RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 011455
(485 letters)
>gnl|CDD|211339 cd02573, PseudoU_synth_EcTruB, Pseudouridine synthase, Escherichia
coli TruB like. This group consists of bacterial
pseudouridine synthases similar to E. coli TruB and
Mycobacterium tuberculosis TruB. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
E. coli TruB and M. tuberculosis TruB make psi55 in the
T loop of tRNAs. Psi55 is nearly universally conserved.
E. coli TruB is not inhibited by RNA containing
5-fluorouridine.
Length = 213
Score = 224 bits (574), Expect = 4e-71
Identities = 69/147 (46%), Positives = 99/147 (67%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP G TS V K+RRL+ KKVGH GTLDP+ATG+L + +G+ATKL K
Sbjct: 3 LLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADK 62
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
Y RLGEAT T DA+ +I+ P + +E+I A +F GEI QVPPM+SA+KV G
Sbjct: 63 TYRATVRLGEATDTDDAEGEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVDG 122
Query: 432 EKMYDKARRGESIELSPRRISIFQFDI 458
+++Y+ AR GE +E PR+++I+ ++
Sbjct: 123 KRLYELARAGEEVERPPRKVTIYSLEL 149
>gnl|CDD|216540 pfam01509, TruB_N, TruB family pseudouridylate synthase (N terminal
domain). Members of this family are involved in
modifying bases in RNA molecules. They carry out the
conversion of uracil bases to pseudouridine. This family
includes TruB, a pseudouridylate synthase that
specifically converts uracil 55 to pseudouridine in most
tRNAs. This family also includes Cbf5p that modifies
rRNA.
Length = 149
Score = 205 bits (525), Expect = 9e-65
Identities = 66/142 (46%), Positives = 91/142 (64%), Gaps = 3/142 (2%)
Query: 330 RRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389
+R++ KKVGH GTLDP+ATG+L VCVGKATKL+ K Y RLG AT T DA+
Sbjct: 1 KRILGAKKVGHTGTLDPLATGVLPVCVGKATKLLQYLLDADKEYRATIRLGVATDTLDAE 60
Query: 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPR 449
+++ P +HI +E I + ASF GEI QVPPM+SA+KV G+++Y+ AR G +E PR
Sbjct: 61 GEIVEEPPVDHITEEKIEEVLASFTGEIEQVPPMYSAVKVNGKRLYELAREGIEVERPPR 120
Query: 450 RISIFQFDIERSLEDRFFFFLF 471
++I+ ++ LE F
Sbjct: 121 PVTIYSLEL---LEFDLPEVTF 139
>gnl|CDD|235113 PRK03287, truB, tRNA pseudouridine synthase B; Provisional.
Length = 298
Score = 193 bits (494), Expect = 3e-58
Identities = 70/162 (43%), Positives = 98/162 (60%), Gaps = 4/162 (2%)
Query: 297 STELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCV 356
+P T G +V+V+KP G TS V + RRL +KVGHAGTLDPMATG+L++ V
Sbjct: 1 MMAMPLTGSG----LVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGV 56
Query: 357 GKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGE 416
+ATKL+ K Y+ RLG+AT+T DA+ V+ + DE I A A+ GE
Sbjct: 57 ERATKLLGHLTLTDKSYTATIRLGQATTTDDAEGEVLASADASAVTDEAIAAAVAALTGE 116
Query: 417 IWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDI 458
I QVP SAIKV G++ Y + R GE +EL R +++ +F++
Sbjct: 117 IMQVPSAVSAIKVDGKRAYARVRAGEEVELPARPVTVSRFEV 158
>gnl|CDD|179469 PRK02755, truB, tRNA pseudouridine synthase B; Provisional.
Length = 295
Score = 171 bits (436), Expect = 1e-49
Identities = 70/153 (45%), Positives = 98/153 (64%), Gaps = 2/153 (1%)
Query: 306 GPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDR 365
G FG + L +KP G TS +LRRL+++K+VGH GTLDP ATG+L + +GKAT+L+
Sbjct: 1 GMFGFLNL-DKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLL-P 58
Query: 366 YQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFS 425
Y K Y G R G TST D ++ +PW H+ +I A FRG+I Q PP +S
Sbjct: 59 YLPGEKTYRGTIRFGVRTSTDDLQGEILSSQPWPHLSLAEIETALPQFRGKIEQRPPQYS 118
Query: 426 AIKVGGEKMYDKARRGESIELSPRRISIFQFDI 458
AI+V GE++Y ARRGE++EL R ++IF+ +
Sbjct: 119 AIQVDGERLYALARRGETMELPARTVTIFRLQL 151
>gnl|CDD|178886 PRK00130, truB, tRNA pseudouridine synthase B; Provisional.
