RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 016811
(382 letters)
>gnl|CDD|211337 cd02570, PseudoU_synth_EcTruA, Eukaryotic and bacterial
pseudouridine synthases similar to E. coli TruA. This
group consists of eukaryotic and bacterial pseudouridine
synthases similar to E. coli TruA, Pseudomonas
aeruginosa truA and human pseudouridine synthase-like 1
(PUSL1). Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. E. coli TruA makes psi38/39 and/or 40 in tRNA.
psi38 and psi39 in tRNAs are highly phylogenetically
conserved. P. aeruginosa truA is required for induction
of type III secretory genes and may act through
modifying tRNAs critical for the expression of type III
genes or their regulators.
Length = 239
Score = 292 bits (751), Expect = 1e-98
Identities = 120/293 (40%), Positives = 149/293 (50%), Gaps = 54/293 (18%)
Query: 62 IAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNVCHVD 121
+ +EY GT FSG Q+Q N RTV G LE+A K G+PV + + RTDAGVHA V H D
Sbjct: 1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAGEPVRVIGAGRTDAGVHALGQVAHFD 60
Query: 122 VERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTYFY 181
+P + +A+N L DI V VP DFHARF A+ RTY Y
Sbjct: 61 TPS--------EIPLEK---LIKALNSLLPP--DIRVLSAEEVPDDFHARFSAKSRTYRY 107
Query: 182 RILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPIRTLD 241
RIL+ P P S F + WHV LD+ AMQEA K+L+G HDFSSFRA+GCQ+ S +RT+
Sbjct: 108 RILNRPVP-SPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGCQSKSTVRTIY 166
Query: 242 ELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARSF 301
V ++ RA F
Sbjct: 167 RADV----------------------------------------YREGDLIVFEIRANGF 186
Query: 302 LYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKY 354
LYH VR IVG L VG G+L+ D++ IL+AK TAA P APA GL L V+Y
Sbjct: 187 LYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYLVKVEY 239
>gnl|CDD|234577 PRK00021, truA, tRNA pseudouridine synthase A; Validated.
Length = 244
Score = 276 bits (709), Expect = 2e-92
Identities = 112/297 (37%), Positives = 140/297 (47%), Gaps = 54/297 (18%)
Query: 58 QRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNV 117
R + +EY GT F G Q+Q N RTV G LE+A K G+PV + + RTDAGVHA V
Sbjct: 2 MRIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAGEPVRVIGAGRTDAGVHALGQV 61
Query: 118 CHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQER 177
H D PP RRA+N L DI V VP DFHARF A+ R
Sbjct: 62 AHFDTPAP--------RPPE---KWRRALNALLPD--DIAVLWAEEVPDDFHARFSAKAR 108
Query: 178 TYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPI 237
Y YRI + P F + WH LD+ AM EA + L+G HDF+SFRASGCQ+ SP+
Sbjct: 109 RYRYRIYNRPAR-PPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASGCQSKSPV 167
Query: 238 RTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIAR 297
RT+ E V+ ++
Sbjct: 168 RTIYEADVT----------------------------------------REGDFIVFDIS 187
Query: 298 ARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKY 354
A FL++ VR IVG L VG G+ D++ +L+AK T A P APA GL L V Y
Sbjct: 188 ANGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYLVEVDY 244
>gnl|CDD|223179 COG0101, TruA, Pseudouridylate synthase [Translation, ribosomal
structure and biogenesis].
Length = 266
Score = 258 bits (662), Expect = 5e-85
Identities = 112/298 (37%), Positives = 141/298 (47%), Gaps = 54/298 (18%)
Query: 58 QRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNV 117
+R + + Y GTRF G Q+Q N RTV G LE+A K G+ V + + RTDAGVHA V
Sbjct: 2 KRIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGGESVRVIGAGRTDAGVHALGQV 61
Query: 118 CHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQER 177
H D P + RA+N L DI V DV VP DFHARF A+ R
Sbjct: 62 VHFDTPA--------DRPLEK---LVRALNALLPP--DIRVLDVAEVPDDFHARFSAKSR 108
Query: 178 TYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPI 237
TY Y I + P F + WHV LDL AM+EA K+L+G HDF+SFR +GCQ+ SP+
Sbjct: 109 TYRYIIYNAPLR-PPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRKAGCQSKSPV 167
Query: 238 RTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIAR 297
RT+ + VS +
Sbjct: 168 RTIYRIDVSRD----------------------------------------GDLIVIDIS 187
Query: 298 ARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYD 355
SFL+H VR IVG L VG G+ V ++ +L+AK A P APA GL L V Y
Sbjct: 188 GNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYP 245
>gnl|CDD|232810 TIGR00071, hisT_truA, tRNA pseudouridine(38-40) synthase. Members
of this family are the tRNA modification enzyme TruA,
tRNA pseudouridine(38-40) synthase. In a few species
(e.g. Bacillus anthracis), TruA is represented by two
paralogs [Protein synthesis, tRNA and rRNA base
modification].
