BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 009530
(532 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|Q96PZ0|PUS7_HUMAN Pseudouridylate synthase 7 homolog OS=Homo sapiens GN=PUS7 PE=1
SV=2
Length = 661
Score = 291 bits (746), Expect = 7e-78, Method: Compositional matrix adjust.
Identities = 176/512 (34%), Positives = 261/512 (50%), Gaps = 106/512 (20%)
Query: 23 NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQ 82
+WP+ G + F LYKENKDT +A+ ++SK L + P F + GTKDKR+++ Q + V K
Sbjct: 249 SWPKSRGSYCHFVLYKENKDTMDAINVLSKYLRVKPNIFSYMGTKDKRAITVQEIAVLKI 308
Query: 83 RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
A +LA LNK L+ +LG+F Y K L LG+L GN FT+ LR + ++D ++ + NSL
Sbjct: 309 TAQRLAHLNKCLMNFKLGNFSYQKNPLKLGELQGNHFTVVLRN-ITGTDDQVQQAMNSLK 367
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREG-ERNEISKAREYYKE 201
GFINY+G+QRFG+ +VPT+ VG +L+ W + +IL PR G E+ + K RE + +
Sbjct: 368 EIGFINYYGMQRFGTTAVPTYQVGRAILQNSWTEVMDLILKPRSGAEKGYLVKCREEWAK 427
Query: 202 TDDIDGTLRKLPRHLVAERAILQCLKKCP-GNYLQALKAIPRTLRMMYVHSYQSFLWNHA 260
T D LRKLP E +L+ L K N + A IPR R+MY+HSYQS++WN+
Sbjct: 428 TKDPTAALRKLPVKRCVEGQLLRGLSKYGMKNIVSAFGIIPRNNRLMYIHSYQSYVWNNM 487
Query: 261 ASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHP 320
S R++ +G + V GDLV KG +++++E
Sbjct: 488 VSKRIEDYGLKP-VPGDLVL-KG----------------------ATATYIEE------- 516
Query: 321 DGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESL 380
D+N+ Y+I DVV+PLPG VIYP + + E Y + D +++
Sbjct: 517 ------------DDVNN--YSIHDVVMPLPGFDVIYPKHKIQEAYREMLTADNLDIDNMR 562
Query: 381 HNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEE 440
H ++++ S++G YR++ +P + WE++ Y D PL TD+D +
Sbjct: 563 HKIRDY---SLSGAYRKIIIRPQNVSWEVVAYDDPKIPLFNTDVDNL------------- 606
Query: 441 AVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESVCGADSQGKQMALK 500
E K P V + S+GK ALK
Sbjct: 607 -------------------------------------EGKTPPVFA-----SEGKYRALK 624
Query: 501 LGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532
+ +LP S YATMAIRE+LK TS+ LN
Sbjct: 625 MDFSLPPSTYATMAIREVLKMDTSIKNQTQLN 656
>sp|Q08647|PUS7_YEAST Multisubstrate pseudouridine synthase 7 OS=Saccharomyces cerevisiae
(strain ATCC 204508 / S288c) GN=PUS7 PE=1 SV=1
Length = 676
Score = 287 bits (735), Expect = 1e-76, Method: Compositional matrix adjust.
Identities = 189/543 (34%), Positives = 284/543 (52%), Gaps = 86/543 (15%)
Query: 2 GRNSKKRK-ERGDNPFDSRGSENWPEQLGK-FLRFHLYKENKDTQEALGLISKMLGILPR 59
RNS+ K E+ + D+ G ENW K F+ F L+KENKDT EA+ +I+K+L + R
Sbjct: 188 NRNSRTNKQEKINQTRDANGVENWGYGPSKDFIHFTLHKENKDTMEAVNVITKLLRVPSR 247
Query: 60 SFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRF 119
+AGTKD+R+V+ QRV++ K +L ALN+ L G+ +G++ + L LG L GN F
Sbjct: 248 VIRYAGTKDRRAVTCQRVSISKIGLDRLNALNRTLKGMIIGNYNFSDASLNLGDLKGNEF 307
Query: 120 TITLRGVV-----VDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEW 174
+ +R V V E+++ SL NGFINYFG+QRFG+ S+ TH +G LL W
Sbjct: 308 VVVIRDVTTGNSEVSLEEIVSNGCKSLSENGFINYFGMQRFGTFSISTHTIGRELLLSNW 367
Query: 175 KSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCL----KKCP 230
K A ++IL ++ + +AR+ + ET D L+++PR +AE A+L L K+
Sbjct: 368 KKAAELILSDQDNVLPKSKEARKIWAETKDAALALKQMPRQCLAENALLYSLSNQRKEED 427
Query: 231 GNYLQ-----ALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDD 285
G Y + A+ IPR LR MYVH+YQS++WN AS R++ HG + +VVGDLV D
Sbjct: 428 GTYSENAYYTAIMKIPRNLRTMYVHAYQSYVWNSIASKRIELHGLK-LVVGDLVI----D 482
Query: 286 TEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDV 345
T ++ ++ D DE D + + K VT DI+S KYT++DV
Sbjct: 483 TSEKSPLIS----------GIDDEDFDE----DVREAQFIRAKAVTQEDIDSVKYTMEDV 528
Query: 346 VLPLPGSRVIYPMN-DVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMD 404
VLP PG V+YP N ++ ++Y + + D ++ V++F S+ G+YR V QKP
Sbjct: 529 VLPSPGFDVLYPSNEELKQLYVDILKADNMDPFNMRRKVRDF---SLAGSYRTVIQKPKS 585
Query: 405 FEWELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDI 464
E+ ++ Y D ++ L TDLD + +
Sbjct: 586 LEYRIIHYDDPSQQLVNTDLDILNNTR--------------------------------- 612
Query: 465 KLSTENNEAACAKEVKQPHVESVCG---ADSQGKQMALKLGLTLPSSCYATMAIRELLKT 521
AKE Q ++++ D G++ A+ L L +S YATMA+REL+K
Sbjct: 613 -----------AKESGQKYMKAKLDRYMPDKGGEKTAVVLKFQLGTSAYATMALRELMKL 661
Query: 522 STS 524
TS
Sbjct: 662 ETS 664
>sp|O74343|YH2X_SCHPO Putative pseudouridine synthase C1A4.09 OS=Schizosaccharomyces
pombe (strain 972 / ATCC 24843) GN=SPBC1A4.09 PE=3 SV=1
Length = 680
Score = 280 bits (717), Expect = 1e-74, Method: Compositional matrix adjust.
Identities = 178/521 (34%), Positives = 269/521 (51%), Gaps = 93/521 (17%)
Query: 23 NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQ 82
+W G++ FHLYKEN+D+ + LG I+++L + R+ AGTKD+R V+ QRV +
Sbjct: 232 SWKALGGEYCHFHLYKENRDSMDCLGKIARLLKVPTRTLSIAGTKDRRGVTCQRVAIHHV 291
Query: 83 RASKLAALN-----KRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKAS 137
RAS+LA LN G LG++ Y L LG L GN F I +R V+ E V++A
Sbjct: 292 RASRLAQLNSGSLKNSTYGFLLGNYSYKNSNLRLGDLKGNEFHIVVRNVITPKEKVVEA- 350
Query: 138 ANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKARE 197
NSL +GFINYFGLQRFG+ SV TH +G LL+ +WK AV +IL PR + +A +
Sbjct: 351 LNSLKEHGFINYFGLQRFGTSSVGTHTIGVRLLQSDWKGAVDLILSPRPEHTGSVKEAID 410
Query: 198 YYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGN---YLQALKAIPRTLRMMYVHSYQS 254
+ T D + +LR LPR ++AE +IL+ + GN YL A + IPR LR +Y H+YQS
Sbjct: 411 LWHSTHDAEASLRILPRRMIAESSILETWSRS-GNQTDYLGAFQRIPRHLRSIYPHAYQS 469
Query: 255 FLWNHAASARVQKHGTEHVVVGDLVF-CKGDDTEKELGCVNPEFEYESSNDADDSSHLDE 313
++WN AS R++ G + VVGDLV+ + + ++ V+PE A D L++
Sbjct: 470 YVWNRVASWRIKNLG-DRPVVGDLVYSTESNGLSQKSPIVDPE--------APDL--LED 518
Query: 314 VPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHL---AE 370
+P + R + ++N+ ++I D+VLPLPG VIYP N+ ++Y + A
Sbjct: 519 LPVSSKLSAR-----PIEEDEVNN--FSIYDIVLPLPGRNVIYPKNETFDIYKSVMNEAS 571
Query: 371 KDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKA 430
D +N++ + S+ G+YR++ +P + E+ + Y + + L TD D++
Sbjct: 572 LDPLNMSRKDREL------SLPGDYRKLLVRPENMEFNFIKYDNMEQQLILTDKDRL--- 622
Query: 431 KLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESVCGA 490
EN + + EV
Sbjct: 623 --------------------------------------ENRSISVSSEV----------- 633
Query: 491 DSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTL 531
GK A+ L LPSS YATMA+RE L+T+T+ + L
Sbjct: 634 ---GKHTAVTLKFVLPSSAYATMALREALRTATASGDQRML 671
>sp|Q08DI8|PUS7_BOVIN Pseudouridylate synthase 7 homolog OS=Bos taurus GN=PUS7 PE=2 SV=1
Length = 659
Score = 270 bits (691), Expect = 2e-71, Method: Compositional matrix adjust.
Identities = 146/407 (35%), Positives = 223/407 (54%), Gaps = 51/407 (12%)
Query: 23 NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQ 82
+WP+ G + F LYKENKDT +A+ L+SK L + P F + GTKDKR+++ Q + V K
Sbjct: 247 SWPKSRGSYCHFVLYKENKDTMDAINLLSKYLRVKPNIFSYMGTKDKRAITVQEIAVLKI 306
Query: 83 RASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG 142
A +LA LNK L+ +LG+F Y K L LG+L GN FT+ LR + +++ ++ + NSL
Sbjct: 307 TAQRLAHLNKCLMNFKLGNFSYQKNPLKLGELQGNHFTVVLRN-ITGTDNQVEQAMNSLK 365
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREG-ERNEISKAREYYKE 201
GFINY+G+QRFG+ +VPT+ VG +L+ W + +IL PR G E+ + K RE + +
Sbjct: 366 EIGFINYYGMQRFGTTAVPTYQVGRAILQNSWAEVMDLILKPRSGAEKGYLVKCREEWAK 425
Query: 202 TDDIDGTLRKLPRHLVAERAILQCLKKCP-GNYLQALKAIPRTLRMMYVHSYQSFLWNHA 260
+ D LRKLP E +L+ L K N + A IPR R+MY+HSYQS++WN+
Sbjct: 426 SKDPAAALRKLPVKRCVEGQLLRGLSKYGMKNIVSAFGIIPRNNRLMYIHSYQSYVWNNM 485
Query: 261 ASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHP 320
S R+ ++G + V GDLV T
Sbjct: 486 VSKRIDEYGLKP-VPGDLVLKGATAT---------------------------------- 510
Query: 321 DGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESL 380
+ D+N+ Y+I DVV+PLPG VIYP + ++E Y + D +++
Sbjct: 511 --------FIEEDDVNN--YSIHDVVMPLPGFDVIYPKHKISEAYREMLTADNLDIDNMR 560
Query: 381 HNVKEFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKI 427
H ++++ S++G YR++ +P + WE++ Y D PL TD+D +
Sbjct: 561 HKIRDY---SLSGAYRKIIIRPQNVSWEVVAYDDPKIPLFNTDVDNL 604
Score = 47.8 bits (112), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 28/41 (68%)
Query: 492 SQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532
S+GK ALK+ +LP S YATMAIRE+LK TS+ LN
Sbjct: 614 SEGKYRALKMDFSLPPSTYATMAIREVLKMDTSIKNQTQLN 654
>sp|Q9H0K6|PUS7L_HUMAN Pseudouridylate synthase 7 homolog-like protein OS=Homo sapiens
GN=PUS7L PE=1 SV=1
Length = 701
Score = 187 bits (475), Expect = 2e-46, Method: Compositional matrix adjust.
