RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase
protein, ribosomal large subunit D [Candidatus Liberibacter asiaticus
str. psy62]
(340 letters)
>gnl|CDD|161659 TIGR00005, rluA_subfam, pseudouridine synthase, RluA family.
modifies uracil-65 in transfer RNAs to pseudouridine.
Length = 299
Score = 315 bits (809), Expect = 1e-86
Identities = 138/316 (43%), Positives = 191/316 (60%), Gaps = 24/316 (7%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83
R+D +LA+ L + SRS ++ LI NG + +NG V+ NP KV GD + VP ++ +
Sbjct: 7 RLDDFLASLLPD-LSRSRIQKLIENGQVKVNGKVTANPKLKVKDGDRITVRVPEEEEHEV 65
Query: 84 AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143
++IPLDIL+ED+DIIVINKP+GLVVHP GN GT++NALL HC I GV+R G
Sbjct: 66 PPQDIPLDILFEDEDIIVINKPSGLVVHPGGGNPFGTVLNALLAHC----PPIAGVERVG 121
Query: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
IVHRLD+DT+G+MVVAK LA ++L Q + + + Y A+V G G ++AP
Sbjct: 122 IVHRLDRDTSGLMVVAKTPLALRELQRQLKNRT----VTKEYVALVHGQFDSGGGTVDAP 177
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
LGR +NR AV A+TH++ +E N+ SL++C LETGRTHQIRVH
Sbjct: 178 LGRVPNNRGLMAVH--PSSEGKPAVTHFRVLE-RFGNA----SLVECELETGRTHQIRVH 230
Query: 264 MAHKGNPLIGDPLYG-KGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQDMDF 322
+ + G+PL GDPLYG K N RQALHA+ L F HP + ++F
Sbjct: 231 LQYLGHPLAGDPLYGNKPVPGNNLNGLLN-------FDRQALHAYELGFIHPATGEILEF 283
Query: 323 QVPIPEDMLTVIRKLN 338
+ P+P D++ ++ L
Sbjct: 284 EAPLPADLVLLLEALR 299
>gnl|CDD|183020 PRK11180, rluD, 23S rRNA pseudouridine synthase D; Provisional.
Length = 325
Score = 255 bits (654), Expect = 1e-68
Identities = 128/326 (39%), Positives = 179/326 (54%), Gaps = 26/326 (7%)
Query: 17 SDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76
S+S R+D+ LA L +SRS +K IL+ + +NG V P KV+ G+ I
Sbjct: 12 SESQLGQRLDQALA-ELFPDYSRSRIKEWILDQRVLVNGKVINKPKEKVLGGEQVAIDAE 70
Query: 77 AAQKLNIAQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSI 136
++ ++IPLDI+YEDDDI+VINKP LVVHP GN GT++NALL++ I
Sbjct: 71 IEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYY----PPI 126
Query: 137 NGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPD 196
V R GIVHRLDKDTTG+MVVAK A +L V+ + + R Y A+ G +
Sbjct: 127 ADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRL----VEALQKREITREYEAVAIGH-MTA 181
Query: 197 SGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGR 256
G ++ P+ R + R AV A+THY+ +E + + L+ LETGR
Sbjct: 182 GGTVDEPISRHPTKRTHMAVH----PMGKPAVTHYRIMEHFR-----VHTRLRLRLETGR 232
Query: 257 THQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSL---ARQALHAHSLSFSH 313
THQIRVHMAH +PL+GD +YG + ++ I +L RQALHA L H
Sbjct: 233 THQIRVHMAHITHPLVGDQVYGG----RPRPPKGASEEFISTLRKFDRQALHATMLRLYH 288
Query: 314 PRNNQDMDFQVPIPEDMLTVIRKLNE 339
P +M++ P+P+DM+ +I L
Sbjct: 289 PITGIEMEWHAPLPQDMVELIEALRA 314
>gnl|CDD|182909 PRK11025, PRK11025, 23S rRNA pseudouridylate synthase C;
Provisional.