Length = 227
Score = 162 bits (412), Expect = 4e-48
Identities = 90/292 (30%), Positives = 126/292 (43%), Gaps = 65/292 (22%)
Query: 58 QRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNV 117
++ + + Y G+ + G Q+Q N RTV G LE+A + ++I + RTD GVHA V
Sbjct: 1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGKKKITIMSAGRTDKGVHAMGQV 60
Query: 118 CHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQER 177
D + +P + + +N L DI V + V +FHARF A +R
Sbjct: 61 ISFDTP--------KEIPDN---KLNAKLNALLP--PDIRVKALAPVNDNFHARFSASKR 107
Query: 178 TYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPI 237
Y Y + R H LDL M+ A K L+G HDFS+F + ++ SPI
Sbjct: 108 HYRY----------ILYNHR--HYYSPLDLEKMRAAAKQLLGKHDFSNFSKAKSKSRSPI 155
Query: 238 RTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIAR 297
RT+ ++ VSE +G +F I
Sbjct: 156 RTISDIKVSE-----------------------------SGEYIIFDI-----------I 175
Query: 298 ARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSL 349
SFL+H VR IVG L VG G+L V ++L AK A APA GL L
Sbjct: 176 GNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANGLYL 227
>gnl|CDD|171495 PRK12434, PRK12434, tRNA pseudouridine synthase A; Reviewed.
Length = 245
Score = 156 bits (396), Expect = 1e-45
Identities = 93/298 (31%), Positives = 146/298 (48%), Gaps = 59/298 (19%)
Query: 60 YLIAVEYIGTRFSGSQKQ-LNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNVC 118
+ ++Y G+R+ G QK N T+ G +E + G+ + I RTDAGVHA + V
Sbjct: 4 IKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTGEEIEIIGCGRTDAGVHALNQVA 63
Query: 119 --HVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQE 176
D E++S+ K +++ +N +L + DI+VT+V V FHAR+ +
Sbjct: 64 NFQTD-EKLSEDK------------IKKYLNEYLPN--DIVVTNVEEVDERFHARYNVKS 108
Query: 177 RTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSP 236
+TY Y+I + +VF + + HV E+LD++AM+EA K LVG HDF+SF + + S
Sbjct: 109 KTYLYKI-WNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAKSKKKST 167
Query: 237 IRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIA 296
+R + SID I ++ ++
Sbjct: 168 VRE------------------------IYSID----------------IMEEDGFVQIRV 187
Query: 297 RARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKY 354
FL++ VR+IVG L VG G+L D+++IL+AK A+ APA GL L V+Y
Sbjct: 188 SGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLENVEY 245
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 153 bits (388), Expect = 2e-44
Identities = 92/293 (31%), Positives = 133/293 (45%), Gaps = 53/293 (18%)
Query: 57 IQRYLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASN 116
++R V Y G+ F G Q Q + RTV GV E+A + Q + + RTD GVHA
Sbjct: 1 MKRVAAVVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFKQRIYTQAAGRTDTGVHANGQ 60
Query: 117 VCHVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQE 176
V + P + + D ++ A+N L DI V V VP +FH RF A++
Sbjct: 61 VIAFNC-------PNDRMTEED---IKNAMNANL--PDDIYVKKVFEVPKNFHPRFDAKK 108
Query: 177 RTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSP 236
R Y Y IL+ E +VF + W ELDL AM++A K L G HDF+SF+ +G +P
Sbjct: 109 RIYHYFILTSKEK-NVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSFK-TGSDERNP 166
Query: 237 IRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIA 296
+RT+ + + + ++ IR
Sbjct: 167 VRTIYRIRILRL------------------------------KKDLILIR---------V 187
Query: 297 RARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSL 349
RSFL VR IVG L VG G+ ++ +L+A+ + A+ APA GL L
Sbjct: 188 EGRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYL 240
>gnl|CDD|173052 PRK14588, PRK14588, tRNA pseudouridine synthase ACD; Provisional.