Identities = 125/421 (29%), Positives = 216/421 (51%), Gaps = 57/421 (13%)
Query: 31 FLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAAL 90
+ F L KEN + EA+G ++ LG++P F +AG KDK++++ Q + V K +L +
Sbjct: 302 YTAFTLRKENLEMFEAIGFLAIKLGVIPSDFSYAGLKDKKAITYQAMVVRKVTPERLKNI 361
Query: 91 NKRLIGIRLGDFCY--VKEGLLLGQLLGNRFTITLRGV---VVDSEDV---IKASANSLG 142
K + R+ F V + L LGQL GN F I +R + + DS ++ I + ++
Sbjct: 362 EKEIEKKRMNVFNIRSVDDSLRLGQLKGNHFDIVIRNLKKQINDSANLRERIMEAIENVK 421
Query: 143 RNGFINYFGLQRFGSG-SVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKE 201
+ GF+NY+G QRFG G V T +G LL+ E A+K+ L P + + + +++A++Y+ +
Sbjct: 422 KKGFVNYYGPQRFGKGRKVHTDQIGLALLKNEMMKAIKLFLTPEDLD-DPVNRAKKYFLQ 480
Query: 202 TDDIDGTLRKLPRHLVAERAILQCLKK---CPGNYLQALKAIPRTLRMMYVHSYQSFLWN 258
T+D GTL +P V ERA+L+ L + +QA ++P ++R+ YVH+Y S +WN
Sbjct: 481 TEDAKGTLSLMPEFKVRERALLEALHRFGMTEEGCIQAWFSLPHSMRIFYVHAYTSKIWN 540
Query: 259 HAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETD 318
A S R++ +G VV GDLV C +D + E +
Sbjct: 541 EAVSYRLETYGAR-VVQGDLV-CLDEDIDDE----------------------------N 570
Query: 319 HPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTE 378
P+ + +LV T + ++ Y I VVLP+ G + YP N V + YH + +DG+
Sbjct: 571 FPNSKIHLV---TEEEGSANMYAIHQVVLPVLGYNIQYPKNKVGQWYHDILSRDGLQTC- 626
Query: 379 SLHNVKEFSITSMT----GNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDKIAKAKLVN 434
F + ++ G YR++ + P + ++L+ D + + +D+ A + L++
Sbjct: 627 ------RFKVPTLKLNIPGCYRQILKHPCNLSYQLMEDHDIDVKTKGSHIDETALSLLIS 680
Query: 435 I 435
Sbjct: 681 F 681
>sp|Q8CE46|PUS7L_MOUSE Pseudouridylate synthase 7 homolog-like protein OS=Mus musculus
GN=Pus7l PE=1 SV=1
Length = 702
Score = 178 bits (451), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 129/414 (31%), Positives = 206/414 (49%), Gaps = 64/414 (15%)
Query: 18 SRGSENWPE--QLGK--FLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVS 73
+RG + PE + GK + F L KEN +T EA+GL++ LG++P F +AG KDKR+++
Sbjct: 285 ARGKRSHPEGCERGKAVYTAFTLQKENLETFEAIGLLAVKLGVIPSDFSYAGLKDKRAIT 344
Query: 74 TQRVTVFKQRASKLAALNKRLIGIRLGDFCY--VKEGLLLGQLLGNRFTIT---LRGVVV 128
Q + V K +L ++ + + R+ F V + L LGQL GN F I LR +
Sbjct: 345 YQSMVVKKVTPERLKSIKEEIEKKRMNVFNIRSVGDCLRLGQLKGNHFEIIIRHLRNQLN 404
Query: 129 DS----EDVIKASANSLGRNGFINYFGLQRFGSGS-VPTHLVGATLLRGEWKSAVKMILD 183
DS E +++A N + GF+NY+G QRFG G + T +G LL+ E A+K+ L
Sbjct: 405 DSANLTERILEAIEN-VKNKGFVNYYGPQRFGKGQKIQTDQIGLALLKNEMVKAIKLFLT 463
Query: 184 PREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKK---CPGNYLQALKAI 240
P + + + ++KA++Y+ T+D GTL +P V ERA+L+ L + ++A +
Sbjct: 464 PEDVD-DPVNKAKQYFLRTEDAKGTLSLMPEFRVRERALLESLHRFGVTEEGCVRAWFSF 522
Query: 241 PRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYE 300
P ++R+ Y+H+Y S +WN AAS R+ +G + VV GDL+ C +D +K
Sbjct: 523 PHSMRIFYIHAYSSRIWNEAASYRLAAYGPK-VVEGDLI-CSDEDADKHF---------- 570
Query: 301 SSNDADDSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMND 360
P + V VT + ++ Y + VVLP+ G V YP N
Sbjct: 571 -------------------PSSK---VHLVTKEEESAHTYALHQVVLPVLGYNVQYPENQ 608
Query: 361 VAEVYHHLAEKDGINLTESLHNVKEFSITSM----TGNYRRVFQKPMDFEWELL 410
V Y +DG+ F + ++ G YR + + P + L+
Sbjct: 609 VGRWYQEALSRDGLQAC-------RFRVPALKLNVPGCYRHIVKHPRNVSHRLV 655
>sp|Q17426|YQ4B_CAEEL Putative pseudouridine synthase B0024.11 OS=Caenorhabditis elegans
GN=B0024.11 PE=3 SV=1
Length = 577
Score = 161 bits (407), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 98/260 (37%), Positives = 142/260 (54%), Gaps = 8/260 (3%)
Query: 18 SRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRV 77
SR + W E++ K F + KENK+T A LI+K L + P + G KDKR+V++QRV
Sbjct: 138 SRKRKLWDEKVPKECHFTICKENKETSFACQLIAKFLNVGPNNIRTHGIKDKRAVTSQRV 197
Query: 78 TVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKAS 137
+V K + LN +L GIR+ Y + + +G GNRF+I LR + DSE ++
Sbjct: 198 SVTKVHERTILDLNSKLRGIRVFGCEYKDDPVQMGAHWGNRFSIVLRSLPDDSEQLLHQR 257
Query: 138 ANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILD---PREGERNEISK 194
+ GFINYFG QRFGS S T +G +++ +W+ AVKMI+ P +
Sbjct: 258 LETFQNTGFINYFGTQRFGSRSSTTAEIGLAIVKRDWEKAVKMIMTNAMPDHLGYGSVGY 317
Query: 195 AREYYKETDDIDGTLRKL---PRHLVAERAILQCLKKCPGNYLQAL-KAIPRTLRMMYVH 250
A + + +T D KL E IL+CL K G + + +AIP R +YVH
Sbjct: 318 AAKCFSQTGDARKAFSKLKGAQAFATVEGNILKCLSK-GGTWQNCITEAIPIQSRSLYVH 376
Query: 251 SYQSFLWNHAASARVQKHGT 270
+YQS +WN AS RV+++GT
Sbjct: 377 AYQSLIWNKVASRRVKEYGT 396
>sp|Q1L8I0|PUS7L_DANRE Pseudouridylate synthase 7 homolog-like protein OS=Danio rerio
GN=pus7l PE=2 SV=1
Length = 643
Score = 155 bits (391), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 117/404 (28%), Positives = 197/404 (48%), Gaps = 66/404 (16%)
Query: 31 FLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKL--- 87
+ F L KEN +T EA+ ++ +LG+LP F +AG KDKR+++ Q + V K +L
Sbjct: 247 YTAFTLRKENLETLEAISYMAAVLGVLPSDFTYAGIKDKRAITYQAMVVKKISPERLLEK 306
Query: 88 -AALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGV-------VVDSEDVIKASAN 139
+ +R G+ + E L LG+L GN F + +R + + + VI+ +
Sbjct: 307 GSEFERR--GMEISRVRPAFEALKLGRLQGNHFELVIRDLKHHGKHGLAELPKVIEEAVE 364
Query: 140 SLGRNGFINYFGLQRFGSGS-VPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREY 198
++ GF+NY+G QRFGSGS V VG LL+ +++VK+ P E + + +KA+ +
Sbjct: 365 NVKNKGFVNYYGPQRFGSGSCVQADQVGLALLKENMEASVKLFFTP-EDDDDLQNKAKRH 423
Query: 199 YKETDDIDGTLRKLPRHLVAERAILQCLKK-------CPGNYLQALKAIPRTLRMMYVHS 251
+ T + +L +P + ER +L+ L + C +L ++P ++R+ Y+HS
Sbjct: 424 FLHTGNAKESLVLMPAYKARERLMLRALHRYGSGQEGCTRGWL----SLPHSMRVFYLHS 479
Query: 252 YQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHL 311
Y S +WN AA R+QK G + V GDLV+ E D++
Sbjct: 480 YCSRVWNQAAKYRLQKLGFK-PVQGDLVWA------------------EPVKGLKDATEE 520
Query: 312 DEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEK 371
P+ + VT+ + + +++D V+LP+PG+ V YP N + + Y +
Sbjct: 521 LSAPQ----------IHVVTSDEEKNEVFSLDQVILPMPGNSVKYPENLLGQWYQDRLAQ 570
Query: 372 DGINLTESLHNVKEFSITSM----TGNYRRVFQKPMDFEWELLT 411
DG+ ES F +T + G YR + KP + + L T
Sbjct: 571 DGL---ESCR----FRVTPLKLNVPGCYRPLLAKPQNITYSLQT 607
>sp|Q466V2|TRUD_METBF Probable tRNA pseudouridine synthase D OS=Methanosarcina barkeri
(strain Fusaro / DSM 804) GN=truD PE=3 SV=1
Length = 438
Score = 150 bits (380), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 91/264 (34%), Positives = 145/264 (54%), Gaps = 8/264 (3%)
Query: 27 QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASK 86
Q GK+L L K + DT ++K+L + + AGTKDKR+++TQ++++F A K
Sbjct: 45 QEGKYLILELIKRDWDTHHLTRTLAKILQVSQKRISVAGTKDKRALTTQKISIFDIDAQK 104
Query: 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIK----ASANSLG 142
+ ++ L + L ++ + LG L GN F IT+R + SE++ K + L
Sbjct: 105 IEKIH--LKDVELKVLGRSRKSVELGDLWGNNFRITIRNITHSSEEIHKLLEKTTNEILA 162
Query: 143 RNGFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKE 201
+NG N+FG+QRFGS THLVG ++ G++ K+A+ I +P E + KAR++ KE
Sbjct: 163 QNGVPNFFGIQRFGSVRPVTHLVGKAIVEGDFEKAALLYIAEPFPDEPEDTRKARQFVKE 222
Query: 202 TDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAA 261
T D L+ P HL ERA++ L P ++ A +P+ L M+VH YQS+++N
Sbjct: 223 TLDFKEGLKIYPLHLGHERAMMNHLIANPDDFAGAFLVLPKNLYRMFVHGYQSYIYNIIL 282
Query: 262 SARVQKH-GTEHVVVGDLVFCKGD 284
R++K V GD+V K +
Sbjct: 283 CRRIEKGLSLNEAVEGDVVCFKNE 306
>sp|C5A1W0|TRUD_THEGJ Probable tRNA pseudouridine synthase D OS=Thermococcus
gammatolerans (strain DSM 15229 / JCM 11827 / EJ3)
GN=truD PE=3 SV=1
Length = 415
Score = 144 bits (364), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 91/247 (36%), Positives = 136/247 (55%), Gaps = 6/247 (2%)
Query: 34 FHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKR 93
F L K N DT + I+K GI R GFAGTKD+ +V+ Q ++V K+ ++ R
Sbjct: 49 FLLKKRNWDTMAVIKEIAKRAGISHRDIGFAGTKDRHAVTYQYISVPAGAKEKVESIQIR 108
Query: 94 LIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG-RNGFINYFGL 152
+ +R F + LG LLGNRF I +R V + D K L + GF NYFG
Sbjct: 109 DVELR---FVSYGRFIKLGHLLGNRFRIIIRDVEGSAFDRTKEIIRELREKGGFPNYFGY 165
Query: 153 QRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKL 212
QRFG V HL+G LL+GE+ A ++ L +G E +AR + ET+D+D L +
Sbjct: 166 QRFGERRVVNHLIGKLLLQGEFDEAARLFLGYADGS-MEGDEARRNFWETEDVDRALEEF 224
Query: 213 PRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEH 272