Length = 317
Score = 124 bits (313), Expect = 3e-29
Identities = 107/352 (30%), Positives = 161/352 (45%), Gaps = 57/352 (16%)
Query: 7 NCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVV 66
S+KI +S A RID +L T LK +S + ++ G + +N K P K+
Sbjct: 4 ETPSVKIVTISADEAGQRIDNFLRTQLK-GVPKSMIYRILRKGEVRVNKKRIK-PEYKLE 61
Query: 67 PGDSFLI---------TVPAAQKLN-IAQENIPLDILYEDDDIIVINKPAGLVVHPAPGN 116
GD I + KL +A + ILYEDD I+V+NKP+G VH G
Sbjct: 62 AGDEVRIPPVRVAEREEEAVSPKLQKVAA--LADVILYEDDHILVLNKPSGTAVHGGSGL 119
Query: 117 WTGTLVNALLYHCHNNLSSINGVK--RPG-----IVHRLDKDTTGVMVVAKNDLAHQKLS 169
G I G++ RP +VHRLD+DT+GV++VAK A + L
Sbjct: 120 SFGV---------------IEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLH 164
Query: 170 EQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKSNRLRRAVKGIDDKTADSAIT 229
EQ + G +++ Y A+V G ++ APL + R V+ + + S T
Sbjct: 165 EQLREKG----MQKDYLALVRGQWQSHVKVVQAPLLKNILQSGERIVR-VSQEGKPSE-T 218
Query: 230 HYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGNPLIGDPLYG-KGFKTKANIV 288
++ E Y FA +L++ TGRTHQIRVH + G+P+ D YG + F
Sbjct: 219 RFKVEERYA----FA-TLVRASPVTGRTHQIRVHTQYAGHPIAFDDRYGDREF------- 266
Query: 289 NNNAKSAILSLARQALHAHSLSFSHPRNNQDMDFQVPIPEDMLTVIRKLNEK 340
+ + L R LHA +L F+HP + M + P+ E + ++KL
Sbjct: 267 --DQQLTGTGLNRLFLHAAALKFTHPGTGEVMRIEAPLDEQLKRCLQKLRNA 316
>gnl|CDD|182971 PRK11112, PRK11112, tRNA pseudouridine synthase C; Provisional.
Length = 257
Score = 116 bits (293), Expect = 7e-27
Identities = 72/265 (27%), Positives = 127/265 (47%), Gaps = 47/265 (17%)
Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTG---------TLVNALLYHCHNNLSSINGVK 140
L+ILY+D+ ++ +NKPAG +VH + W T+ + + H
Sbjct: 2 LEILYQDEWLVAVNKPAGWLVHRS---WLDRHETVFVMQTVRDQIGQHVFT--------- 49
Query: 141 RPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGII 200
HRLD+ T+GV+++A + + L++QF H ++++ Y+A+V G L + ++
Sbjct: 50 ----AHRLDRPTSGVLLMALSSEVARLLAQQFEQH----QIQKTYHAIVRGW-LMEEAVL 100
Query: 201 NAPLGRCKSNRLRRAVKGID-DKTADSAITHYQ---TIEIYNKNSNFAV---SLLKCHLE 253
+ PL K + A K DK A+THY+ T+E+ + SL++ +
Sbjct: 101 DYPL---KEELDKIADKFAREDKAPQPAVTHYRGLATVEMPVATGRYPTTRYSLVELEPK 157
Query: 254 TGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSH 313
TGR HQ+R HMAH +P+IGD +G ++ N + + +R LHA LS +H
Sbjct: 158 TGRKHQLRRHMAHLRHPIIGDTKHG-------DLRQNRSLAEHFGCSRLMLHASELSLTH 210
Query: 314 PRNNQDMDFQVPIPEDMLTVIRKLN 338
P + + + E ++ +
Sbjct: 211 PFTGEPLTITAGLDETWQQLLSQFG 235
>gnl|CDD|182274 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A;
Provisional.
