RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus
Liberibacter asiaticus str. psy62]
(209 letters)
>gnl|CDD|178795 PRK00015, rnhB, ribonuclease HII; Validated.
Length = 197
Score = 265 bits (680), Expect = 7e-72
Identities = 100/199 (50%), Positives = 132/199 (66%), Gaps = 3/199 (1%)
Query: 7 PERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHK 66
P E + ++ + +AG+DE GRG LAGPVV AA+ILDP+ G+NDSKK+S K
Sbjct: 1 RLEPMLSFERALLKQGLGLIAGVDEAGRGPLAGPVVAAAVILDPDRPIEGLNDSKKLSEK 60
Query: 67 KREELYEKITSSAI-ISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSI 125
KREELYE+I A+ S+ AS + ID+ NI +ATL A+ AVE L V P L+DG +
Sbjct: 61 KREELYEEIKEKALAYSVGIASPEEIDELNILEATLLAMRRAVEGL-VKPDYVLVDGNRV 119
Query: 126 PEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQ 185
P+ LP A++KGD+ S SIAAASI+AKVTRDRLM K+YP YGF H GY T +H
Sbjct: 120 PK-LPIPQEAIVKGDAKSPSIAAASILAKVTRDRLMEELDKEYPGYGFAKHKGYGTKEHL 178
Query: 186 QVIKEKGPSCIHRLTFRPL 204
+ + + GP+ IHR +F P+
Sbjct: 179 EALAKYGPTPIHRRSFAPV 197
>gnl|CDD|184399 PRK13925, rnhB, ribonuclease HII; Provisional.
Length = 198
Score = 180 bits (460), Expect = 1e-46
Identities = 80/183 (43%), Positives = 111/183 (60%), Gaps = 5/183 (2%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSAI- 80
+AG+DEVGRGAL GPV AA+IL P G+ DSKK+S K+R +L I + A
Sbjct: 10 IAGVDEVGRGALFGPVFAAAVILSEKAEPQLLQAGLTDSKKLSPKRRAQLVPLILTLASD 69
Query: 81 ISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGD 140
I AS + ID+ I +AT A+ A++ L+ P L+DG P ++KGD
Sbjct: 70 WGIGQASAREIDRLGIRQATELAMLRALKKLKSPPSLCLVDGNLPLRLWPGPQRTIVKGD 129
Query: 141 SISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRLT 200
S S +IAAASI+AKV RD L++ KKYP YG + + GY TA+H+Q + + GP+ +HR +
Sbjct: 130 SKSAAIAAASILAKVWRDDLIKRLAKKYPGYGLEKNKGYGTAQHRQALLKLGPTPLHRKS 189
Query: 201 FRP 203
F P
Sbjct: 190 FLP 192
>gnl|CDD|184400 PRK13926, PRK13926, ribonuclease HII; Provisional.
Length = 207
Score = 158 bits (401), Expect = 9e-40
Identities = 85/204 (41%), Positives = 115/204 (56%), Gaps = 5/204 (2%)
Query: 5 SIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKIS 64
+ P P + E + VAG+DE GRGA AGPVVVAA+IL P PF DSK +S
Sbjct: 3 TPPLEPDWAYEREHWRRGYLRVAGVDEAGRGAWAGPVVVAAVILPPGEYPF--RDSKTLS 60
Query: 65 HKKREELYEKITSSAII-SISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGR 123
RE L E++ A+ ++ A ID+ N+ KAT A A+ L V P + + D
Sbjct: 61 PAAREALAEEVRRVALAWAVGHAEAAEIDRLNVLKATHLAAARALARLAVAPEALVTDYL 120
Query: 124 SIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAK 183
+P LP A K D++S ++AAAS++AK RDRLMR +YP YGF H GY T
Sbjct: 121 RLPTPLPLLA--PPKADALSPTVAAASLLAKTERDRLMRELDARYPGYGFARHKGYGTPA 178
Query: 184 HQQVIKEKGPSCIHRLTFRPLRNL 207
H++ + GPS +HR +F P+R L
Sbjct: 179 HREALAALGPSPVHRRSFAPVRRL 202
>gnl|CDD|173015 PRK14550, rnhB, ribonuclease HII; Provisional.