PR L ER +L KK G++ +A ++P + +++H+YQS+L+N S R+++
Sbjct: 225 PRFLRYERTLLYTYKKT-GSWKKAFLSLPLPIMRIFIHAYQSYLFNLYLSRRIEELPLNE 283
Query: 273 VVVGDLV 279
+VGD+V
Sbjct: 284 PLVGDIV 290
>sp|O28596|TRUD_ARCFU Probable tRNA pseudouridine synthase D OS=Archaeoglobus fulgidus
(strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC
100126) GN=truD PE=3 SV=1
Length = 411
Score = 144 bits (363), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 88/243 (36%), Positives = 139/243 (57%), Gaps = 6/243 (2%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G FL + K+N DT ++S LGI + FAGTKDKR+++ Q +++ + ++
Sbjct: 42 GDFLIIRVEKKNWDTLNFARVLSNALGISQKRISFAGTKDKRALTVQYFSIYGVKKEEIE 101
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFIN 148
+N L ++ Y + + LG LLGN F I + G D E + + + N L G N
Sbjct: 102 RVN--LKDAKIEVIGYARRAIQLGDLLGNFFRIRVYG-CRDGE-IFQETRNELMEKGTPN 157
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKM-ILDPREGERNEISKAREYYKETDDIDG 207
+FGLQRFGS TH VG +L+ ++ A + + P EGE E+ K RE ET D
Sbjct: 158 FFGLQRFGSIRFITHEVGKLILQNNYEEAFWVYVAKPFEGENEEVRKIREILWETRDAKL 217
Query: 208 TLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQK 267
LR+LP++L ER +LQ L++ +AL ++P+ L+MM+VH+YQS+++N S R+++
Sbjct: 218 GLRELPKYLRYERNLLQKLREGKSEE-EALLSLPKNLKMMFVHAYQSYIFNRLLSERIRQ 276
Query: 268 HGT 270
G+
Sbjct: 277 FGS 279
>sp|Q8TXJ7|TRUD_METKA Probable tRNA pseudouridine synthase D OS=Methanopyrus kandleri
(strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
GN=truD PE=3 SV=1
Length = 400
Score = 143 bits (361), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 103/275 (37%), Positives = 146/275 (53%), Gaps = 17/275 (6%)
Query: 34 FHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKR 93
F+L K + DT +A+ I++ L R FG AG KDKR+V++QRVTV LA L R
Sbjct: 55 FYLEKYDWDTMKAVRRIAQALRKHHRHFGIAGMKDKRAVTSQRVTVRGVPPGVLARL--R 112
Query: 94 LIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQ 153
+ +++ + L G L GNRF IT+RG V + LG G NY+GLQ
Sbjct: 113 IRDLKIVPMGRARRKLRPGDLWGNRFVITVRGAKVRRLPEALRTVRELG--GVPNYYGLQ 170
Query: 154 RFGSGSVPTHLVGATLLRGEWKSAVKMILD---PREGERNEISKAREYYKE-TDDIDGTL 209
RFGS TH+VG ++ +W+ AVK L PRE E +AR + KE + L
Sbjct: 171 RFGSRRPVTHVVGKYVVLEDWEKAVKTFLTLEYPRESP--EALEARRWLKEHWGEFKEAL 228
Query: 210 RKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHG 269
R+ P+ L ER IL+ L + P +Y+ A + +P +R M+VH+YQS+L+N S R+ +
Sbjct: 229 RRFPKFLDYERHILEHLARHPHDYINAFRRLPMWIRRMFVHAYQSYLFNRILSERIARGL 288
Query: 270 TEHVVVGDLVFCKGDDTEKELGCVN-PEFEYESSN 303
H V +GD T+ L V P F E S+
Sbjct: 289 PVHRPV------EGDVTQDGLPTVPLPGFRTELSD 317
>sp|O27572|TRUD_METTH Probable tRNA pseudouridine synthase D OS=Methanothermobacter
thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM
10044 / NBRC 100330 / Delta H) GN=truD PE=3 SV=1
Length = 415
Score = 140 bits (353), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 89/252 (35%), Positives = 139/252 (55%), Gaps = 11/252 (4%)
Query: 38 KENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGI 97
KE + T + L I++ L + R GFAG KDKR+V+ Q + V S++ A+ +R+ +
Sbjct: 48 KEGRTTLDVLLDIARELHLDRRRMGFAGMKDKRAVTRQWICVSNTAPSEVKAIEERIRNV 107
Query: 98 RLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSE-DVIKASANSLGRNGFINYFGLQRFG 156
+ ++ L +GQLLGNRF I +R +D + KA+ L G NY+G QRFG
Sbjct: 108 KFLRVTANEKKLRMGQLLGNRFRILIRDTEIDEPLETAKATLQELEDKGVPNYYGWQRFG 167
Query: 157 SGSVPTHLVGATLLRGEWKSAV-KMILDPREGERNEISKAREYYKETDDIDGTLRKLPRH 215
S THLVG L+ G+ K AV I +P EGE +S+AR Y + D++ +P
Sbjct: 168 SPRANTHLVGRALVHGDVKGAVDSYIGNPLEGESEIVSEARRAY-DRGDLEEAYELMPSS 226
Query: 216 LVAERAILQCLKK-------CPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH 268
+ ER +L+ + + +Y++A+ A+P+ L+ M+VH+YQS+L+N A S R
Sbjct: 227 MRYERMMLRPMLRDLRRGEFSDESYVRAIHALPKPLKRMFVHAYQSYLFNRAVSERAALG 286
Query: 269 GTEHVVVGDLVF 280
H + GD+V
Sbjct: 287 INTH-IPGDIVI 297
>sp|B6YTE4|TRUD_THEON Probable tRNA pseudouridine synthase D OS=Thermococcus onnurineus
(strain NA1) GN=truD PE=3 SV=1
Length = 416
Score = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 90/252 (35%), Positives = 140/252 (55%), Gaps = 7/252 (2%)
Query: 30 KFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA 89
K+ F L K N DT A+ I+K GI + GFAGTKD+ +V+ Q ++V + K+ A
Sbjct: 45 KYAIFLLKKRNWDTMAAVKEIAKRAGISYKDIGFAGTKDRHAVTYQYISVPRDAKEKVEA 104
Query: 90 LNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSL-GRNGFIN 148
+ + I +R F L LG LLGNRF I +R V + + K L + GF N
Sbjct: 105 VRIKDIELR---FVSYGRALKLGHLLGNRFKIIVRDVDESAFERTKEIVRELRSKGGFPN 161
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGT 208
YFG QRFG V HL+G LL+G+++ A ++ L G E +AR+ + ET D++
Sbjct: 162 YFGYQRFGERRVTNHLIGKLLLKGDFEGAARLFLGAHGGG-MEGDEARKNFWETGDVNRA 220
Query: 209 LRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH 268
L + P L ERA+L K+ G++ +A ++P + +++H+YQS+L+N S R+++
Sbjct: 221 LEEFPGFLRYERAMLYRYKET-GSWRKAFLSLPLPIMRIFIHAYQSYLFNLYISRRIEEG 279
Query: 269 -GTEHVVVGDLV 279
+VGD+V
Sbjct: 280 LPLNEALVGDIV 291
>sp|Q5JDB6|TRUD_PYRKO Probable tRNA pseudouridine synthase D OS=Pyrococcus kodakaraensis
(strain ATCC BAA-918 / JCM 12380 / KOD1) GN=truD PE=3
SV=1
Length = 416
Score = 136 bits (342), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 89/252 (35%), Positives = 140/252 (55%), Gaps = 7/252 (2%)
Query: 30 KFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA 89
K+ F L K N +T A+ I+K GI R GFAGTKD+ +V+ Q ++V + ++
Sbjct: 45 KYAIFLLKKRNWETMAAVKEIAKRAGINYREIGFAGTKDRHAVTYQYISVPAEARERVEQ 104
Query: 90 LNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG-RNGFIN 148
++ R I +R F + LG LLGNRF I +R V D+ D K L + GF N
Sbjct: 105 VSIRDIELR---FVSYGRFIKLGHLLGNRFRIIVRDVSEDAFDRTKEIVRELREKGGFPN 161
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGT 208
YFG QRFG V H++G LL+G+++ A ++ L +G E +AR+ + ET D++
Sbjct: 162 YFGYQRFGERRVVNHIIGKLLLQGDFEGAARLFLGAHDGS-MEGDEARKNFWETGDVERA 220
Query: 209 LRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH 268
L + P L ER +L K GN+ +A ++P + +++H+YQS+L+N S R+++
Sbjct: 221 LEEFPGFLRYERTLLHRYKDT-GNWKRAFLSLPLPIMRIFIHAYQSYLFNLYLSRRIEEG 279
Query: 269 -GTEHVVVGDLV 279
+VGD+V
Sbjct: 280 LPLNEPLVGDIV 291
>sp|Q12WH6|TRUD_METBU Probable tRNA pseudouridine synthase D OS=Methanococcoides burtonii
(strain DSM 6242) GN=truD PE=3 SV=1
Length = 439
Score = 135 bits (339), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 104/348 (29%), Positives = 175/348 (50%), Gaps = 43/348 (12%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
GK+L L K N +T + ++++L I + GFAGTKDKR+V+TQ+++++ L
Sbjct: 48 GKYLILELTKRNWETHHLIRDLTRILRISQKRVGFAGTKDKRAVTTQKISIYDMEEEALQ 107
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDV----IKASANSLGRN 144
N L L + L LG L GN F IT+R + +D +++ + +A+ +
Sbjct: 108 --NVHLKDTELKILGRSNKSLELGDLTGNEFIITVRDIDLDEKELESRLSQTTASIKEQG 165
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKETD 203
G N+FG+QRFG+ TH+VG +++R + K+A+ I E + + R ET
Sbjct: 166 GVPNFFGIQRFGALRPITHVVGESIVRNDIEKAAMAYIAASYPDEPEDTQEVRNRVFETK 225
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
D L+ P L ERA++ L P +Y + + +P +R M+VH+YQS+++N +
Sbjct: 226 DYIEGLKGYPLQLRYERAMMHHLVSKPEDYAGSFETLPANIRKMFVHAYQSYIYNTIICS 285
Query: 264 RVQKH-GTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDG 322
R++K VVGD+V C +++ D S + V E D+ DG
Sbjct: 286 RIKKGLPLNRAVVGDIV-C-----------------FKNKAGLPDKSRNERVTE-DNIDG 326
Query: 323 RHNLVKT----VTA------ADINSG------KYTIDDVVLPLPGSRV 354
+NLVK VTA +++ SG + I+++ +P+ G +V
Sbjct: 327 MNNLVKRNRAFVTAPLVGYSSELASGVPGEIEREVIEELNVPIEGFKV 374
>sp|Q8TKX2|TRUD_METAC Probable tRNA pseudouridine synthase D OS=Methanosarcina
acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 /
C2A) GN=truD PE=3 SV=1
Length = 441
Score = 130 bits (327), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 83/257 (32%), Positives = 137/257 (53%), Gaps = 8/257 (3%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G++L L K + DT ++K+L I + AGTKDKR+++TQ++++F A ++
Sbjct: 50 GRYLVLELTKRDWDTHHFTRTLAKILQISQKRISVAGTKDKRALTTQKISIFDIDALEIE 109
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSED----VIKASANSLGRN 144
++ L + L ++ + LG L GN F IT+R + E+ + K ++ L +