Length = 219
Score = 114 bits (287), Expect = 3e-26
Identities = 83/242 (34%), Positives = 119/242 (49%), Gaps = 43/242 (17%)
Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKR--PGI--V 145
L ILY+D+ I+V+NKP+GL+ P G L H + S + ++R P V
Sbjct: 14 LVILYQDEHIMVVNKPSGLLSVP------GRLEE------HKD-SVMTRIQRDYPQAESV 60
Query: 146 HRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLG 205
HRLD T+GV+VVA A ++L QF + K+ Y A VWG P P G+++ PL
Sbjct: 61 HRLDMATSGVIVVALTKAAERELKRQF----REREPKKQYVARVWGHPSPAEGLVDLPLI 116
Query: 206 RCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMA 265
NR ++ V +T A T Y+ +E N+ A +LK TGR+HQ+RVHM
Sbjct: 117 CDWPNRPKQKVCY---ETGKPAQTEYEVVEYAADNT--ARVVLKP--ITGRSHQLRVHML 169
Query: 266 HKGNPLIGDPLYGKGFKTKANIVNNNAKSAILSLA-RQALHAHSLSFSHPRNNQDMDFQV 324
G+P++GD Y A ++A R LHA L+ +HP M F+
Sbjct: 170 ALGHPILGDRFY--------------ASPEARAMAPRLLLHAEMLTITHPAYGNSMTFKA 215
Query: 325 PI 326
P
Sbjct: 216 PA 217
>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 = 96.1 bits (239), Expect = 1e-20
Identities = 65/229 (28%), Positives = 107/229 (46%), Gaps = 41/229 (17%)
Query: 90 LDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLD 149
+IL+ D ++INK G+ VH G TG L +++ GV + +VHRLD
Sbjct: 2 FEILFTHPDFLLINKHPGISVHKDDGE-TGLL---------QEVATQLGVGQVWLVHRLD 51
Query: 150 KDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAPLGRCKS 209
K T+G++++A N + +LS+ F ++++ Y A+ P G+I +
Sbjct: 52 KMTSGILLLALNAESASELSQGFAKR----KIEKTYLALSSKKPKKKQGLICGDM----- 102
Query: 210 NRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVHMAHKGN 269
+ RR + + + AIT + + F +LK H TG+THQ+RV M G+
Sbjct: 103 EKSRRGSWKLVNSQENPAITRFFSASAATGLRLF---ILKPH--TGKTHQLRVAMKSLGS 157
Query: 270 PLIGDPLYGKGFKTKANIVNNNAKSAILSLARQALHAHSLSFSHPRNNQ 318
P++GDPLYG ++ R LHA +L F + +N
Sbjct: 158 PILGDPLYGTTDESD----------------RGYLHAFALRFDY-QNEV 189
>gnl|CDD|183115 PRK11394, PRK11394, 23S rRNA pseudouridine synthase E; Provisional.
Length = 217
Score = 40.1 bits (93), Expect = 8e-04
Identities = 44/167 (26%), Positives = 65/167 (38%), Gaps = 27/167 (16%)
Query: 136 INGVKRPGIVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLP 195
+ GV G RLD+D+ G++V+ N +L++ GK R + YY V GIP
Sbjct: 69 VQGVYAAG---RLDRDSEGLLVLTNNGALQARLTQP----GK--RTGKIYYVQVEGIPTQ 119
Query: 196 DSGIINAPLGRCKSNRLRRAVKGIDDKTADSAITHYQTIE-IYNKN------SNFAVSLL 248
D+ LR V D T + ++ +N + S L
Sbjct: 120 DA-----------LEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTSWL 168
Query: 249 KCHLETGRTHQIRVHMAHKGNPLIGDPLYGKGFKTKANIVNNNAKSA 295
K L GR Q+R AH G P + Y G + N+ N + A
Sbjct: 169 KITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREA 215
>gnl|CDD|161704 TIGR00093, TIGR00093, pseudouridine synthase. This model
identifies panels of pseudouridine synthase enzymes that
RNA modifications involved in maturing the protein
translation apparatus. Counts per genome vary: two in
Staphylococcus aureus, three in Pseudomonas putida, four
in E. coli, etc.
Length = 128
Score = 37.3 bits (87), Expect = 0.006
Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 27/127 (21%)
Query: 145 VHRLDKDTTGVMVVAKN-DLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203
RLD+D+ G++++ + +L H+ ++ Y V G +
Sbjct: 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGH-------HCEKTYLVTVEGPVTDE------- 46
Query: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIRVH 263
LR+ V+ ++D A + I + ++L + GR Q+R
Sbjct: 47 ----DLEALRKGVQ-LEDGPTKPAKL--EVITEPGFPTWLRITLSE-----GRNRQVRRM 94
Query: 264 MAHKGNP 270
A G P
Sbjct: 95 FAAVGFP 101
>gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain.
Length = 60
Score = 36.8 bits (86), Expect = 0.008
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 24 RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVP 76
R+D++LA L SRS + LI G + +NG P+ V PGD +I+V
Sbjct: 2 RLDKFLA-RLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGD--VISVR 51
>gnl|CDD|129570 TIGR00478, tly, hemolysin TlyA family protein. Hemolysins are
exotoxins that attack blood cell membranes and cause
cell rupture, often by forming a pore in the membrane.
At least two members of this protein family have been
characterized indirectly as pore-forming hemolysins,
one from the spirochete Serpula (Treponema)
hyodysenteriae and one from Mycobacterium tuberculosis.
However, homology domains in this protein suggest
methyltransferase activity (pfam01728) and RNA-binding
activity (pfam01479).