Length = 204
Score = 93.5 bits (232), Expect = 4e-20
Identities = 61/183 (33%), Positives = 90/183 (49%), Gaps = 10/183 (5%)
Query: 28 GIDEVGRGALAGPVVVAAIILDPNN----IPFGINDSKKISHKKREELYEKITSSAIIS- 82
GIDE GRG LAG + VA + + + G+ DSKK+S KKR L +KI + +
Sbjct: 4 GIDEAGRGCLAGSLFVAGVACNEKTALEFLKMGLKDSKKLSPKKRFFLEDKIKTHGEVGF 63
Query: 83 -ISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRS---IPEDLPCQAFAVIK 138
+ S ID + AI +EN + IDG + + + P +IK
Sbjct: 64 FVVKKSANEIDSLGLGACLKLAIQEILENGCSLANEIKIDGNTAFGLNKRYP-NIQTIIK 122
Query: 139 GDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHR 198
GD IA AS++AK +DR M H + +YG+D + GY T +H + I + G + HR
Sbjct: 123 GDETIAQIAMASVLAKAFKDREMLELHALFKEYGWDKNCGYGTKQHIEAIIKLGATPFHR 182
Query: 199 LTF 201
+F
Sbjct: 183 HSF 185
>gnl|CDD|129812 TIGR00729, TIGR00729, ribonuclease H, mammalian HI/archaeal HII
subfamily. Archaeal members of this subfamily of RNase
H are designated RNase HII and one has been shown to be
active as a monomer. A member from Homo sapiens was
characterized as RNase HI, large subunit.
Length = 206
Score = 82.9 bits (205), Expect = 5e-17
Identities = 53/176 (30%), Positives = 80/176 (45%), Gaps = 24/176 (13%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNI----PFGINDSKKISHKKREELYEKITSS--- 78
VAGIDE GRG + GP+VV ++ G+ DSKK++ +REEL+ KI +
Sbjct: 1 VAGIDEAGRGPVIGPLVVGVFAIEEKREEELRKLGVKDSKKLTPGRREELFSKIRNKLGR 60
Query: 79 -AIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALID------GRSIPEDLPC 131
++ I+ N+++ ++ A L P +D R E
Sbjct: 61 YEVLKITPEEIDRERNINLNENEIEKFSKAAIILIEKPSEVYVDSVDVNPKRFKREIKIK 120
Query: 132 QAFAVI------KGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPT 181
+ I K D+ ++AASIIAKV RDR + +KY D+G GYP+
Sbjct: 121 ERIEGIKVIAEHKADAKYPVVSAASIIAKVERDREIESLKRKYGDFG----SGYPS 172
>gnl|CDD|184738 PRK14551, rnhB, ribonuclease HII; Provisional.
Length = 212
Score = 71.7 bits (176), Expect = 1e-13
Identities = 50/176 (28%), Positives = 82/176 (46%), Gaps = 27/176 (15%)
Query: 25 PVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISIS 84
G+DE G+G + G + AA+ DP +P GI+DSK++S ++REEL ++ I++
Sbjct: 1 MRFGVDEAGKGPVLGSMFAAAVRADPAALPDGIDDSKRLSPERREELAAELREDDAIAVG 60
Query: 85 SA--SHQYID--KHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKGD 140
A ID + +++ T+ A A+ + + L D D+ FA D
Sbjct: 61 VAEIPPARIDDPETDMNTLTVAAHAEALSGVATDGITGLCDA----GDVDAGRFARRVAD 116
Query: 141 SISLSIA---------------AASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPT 181
++L ++ AASI+AKV RD + +Y D G GYP+
Sbjct: 117 RVALDVSVSAEHGADEEDPLVGAASIVAKVARDAHVAALAAEYGDVG----SGYPS 168
>gnl|CDD|179201 PRK00996, PRK00996, ribonuclease HIII; Provisional.