Sbjct: 110 KIH--LKDVELKVLGRSRKSVELGDLWGNEFIITIRDISSSPEETRTILEKTNSKVLTQG 167
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKA-REYYKETD 203
G N+FG+QRFGS THLVG ++ G ++ A + + E E +KA R++ KET
Sbjct: 168 GVPNFFGVQRFGSVRSVTHLVGKAIVEGNFEKAAMLYIAEPFPEEPEETKAARQFVKETR 227
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
D L+ P L ERA++ L P +Y A +P+ L M+VH+YQS+++N
Sbjct: 228 DFKEGLKTYPLRLGHERAMMNHLISNPEDYSGAFSVLPKNLYRMFVHAYQSYIYNMILCR 287
Query: 264 RVQKH-GTEHVVVGDLV 279
R++ V GD+V
Sbjct: 288 RIESGISLNRAVEGDIV 304
>sp|Q8Q0M2|TRUD_METMA Probable tRNA pseudouridine synthase D OS=Methanosarcina mazei
(strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833
/ OCM 88) GN=truD PE=1 SV=1
Length = 438
Score = 127 bits (318), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 85/257 (33%), Positives = 141/257 (54%), Gaps = 8/257 (3%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
GK+L L K + DT +S++L + + AGTKDKR+++TQ++++F AS++
Sbjct: 47 GKYLIVELTKRDWDTHHLTRTLSRILQVSQKRISVAGTKDKRALTTQKISIFDTDASEIE 106
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGV---VVDSEDVIKASANS-LGRN 144
++ L I L ++ + LG L GN F IT+R + ++E ++K + + L +
Sbjct: 107 KIH--LKDIELKVLGRSRKSVELGDLWGNDFRITVRNIENSPEETEALLKKTTDEILAQG 164
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKETD 203
G N+FG+QRFGS THLVG ++ G + K+A+ I +P E E AR++ K+T
Sbjct: 165 GVPNFFGIQRFGSVRPVTHLVGKAIVEGNFEKAALLYIAEPFPEEPEETKNARQFVKDTL 224
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
D L+ P L ERA++ L P +Y + + +P+ L M+VH YQS+++N
Sbjct: 225 DFKEGLKTYPLRLGHERAMMNHLIANPEDYSGSFRVLPQNLYRMFVHGYQSYIYNIILCR 284
Query: 264 RVQKH-GTEHVVVGDLV 279
R++ V GD+V
Sbjct: 285 RIEAGIPLNRAVEGDIV 301
>sp|P60347|TRUD_GEOSL tRNA pseudouridine synthase D OS=Geobacter sulfurreducens (strain
ATCC 51573 / DSM 12127 / PCA) GN=truD PE=3 SV=1
Length = 408
Score = 124 bits (311), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 83/245 (33%), Positives = 132/245 (53%), Gaps = 9/245 (3%)
Query: 38 KENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGI 97
K T EA+ + + G R G+AG KD R ++ Q V++ + +++ LN + GI
Sbjct: 52 KRGITTLEAIRRLCRATGAPERDTGYAGMKDARGITRQTVSLPRVTPAEVMGLN--IPGI 109
Query: 98 RLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFG- 156
R+ + L LG L GNRF + LR V D+ D +A + L R G N FG QR+G
Sbjct: 110 RILSADRHRNKLRLGHLAGNRFRLRLRETVPDAADRARAILDVLARRGVPNRFGEQRYGI 169
Query: 157 SGSVPTHLVGATLLRGEWKSAVKMIL-DPREGERNEISKAREYYKETDDIDGTLRKLPRH 215
G+ +HLVG +L G+W+ AV +++ DP + E A E Y++ D+ G+L P H
Sbjct: 170 QGN--SHLVGRAMLAGDWRGAVDLLMGDPAKVEGERWRAAIEAYRQ-GDLAGSLSLFPGH 226
Query: 216 LVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVV 275
ER +LQ L K P ++ +A+ + L+ +Y+ + QS L++ R+Q +HV+
Sbjct: 227 CRTERDVLQRLAKRPDDFERAVHGVHPRLKKLYLSACQSALFDRVLETRLQT--IDHVME 284
Query: 276 GDLVF 280
GDL +
Sbjct: 285 GDLAW 289
>sp|Q58008|TRUD1_METJA Probable tRNA pseudouridine synthase D 1 OS=Methanocaldococcus
jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
10045 / NBRC 100440) GN=truD1 PE=3 SV=2
Length = 392
Score = 123 bits (308), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 81/258 (31%), Positives = 138/258 (53%), Gaps = 13/258 (5%)
Query: 17 DSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQR 76
+ + ENW G ++ F L K N T +A+ I+ +G + FGFAG KDK +V+TQR
Sbjct: 44 EFKDEENWK---GNYIHFTLEKRNWTTLDAIREIANRVGKQRKHFGFAGNKDKYAVTTQR 100
Query: 77 VTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKA 136
V F + L + ++ GI L DF + LG L GNRFTI +R + +++ +A
Sbjct: 101 VGCFNVKLEDLMKV--KIKGIILRDFQKTNRKIRLGDLWGNRFTIRVREPELKGKELEEA 158
Query: 137 SANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILD---PREGERNEIS 193
F+NY+G+QRFG+ TH+VG ++ +W+ A P + +++++
Sbjct: 159 LNKLCKLKYFLNYYGVQRFGTTRPITHIVGRFIIERDWEGAFHAYCGTPLPYDDKKSKL- 217
Query: 194 KAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQ 253
ARE E ++ +K P+ ER +++ + G+Y +A +P LR M++++YQ
Sbjct: 218 -ARELVDE-ENFKEAYKKFPKAFFYERRMIKAYIET-GSYQKAFMILPPYLRCMFINAYQ 274
Query: 254 SFLWNHAASARVQKHGTE 271
S+L+N + R + +G E
Sbjct: 275 SYLFNEIINRRFE-YGFE 291
>sp|Q978K9|TRUD_THEVO Probable tRNA pseudouridine synthase D OS=Thermoplasma volcanium
(strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 /
GSS1) GN=truD PE=3 SV=1
Length = 409
Score = 122 bits (307), Expect = 5e-27, Method: Compositional matrix adjust.
Identities = 111/424 (26%), Positives = 198/424 (46%), Gaps = 53/424 (12%)
Query: 25 PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRA 84
P+ GK+ + DT I++ L + + FAGTKDKR+V Q +
Sbjct: 30 PDPNGKYTIIKARVRDWDTNRIAAEIARRLHMSRKRVTFAGTKDKRAVKLQYFCI-NSAD 88
Query: 85 SKLAALNKRLIGIRLGDFCYVK-----EGLLLGQLLGNRFTITLRGVVVDSEDVIKASAN 139
+A+L+ GI+ DF ++ L LG L+ N F I G+ D E + +
Sbjct: 89 VDVASLS----GIK--DFEVIESFKSSHYLTLGDLIANHFKIRFYGI--DPEMFRERYVH 140
Query: 140 SLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYY 199
+ + GF N+FG QRFGS TH +G +++GE++ AVK + E+ + R+++
Sbjct: 141 IISKGGFPNFFGDQRFGSRRRNTHEIGKLIIKGEYEEAVKKYI---YDEKYDKESYRKHF 197
Query: 200 KETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNH 259
+T D L + P L ER+++ + G + A ++P+ L +M+VH+YQS+L+N
Sbjct: 198 IDTLDYKTALERFPHSLSFERSLIGYYARN-GTFKGAFDSLPKNLTIMFVHAYQSYLFNR 256
Query: 260 AASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDH 319
R++ +G V+ GD+ F V+ F + S + +S+
Sbjct: 257 ILDERLKIYGLNAVLPGDIAF-----------PVDAYFNPDKSKPIEVNSY--------- 296
Query: 320 PDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTES 379
R + K V++ I + LP+ G + +D +V + + +++GI+ +
Sbjct: 297 --NREKISKLVSSDKIR--------ISLPIFGYKTWIDNSDFGDVEYGILKEEGIS-QDD 345
Query: 380 LHNVKEFSITSMTGNYRRVFQKPMDFEWE--LLTYIDGNKPLAETDLDKIAKAKLVNIVK 437
N K+F+ S +G+ R + KP++F E ++ + G A L I + K N+
Sbjct: 346 FKN-KDFAYLSSSGDRRIISAKPINFSLENNVVEFTLGKGIYATVFLSSIGRLK-ENVYS 403
Query: 438 EEEA 441
+ EA
Sbjct: 404 DSEA 407
>sp|Q6L1R2|TRUD_PICTO Probable tRNA pseudouridine synthase D OS=Picrophilus torridus
(strain ATCC 700027 / DSM 9790 / JCM 10055 / NBRC
100828) GN=truD PE=3 SV=1
Length = 414
Score = 120 bits (302), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 120/426 (28%), Positives = 200/426 (46%), Gaps = 64/426 (15%)
Query: 15 PFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVST 74
PFD + +N GK+L + DT + +++ + I + +AGTKDKR+V+T
Sbjct: 42 PFDIKKDDN-----GKYLIIKARLYDWDTNRFVMYLARHMNISRKRITYAGTKDKRAVTT 96
Query: 75 QRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSE-DV 133
Q + R ++N GI + + + + LG L GNRF I VD D+
Sbjct: 97 QYFCINTDRMFS-GSIN----GIEIIEQFRSNDIIKLGDLYGNRFLIK-----VDYPGDL 146
Query: 134 IKASANSLG----RNGFINYFGLQRFGSGSVPTHLVGATLLRGEW-KSAVKMILDPREGE 188
K S+ +L + GF N+FG+QRFGS TH +G +++GE+ K+A K + D +
Sbjct: 147 EKDSSETLKEINEKGGFPNFFGVQRFGSMRSNTHYIGKMIIKGEYEKAADKYLYD----D 202
Query: 189 RNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMY 248
+ + R Y + D +L++ P +L ER+IL + GN A A+P+ L +M+
Sbjct: 203 NFDTEEYRINYGKNMDAKNSLKEYPGNLTFERSILGAI--ASGNKSSAFNALPKNLSIMF 260
Query: 249 VHSYQSFLWNHAASARVQKH--GTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDAD 306
VH++QS+L+N S R+ KH + V+ GDL++ D NP
Sbjct: 261 VHAFQSYLFNKMLSERM-KHVKDLKTVIEGDLLYNIDD-------YFNP----------- 301
Query: 307 DSSHLDEVPETDHPDGRHNLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYH 366
D L E R+NL + ++ + V+PLPG P ++
Sbjct: 302 DKKRLIEA-------NRYNLEMLNNLSSMDKIR-----PVIPLPGFDTRMPDGLQRDIML 349
Query: 367 HLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEW---ELLTYIDGNKPLAETD 423
+ E + ++L + E+S S +G+YR + KP++ ++ L +I G A +
Sbjct: 350 KVLEDENVSL-QDFKIPGEYSYMSSSGDYRIISAKPINLKFPEKNKLDFILGRGIYATSF 408
Query: 424 LDKIAK 429
L +I K
Sbjct: 409 LREIIK 414
>sp|Q9HLL3|TRUD_THEAC Probable tRNA pseudouridine synthase D OS=Thermoplasma acidophilum
(strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 /
AMRC-C165) GN=truD PE=3 SV=1
Length = 411
Score = 119 bits (299), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 84/246 (34%), Positives = 118/246 (47%), Gaps = 24/246 (9%)
Query: 42 DTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGD 101
DT + I+ L I + +AGTKDKR+ Q + + A G R+ D
Sbjct: 53 DTNRIVEEIASALRISRKRISYAGTKDKRARKIQYFCINAPVDVSVLAFK----GFRIID 108
Query: 102 FCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGR-NGFINYFGLQRFGSGSV 160