Length = 290
Score = 166 bits (423), Expect = 6e-48
Identities = 68/145 (46%), Positives = 102/145 (70%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP G TSF V K+R++ K+KKVGH GTLDP+A+G+L VC+GKATK+VD K Y
Sbjct: 7 ILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTY 66
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEK 433
+LG T T+D + +++ + H+ +E+IR+A SF+GEI QVPPM+SA+K+ G+K
Sbjct: 67 RAEIKLGVETDTYDREGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKINGKK 126
Query: 434 MYDKARRGESIELSPRRISIFQFDI 458
+Y+ AR+G +E R+I+I+ +I
Sbjct: 127 LYELARQGIEVEREARKITIYDIEI 151
>gnl|CDD|129523 TIGR00431, TruB, tRNA pseudouridine(55) synthase. TruB, the tRNA
pseudouridine 55 synthase, converts uracil to
pseudouridine in the T loop of most tRNAs in all three
domains of life. This model is built on a seed alignment
of bacterial proteins only. Saccharomyces cerevisiae
protein YNL292w (Pus4) has been shown to be the
pseudouridine 55 synthase of both cytosolic and
mitochondrial compartments, active at no other position
on tRNA and the only enzyme active at that position in
the species. A distinct yeast protein YLR175w,
(centromere/microtubule-binding protein CBF5) is an rRNA
pseudouridine synthase, and the archaeal set is much
more similar to CBF5 than to Pus4. It is unclear whether
the archaeal proteins found by this model are tRNA
pseudouridine 55 synthases like TruB, rRNA pseudouridine
synthases like CBF5, or (as suggested by the absence of
paralogs in the Archaea) both. CBF5 likely has
additional, eukaryotic-specific functions. The trusted
cutoff is set above the scores for the archaeal homologs
of unknown function, so yeast Pus4p scores between
trusted and noise [Protein synthesis, tRNA and rRNA base
modification].
Length = 209
Score = 162 bits (413), Expect = 2e-47
Identities = 65/143 (45%), Positives = 93/143 (65%), Gaps = 1/143 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP+G TSF K+RRL+ VKKVGH GTLDP ATG+L + VGKATKL + K
Sbjct: 5 LLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDK 64
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
Y RLG T T D D +++ P + D+ A +FRGEI Q+PPM+SA+KV G
Sbjct: 65 EYRAEIRLGVRTDTLDPDGQIVETRPVNPTTE-DVEAALPTFRGEIEQIPPMYSALKVNG 123
Query: 432 EKMYDKARRGESIELSPRRISIF 454
+++Y+ AR+G +E R ++++
Sbjct: 124 KRLYEYARQGIEVERKARPVTVY 146
>gnl|CDD|234959 PRK01550, truB, tRNA pseudouridine synthase B; Provisional.
Length = 304
Score = 161 bits (410), Expect = 6e-46
Identities = 69/154 (44%), Positives = 100/154 (64%), Gaps = 1/154 (0%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
+L++KP+G TS KLR++++ KKVGH GTLDP +G+L +CVG+ATK+ + K
Sbjct: 5 LLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDEGK 64
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPW-EHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
Y G LG +T+T DAD V++ +P I E+I A AS G I Q+PPM+SA+KV
Sbjct: 65 TYEGEVTLGFSTTTEDADGEVVETKPVDRPITREEIEAALASLTGTIEQIPPMYSAVKVN 124
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLED 464
G+K+Y+ AR G +E R+I+I +F + S ED
Sbjct: 125 GKKLYEYARAGIEVERPVRQITIHEFVLLDSRED 158
>gnl|CDD|211323 cd00506, PseudoU_synth_TruB_like, Pseudouridine synthase, TruB
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M.
tuberculosis TruB, S. cerevisiae Cbf5 and human
dyskerin. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruB, M. tuberculosis TruB and S.
cerevisiae Pus4, make psi55 in the T loop of tRNAs.