Length = 228
Score = 31.3 bits (71), Expect = 0.34
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 38 SRSYVKILILNGFISINGMVSKNPNRKV 65
SR K LIL GF+ +NG P+ V
Sbjct: 14 SREKAKRLILKGFVLVNGKKVDKPSALV 41
>gnl|CDD|178682 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 30.2 bits (68), Expect = 0.73
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 2 QQTLDNCSSIKISLLSDSTAEGRIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKN 60
++T DNCSS K + D T R L E+FS +++ + + G S+N V K+
Sbjct: 859 KKTCDNCSSSKSLIDKDVTEIARQLVELVKLTGERFSSAHI-LEVYRG--SLNQYVKKH 914
>gnl|CDD|178017 PLN02394, PLN02394, trans-cinnamate 4-monooxygenase.
Length = 503
Score = 29.7 bits (67), Expect = 1.1
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 102 INKPAGLVVHPAPGNW--TGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVA 159
+ P G P GNW G +N H NL+ + K+ G V L ++VV+
Sbjct: 29 LKLPPGPAAVPIFGNWLQVGDDLN------HRNLAEMA--KKYGDVFLLRMGQRNLVVVS 80
Query: 160 KNDLAHQKLSEQFVDHGKSTR 180
+LA + L Q V+ G TR
Sbjct: 81 SPELAKEVLHTQGVEFGSRTR 101
>gnl|CDD|152404 pfam11969, DcpS_C, Scavenger mRNA decapping enzyme C-term binding.
This family consists of several scavenger mRNA decapping
enzymes (DcpS) and is the C-terminal region. DcpS is a
scavenger pyrophosphatase that hydrolyses the residual
cap structure following 3' to 5' decay of an mRNA. The
association of DcpS with 3' to 5' exonuclease exosome
components suggests that these two activities are linked
and there is a coupled exonucleolytic decay-dependent
decapping pathway. The C-terminal domain contains a
histidine triad (HIT) sequence with three histidines
separated by hydrophobic residues. The central histidine
within the DcpS HIT motif is critical for decapping
activity and defines the HIT motif as a new mRNA
decapping domain, making DcpS the first member of the
HIT family of proteins with a defined biological
function.
Length = 113
Score = 28.7 bits (65), Expect = 2.3
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 83 IAQENIPLDILYEDDDIIVIN 103
I P I+YEDD +
Sbjct: 7 IINGEEPERIVYEDDGFVAFK 27
>gnl|CDD|184908 PRK14944, PRK14944, DNA polymerase III subunit beta; Provisional.
Length = 375
Score = 28.3 bits (63), Expect = 3.2
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 53 INGMVSKNPNRKVVPGDSF-----LITVPAAQKLNIAQENIPLDILYEDDDIIVINK 104
IN SKN R ++ G + L+ A ++Q+ I LD Y + +I++ NK
Sbjct: 145 INISTSKNEKRPILTGLNLIYQKNLLKALATDSFRMSQKKIKLDFNYHNFNIVIPNK 201
>gnl|CDD|179429 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 27.3 bits (61), Expect = 5.8
Identities = 22/83 (26%), Positives = 30/83 (36%), Gaps = 31/83 (37%)
Query: 99 IIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVV 158
II + K AG+ H A ++ L I K+ G LD D GV+ +
Sbjct: 5 IINLKKEAGMTSHDA------------VFK----LRKILQTKKIGHGGTLDPDVVGVLPI 48
Query: 159 AKNDLAHQKLSEQFVDHGKSTRL 181
A GK+TRL
Sbjct: 49 AV---------------GKATRL 56
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 26.9 bits (60), Expect = 7.3
Identities = 22/82 (26%), Positives = 30/82 (36%), Gaps = 31/82 (37%)
Query: 100 IVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPGIVHRLDKDTTGVMVVA 159
+ ++KPAGL H C L + +KR G LD TGV+ +A
Sbjct: 6 LNLDKPAGLTSH----------------DCVARLRRLLRLKRVGHGGTLDPAATGVLPIA 49
Query: 160 KNDLAHQKLSEQFVDHGKSTRL 181
GK+TRL
Sbjct: 50 L---------------GKATRL 56
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
0.318 0.134 0.395
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,473,326
Number of extensions: 345636
Number of successful extensions: 726
Number of sequences better than 10.0: 1
Number of HSP's gapped: 706
Number of HSP's successfully gapped: 22
Length of query: 340
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 246
Effective length of database: 3,963,321
Effective search space: 974976966
Effective search space used: 974976966
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 (21.7 bits)
S2: 57 (26.0 bits)