L LG L N F I +G S+D I+ + GF NYFG QRFGS
Sbjct: 109 RFRSDHYLRLGDLTANHFRIRFQGA---SDDYIEQRYEKMMECGGFPNYFGQQRFGSRRR 165
Query: 161 PTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAER 220
TH VG ++ G ++ AV++ L ER +I R + ET D + L K PR L ER
Sbjct: 166 NTHDVGRLIVTGRYEDAVRLYL---YDERYDIEDYRREFIETLDYNRALEKFPRTLRFER 222
Query: 221 AILQCLKKCPGNYLQ------ALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVV 274
+I+ G Y Q A A+P+ L +M+VH+YQS+L+N S R++K+G +
Sbjct: 223 SII-------GYYAQHHTFKGAFDALPKNLSIMFVHAYQSYLFNRMLSLRIEKYGLNRAI 275
Query: 275 VGDLVF 280
GD F
Sbjct: 276 PGDTAF 281
>sp|C6A1K9|TRUD_THESM Probable tRNA pseudouridine synthase D OS=Thermococcus sibiricus
(strain MM 739 / DSM 12597) GN=truD PE=3 SV=1
Length = 422
Score = 117 bits (294), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 85/257 (33%), Positives = 141/257 (54%), Gaps = 15/257 (5%)
Query: 32 LRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTV----FKQRASKL 87
L + + K+N +T A+ I+K +GI ++ GFAGTKD+ +++ Q +++ + +
Sbjct: 47 LIYLIKKQNWETMAAIKEIAKRIGIDYKNVGFAGTKDRHAITYQYISICSENLESIKESI 106
Query: 88 AALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGR---- 143
A+LN + GI L F + L LG L+GN F I LRG+ D E ++ + L
Sbjct: 107 ASLN--IEGISL-KFVGRGKPLKLGMLIGNHFQIILRGLE-DPERALERTKKILKELKLK 162
Query: 144 NGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETD 203
GF NYFG QRFG V H VG LL+G+++ A L G+ +AR+ + +T
Sbjct: 163 GGFPNYFGSQRFGERRVINHEVGKLLLKGDFEGAALKFLGEYTGDMTG-DEARKDFLKTG 221
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
D++ L + P L ERA+L ++ ++ +A +PR + +++HSYQS+L+N A S
Sbjct: 222 DVEKALEEFPNFLRYERAMLYKYRETR-SWKKAFAVLPRPIVRIFIHSYQSYLFNKALSR 280
Query: 264 RVQKH-GTEHVVVGDLV 279
R+++ + GD+V
Sbjct: 281 RIEEGLSLNEALSGDIV 297
>sp|Q8U0N1|TRUD_PYRFU Probable tRNA pseudouridine synthase D OS=Pyrococcus furiosus
(strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) GN=truD
PE=3 SV=1
Length = 407
Score = 116 bits (291), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 81/237 (34%), Positives = 131/237 (55%), Gaps = 17/237 (7%)
Query: 34 FHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKR 93
+ L K+N +T A+ I+K +G+ GFAGTKD+ +V+ Q +++ + +N
Sbjct: 47 YILKKKNWETMAAIKEIAKRVGVHYSEIGFAGTKDRHAVTYQYISICRD-------VNLE 99
Query: 94 LIGIRLGDFCYVKEG--LLLGQLLGNRFTITLRGVVVDSEDVIKASA--NSLGRNGFINY 149
+ IR + +V G L LG LLGN F I +R +S + S + + GF NY
Sbjct: 100 EVKIRDIELKFVGYGRPLKLGFLLGNFFKIRVR----ESNPSLLPSVIEEAKEKGGFPNY 155
Query: 150 FGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTL 209
FG+QRFG H+VG LL G+++ A ++ L G+ E +AR + ET D+D L
Sbjct: 156 FGIQRFGEKRSVNHVVGKLLLLGKYEEAAEVFLG-FPGKGMEGDEARRKFLETKDVDLAL 214
Query: 210 RKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQ 266
R+ P L ERA+L K+ G++ +A +PR + +++HS+QS+L+N S R++
Sbjct: 215 REFPNFLRYERAMLYRYKET-GSWKKAFLVLPRPILRIFIHSFQSYLFNLYLSRRIE 270
>sp|Q39R76|TRUD_GEOMG tRNA pseudouridine synthase D OS=Geobacter metallireducens (strain
GS-15 / ATCC 53774 / DSM 7210) GN=truD PE=3 SV=1
Length = 404
Score = 116 bits (290), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 84/251 (33%), Positives = 133/251 (52%), Gaps = 11/251 (4%)
Query: 35 HLY----KENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAAL 90
H+Y K T +A+ +++ L + R G+AG KD R V+ Q V++ + + ++ AL
Sbjct: 42 HVYALIEKRGVTTLDAIRRLARALKLSERDVGYAGMKDARGVTRQTVSLPRMKPEEVLAL 101
Query: 91 NKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYF 150
L GIR+ + L LG L GNRF I +RGVV D+ +A L R G N F
Sbjct: 102 E--LPGIRILSAERHRNKLKLGHLAGNRFRIRVRGVVSDAVARAEAILAVLERRGVPNRF 159
Query: 151 GLQRFGSGSVPTHLVGATLLRGEWKSAVKMIL-DPREGERNEISKAREYYKETDDIDGTL 209
G QR+G+ +HL+G +L G+W +AV +++ DP + A E Y+ +++ +
Sbjct: 160 GEQRYGAQGN-SHLIGRAMLAGDWCAAVDLLMGDPAKVTGEAWRSAIEAYQR-GELEESQ 217
Query: 210 RKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHG 269
R P H ER ++Q L K P ++ A +A+ LR +Y+ + QS L++H AR+
Sbjct: 218 RLFPGHCRTERDVIQRLVKRPDDFEGAFRAVNPRLRKLYLSACQSALFDHVVEARLDSLD 277
Query: 270 TEHVVVGDLVF 280
T V GDL +
Sbjct: 278 T--VQEGDLAW 286
>sp|O59207|TRUD_PYRHO Probable tRNA pseudouridine synthase D OS=Pyrococcus horikoshii
(strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139
/ OT-3) GN=truD PE=3 SV=1
Length = 409
Score = 115 bits (287), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 80/247 (32%), Positives = 135/247 (54%), Gaps = 10/247 (4%)
Query: 34 FHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKR 93
+ L K+N +T A+ I+K +GI GFAGTKD+ +V+ Q +++ ++ + A+
Sbjct: 48 YLLKKKNWETMAAIKEIAKRIGIHYSEIGFAGTKDRHAVTYQYISICREVDLENVAIKD- 106
Query: 94 LIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQ 153
+ +R F L LG LLGN F I +R + I A G GF NYFG+Q
Sbjct: 107 -VTLR---FVGYGRPLKLGLLLGNFFKIRVRDTTPELLPNILKEAKEKG--GFPNYFGIQ 160
Query: 154 RFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLP 213
RFG H+VG LL G+++ A ++ L G E +AR+ + ET ++D L + P
Sbjct: 161 RFGEKRSVNHIVGKLLLLGKYEEAAEVFLG-YPGNGMEGDEARKKFLETKNVDLALEEFP 219
Query: 214 RHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQK-HGTEH 272
+ L ERA+L ++ G++ ++ A+PR + +++H++QS+L+N S R+++
Sbjct: 220 KFLRYERAMLYKYRET-GSWKRSFLALPRPILRIFIHAFQSYLFNLYISRRIEEGFPLNE 278
Query: 273 VVVGDLV 279
+ GD+V
Sbjct: 279 ALPGDIV 285
>sp|Q9V107|TRUD_PYRAB Probable tRNA pseudouridine synthase D OS=Pyrococcus abyssi (strain
GE5 / Orsay) GN=truD PE=3 SV=1
Length = 406
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 79/244 (32%), Positives = 132/244 (54%), Gaps = 9/244 (3%)
Query: 38 KENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGI 97
K N +T A+ I+K +GI GFAGTKD+ +V+ Q ++V + ++ L R + +
Sbjct: 47 KRNWETIAAIKEIAKRIGIHYSEIGFAGTKDRHAVTYQYISVCRDVRKEVEKLKIRDVEL 106
Query: 98 RLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLG-RNGFINYFGLQRFG 156
+ F L LG LLGN F I +R V ++I L + GF NYFG+QRFG
Sbjct: 107 K---FVGYGRPLKLGFLLGNFFLIRVRDV--KRPELIPKIIEELKIKGGFPNYFGIQRFG 161
Query: 157 SGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHL 216
H+VG LL G+++ A ++ L G E +AR+ + ET D+D L + P+ L
Sbjct: 162 EKRSVNHIVGKLLLEGKYEEAAEVFLG-YPGNGMEGDEARKRFLETKDVDLALEEFPKFL 220
Query: 217 VAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH-GTEHVVV 275
ERA+L ++ ++ +A +PR + +++H++Q++L+N S R+++ +
Sbjct: 221 RYERAMLYRYRET-RSWKKAFLVLPRPILRIFIHAFQAYLFNLYLSRRIEEGLPLNEAIP 279
Query: 276 GDLV 279
GD+V
Sbjct: 280 GDIV 283
>sp|Q5V1E6|TRUD_HALMA Probable tRNA pseudouridine synthase D OS=Haloarcula marismortui
(strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
GN=truD PE=3 SV=1
Length = 460
Score = 113 bits (283), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 91/288 (31%), Positives = 133/288 (46%), Gaps = 33/288 (11%)
Query: 32 LRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALN 91
L F N +T + +S LGI +AGTKDKR+V+TQ +V A L +
Sbjct: 57 LVFRAELRNWETNDFASKLSDRLGISRERVSWAGTKDKRAVTTQLFSVKGVAAGDLPEIG 116
Query: 92 KRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLR---------GVVVD------SEDVIKA 136
I + +L G L GN F I +R VV D +D + +
Sbjct: 117 GTDIEV----IGRAGRPILFGDLAGNAFEIVVRDTENTDNAASVVADLRAFANGDDSVTS 172
Query: 137 SANSLGRN--------GFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAV-KMILDPREG 187
S G NYFG QRFGS TH VG + RGEWK AV + +P E
Sbjct: 173 EGWSSDATLPDGDTTVGVPNYFGQQRFGSRRPVTHEVGLAIARGEWKDAVLAYVGNPNER 232
Query: 188 ERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKC----PGNYLQALKAIPRT 243
E +AR Y ET D G L +LP L ER+I L + P ++ +AL+A+P
Sbjct: 233 EPESTQEARGYVDETHDWAGALDRLPGALGYERSICHRLVENGASEPADFREALEALPSN 292
Query: 244 LRMMYVHSYQSFLWNHAASARVQKH-GTEHVVVGDLVFCKGDDTEKEL 290
L+ ++V++ QS+++N S R+++ + V GD+V + D ++
Sbjct: 293 LQSLFVNAAQSYVFNRILSERLERGLPFDRPVEGDVVCFRDSDAPEDF 340
>sp|B9M644|TRUD_GEOSF tRNA pseudouridine synthase D OS=Geobacter sp. (strain FRC-32)
GN=truD PE=3 SV=1
Length = 397
Score = 111 bits (278), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 78/251 (31%), Positives = 131/251 (52%), Gaps = 11/251 (4%)
Query: 35 HLYKENKD----TQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAAL 90
H+Y E + T EA+ ++K LGI R G+AG KD + ++ Q +++ R + L
Sbjct: 39 HIYAEIEKRGITTLEAIRRLAKALGIGERDVGYAGMKDAKGITRQTISL--PRVAPEQVL 96
