RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780608|ref|YP_003065021.1| ribosomal large subunit
pseudouridine synthase C [Candidatus Liberibacter asiaticus str.
psy62]
(346 letters)
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C;
Provisional.
Length = 317
Score = 175 bits (446), Expect = 1e-44
Identities = 109/312 (34%), Positives = 173/312 (55%), Gaps = 16/312 (5%)
Query: 7 VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
V+ V + DE R+D + + + + +ILR G+VRV+KKR+K ++++G VR
Sbjct: 8 VKIVTISADEAGQRIDNFLRTQLKGVPKSMIYRILRKGEVRVNKKRIKPEYKLEAGDEVR 67
Query: 67 IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
IPPV A E++ S L K + L ++LYED I V NKP+G +V GGSG++
Sbjct: 68 IPPVRVA------EREEEAVSPKLQKVAA-LADVILYEDDHILVLNKPSGTAVHGGSGLS 120
Query: 127 YHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSL 186
+ + L++ + + + L HRLD++TSG+L+VA+ R+A + L E R + +QK Y +L
Sbjct: 121 FGVIEGLRA-LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLAL 179
Query: 187 VWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWL-EM 245
V G ++ + + LLK G+ +V+ +++G + + FKV + +A F L
Sbjct: 180 VRGQWQSHVKVVQAPLLKNILQSGE--RIVRVSQEGKP-SETRFKVEERYA--FATLVRA 234
Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYC-ANFKGNFTSPIQNKLYLHARYMDLPHPEGG- 303
P TGRTHQ+RVH + G PI D +Y F T N+L+LHA + HP G
Sbjct: 235 SPVTGRTHQIRVHTQYAGHPIAFDDRYGDREFDQQLTGTGLNRLFLHAAALKFTHPGTGE 294
Query: 304 RLQITAPLPAHM 315
++I APL +
Sbjct: 295 VMRIEAPLDEQL 306
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family.
modifies uracil-65 in transfer RNAs to pseudouridine.
Length = 299
Score = 171 bits (436), Expect = 2e-43
Identities = 91/317 (28%), Positives = 150/317 (47%), Gaps = 41/317 (12%)
Query: 15 DEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINAL 74
++ RLD + + P ++ +QK++ +GQV+V+ K V N +++ RI +
Sbjct: 2 EQAGQRLDDFLASLLPDLSRSRIQKLIENGQVKVNGK-VTANPKLKVKDGDRITVRVPEE 60
Query: 75 --NHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYH--ID 130
+ + + LD +L+ED I V NKP+G+ V G G + ++
Sbjct: 61 EEHEVPPQDIPLD---------------ILFEDEDIIVINKPSGLVVHPGGGNPFGTVLN 105
Query: 131 GFLKSWVDSKG-QKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
L G ++ + HRLD++TSG++VVA+T A + L + R + K Y +LV G
Sbjct: 106 ALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYVALVHG 165
Query: 190 IPKNKK-ECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPH 248
+ A ++ G VH + +G A++HF+V++ F +E +
Sbjct: 166 QFDSGGGTVDAPLGRVPNNRGLMAVH---PSSEGKP-AVTHFRVLERF-GNASLVECELE 220
Query: 249 TGRTHQLRVHALHMGCPIVGDHKY--------CANFKGNFTSPIQNKLYLHARYMDLPHP 300
TGRTHQ+RVH ++G P+ GD Y N NF ++ LHA + HP
Sbjct: 221 TGRTHQIRVHLQYLGHPLAGDPLYGNKPVPGNNLNGLLNF-----DRQALHAYELGFIHP 275
Query: 301 EGGR-LQITAPLPAHMV 316
G L+ APLPA +V
Sbjct: 276 ATGEILEFEAPLPADLV 292
>gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A;
Provisional.
