 0.144 0.449
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,648,969
Number of extensions: 209140
Number of successful extensions: 1478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1416
Number of HSP's successfully gapped: 291
Length of query: 281
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 188
Effective length of database: 4,254,100
Effective search space: 799770800
Effective search space used: 799770800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 57 (25.7 bits)