Query: 91 NKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYF 150
L GI++ + L +G L GNRF I + GV D+ + A + L + G N+F
Sbjct: 97 GLELPGIKVLSAVPHRNKLKVGHLRGNRFRIRIGGVGADAATIAIAVLDILEKRGVPNFF 156
Query: 151 GLQRFGSGSVPTHLVGATLLRGEWKSAV-KMILDPREGERNEISKAREYYKETDDIDGTL 209
G QR+G+ +HL+G +LR +++ AV +I +P + +A E +K D+ +L
Sbjct: 157 GEQRYGAQG-NSHLIGGAILRNDYRGAVDALIGEPDKVTDERWRRAIEAFK-AGDLAKSL 214
Query: 210 RKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHG 269
P H ER +LQ L K P + +A +A+ LR +Y+ ++Q+ L++ R+
Sbjct: 215 ETFPPHCRTERELLQKLVKQPEAHEKAFRAVHPRLRKLYLSAFQADLFDRVVQQRMDS-- 272
Query: 270 TEHVVVGDLVF 280
+ VV GD+ F
Sbjct: 273 LDQVVHGDVAF 283
>sp|A4FYL2|TRUD_METM5 Probable tRNA pseudouridine synthase D OS=Methanococcus maripaludis
(strain C5 / ATCC BAA-1333) GN=truD PE=3 SV=1
Length = 390
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 78/248 (31%), Positives = 130/248 (52%), Gaps = 8/248 (3%)
Query: 20 GSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTV 79
G E+ + G F+ F + K N +T +AL I + ++FGFAGTKDK +V+TQR
Sbjct: 45 GFEDVEKWHGSFIHFTVEKTNWNTMDALKQIVRTTKTKRKNFGFAGTKDKFAVTTQRFGC 104
Query: 80 FKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASAN 139
F + +L +N + I IR D + L +G L GN+FTI +RG+ + +++ + S
Sbjct: 105 FGLKKEQLENINIKDIVIR--DVQKSNKKLRMGDLWGNKFTIKIRGLDLSKKEIKRIS-- 160
Query: 140 SLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYY 199
L + +NY+G+QRFG TH+VG + +++SA E + +AR+
Sbjct: 161 DLKLDYVLNYYGIQRFGLIRPITHIVGKFIYERDFESAFYTYCGTPISETGDSLEARQLV 220
Query: 200 KETDDIDGTLRKLPR-HLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWN 258
+ + L+ R H +R I Q LK ++ A A+P L M+V++YQ++L+N
Sbjct: 221 -DVGEFKKALKLFNRNHDYEKRLIQQYLK--YKDFKMAFTALPPQLNSMFVNAYQAYLFN 277
Query: 259 HAASARVQ 266
+ R +
Sbjct: 278 EMINKRFE 285
>sp|A6UV17|TRUD_META3 Probable tRNA pseudouridine synthase D OS=Methanococcus aeolicus
(strain Nankai-3 / ATCC BAA-1280) GN=truD PE=3 SV=1
Length = 402
Score = 108 bits (269), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 78/264 (29%), Positives = 133/264 (50%), Gaps = 10/264 (3%)
Query: 22 ENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFK 81
EN + G F+ F + K N +T +A+ +++ ++FGFAGTKDK +++TQRV F
Sbjct: 48 ENKHDWNGSFIHFTMEKINWNTMDAIRELARRTKTKRKNFGFAGTKDKFALTTQRVGCFG 107
Query: 82 QRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDS--EDVIKASAN 139
+ KL + + I + D L +G L GN+FTI +R D D+ K
Sbjct: 108 IKPEKLEEIKNSIKDITIRDIQKTNIKLRMGHLWGNKFTIKIRLNETDKYYNDISKYEEI 167
Query: 140 SLGRN--GFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKARE 197
+N +NY+G QRFG+ TH+VG + +++SA E + +ARE
Sbjct: 168 LKNKNLDYILNYYGTQRFGTFRPITHIVGKFIYNRDFESAFYTYCGAPINETGVVKEARE 227
Query: 198 YYKETDDIDGTLRKLPR--HLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSF 255
+ + + L+ P+ + + I +K GNY + K +P L M+V++YQS+
Sbjct: 228 MV-DNGEFEKALKLFPKKSYYNEIKMIRHYIK--TGNYKECFKVLPPQLSSMFVNAYQSY 284
Query: 256 LWNHAASARVQKHGTEHVVVGDLV 279
L+N + R + + + ++ GD+V
Sbjct: 285 LFNEMINIRHRDYSFD-ILDGDVV 307
>sp|P60348|TRUD_NANEQ Probable tRNA pseudouridine synthase D OS=Nanoarchaeum equitans
(strain Kin4-M) GN=truD PE=3 SV=1
Length = 374
Score = 106 bits (264), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 72/255 (28%), Positives = 129/255 (50%), Gaps = 23/255 (9%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G + + L K+N T +A+ +I+K + F+G KDK++++ Q ++++K +
Sbjct: 42 GDYTIYVLKKKNLSTTQAIKIIAKQFRLSKYRISFSGEKDKKAITYQLISIYKGPKKSMF 101
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFIN 148
N L I L D + + LG LGN F I + + + G + F N
Sbjct: 102 LDNLELYYIGLSD-----KPVKLGSHLGNYFEIKV------------YAESPKGFDVFPN 144
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAR----EYYKETDD 204
YF +QRFG + HL+G L++ E + A K++L E + K R EY+ +
Sbjct: 145 YFDVQRFGDKRLVNHLIGKHLIKNECEEAAKILLTFVGKESKKTIKVRQLIKEYWNNIEK 204
Query: 205 IDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASAR 264
+ + +P+ L E+A LQ + +Y +A KAIP+ + M+++HSYQS+++N
Sbjct: 205 LKKVIPLMPKALDIEKAYLQSFIE-KKDYCKAFKAIPKWILMLFIHSYQSYIFNETLKMY 263
Query: 265 VQKHGTEHVVVGDLV 279
+ K+ T+ + + DL+
Sbjct: 264 L-KNKTKIIKIRDLL 277
>sp|A6USB0|TRUD_METVS Probable tRNA pseudouridine synthase D OS=Methanococcus vannielii
(strain SB / ATCC 35089 / DSM 1224) GN=truD PE=3 SV=1
Length = 390
Score = 106 bits (264), Expect = 5e-22, Method: Compositional matrix adjust.
Identities = 72/236 (30%), Positives = 125/236 (52%), Gaps = 6/236 (2%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G F+ F L K N +T +AL I + ++FGFAGTKDK +V+TQR+ F + +L
Sbjct: 54 GSFIHFTLEKRNWNTMDALSAIVRATKTKRKNFGFAGTKDKFAVTTQRMGCFGLKKEQLE 113
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFIN 148
++ ++ I + D + L +G L GNRFTI +R ++ + + + + L + +N
Sbjct: 114 SV--KIPEIIIKDIQKSNKKLRMGDLFGNRFTINIRD--IEKKYMELENLSDLKLDHVLN 169
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGT 208
YFG+QRFG TH+VG + +++SA E + +ARE ++ + G
Sbjct: 170 YFGIQRFGLKRPITHIVGKFIYERDFESAFYTYCGTPISETGDEKEARELV-DSGNFKGA 228
Query: 209 LRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASAR 264
L+ + E+ ++Q K ++ A A+P L M+V++YQ++L+N + R
Sbjct: 229 LKLFSKGNEYEKRLIQQYFKYK-DFKMAFTALPPQLNSMFVNAYQAYLFNEMVNER 283
>sp|Q3IMF3|TRUD_NATPD Probable tRNA pseudouridine synthase D OS=Natronomonas pharaonis
(strain DSM 2160 / ATCC 35678) GN=truD PE=3 SV=1
Length = 435
Score = 105 bits (263), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 85/263 (32%), Positives = 125/263 (47%), Gaps = 18/263 (6%)
Query: 32 LRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALN 91
L F DT + +S LG+ +AGTKDK +V+TQ +F R A +
Sbjct: 59 LVFRATLREWDTNDFASAVSNALGVSRERVSWAGTKDKHAVTTQ---LFSVRHDDAALPD 115
Query: 92 KRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSL-----GRNGF 146
L G + +L G L GN F + +R D + +A+A L G G
Sbjct: 116 --LDGADIEPIGRAGRPVLFGDLAGNEFELVIRDP--DRPEHAEATAAELCDFGGGEAGV 171
Query: 147 INYFGLQRFGSGSVPTHLVGATLLRGEWK-SAVKMILDPREGERNEISKAREYYKETDDI 205
NYFG QRFGS TH VG +L G+W+ +AV+ + + E E + RE D
Sbjct: 172 PNYFGTQRFGSRRPITHRVGLDVLDGDWEAAAVRYVCESSEREPERTQEVREGIDADRDW 231
Query: 206 DGTLRKLPRHLVAERAILQCL---KKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAAS 262
+LP L ERAI L + P +Y AL+ +P L+ M+V++ QS+++N S
Sbjct: 232 AAAGERLPGSLRFERAIANRLAEGAESPDDYRAALEELPSNLQRMFVNAAQSYVFNRILS 291
Query: 263 ARVQKH-GTEHVVVGDLVFCKGD 284
R+++ + VVGD+V C D
Sbjct: 292 ERLRRGLPFDEPVVGDVV-CFSD 313
>sp|Q6LZL0|TRUD2_METMP Probable tRNA pseudouridine synthase D 2 OS=Methanococcus
maripaludis (strain S2 / LL) GN=truD2 PE=3 SV=2
Length = 390
Score = 104 bits (259), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 77/247 (31%), Positives = 128/247 (51%), Gaps = 8/247 (3%)
Query: 20 GSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTV 79
G E+ + G F+ F + K N +T +AL I + ++FGFAGTKDK +V+TQR
Sbjct: 45 GFEDVEKWHGSFIHFTVEKTNWNTMDALKQIVRATKTKRKNFGFAGTKDKFAVTTQRFGC 104
Query: 80 FKQRASKLAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASAN 139
F + +L +N + I IR D + L +G L GN+FTI +R + + +++ + S
Sbjct: 105 FGLKKEQLENINIKDIVIR--DVQKTNKKLRMGGLWGNKFTIKIRDLNLSEKEIKRIS-- 160
Query: 140 SLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYY 199
L + +NY+G+QRFG TH+VG + +++SA E + +AR+
Sbjct: 161 DLKLDYVLNYYGIQRFGLIRPITHIVGKFIYERDFESAFYTYCGTPINETGDSLEARQLV 220
Query: 200 KETDDIDGTLRKLPR-HLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWN 258
+ + L+ R H +R I Q LK ++ A A+P L M+V++YQ++L+N
Sbjct: 221 -DMGEFKKALKLFNRGHDYEKRLIQQYLKY--KDFKMAFTALPPQLNSMFVNAYQAYLFN 277
Query: 259 HAASARV 265
+ R
Sbjct: 278 EMINKRF 284
>sp|C6E4K4|TRUD_GEOSM tRNA pseudouridine synthase D OS=Geobacter sp. (strain M21) GN=truD
PE=3 SV=1
Length = 398
Score = 104 bits (259), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 77/246 (31%), Positives = 124/246 (50%), Gaps = 7/246 (2%)
Query: 36 LYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLI 95
L K T EAL ++K LG+ R G+AG KD ++ Q +++ + K+ AL +
Sbjct: 44 LEKRGIATLEALRRLAKALGVQERDLGYAGMKDAIGITRQTISIPRVAPEKVLALE--IP 101
Query: 96 GIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRF 155
GI + L LG L GNRF I +R V + +A+ + R G N FG+QR+
Sbjct: 102 GITVLSASMHGNKLRLGHLKGNRFVIRVRDVAQGAAGNAEAALEIMTRRGVPNRFGVQRY 161
Query: 156 GSGSVPTHLVGATLLRGEWKSAV-KMILDPREGERNEISKAREYYKETDDIDGTLRKLPR 214