Pus4 catalyses the formation of psi55 in both
cytoplasmic and mitochondrial tRNAs. Psi55 is almost
universally conserved. S. cerevisiae Cbf5 and human
dyskerin are nucleolar proteins that, with the help of
guide RNAs, make the hundreds of psueudouridnes present
in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin
is the catalytic subunit of eukaryotic box H/ACA small
nucleolar ribonucleoprotein (snoRNP) particles.
Mutations in human dyskerin cause X-linked dyskeratosis
congenitas.
Length = 210
Score = 157 bits (399), Expect = 1e-45
Identities = 62/146 (42%), Positives = 94/146 (64%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+ V+KP+G +S V +RR+ +KVGH GTLDP ATG+L+V +GKATKL+
Sbjct: 2 LFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAAT 61
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y+ + RLG+AT T+DA VI+ P++HI E + +A + G+I QVPP++SA+K
Sbjct: 62 KDYTAIGRLGQATDTFDATGQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQ 121
Query: 431 GEKMYDKARRGESIELSPRRISIFQF 456
G++ Y+ ARRG + R +I++
Sbjct: 122 GQRAYELARRGLLVPDEARPPTIYEL 147
>gnl|CDD|235442 PRK05389, truB, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 158 bits (403), Expect = 7e-45
Identities = 65/158 (41%), Positives = 88/158 (55%), Gaps = 2/158 (1%)
Query: 312 VLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIK 371
++++KP G TS K++ L +K GHAGTLDP+A+G+L + +G+ATK V K
Sbjct: 16 LILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTVPYVMDGTK 75
Query: 372 GYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
Y GE T D + V DE+IR A +F GEI QVPP FSAIK+ G
Sbjct: 76 RYRFTVAWGEERDTDDLEGEVTATSD-VRPTDEEIRAALPAFTGEIMQVPPQFSAIKIDG 134
Query: 432 EKMYDKARRGESIELSPRRISIFQFD-IERSLEDRFFF 468
E+ YD AR GE++EL R + I + +ER D F
Sbjct: 135 ERAYDLAREGETVELPARPVEIDRLTLVERPDADHAVF 172
>gnl|CDD|235042 PRK02484, truB, tRNA pseudouridine synthase B; Provisional.
Length = 294
Score = 151 bits (384), Expect = 3e-42
Identities = 61/145 (42%), Positives = 91/145 (62%), Gaps = 1/145 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ K G TS KLR++++ KK+GH GTLDP G+L + VGKAT+L++ K Y
Sbjct: 8 LKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAGKVY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDED-IRKAAASFRGEIWQVPPMFSAIKVGGE 432
G LG +T+T DA V+ P E+ + +A SF G+I Q+PPM+SA+KV G+
Sbjct: 68 EGEITLGYSTTTEDASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKVNGK 127
Query: 433 KMYDKARRGESIELSPRRISIFQFD 457
K+Y+ AR GE +E R+++I+QF+
Sbjct: 128 KLYEYARAGEEVERPKRQVTIYQFE 152
>gnl|CDD|235333 PRK05033, truB, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 146 bits (372), Expect = 3e-40
Identities = 61/154 (39%), Positives = 93/154 (60%), Gaps = 9/154 (5%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK----LVDRY 366
++L++KP+G +S K++RL K GH G LDP+ATG+L +C+G+ATK L+D
Sbjct: 12 VLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKFSQYLLDSD 71
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSA 426
K Y RLG+ T T DAD V++ P + E + A FRG+I QVP M+SA
Sbjct: 72 ----KRYRVTARLGQRTDTSDADGEVVEERPVT-LSAEQLEAALEKFRGDIEQVPSMYSA 126
Query: 427 IKVGGEKMYDKARRGESIELSPRRISIFQFDIER 460
+K G+ +Y+ AR+G +E R I+I++ ++ R
Sbjct: 127 LKYQGQPLYEYARQGIEVEREARPITIYELELIR 160
>gnl|CDD|234986 PRK01851, truB, tRNA pseudouridine synthase B; Provisional.
Length = 303
Score = 146 bits (370), Expect = 4e-40
Identities = 61/148 (41%), Positives = 86/148 (58%), Gaps = 1/148 (0%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++L++KP G +S + +RL++ KK GH GTLDP+ATGLL +C G+ATK
Sbjct: 18 VLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDAD 77
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y RLG TST DA+ V+ P + A A F GEI QVPPM+SA+K
Sbjct: 78 KTYEATLRLGVRTSTGDAEGEVLATRP-VDCDPAALEAALARFTGEIRQVPPMYSALKKD 136
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDI 458
G+ +Y+ AR G ++E R ++I D+
Sbjct: 137 GKPLYEYARAGITVEREARDVTIHALDL 164
>gnl|CDD|179199 PRK00989, truB, tRNA pseudouridine synthase B; Provisional.