Length = 219
Score = 100 bits (249), Expect = 7e-22
Identities = 72/208 (34%), Positives = 110/208 (52%), Gaps = 18/208 (8%)
Query: 100 ILLYEDSKIYVFNKPAGI-SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGIL 158
++LY+D I V NKP+G+ SV G + H D + + + + HRLD TSG++
Sbjct: 15 VILYQDEHIMVVNKPSGLLSVPGR--LEEHKDSVM-TRIQRDYPQAESVHRLDMATSGVI 71
Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
VVA T+AA + L FR R +K Y + VWG P + + L+ D+ + KQ
Sbjct: 72 VVALTKAAERELKRQFREREPKKQYVARVWGHPSPAEGLVDLPLI------CDWPNRPKQ 125
Query: 219 N---EKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCAN 275
E G A + ++V++ A + ++P TGR+HQLRVH L +G PI+GD Y A+
Sbjct: 126 KVCYETGKP-AQTEYEVVEYAADNTARVVLKPITGRSHQLRVHMLALGHPILGDRFY-AS 183
Query: 276 FKGNFTSPIQNKLYLHARYMDLPHPEGG 303
+ +P +L LHA + + HP G
Sbjct: 184 PEARAMAP---RLLLHAEMLTITHPAYG 208
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
Length = 257
Score = 99.4 bits (248), Expect = 1e-21
Identities = 69/247 (27%), Positives = 110/247 (44%), Gaps = 63/247 (25%)
Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSK-------------GQKPRLT 147
+LY+D + NKPAG V +SW+D GQ
Sbjct: 4 ILYQDEWLVAVNKPAGWLVH-------------RSWLDRHETVFVMQTVRDQIGQHVFTA 50
Query: 148 HRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSH 207
HRLD+ TSG+L++A + A+ L + F +IQK Y ++V G WL++++
Sbjct: 51 HRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYHAIVRG-----------WLMEEAV 99
Query: 208 IGGDYVHVVK---------QNEKGANYAISHFKV---------IDCFA-QKFCWLEMQPH 248
+ DY + + +K A++H++ + ++ +E++P
Sbjct: 100 L--DYPLKEELDKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157
Query: 249 TGRTHQLRVHALHMGCPIVGDHKYCANFKGN--FTSPIQ-NKLYLHARYMDLPHP-EGGR 304
TGR HQLR H H+ PI+GD K+ + + N ++L LHA + L HP G
Sbjct: 158 TGRKHQLRRHMAHLRHPIIGDTKH-GDLRQNRSLAEHFGCSRLMLHASELSLTHPFTGEP 216
Query: 305 LQITAPL 311
L ITA L
Sbjct: 217 LTITAGL 223
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional.
Length = 325
Score = 93.2 bits (232), Expect = 9e-20
Identities = 75/240 (31%), Positives = 118/240 (49%), Gaps = 31/240 (12%)
Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF----LKSWVDSKGQKPR--LTHRLDQET 154
++YED I V NKP + V G+G DG L + PR + HRLD++T
Sbjct: 86 IVYEDDDILVINKPRDLVVHPGAGNP---DGTVLNALLHYYPPIADVPRAGIVHRLDKDT 142
Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNK---KECIANWLLKKSHIGGD 211
+G++VVA+T A L E+ + R I + Y ++ G E I+ K++H+
Sbjct: 143 TGLMVVAKTVPAQTRLVEALQKREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMA-- 200
Query: 212 YVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHK 271
VH G A++H+++++ F + L ++ TGRTHQ+RVH H+ P+VGD
Sbjct: 201 -VH-----PMGKP-AVTHYRIMEHF-RVHTRLRLRLETGRTHQIRVHMAHITHPLVGDQV 252
Query: 272 YCA------NFKGNFTSPIQN--KLYLHARYMDLPHP-EGGRLQITAPLPAHMVKTWDSL 322
Y F S ++ + LHA + L HP G ++ APLP MV+ ++L
Sbjct: 253 YGGRPRPPKGASEEFISTLRKFDRQALHATMLRLYHPITGIEMEWHAPLPQDMVELIEAL 312
>gnl|CDD|130682 TIGR01621, RluA-like, pseudouridine synthase Rlu family protein,
TIGR01621. This model represents a clade of sequences
within the pseudouridine synthase superfamily
(pfam00849). The superfamily includes E. coli proteins:
RluA, RluB, RluC, RluD, and RsuA. The sequences modeled
here are most closely related to RluA. Neisseria, among
those species hitting this model, does not appear to
have an RluA homolog. It is presumed that these
sequences function as pseudouridine synthases, although
perhaps with different specificity.
Length = 217
Score = 88.4 bits (219), Expect = 2e-18
Identities = 63/213 (29%), Positives = 95/213 (44%), Gaps = 22/213 (10%)
Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPR--LTHRLDQETSGIL 158
+L+ + NK GISV G + L V ++ + L HRLD+ TSGIL
Sbjct: 4 ILFTHPDFLLINKHPGISVHKDDG-----ETGLLQEVATQLGVGQVWLVHRLDKMTSGIL 58
Query: 159 VVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
++A +A L++ F R+I+K Y +L PK K+ I ++KS G K
Sbjct: 59 LLALNAESASELSQGFAKRKIEKTYLALSSKKPKKKQGLICGD-MEKSRRG-----SWKL 112
Query: 219 NEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKG 278
N AI+ F A ++PHTG+THQLRV +G PI+GD Y +
Sbjct: 113 VNSQENPAITRFFSASA-ATGLRLFILKPHTGKTHQLRVAMKSLGSPILGDPLYGTTDE- 170
Query: 279 NFTSPIQNKLYLHARYMDLPHPEGGRLQITAPL 311
++ YLHA + + + +Q
Sbjct: 171 ------SDRGYLHAFALRFDY-QNEVIQWLCDP 196
>gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 33.3 bits (77), Expect = 0.095
Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVIN 72
RLD++ + +K++ G+V+V+ K+V + ++ G V+ +
Sbjct: 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55
>gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional.