Length = 304
Score = 67.6 bits (166), Expect = 2e-12
Identities = 46/184 (25%), Positives = 75/184 (40%), Gaps = 37/184 (20%)
Query: 1 MFCNSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPF----G 56
+ + + + G DEVG+G GP+ VAA+ +D IPF G
Sbjct: 64 FWKKTKKKGVAKSGYEEPLSFQNLSLIGSDEVGKGDYFGPLTVAAVYVDKEQIPFLKKLG 123
Query: 57 INDSKKISHKKREELYEKITSSAIISISSASHQ-----YIDKHNIHKATLDAIYH--AVE 109
+ DSKK++ K ++ ++ S+ S + +N +K L A H A++
Sbjct: 124 VKDSKKLTDTKIRQIAPQLREKIPHSVLLLSPEKYNELQAKGYNQNK--LKAWLHNQAID 181
Query: 110 NL-QVI----PRSALID---------------GRSIPEDLPCQAFAVIKGDSISLSIAAA 149
NL Q I P +ID +++ + K +S L++AAA
Sbjct: 182 NLLQKIAGIQPEKIVIDQFASPEVYQKYLKKEKNKFRDNVTFET----KAESKHLAVAAA 237
Query: 150 SIIA 153
SIIA
Sbjct: 238 SIIA 241
>gnl|CDD|129799 TIGR00716, rnhC, ribonuclease HIII. Two types of ribonuclease H in
Bacillus subtilis, RNase HII (rnhB) and RNase HIII
(rnhC), are both known experimentally and are quite
similar to each other. The only RNase H homolog in the
Mycoplasmas resembles rnhC. Archaeal forms resemble HII
more closely than HIII. This model describes bacterial
RNase III.
Length = 284
Score = 44.9 bits (106), Expect = 1e-05
Identities = 43/200 (21%), Positives = 75/200 (37%), Gaps = 29/200 (14%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITS---S 78
V G DE G+G + GP+V+ + + N DSK++S K+ E L + +
Sbjct: 83 VIGCDESGKGDIFGPLVLCCVYIPEENYLKVSSLNPRDSKRLSDKRIERLALNLKPLVKA 142
Query: 79 AIISISSASHQYIDKHNIHKATLDAIYHA--VENLQVIP---RSALIDGRSIPEDLPCQA 133
+ + + + + + A +H +E L ++D +
Sbjct: 143 YCYELKPEKYNKLYRKFRNLNKMMAHFHKLLIERLLKEECGVSEVVVDQFAPSNPFFNHL 202
Query: 134 FA--VIKGDSI-------SLSIAAASIIAK----VTRDRLMRIAHKKYPDYGFDSHVGYP 180
++ D I +L++AAASI A+ + L R K P G V
Sbjct: 203 KGRDIVGEDVIFETEAERNLAVAAASIFARYKFLQSLKELERELGIKLPK-GASKEVKEL 261
Query: 181 TAKHQQVIKEKGPSCIHRLT 200
+I +KGPS + R
Sbjct: 262 AKS---LILKKGPSALERFI 278
>gnl|CDD|178664 PLN03117, PLN03117, Branched-chain-amino-acid aminotransferase;
Provisional.
Length = 355
Score = 30.3 bits (68), Expect = 0.33
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 122 GRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF 173
G++I E C F ++KG+ +S + +I+ VTR + +A D G+
Sbjct: 229 GKNIEELSACNIF-ILKGNIVSTPPTSGTILPGVTRKSISELAR----DIGY 275
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 28.3 bits (63), Expect = 1.4
Identities = 15/50 (30%), Positives = 29/50 (58%), Gaps = 2/50 (4%)
Query: 66 KKREELYE--KITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQV 113
K+R EL+ +IT AI++ ++ SH+YI + +D I A ++++
Sbjct: 354 KERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRM 403
>gnl|CDD|181217 PRK08063, PRK08063, enoyl-(acyl carrier protein) reductase;
Provisional.