G+ TH +GA +LR E+KSAV ++I DP A E Y+ ++ +L P
Sbjct: 162 GAQG-NTHEIGAAMLRREFKSAVDRLIGDPAAVTDERWRLAIEAYRR-GEVAESLALFPG 219
Query: 215 HLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKHGTEHVV 274
H ER +L L + P + +A ++ ++ +Y+ ++QS L++ R+ + V
Sbjct: 220 HFRVERELLTRLVQRPDGFERAFNSVQPRMKRLYLSAFQSSLFDLVLGKRLDSF--DQVN 277
Query: 275 VGDLVF 280
VGD+ F
Sbjct: 278 VGDIAF 283
>sp|Q9HSG5|TRUD_HALSA Probable tRNA pseudouridine synthase D OS=Halobacterium salinarum
(strain ATCC 700922 / JCM 11081 / NRC-1) GN=truD PE=3
SV=2
Length = 434
Score = 104 bits (259), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 77/244 (31%), Positives = 117/244 (47%), Gaps = 10/244 (4%)
Query: 42 DTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGD 101
DT + ++ +G+ +AGTKD+ +V+TQ V A+++ + I +
Sbjct: 67 DTNDFARELANTVGMSRERVRWAGTKDRHAVTTQLFAVRDLDAAQVPEIRNADIEV---- 122
Query: 102 FCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSL---GRNGFINYFGLQRFGSG 158
GL G L GN F I +R A + G G NYFG QRFGS
Sbjct: 123 VGRAGRGLEFGDLAGNAFEIVVRDPDAPERAAAVADELAAFGGGTVGTPNYFGQQRFGSK 182
Query: 159 SVPTHLVGATLLRGEWKSAVKMILD-PREGERNEISKAREYYKETDDIDGTLRKLPRHLV 217
TH VG +LR +W++A L P E E + +AREY ET D G L + P+ L
Sbjct: 183 RPVTHEVGLAILRDDWEAAAMAYLGAPTEHEPADSQRAREYVAETRDWTGALAEFPQRLR 242
Query: 218 AERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH-GTEHVVVG 276
ER +L L G++ A++ P L+ ++VH+ QS+++N S R+ + V G
Sbjct: 243 YERTMLHELADG-GSFRDAVETFPSNLQQLFVHAAQSYVFNRIVSERMARGLPFGEPVAG 301
Query: 277 DLVF 280
D+V+
Sbjct: 302 DVVW 305
>sp|B0R2Y4|TRUD_HALS3 Probable tRNA pseudouridine synthase D OS=Halobacterium salinarum
(strain ATCC 29341 / DSM 671 / R1) GN=truD PE=3 SV=1
Length = 434
Score = 104 bits (259), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 77/244 (31%), Positives = 117/244 (47%), Gaps = 10/244 (4%)
Query: 42 DTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGD 101
DT + ++ +G+ +AGTKD+ +V+TQ V A+++ + I +
Sbjct: 67 DTNDFARELANTVGMSRERVRWAGTKDRHAVTTQLFAVRDLDAAQVPEIRNADIEV---- 122
Query: 102 FCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSL---GRNGFINYFGLQRFGSG 158
GL G L GN F I +R A + G G NYFG QRFGS
Sbjct: 123 VGRAGRGLEFGDLAGNAFEIVVRDPDAPERAAAVADELAAFGGGTVGTPNYFGQQRFGSK 182
Query: 159 SVPTHLVGATLLRGEWKSAVKMILD-PREGERNEISKAREYYKETDDIDGTLRKLPRHLV 217
TH VG +LR +W++A L P E E + +AREY ET D G L + P+ L
Sbjct: 183 RPVTHEVGLAILRDDWEAAAMAYLGAPTEHEPADSQRAREYVAETRDWTGALAEFPQRLR 242
Query: 218 AERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQKH-GTEHVVVG 276
ER +L L G++ A++ P L+ ++VH+ QS+++N S R+ + V G
Sbjct: 243 YERTMLHELADG-GSFRDAVETFPSNLQQLFVHAAQSYVFNRIVSERMARGLPFGEPVAG 301
Query: 277 DLVF 280
D+V+
Sbjct: 302 DVVW 305
>sp|O67616|TRUD_AQUAE tRNA pseudouridine synthase D OS=Aquifex aeolicus (strain VF5)
GN=truD PE=3 SV=1
Length = 385
Score = 102 bits (255), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 79/267 (29%), Positives = 127/267 (47%), Gaps = 15/267 (5%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G++ F L K++ T +A+ IS GI ++ GFAG KDK++V+ Q ++V K+
Sbjct: 26 GQYAYFLLKKKDMTTLDAVRHISHRFGIPLKNIGFAGLKDKKAVTEQYISVKDLNEEKIR 85
Query: 89 ALN-KRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFI 147
++ R + L + +GL LG++ GN F + +RGV V + G
Sbjct: 86 KMDGYRTENLELKFLGFSDKGLELGEIEGNYFEVVVRGVTKYHRRVFPRMKELVENYGCE 145
Query: 148 NYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDG 207
NYFG QRFGS + LLR E++ A+K L +R + R K D D
Sbjct: 146 NYFGEQRFGSVKHAEEFIVKYLLRHEYEEAMKEYLTSLGDKRLK----RLLRKAWRDWDR 201
Query: 208 TLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQK 267
L +P+ E +++ L++ ++ A +P+ +R+M+V +YQS+LWN
Sbjct: 202 FLSLMPKGAKPELEVVKALRRGE-SFKNAFMVLPKNIRLMFVFAYQSYLWNRYLYT---- 256
Query: 268 HGTEHVVVGDLVFCKGDDTEKELGCVN 294
VV L +CK + EL N
Sbjct: 257 -----FVVRYLKYCKTPFLKWELAFFN 278
>sp|Q58759|TRUD2_METJA Probable tRNA pseudouridine synthase D 2 OS=Methanocaldococcus
jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
10045 / NBRC 100440) GN=truD2 PE=3 SV=2
Length = 422
Score = 95.5 bits (236), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 83/285 (29%), Positives = 135/285 (47%), Gaps = 28/285 (9%)
Query: 34 FHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRAS-KLAALNK 92
+ L K N ++ +A I+K I + G+ G KD+ +++TQ +++ K+ L N
Sbjct: 55 YKLTKRNIESLKAFSYIAKKFKIPLKDIGYCGLKDRHALTTQYISIPKKYGKLSLDEPNL 114
Query: 93 RLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASAN-SLGRNGFINYFG 151
+L I F LLLG L GNRFTIT+RG+ ED+ K N G NYF
Sbjct: 115 KLELIGESKF------LLLGDLEGNRFTITVRGL--KKEDIPKIKENLKYLEFGAPNYFD 166
Query: 152 LQRFGSGSVPTHLVGATLLRGEWKSAVKMILDP-REGERNEISKAREYY-KETDDIDGTL 209
QRFGS + +++G ++ AVK++L ++ E+ I + + K D D
Sbjct: 167 SQRFGS-VFDKKFIAKEVIKGNYEEAVKILLTKYKKSEKKLIKDLKRFIDKNWGDWDKIW 225
Query: 210 RKLPRHLVAERAILQCLK--KCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQK 267
+ + + R + +K K +Y +AL + L+ ++V +YQS+LWN ++K
Sbjct: 226 EYIKENNIKSRLYVNMVKELKKSNDYKKALSYVDDRLKKIFVAAYQSYLWNECVKELLRK 285
Query: 268 HGTEHVVV------GDLVFCKGDDTE-------KELGCVNPEFEY 299
+ E V G L+F K D E K+ + P+ EY
Sbjct: 286 YVPEEDRVYYEYECGTLMFYKKMDEEVFNILKDKKFPTIAPDIEY 330
>sp|Q8ZTR2|TRUD_PYRAE Probable tRNA pseudouridine synthase D OS=Pyrobaculum aerophilum
(strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC
100827) GN=truD PE=3 SV=1
Length = 413
Score = 94.7 bits (234), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 99/418 (23%), Positives = 174/418 (41%), Gaps = 70/418 (16%)
Query: 27 QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASK 86
++G + H+ K N DT + + +++ LG+ R G KD ++V++Q ++V
Sbjct: 56 RVGNWTWIHVVKRNVDTIKLVLRLARALGLSHRDVSVGGLKDTKAVTSQIISV----RGP 111
Query: 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGF 146
+A L + L G++ + + + Q+ GNRFTI LR V+ + + +L +
Sbjct: 112 VANLPQ-LPGVQFLGMWSMDKPITPSQIYGNRFTIILRD--VERISCAEGALEALKKTAA 168
Query: 147 INYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDID 206
NY+G QRFG+ THL+G LL+ + +++ +E++K D
Sbjct: 169 PNYYGYQRFGTIRPVTHLLGKALLKKDPHLFFEVMFCKIFSRESEVAKRAREAACKGDYA 228
Query: 207 GTLRKLPRHLVAERAILQCLKKCPGNY--LQALKAIPRTLRMMYVHSYQSFLWNHAASAR 264
L P+ V ER LK+ G Y A+ AIP + +Y+ + QS+++N S R
Sbjct: 229 KALELFPKKFVEERVF---LKRLAGGYDMWNAIMAIPPQILRVYIEAAQSYIFNRFLSIR 285
Query: 265 VQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRH 324
++ + V GDLV +N + Y +
Sbjct: 286 MEIGPIDRPVEGDLV------------EINRQIAYYAEGLG------------------- 314
Query: 325 NLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVK 384
+VVLP+ G+ V P V E + ++G++ + L +
Sbjct: 315 ------------------GEVVLPVVGAGVRMPRGKVGEALLRVLREEGLDPSAFLKMPR 356
Query: 385 EFSITSMTGNYRRVFQKPMDFEWELLTYIDGNKPLAETDLDK--IAKAKLVNIVKEEE 440
+ G YRRV +P FE++++ GN + L + A L +VK E
Sbjct: 357 GLRV---YGTYRRVRLEPAGFEYKIM----GNDVFMQFTLPRGSYATVLLREVVKPAE 407
>sp|A4WLG8|TRUD_PYRAR Probable tRNA pseudouridine synthase D OS=Pyrobaculum arsenaticum
(strain DSM 13514 / JCM 11321) GN=truD PE=3 SV=1
Length = 413
Score = 91.3 bits (225), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 76/258 (29%), Positives = 120/258 (46%), Gaps = 10/258 (3%)
Query: 27 QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASK 86
++G + H+ K N DT + ++K LG+ PR G KD R+V++ ++V
Sbjct: 56 RVGGWTWIHVVKRNVDTIRLMIRLAKALGVSPREVSVGGIKDTRAVASHIISV----RGA 111
Query: 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGF 146
+ L + + G++ + + ++ GNRFTI LR V+ D + +L
Sbjct: 112 VKGLPE-IPGVKFLGMWSMDRPMSPSEIYGNRFTIVLRD--VERVDCAVEALEALKSAAV 168
Query: 147 INYFGLQRFGSGSVPTHLVGATLLRGEWKSAV-KMILDPREGERNEISKAREYYKETDDI 205
NY+G QRFG+ +HL+G LLR + M E E KARE +
Sbjct: 169 PNYYGYQRFGTIRPVSHLLGRALLRKSPEEFFDAMFCKIFEHESAAAKKARE-LACRGEY 227
Query: 206 DGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARV 265
L PR V ERA L+ L + + A+ IP + +YV + QS+L+N SAR+
Sbjct: 228 QKALETFPRRFVEERAFLRRLAQG-YDMWNAIMGIPLQILRIYVEAAQSYLFNRFLSARL 286
Query: 266 QKHGTEHVVVGDLVFCKG 283
+ + + GDLV G
Sbjct: 287 ELGPLDKPLEGDLVEVGG 304
>sp|Q3A6I8|TRUD_PELCD tRNA pseudouridine synthase D OS=Pelobacter carbinolicus (strain
DSM 2380 / Gra Bd 1) GN=truD PE=3 SV=1
Length = 398