Length = 217
Score = 33.2 bits (75), Expect = 0.098
Identities = 42/166 (25%), Positives = 70/166 (42%), Gaps = 16/166 (9%)
Query: 104 EDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVART 163
+ +++ +FNKP + Q LK ++ +G RLD+++ G+LV+
Sbjct: 37 QPTRVILFNKPYDVLPQFTDEAGRKT---LKEFIPVQGVYA--AGRLDRDSEGLLVLTNN 91
Query: 164 RAAAQHLTESFRMRRIQKIYWSLVWGIP-KNKKECIANWL-LKKSHIGGDYVHVVKQNE- 220
A LT+ +R KIY+ V GIP ++ E + N + L +V +
Sbjct: 92 GALQARLTQP--GKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 149
Query: 221 -KGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCP 265
N I K I WL++ + GR Q+R H+G P
Sbjct: 150 LWPRNPPIRERKSIPT-----SWLKITLYEGRNRQVRRMTAHVGFP 190
>gnl|CDD|131605 TIGR02554, PrgH, type III secretion system protein PrgH/EprH. In
Samonella, this gene is part of a four-gene operon
PrgHIJK and in general is found in type III secretion
operons. PrgH has been shown to be required for
secretion, as well as being a structural component of
the needle complex.
Length = 389
Score = 29.5 bits (66), Expect = 1.2
Identities = 8/27 (29%), Positives = 10/27 (37%)
Query: 11 VVENDEENMRLDRWFKNHYPHINFVNL 37
V E R+ RW P + F L
Sbjct: 219 VAVIGAERQRVSRWLDEAGPQLAFYRL 245
>gnl|CDD|148052 pfam06218, NPR2, Nitrogen permease regulator 2. This family of
regulators are involved in post-translational control of
nitrogen permease.
Length = 400
Score = 28.8 bits (65), Expect = 2.2
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 64 VVRIPPVINALNHIIKEQKILDSSVNLTK 92
+ +I P IN +N + + + D NL K
Sbjct: 199 MQKILPYINGINSVARIAALADVDYNLVK 227
>gnl|CDD|182468 PRK10446, PRK10446, ribosomal protein S6 modification protein;
Provisional.
Length = 300
Score = 28.3 bits (63), Expect = 2.6
Identities = 29/93 (31%), Positives = 46/93 (49%), Gaps = 13/93 (13%)
Query: 84 LDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQK 143
L+ SV + + D L+S+ L I + P +GIA+ D +D G
Sbjct: 88 LNESVAIARARDKLRSMQLLARQGI---DLPV-------TGIAHSPDD-TSDLIDMVGGA 136
Query: 144 PRLTHRLDQETSGI-LVVARTRAAAQHLTESFR 175
P L +L + T GI +V+A TR AA+ + ++FR
Sbjct: 137 P-LVVKLVEGTQGIGVVLAETRQAAESVIDAFR 168
>gnl|CDD|139571 PRK13434, PRK13434, F0F1 ATP synthase subunit delta; Provisional.
Length = 184
Score = 27.2 bits (60), Expect = 5.7
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 3/62 (4%)
Query: 34 FVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKH 93
F+ L +I + V +DKK+ + +I S + P ++ L I+ E+ S L
Sbjct: 84 FIYLPEIQKDFTVELDKKKGRVRAQIVSYPSLE-PAQVDKLGSILSEK--FKSEFILEVS 140
Query: 94 SD 95
D
Sbjct: 141 ED 142
>gnl|CDD|148071 pfam06243, PaaB, Phenylacetic acid degradation B. Phenylacetic
acid degradation protein B (PaaB) is thought to be part
of a multicomponent oxygenase involved in
phenylacetyl-CoA hydroxylation.
Length = 92
Score = 26.9 bits (60), Expect = 8.6
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 277 KGNFTSPIQNKLYLHARYMDLPHPEG 302
K +F +P +K+Y H + ++P G
Sbjct: 65 KDSFFAPADDKVYRHPTFYEVPDGVG 90
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
0.323 0.138 0.430
Gapped
Lambda K H
0.267 0.0670 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,661,891
Number of extensions: 354239
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 597
Number of HSP's successfully gapped: 20
Length of query: 346
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 252
Effective length of database: 3,963,321
Effective search space: 998756892
Effective search space used: 998756892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 58 (26.2 bits)