Length = 272
Score = 149 bits (378), Expect = 1e-42
Identities = 101/306 (33%), Positives = 131/306 (42%), Gaps = 54/306 (17%)
Query: 64 VEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNVCHVDVE 123
+EY GT F+GSQ Q + RTV G LE A+ + I L+ RTDAGVHA V HV +
Sbjct: 8 LEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQERRRIVLAGRTDAGVHARGQVAHVQTD 67
Query: 124 RISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTYFYRI 183
H + + R +N L DI V + P DFHARF A +R Y Y I
Sbjct: 68 -----------TRHSLATIWRGLNAHLPE--DIGVQNAWEAPPDFHARFSAIQREYRYVI 114
Query: 184 LSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPIRTLDEL 243
P P + H LD+ AM A K+L+G HDF++F + Q S +RT
Sbjct: 115 DCAPAPSPQLRH-QVLHYAGTLDVAAMDAALKLLIGTHDFAAF-TTAPQEGSTVRT---C 169
Query: 244 HVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARSFLY 303
+ + T F P+L + EV A A FL
Sbjct: 170 YWARCTDTEWF-----GRPLL--------------------------AIEVAANA--FLQ 196
Query: 304 HQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYDLPEDDQTD 363
H VR IVG L VG G +TV +L ++ A P APA GL L V+Y
Sbjct: 197 HMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGLYLTAVRYP---PGLIR 253
Query: 364 AAESLE 369
E +
Sbjct: 254 WVEPSK 259
>gnl|CDD|211322 cd00497, PseudoU_synth_TruA_like, Pseudouridine synthase, TruA
family. This group consists of eukaryotic, bacterial
and archeal pseudouridine synthases similar to
Escherichia coli TruA, Saccharomyces cerevisiae Pus1p,
S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and
human PUS1. Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. S. cerevisiae PUS1 catalyzes the formation of
psi34 and psi36 in the intron containing tRNAIle, psi35
in the intron containing tRNATyr, psi27 and/or psi28 in
several yeast cytoplasmic tRNAs and, psi44 in U2 small
nuclear RNA (U2 snRNA). The presence of the intron is
required for the formation of psi 34, 35 and 36. In
addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C.
elegans Pus1p does not modify psi44 in U2 snRNA. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44
in U2 snRNA and, psi38 and psi39 in tRNAs are highly
phylogenetically conserved. Psi 26,27,28,34,35,36,65
and 67 in tRNAs are less highly conserved. Mouse Pus1p
regulates nuclear receptor activity through
pseudouridylation of Steroid Receptor RNA Activator.
Missense mutation in human PUS1 causes mitochondrial
myopathy and sideroblastic anemia (MLASA).
Length = 215
Score = 128 bits (323), Expect = 3e-35
Identities = 85/291 (29%), Positives = 111/291 (38%), Gaps = 76/291 (26%)
Query: 64 VEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNVCHVDVE 123
Y GT++ G Q+Q + TV G L A K P I ++RTD GV A V ++ E
Sbjct: 1 FGYDGTKYHGFQRQNDVPTVEGELIIALLKAGNIPYFIKAAARTDRGVSALGQVVAIETE 60
Query: 124 RISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTYFYRI 183
R L P A+N L GDI V V VP DFHA RTY Y I
Sbjct: 61 RR--------LTPE-------ALNGILP--GDIRVFAVHSVPPDFHAPRYCDHRTYRYYI 103
Query: 184 LSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPIRTLDEL 243
S P LD ++ A +G HDF++F + + +RT+
Sbjct: 104 PSFP-----------------LDDERLKSAASRFLGTHDFTNFSKKDTR--NTVRTIIS- 143
Query: 244 HVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARSFLY 303
+P + V +A+SFL+
Sbjct: 144 -----------IECKDLNPFV-----------------VVEF-----------KAKSFLW 164
Query: 304 HQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKY 354
HQVR +VG L VG G + S V R+L APA GL L VKY
Sbjct: 165 HQVRRMVGFLMLVGEGLHSPSSVSRLLAGPAPPIPMVPAPAEGLLLVDVKY 215
>gnl|CDD|237759 PRK14589, PRK14589, tRNA pseudouridine synthase ACD; Provisional.