Length = 230
Score = 142 bits (359), Expect = 2e-39
Identities = 66/145 (45%), Positives = 97/145 (66%), Gaps = 4/145 (2%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVG-KATKLVDRYQGM 369
++LV+KP+G TSF++ L +L+ VKK+GHAGTLDP ATG++++ +G K T+L D
Sbjct: 11 ILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDILLFE 70
Query: 370 IKGYSGVFRLGEATSTWDADSPVIQREPWEHIKD-EDIRKAAASFRGEIWQVPPMFSAIK 428
K Y+ V LG T ++D D ++ R + I E++ AA+ F+GEI QVPPMFSA K
Sbjct: 71 DKEYAAVAHLGTTTDSYDCDGKIVGRS--KKIPTLEEVLSAASYFQGEIQQVPPMFSAKK 128
Query: 429 VGGEKMYDKARRGESIELSPRRISI 453
V G+K+Y+ AR+G SIE P + +
Sbjct: 129 VQGKKLYEYARQGLSIERRPSTVQV 153
>gnl|CDD|223208 COG0130, TruB, Pseudouridine synthase [Translation, ribosomal
structure and biogenesis].
Length = 271
Score = 141 bits (357), Expect = 1e-38
Identities = 53/161 (32%), Positives = 81/161 (50%), Gaps = 35/161 (21%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP G TS V ++R++ V+K GH GTLDP+ATG+L +C+G+ATKLV
Sbjct: 17 VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDAD 76
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVG 430
K Y RLG+ T + +E++R A +F GEI+Q+PPMFSA+K
Sbjct: 77 KEYVATVRLGDQTDS-----------------EEEVRAALEAFTGEIYQIPPMFSAVK-- 117
Query: 431 GEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLF 471
E+ R+I+I+ L+
Sbjct: 118 -------------REVERRKITIYDLLE---LDFDRNLVTL 142
>gnl|CDD|172614 PRK14124, PRK14124, tRNA pseudouridine synthase B; Provisional.
Length = 308
Score = 138 bits (350), Expect = 3e-37
Identities = 64/145 (44%), Positives = 91/145 (62%), Gaps = 1/145 (0%)
Query: 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKG 372
+ KPKG TS V ++R+ +K +KVGHAGTLDP ATG+LIV V KAT+L++ + K
Sbjct: 7 VAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKV 66
Query: 373 YSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGE 432
Y RLG T T+D V++ ++ +E+IR+A SF GE QVPP +SA K GE
Sbjct: 67 YYVKMRLGLITETFDITGEVVEERE-CNVTEEEIREAIFSFVGEYKQVPPAYSAKKYKGE 125
Query: 433 KMYDKARRGESIELSPRRISIFQFD 457
++Y AR G+ I L P+ + I++
Sbjct: 126 RLYKLAREGKIINLPPKEVKIYEIW 150
>gnl|CDD|184521 PRK14122, PRK14122, tRNA pseudouridine synthase B; Provisional.
Length = 312
Score = 134 bits (339), Expect = 1e-35
Identities = 57/145 (39%), Positives = 83/145 (57%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
V+KP G TS V + RR + ++VGH GTLDP+ATG+L++C +TKLV K Y
Sbjct: 6 VDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAEDKEY 65
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEK 433
G T T DA+ P+ + P + ++D+ A F G QVPP +SAIKVGG +
Sbjct: 66 LAWVSFGATTPTLDAEGPISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKVGGVR 125
Query: 434 MYDKARRGESIELSPRRISIFQFDI 458
Y+ AR G ++EL R + + ++
Sbjct: 126 AYEAARAGGALELPARPVVYHELEL 150
>gnl|CDD|179870 PRK04642, truB, tRNA pseudouridine synthase B; Provisional.