Length = 250
Score = 27.4 bits (61), Expect = 2.7
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 6/45 (13%)
Query: 71 LYEKITSSAIISISS-ASHQYIDKH---NIHKATLDAI--YHAVE 109
L EK+ IIS+SS S +Y++ + + KA L+A+ Y AVE
Sbjct: 127 LMEKVGGGKIISLSSLGSIRYLENYTTVGVSKAALEALTRYLAVE 171
>gnl|CDD|150830 pfam10216, ChpXY, CO2 hydration protein (ChpXY). This small family
of proteins includes paralogues ChpX and ChpY in
Synechococcus sp. PCC7942 and other cyanobacteria,
associated with distinct NAD(P)H dehydrogenase
complexes. These proteins collectively enable
light-dependent CO2 hydration and CO2 uptake; loss of
both blocks growth at low CO2 concentrations.
Length = 353
Score = 26.5 bits (59), Expect = 4.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 147 AAASIIAKVTRDRLMRIAHKKYPDY 171
A +I AK + L+ HK +PD+
Sbjct: 109 ADRAIRAKFKGNPLLLGLHKLFPDF 133
>gnl|CDD|177901 PLN02259, PLN02259, branched-chain-amino-acid aminotransferase 2.
Length = 388
Score = 26.6 bits (58), Expect = 5.2
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 120 IDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIA 164
+ + + E C F V+KG +IS +I+ +TR +M IA
Sbjct: 264 VKKKYLEEASSCNVF-VVKGRTISTPATNGTILEGITRKSVMEIA 307
>gnl|CDD|182774 PRK10846, PRK10846, bifunctional folylpolyglutamate synthase/
dihydrofolate synthase; Provisional.
Length = 416
Score = 25.8 bits (57), Expect = 7.4
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 120 IDGRSIPEDLPCQAFAVI---KGDSISLS 145
I G+ +PE +FA I +GD ISL+
Sbjct: 95 IQGQELPESAHTASFAEIEAARGD-ISLT 122
>gnl|CDD|150545 pfam09885, DUF2112, Uncharacterized protein conserved in archaea
(DUF2112). This domain, found in various hypothetical
archaeal proteins, has no known function.
Length = 143
Score = 26.1 bits (58), Expect = 7.5
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 33 GRGALAGPVVV---AAIILDPNNIPFG 56
GR +L GP++ AAII+ I FG
Sbjct: 69 GRMSLIGPLIEEAEAAIIVGDAPILFG 95
>gnl|CDD|152733 pfam12298, Bot1p, Eukaryotic mitochondrial regulator protein.
This family of proteins is found in eukaryotes.
Proteins in this family are typically between 168 and
381 amino acids in length. Bot1p localizes to the
mitochondria in live cells and cofractionates with
purified mitochondrial ribosomes. Bot1p has a novel
function in the control of cell respiration by acting
on the mitochondrial protein synthesis machinery.
Observations also indicate that in fission yeast,
alterations of mitochondrial function are linked to
changes in cell cycle and cell morphology control
mechanisms.
Length = 171
Score = 25.8 bits (57), Expect = 8.4
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 54 PFGINDSKK----ISHKKREELYEKITSSAIISISSASHQY 90
PF +N K IS + RE++YE +T +S+ S +Y
Sbjct: 4 PFPLNPYFKTNPVISEELREKIYEDVTVDG-LSVQEVSVKY 43
>gnl|CDD|178895 PRK00140, rplK, 50S ribosomal protein L11; Validated.
Length = 141
Score = 25.9 bits (58), Expect = 8.7
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 150 SIIAKVTRDRLMRIAHKKYPD 170
+ K+TR ++ IA K PD
Sbjct: 95 EKVGKITRAQVREIAETKMPD 115
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
0.320 0.135 0.397
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,462,360
Number of extensions: 217110
Number of successful extensions: 487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 470
Number of HSP's successfully gapped: 29
Length of query: 209
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 120
Effective length of database: 4,071,361
Effective search space: 488563320
Effective search space used: 488563320
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 (21.8 bits)
S2: 55 (24.9 bits)