Length = 265
Score = 111 bits (280), Expect = 1e-28
Identities = 96/321 (29%), Positives = 120/321 (37%), Gaps = 91/321 (28%)
Query: 64 VEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFI----GQPVSISLSSRTDAGVHAASNVCH 119
+ YIGTRF GSQ Q + RTV G A + + +L+ RTD GVHA V
Sbjct: 7 ISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQVL- 65
Query: 120 VDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTY 179
S KP A+N L DI T VP FH R+ A RTY
Sbjct: 66 ----AFSTHKP---------ERAVEALNGQLPP--DIWCTGWAEVPESFHPRYDAISRTY 110
Query: 180 FYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSF-RASGCQANSPIR 238
Y P D+ AM++A +G HDFS F R G SP+R
Sbjct: 111 RYYFSRPP-----------------SDINAMRDAAGEFIGTHDFSCFARVEG---KSPVR 150
Query: 239 TLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARA 298
T+ + V +GG VF EV A
Sbjct: 151 TILRIRVFS-----------------------------DGGFPVF---------EV--TA 170
Query: 299 RSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYDLPE 358
+SFL+H VR + G L +G GE+ D+ER+L P APA GL L V L
Sbjct: 171 QSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKRKVKP-APAEGLVLWDVDCGLTF 229
Query: 359 DDQTDAAESLETCPDPVSRKR 379
DP S +R
Sbjct: 230 T---------PIPADPRSVRR 241
>gnl|CDD|211343 cd02866, PseudoU_synth_TruA_Archea, Archeal pseudouridine
synthases. This group consists of archeal pseudouridine
synthases.Pseudouridine synthases catalyze the
isomerization of specific uridines in an RNA molecule to
pseudouridines (5-ribosyluracil, psi). No cofactors are
required. This group of proteins make Psedouridine in
tRNAs.
Length = 219
Score = 105 bits (265), Expect = 7e-27
Identities = 85/294 (28%), Positives = 115/294 (39%), Gaps = 80/294 (27%)
Query: 64 VEYIGTRFSGSQKQLNCRTVVGVLEEAFHK--FIGQPVSISLSSRTDAGVHAASNVCHVD 121
+ Y GT F G Q+Q + RTV G L +A + I + + RTD GVHA NV +
Sbjct: 3 IAYDGTNFHGFQRQPDVRTVEGELIKALEELGIIESRARLYSAGRTDRGVHALGNVVVFE 62
Query: 122 VERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTYFY 181
E+ P +N L DI V VP DF R A + Y Y
Sbjct: 63 TEK----------EPI-----PPMINAKLPK--DIWVLAGAKVPEDFDPRRWAHRKYYRY 105
Query: 182 RILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSF-RASGCQANSPIRTL 240
+ S D+ AM+EA K L+G HDFS+F + G P+RT+
Sbjct: 106 NLGSD------------------YDVEAMKEAAKKLIGTHDFSNFSKRDG--RKDPVRTI 145
Query: 241 DELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARARS 300
+ + +SE NG +V+ S
Sbjct: 146 ERIEISE-----------------------------NGEFITI---------DVV--GES 165
Query: 301 FLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKY 354
FL++ VR IVG L VG G+ VE++L + P AP GL L VKY
Sbjct: 166 FLWNMVRRIVGALSEVGKGKRENEWVEKLLDGEFRPEGVPPAPPEGLILVDVKY 219
>gnl|CDD|211335 cd02568, PseudoU_synth_PUS1_PUS2, Pseudouridine synthase, PUS1/
PUS2 like. This group consists of eukaryotic
pseudouridine synthases similar to Saccharomyces
cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis
elegans Pus1p and human PUS1. Pseudouridine synthases
catalyze the isomerization of specific uridines in an
RNA molecule to pseudouridines (5-ribosyluracil, psi).
No cofactors are required. S. cerevisiae Pus1p catalyzes
the formation of psi34 and psi36 in the
intron-containing tRNAIle, psi35 in the
intron-containing tRNATyr, psi27 and/or psi28 in several
yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear
RNA (U2 snRNA). The presence of the intron is required
for the formation of psi 34, 35 and 36. In addition S.
cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans
Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p
makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle,
psi 34/36 in tRNAIle and, psi 32 and potentially 67 in
tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are
highly phylogenetically conserved. Psi
26,27,28,34,35,36,65 and 67 in tRNAs are less highly
conserved. Mouse Pus1p regulates nuclear receptor
activity through pseudouridylation of Steroid Receptor
RNA Activator. Missense mutation in human PUS1 causes
mitochondrial myopathy and sideroblastic anemia (MLASA).