Length = 300
Score = 127 bits (321), Expect = 2e-33
Identities = 59/147 (40%), Positives = 83/147 (56%)
Query: 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRY 366
++L++KP G +S RRL++ +K GH G+LDP+ATGLL +C G+ATK+
Sbjct: 8 RLDGILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLL 67
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSA 426
G K Y LG T T DAD V++ P + ++ A A G I Q P++SA
Sbjct: 68 LGSAKAYDAEIVLGVTTDTDDADGQVLRERPVPDLSAAALQAALAPLIGRIRQRAPIYSA 127
Query: 427 IKVGGEKMYDKARRGESIELSPRRISI 453
+K GGE +Y KARRGE IE R + +
Sbjct: 128 LKQGGEPLYAKARRGEVIEAPVREVEV 154
>gnl|CDD|184522 PRK14123, PRK14123, tRNA pseudouridine synthase B; Provisional.
Length = 305
Score = 127 bits (320), Expect = 4e-33
Identities = 60/155 (38%), Positives = 90/155 (58%), Gaps = 4/155 (2%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
V K +G TS V KLR+++K KK+GH GTLDP G+L VC+G AT++ D M K Y
Sbjct: 8 VYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWE--HIKDEDIRKAAASFRGEIWQVPPMFSAIKVGG 431
+G +T+T D ++ + +DI + F+G I Q+PPM+S++KV G
Sbjct: 68 EATVSIGRSTTTEDQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVKVNG 127
Query: 432 EKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466
+K+Y+ AR E++E R+++I DI R E F
Sbjct: 128 KKLYEYARNNETVERPKRKVNI--KDIGRISELDF 160
>gnl|CDD|211344 cd02867, PseudoU_synth_TruB_4, Pseudouridine synthase homolog 4.
This group consists of Eukaryotic TruB proteins similar
to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4,
makes psi55 in the T loop of both cytoplasmic and
mitochondrial tRNAs. Psi55 is almost universally
conserved. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi).
Length = 312
Score = 126 bits (319), Expect = 6e-33
Identities = 67/196 (34%), Positives = 98/196 (50%), Gaps = 35/196 (17%)
Query: 314 VNKPKGWTSFTVCGKL-------------------------RRLVKVK----KVGHAGTL 344
+NKP G TS V L RR K K+GH GTL
Sbjct: 5 INKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTL 64
Query: 345 DPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDE 404
DP+ATG+L+V VG TK + Y K Y G +T+T+D + +++++P+ HI E
Sbjct: 65 DPLATGVLVVGVGAGTKQLQDYLSCSKTYEATGLFGASTTTYDREGKILKKKPYSHITRE 124
Query: 405 DIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLED 464
DI + A FRG+I QVPP++SA+K+ G+++Y+ AR G+ + PR I Q + E
Sbjct: 125 DIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYAREGKPL---PRPIERRQVVVS---EL 178
Query: 465 RFFFFLFPLPLKLLDV 480
++ P PL V
Sbjct: 179 LVKDWIEPGPLFTRTV 194
>gnl|CDD|134035 PRK00020, truB, tRNA pseudouridine synthase B; Provisional.
Length = 244
Score = 118 bits (298), Expect = 1e-30
Identities = 53/154 (34%), Positives = 87/154 (56%), Gaps = 2/154 (1%)
Query: 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRY 366
++L++KP G +S + +R V K GH GTLDP ATGLL+ C+G+ATK+ R
Sbjct: 8 ALDGVLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRM 67
Query: 367 QGMIKGYSGVFRLGEATSTWDADSPVIQREP--WEHIKDEDIRKAAASFRGEIWQVPPMF 424
K Y + GE T + D ++ R P + +++ +R + F G I Q+PPM+
Sbjct: 68 LEADKTYQATLQFGEETDSGDLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMY 127
Query: 425 SAIKVGGEKMYDKARRGESIELSPRRISIFQFDI 458
SA+K G+ +Y+ AR G ++ PR+++I ++
Sbjct: 128 SALKRDGKPLYEYARAGIELDRPPRQVTIRHIEL 161
>gnl|CDD|179381 PRK02193, truB, tRNA pseudouridine synthase B; Provisional.
Length = 279
Score = 104 bits (262), Expect = 3e-25
Identities = 55/147 (37%), Positives = 85/147 (57%)
Query: 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKG 372
L+ KPKG +SF + +KK+GH GTLDP+A+GLL+V + TKL+D K
Sbjct: 4 LLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKT 63
Query: 373 YSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGE 432
Y + G ++T+D++ +I + E++ +A + G QVPP+FSA KV G+
Sbjct: 64 YIAKIKFGFISTTYDSEGQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGK 123
Query: 433 KMYDKARRGESIELSPRRISIFQFDIE 459
+ YD AR+G+ IEL P I I + ++
Sbjct: 124 RAYDLARQGKQIELKPIEIKISKIELL 150
>gnl|CDD|179739 PRK04099, truB, tRNA pseudouridine synthase B; Provisional.