Score = 90.9 bits (224), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 73/254 (28%), Positives = 134/254 (52%), Gaps = 10/254 (3%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G+ L + K T E L +S+ L + R+ G+AG KD ++ + Q ++V A +
Sbjct: 37 GEHLYLEVEKRGMTTFELLKRLSRALQVNERAMGYAGLKDAQATTRQFISVTDCSAEQAL 96
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFIN 148
AL +L IR+ + L LG L GNRFTIT+R + D+ + + + L G N
Sbjct: 97 AL--QLQDIRILSARRHRNKLRLGHLAGNRFTITIRDIDSDALEKARDILHVLQMTGVPN 154
Query: 149 YFGLQRFGS-GSVPTHLVGATLLRGEW-KSAVKMILDPREGERNEISKAREYYKETDDID 206
+FG QR+G+ G+ +HL+G +++ + ++A +I DP + E + Y E + ++
Sbjct: 155 FFGEQRYGALGN--SHLIGQAIVQKNFSQAAAHIIGDPDKIIHPEWRQGAILYAE-NRLE 211
Query: 207 GTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQ 266
+ LPR + ER +++ L++ +A++ +P L +Y+ +YQS L++ S R++
Sbjct: 212 EAEQALPRRMRNERNLVRSLRQGRSAE-KAVRRLPGKLLRLYLSAYQSHLFDRLVSMRLE 270
Query: 267 KHGTEHVVVGDLVF 280
E + GD+ +
Sbjct: 271 S--LETLWTGDIAY 282
>sp|A1RRV7|TRUD_PYRIL Probable tRNA pseudouridine synthase D OS=Pyrobaculum islandicum
(strain DSM 4184 / JCM 9189) GN=truD PE=3 SV=1
Length = 412
Score = 90.5 bits (223), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 68/257 (26%), Positives = 125/257 (48%), Gaps = 8/257 (3%)
Query: 27 QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASK 86
++G + H+ K+N DT + L ++K LG+ R G KD R+V++Q +++ + +
Sbjct: 56 RVGSWTWIHVVKKNTDTLKLLLYLAKTLGLKARDISIGGIKDTRAVTSQIISI-RGDVTN 114
Query: 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGF 146
L + + F + + + + GNRFTITLR V+ D +A+ +L
Sbjct: 115 LPKIRN----VEFLSFWPMDKPITPSLIYGNRFTITLRN--VEKVDCAEATLKTLQYIAL 168
Query: 147 INYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDID 206
NY+G QRFG+ +HL+G L++ + + ++ ++++K D
Sbjct: 169 PNYYGYQRFGTIRPVSHLLGKALVKKDAEEFFDIMFCKIFAYESDVAKKAREAACKGDYR 228
Query: 207 GTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQ 266
L P+ + ERA+L+ L + + A+ +IP + +YV + QS+L+N S R++
Sbjct: 229 RALEIFPKRFIEERAVLRGLLRGLDLW-NAIMSIPIQILRIYVEALQSYLFNLFLSKRME 287
Query: 267 KHGTEHVVVGDLVFCKG 283
+ GDLV G
Sbjct: 288 LGPLNRPIEGDLVEING 304
>sp|B1Y9W7|TRUD_PYRNV Probable tRNA pseudouridine synthase D OS=Pyrobaculum neutrophilum
(strain DSM 2338 / JCM 9278 / V24Sta) GN=truD PE=3 SV=1
Length = 412
Score = 87.4 bits (215), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 81/263 (30%), Positives = 129/263 (49%), Gaps = 14/263 (5%)
Query: 27 QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASK 86
++G + H+ K N DT + + ++K LG+ R G KD R+V++Q V+V A
Sbjct: 56 RVGGWTWIHVVKRNVDTVKLVLRLAKALGLRSRDISIGGIKDTRAVTSQIVSVRGNVADL 115
Query: 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGF 146
N + +G+ D + + + GNRFTI LR V+ + +A+ +LG+
Sbjct: 116 PKIPNVQFLGLWPMD-----KPIAPSLIYGNRFTIVLRN--VERRECAEAALAALGKAAL 168
Query: 147 INYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMI---LDPREGERNEISKAREYYKETD 203
NY+G QRFG+ +HL+G LLR + + ++ + P E E + KARE
Sbjct: 169 PNYYGYQRFGTIRPVSHLLGKALLRKDAEGFFHVMFCKIFPYESEAAK--KARE-LACRG 225
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASA 263
+ L PR V ERA+L+ L + + A AIP + +Y+ + QS L+N S
Sbjct: 226 EYQKALEAFPRGFVEERALLRRLVRG-SDLWNAAMAIPLQILRIYIEAAQSHLFNLLLSK 284
Query: 264 RVQKHGTEHVVVGDLVFCKGDDT 286
R++ + V GDLV G T
Sbjct: 285 RMELGPLDRPVEGDLVEVNGQVT 307
>sp|Q8F8N2|TRUD_LEPIN tRNA pseudouridine synthase D OS=Leptospira interrogans serogroup
Icterohaemorrhagiae serovar Lai (strain 56601) GN=truD
PE=3 SV=1
Length = 408
Score = 80.5 bits (197), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 16/245 (6%)
Query: 26 EQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRAS 85
++ GK++ F L K +T +AL ISK + G+AG KD+ + ++Q ++
Sbjct: 34 QKTGKWMIFRLQKSGWNTLDALLRISKESKVSIFEIGYAGKKDRHASTSQYIS-----CQ 88
Query: 86 KLAALNKRLIG-IRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRN 144
K + K L I+L + K+ L +GNRF + LR ++ + I+ + + +N
Sbjct: 89 KPLRVPKELTKVIQLDKIGFSKKSLSTELNVGNRFQLVLRNLLEKEIESIRNNFEKITKN 148
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMIL-DPREGERNEISKAREYYKETD 203
GFINY+ QRF L +G+ ++ +K+IL DP GE+ + AR+ K
Sbjct: 149 GFINYYDSQRFSRFHSEFRLPILPFFKGDAETCLKLILTDPFPGEKKQ---ARDRKKILY 205
Query: 204 DIDGTLRKLPRHLVA--ERAILQCLKK----CPGNYLQALKAIPRTLRMMYVHSYQSFLW 257
D+ G + + + E+ I LKK Y + P +M V S+QS +W
Sbjct: 206 DLWGNWSQCEKWSKSKLEKNIFSNLKKEKKPTQKTYSDLILRFPEEELLMLVSSFQSLIW 265
Query: 258 NHAAS 262
N S
Sbjct: 266 NEFVS 270
>sp|Q72N01|TRUD_LEPIC tRNA pseudouridine synthase D OS=Leptospira interrogans serogroup
Icterohaemorrhagiae serovar copenhageni (strain Fiocruz
L1-130) GN=truD PE=3 SV=2
Length = 408
Score = 80.5 bits (197), Expect = 3e-14, Method: Compositional matrix adjust.
Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 16/245 (6%)
Query: 26 EQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRAS 85
++ GK++ F L K +T +AL ISK + G+AG KD+ + ++Q ++
Sbjct: 34 QKTGKWMIFRLQKSGWNTLDALLRISKESKVSIFEIGYAGKKDRHASTSQYIS-----CQ 88
Query: 86 KLAALNKRLIG-IRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRN 144
K + K L I+L + K+ L +GNRF + LR ++ + I+ + + +N
Sbjct: 89 KPLRVPKELTKVIQLDKIGFSKKSLSTELNVGNRFQLVLRNLLEKEIESIRNNFEKITKN 148
Query: 145 GFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMIL-DPREGERNEISKAREYYKETD 203
GFINY+ QRF L +G+ ++ +K+IL DP GE+ + AR+ K
Sbjct: 149 GFINYYDSQRFSRFHSEFRLPILPFFKGDAETCLKLILTDPFPGEKKQ---ARDRKKILY 205
Query: 204 DIDGTLRKLPRHLVA--ERAILQCLKK----CPGNYLQALKAIPRTLRMMYVHSYQSFLW 257
D+ G + + + E+ I LKK Y + P +M V S+QS +W
Sbjct: 206 DLWGNWSQCEKWSKSKLEKNIFSNLKKEKKPTQKTYSDLILRFPEEELLMLVSSFQSLIW 265
Query: 258 NHAAS 262
N S
Sbjct: 266 NEFVS 270
>sp|Q6M1A3|TRUD1_METMP Probable tRNA pseudouridine synthase D 1 OS=Methanococcus
maripaludis (strain S2 / LL) GN=truD1 PE=3 SV=1
Length = 389
Score = 75.9 bits (185), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 60/238 (25%), Positives = 117/238 (49%), Gaps = 16/238 (6%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G + + L K + +A+ +SK + + G+ G KD+ +++TQ V++ K+ KL+
Sbjct: 24 GNYFLYKLQKNGIENLKAISYLSKNFEVPTKEIGYCGLKDRHAITTQYVSIPKEYG-KLS 82
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRN---G 145
L +L +++ L +G+L GNRF I R VD ++ +K + N RN G
Sbjct: 83 LDEDNL---KLEYVGTIEKPLKIGRLYGNRFEIIARA--VDKDEFLKIADNI--RNLSSG 135
Query: 146 FINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMILDPR-EGERNEISKAREYY-KETD 203
NY+ QRFGS + +L+G ++ VK++L + E+ ++ + + K
Sbjct: 136 APNYYDDQRFGS-VFNGKFIAKEILKGNYEEVVKILLTSYTKSEKKQLKDLKRFIAKNWG 194
Query: 204 DIDGTLRKLPRHLVAERAILQCLKKCP--GNYLQALKAIPRTLRMMYVHSYQSFLWNH 259
+ D L + + + + +K ++ +A K + L+ +++ +YQS+LWN
Sbjct: 195 NWDECLEYIDKKQIRSKMFRNMVKSLTYENDFKKAFKYVDNRLKELFISAYQSYLWNE 252
>sp|A7H5G6|TRUD_CAMJD tRNA pseudouridine synthase D OS=Campylobacter jejuni subsp. doylei
(strain ATCC BAA-1458 / RM4099 / 269.97) GN=truD PE=3
SV=1
Length = 372
Score = 72.0 bits (175), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 51/152 (33%), Positives = 82/152 (53%), Gaps = 3/152 (1%)
Query: 29 GKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88
G+ L H+ K++ T EAL ++S+ G+ R FG+AG KDK+ + Q +++ K+ S L+
Sbjct: 46 GEHLILHINKKDLSTNEALKILSEQSGVKMRDFGYAGLKDKQGSTFQYLSIPKKFESFLS 105
Query: 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFIN 148
+ + I L F + + L +G L GN F I L+ V+ ++ +L + GF N
Sbjct: 106 NFSHSKLKI-LETFTH-ENKLRIGHLKGNSFFIRLKKVMPSDALKLEQVLMNLDKQGFAN 163
Query: 149 YFGLQRFGSGSVPTHLVGATLLRGEWKSAVKM 180
YFG QRFG + G +LRG+ +KM
Sbjct: 164 YFGYQRFGKFG-DNYKEGLEILRGKKMKNIKM 194
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.316 0.133 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 200,457,810
Number of Sequences: 539616
Number of extensions: 8710819
Number of successful extensions: 22627
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 89
Number of HSP's successfully gapped in prelim test: 130
Number of HSP's that attempted gapping in prelim test: 21873
Number of HSP's gapped (non-prelim): 521
length of query: 532
length of database: 191,569,459
effective HSP length: 122
effective length of query: 410
effective length of database: 125,736,307
effective search space: 51551885870
effective search space used: 51551885870
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 64 (29.3 bits)