Length = 273
Score = 101 bits (254), Expect = 3e-24
Identities = 58/150 (38%), Positives = 77/150 (51%), Gaps = 13/150 (8%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+ + NKP G +S +L+R VKK G +GTLDP A G+LIV G+ TKL +
Sbjct: 4 LFVANKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTP 63
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKD------EDIRKAAASFRGEIWQVPPMF 424
K Y LG A SP + E E I+ + I K S +GEI PP F
Sbjct: 64 KTYRATLWLG-------ASSPSLDIENIESIQIIKPFDKDLIEKILKSLQGEISYTPPKF 116
Query: 425 SAIKVGGEKMYDKARRGESIELSPRRISIF 454
SA K+ G++ Y+ AR+GE EL P + IF
Sbjct: 117 SAKKINGKRAYELARKGEEFELKPITMEIF 146
>gnl|CDD|211338 cd02572, PseudoU_synth_hDyskerin, Pseudouridine synthase, human
dyskerin like. This group consists of eukaryotic and
archeal pseudouridine synthases similar to human
dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila
melanogaster Mfl (minifly protein). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactor is required. S.
cerevisiae Cbf5 and human dyskerin are nucleolar
proteins that, with the help of guide RNAs, make the
hundreds of psueudouridnes present in rRNA and small
nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic
subunit of eukaryotic box H/ACA small nucleolar
ribonucleoprotein (snoRNP) particles. D. melanogaster
mfl hosts in its fourth intron, a box H/AC snoRNA gene.
In addition dyskerin is likely to have a structural role
in the telomerase complex. Mutations in human dyskerin
cause X-linked dyskeratosis congenitas. Mutations in
Drosophila Mfl results in miniflies that suffer
abnormalities.
Length = 182
Score = 98.9 bits (247), Expect = 3e-24
Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 18/118 (15%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
++ ++KP G +S V ++R++ V+K GH+GTLDP TG L VC+ +AT+LV Q
Sbjct: 4 VINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAG 63
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y V RL + +E +R+ F G I+Q PP+ SA+K
Sbjct: 64 KEYVCVMRLHDDVD------------------EEKVRRVLEEFTGAIFQRPPLISAVK 103
>gnl|CDD|179300 PRK01528, truB, tRNA pseudouridine synthase B; Provisional.
Length = 292
Score = 93.5 bits (232), Expect = 3e-21
Identities = 53/141 (37%), Positives = 80/141 (56%), Gaps = 1/141 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP+G +S + +++++ K+GHAGTLD A G+L + VG+ATKLV K Y
Sbjct: 8 IYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEK 433
+ G+ T + D VI + + K E+ + F G I Q+PP FSA+KV G +
Sbjct: 68 IFTVKFGKQTDSGDYAGKVIATKDYIPSK-EEAYAVCSKFIGNITQIPPAFSALKVNGVR 126
Query: 434 MYDKARRGESIELSPRRISIF 454
Y AR G+ +EL PR I+I+
Sbjct: 127 AYKLAREGKEVELKPRNITIY 147
>gnl|CDD|232971 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This
family, found in archaea and eukaryotes, includes the
only archaeal proteins markedly similar to bacterial
TruB, the tRNA pseudouridine 55 synthase. However, among
two related yeast proteins, the archaeal set matches
yeast YLR175w far better than YNL292w. The first, termed
centromere/microtubule binding protein 5 (CBF5), is an
apparent rRNA pseudouridine synthase, while the second
is the exclusive tRNA pseudouridine 55 synthase for both
cytosolic and mitochondrial compartments. It is unclear
whether archaeal proteins found by this model modify
tRNA, rRNA, or both [Protein synthesis, tRNA and rRNA
base modification].
Length = 322
Score = 91.0 bits (226), Expect = 3e-20
Identities = 44/118 (37%), Positives = 62/118 (52%), Gaps = 18/118 (15%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V ++KP G +S V +RR++ V+K GH GTLDP TG+L VC+ +AT+LV Q
Sbjct: 36 VVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSQQEAP 95
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y + RL K+EDI + F G I+Q PP+ SA+K
Sbjct: 96 KEYVCLMRLHRD------------------AKEEDILRVLKEFTGRIFQRPPLKSAVK 135
>gnl|CDD|237834 PRK14846, truB, tRNA pseudouridine synthase B; Provisional.
Length = 345
Score = 89.3 bits (221), Expect = 2e-19
Identities = 50/143 (34%), Positives = 77/143 (53%), Gaps = 1/143 (0%)
Query: 314 VNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGY 373
+ KP+G +S + +++++ K+GHAGTLD A G+L VG+ATKL+ K Y
Sbjct: 8 IYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTY 67
Query: 374 SGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEK 433
+ G T++ D VI + E+ + F G + Q+PP FSA+KV G +
Sbjct: 68 IFTVKFGMQTNSGDCAGKVIATKDCIP-SQEEAYAVCSKFIGNVTQIPPAFSALKVNGVR 126
Query: 434 MYDKARRGESIELSPRRISIFQF 456
Y AR G+ +EL PR I+I+
Sbjct: 127 AYKLAREGKKVELKPRNITIYDL 149
>gnl|CDD|179806 PRK04270, PRK04270, H/ACA RNA-protein complex component Cbf5p;
Reviewed.
Length = 300
Score = 86.8 bits (216), Expect = 6e-19
Identities = 47/120 (39%), Positives = 62/120 (51%), Gaps = 22/120 (18%)
Query: 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMI 370
+V ++KP G TS V +R ++ V+K GH GTLDP TG+L V +GKATK+V
Sbjct: 24 VVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESG 83
Query: 371 KGYSGVFRLGEATSTWDADSPVIQREPWEH--IKDEDIRKAAASFRGEIWQVPPMFSAIK 428
K Y V L H + +EDIRK F GEI+Q PP+ SA+K
Sbjct: 84 KEYVCVMHL--------------------HGDVPEEDIRKVFKEFTGEIYQKPPLKSAVK 123
>gnl|CDD|211324 cd01291, PseudoU_synth, Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). Pseudouridine
synthases contains the RsuA/RluD, TruA, TruB and TruD
families. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases. Some psi sites such
as psi55,13,38 and 39 in tRNA are highly conserved,
being in the same position in eubacteria, archeabacteria
and eukaryotes. Other psi sites occur in a more
restricted fashion, for example psi2604in 23S RNA made
by E.coli RluF has only been detected in E.coli. Human
dyskerin with the help of guide RNAs makes the hundreds
of psueudouridnes present in rRNA and small nuclear RNAs
(snRNAs). Mutations in human dyskerin cause X-linked
dyskeratosis congenitas. Missense mutation in human PUS1
causes mitochondrial myopathy and sideroblastic anemia
(MLASA).
Length = 87
Score = 41.4 bits (98), Expect = 6e-05
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 314 VNKPKGWTSFTVCGKLRRL-VKVKKVGHAGTLDPMATGLLIVC 355
+ KP G T + L + K+VG+AG D A +V
Sbjct: 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase,
humanTRUB2_like. This group consists of eukaryotic
pseudouridine synthases similar to human TruB
pseudouridine synthase homolog 2 (TRUB2). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi).
Length = 226
Score = 34.7 bits (80), Expect = 0.076
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 344 LDPMATGLLIVCVGKATKLVDR-YQGM-IKGYSGVFRLGEATSTWDADSPVIQREPWEHI 401
LD ++G+L++ V KL+ Y + Y+ LG+AT + VI++ ++HI
Sbjct: 40 LDAFSSGVLVLGVNHGNKLLSHLYSNHPTRVYTIRGLLGKATENFFHTGRVIEKTTYDHI 99
Query: 402 KDEDIRKAAASFRGE 416
E I + A +
Sbjct: 100 TREKIERLLAVIQSG 114
>gnl|CDD|216150 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase. Members
of this family are involved in modifying bases in RNA
molecules. They carry out the conversion of uracil bases
to pseudouridine. This family includes RluD, a
pseudouridylate synthase that converts specific uracils
to pseudouridine in 23S rRNA. RluA from E. coli converts
bases in both rRNA and tRNA.
Length = 149
Score = 32.0 bits (73), Expect = 0.26
Identities = 12/71 (16%), Positives = 24/71 (33%), Gaps = 11/71 (15%)
Query: 312 VLVNKPKGWTS---------FTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKL 362
++VNKP G L + ++ LD +GLL+ + K +
Sbjct: 2 IVVNKPAGVPVHPTDPSDLLSLTALLLVAELGKFRLYPVHRLDRNTSGLLL--LAKDGEA 59
Query: 363 VDRYQGMIKGY 373
++ +
Sbjct: 60 ANKLNKLFPER 70
>gnl|CDD|187793 cd09662, Csm5_III-A, CRISPR/Cas system-associated RAMP superfamily
protein Csm5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 365
Score = 30.1 bits (68), Expect = 2.9
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 220 KAGGKSEEKKYNKEDDKRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKV 279
K G E ++Y + D E+ + +K EEF K K+V
Sbjct: 233 KRGLDRENERYLPCLPFNK--LIIIKINDASDHTKNEEAETELSDVQKAYEEFRKLEKEV 290
Query: 280 PNKENEV 286
NK E+
Sbjct: 291 NNKVGEI 297
>gnl|CDD|211325 cd02550, PseudoU_synth_Rsu_Rlu_like, Pseudouridine synthase,
Rsu/Rlu family. This group is comprised of eukaryotic,
bacterial and archeal proteins similar to eight site
specific Escherichia coli pseudouridine synthases: RsuA,
RluA, RluB, RluC, RluD, RluE, RluF and TruA.
Pseudouridine synthases catalyze the isomerization of
specific uridines in a n RNA molecule to pseudouridines
(5-ribosyluracil, psi) requiring no cofactors. E. coli
RluC for example makes psi955, 2504 and 2580 in 23S RNA.
Some psi sites such as psi1917 in 23S RNA made by RluD
are universally conserved. Other psi sites occur in a
more restricted fashion, for example psi2819 in 21S
mitochondrial ribosomal RNA made by S. cerevisiae Pus5p
is only found in mitochondrial large subunit rRNAs from
some other species and in gram negative bacteria. The E.
coli counterpart of this psi residue is psi2580 in 23S
rRNA. psi2604in 23S RNA made by RluF has only been
detected in E.coli.
Length = 154
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 9/63 (14%)
Query: 312 VLVNKPKGWTS-------FTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVD 364
+++NKP G + +V AG LD +GLL+ + +L
Sbjct: 2 LVLNKPSGLVCHPTDRDRDPTVVVRLDKLHGPRVHAAGRLDKDTSGLLL--LTNDGRLQR 59
Query: 365 RYQ 367
R
Sbjct: 60 RLT 62
>gnl|CDD|217233 pfam02794, HlyC, RTX toxin acyltransferase family. Members of this
family are enzymes EC:2.3.1.-. involved in fatty
acylation of the protoxins (HlyA) at lysine residues,
thereby converting them to the active toxin. Acyl-acyl
carrier protein (ACP) is the essential acyl donor. This
family show a number of conserved residues that are
possible candidates for participation in acyl transfer.
Site-directed mutagenesis of the single conserved
histidine residue in E. coli hlyC resulted in complete
inactivation of the enzyme.
Length = 134
Score = 28.0 bits (63), Expect = 6.0
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 184 HYKMVY-QLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGG 223
H + +Y L ++ FP Q + D + K M + G
Sbjct: 92 HARAIYRDLRRRIFPGQKVRALRYDKGGQKRGKIMEFRGGA 132
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.3 bits (65), Expect = 6.6
Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 3/111 (2%)
Query: 180 EKDKHYKMVYQLEKKYFPDQCLDKAFLDPSADQNVKKMRKKAGGKSEEKKYNKEDDKRLV 239
K K ++ E+K +Q K + + +KK ++ K+ E+ E+DK+
Sbjct: 1618 AKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA 1677
Query: 240 FFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKENEVGSGE 290
++ KK+E+D + K KK EE K + K E+ E
Sbjct: 1678 ---EEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAE 1725
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 28.8 bits (64), Expect = 8.9
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 9/66 (13%)
Query: 77 VNSTNSDENQNPDGELGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGT 136
V+S +DE NP + +SW DKK +K+ ++ + A++ Q+M
Sbjct: 101 VDSELNDEYGNPIWKNRVESWKDKKNKKKKSAKKKEAHKAQIPP---------EQQMEEK 151
Query: 137 DSEDEY 142
S D Y
Sbjct: 152 PSADAY 157
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.135 0.397
Gapped
Lambda K H
0.267 0.0629 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,101,087
Number of extensions: 2471095
Number of successful extensions: 2360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2322
Number of HSP's successfully gapped: 72
Length of query: 485
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 384
Effective length of database: 6,457,848
Effective search space: 2479813632
Effective search space used: 2479813632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.5 bits)