Length = 245
Score = 91.9 bits (229), Expect = 2e-21
Identities = 74/306 (24%), Positives = 107/306 (34%), Gaps = 74/306 (24%)
Query: 62 IAVEYIGTRFSGSQKQ-LNCRTVVGVLEEAFHK-------FIGQP--VSISLSSRTDAGV 111
+ Y GT + G Q +T+ G LE A K G P + S ++RTD GV
Sbjct: 1 LLFGYCGTGYHGMQYNPGAYKTIEGELERALFKAGAISESNAGDPKKIGFSRAARTDKGV 60
Query: 112 HAASNVC--HVDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFH 169
HAA NV V ++ E L +N L S DI V + V F+
Sbjct: 61 HAARNVVSLKVIIDDPEGLGILEDLV--------EKLNSHLPS--DIRVFGITRVTKSFN 110
Query: 170 ARFRAQERTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRAS 229
AR RTY Y + P E L+ E K VG H+F +F
Sbjct: 111 ARKACDSRTYEYLL-----PTFALE-----------TLQRFNEILKEYVGTHNFHNF--- 151
Query: 230 GCQANSPIRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPN-GGSNVFGIRKK 288
++ E D S+ + + S F I +
Sbjct: 152 ------TVKKKFE-------------------------DPSANRFIKSFYVSEPFVIEEG 180
Query: 289 HRSYEVIARARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLS 348
+ +SF+ HQ+R ++G+ A+ G S +E K P+AP GL
Sbjct: 181 LEWISIKIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIELSFN-KDKIIIIPLAPGLGLL 239
Query: 349 LGFVKY 354
L +
Sbjct: 240 LERPHF 245
>gnl|CDD|211336 cd02569, PseudoU_synth_ScPus3, Pseudouridine synthase,
Saccharomyces cerevisiae Pus3 like. This group consists
of eukaryotic pseudouridine synthases similar to S.
cerevisiae Pus3p, mouse Pus3p and, human PUS2.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). No cofactors are required. S.
cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse
Pus3p has been shown to makes psi38 and, possibly also
psi 39, in tRNAs. Psi38 and psi39 are highly conserved
in tRNAs from eubacteria, archea and eukarya.
Length = 256
Score = 88.9 bits (221), Expect = 3e-20
Identities = 72/277 (25%), Positives = 98/277 (35%), Gaps = 85/277 (30%)
Query: 66 YIGTRFSGSQKQLNCR-TVVGVLEEAFHK--FI--GQPVSISLSSRTDAGVHAASNVCHV 120
Y+G ++G Q TV L EA K I Q + S RTD GV A V +
Sbjct: 5 YLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQVISL 64
Query: 121 DVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGD-------IMVTDVRC-----VPSDF 168
DV S KP + L P + E ++ D+R VP DF
Sbjct: 65 DVR--SNLKPEDGLDPSTDVKSTA-----DEEELPYCKILNRVLPPDIRILAWAPVPPDF 117
Query: 169 HARFRAQERTYFYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRA 228
ARF RTY Y F K +LD+ M++A K+L+G HDF +F
Sbjct: 118 SARFSCVSRTYRY----------FFPKG-------DLDIELMRKAAKLLLGEHDFRNF-- 158
Query: 229 SGC------QANSPIRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNV 282
C Q + +R + V V G +
Sbjct: 159 --CKMDVANQVTNYVRRVLSAEVEPV-------------------------DQHPDGDGL 191
Query: 283 FGIRKKHRSYEVIARARSFLYHQVRLIVGVLKAVGTG 319
Y R +FL+HQVR ++ VL +G G
Sbjct: 192 ---------YYFEVRGSAFLWHQVRCMMAVLFLIGQG 219
>gnl|CDD|216487 pfam01416, PseudoU_synth_1, tRNA pseudouridine synthase. Involved
in the formation of pseudouridine at the anticodon stem
and loop of transfer-RNAs Pseudouridine is an isomer of
uridine (5-(beta-D-ribofuranosyl) uracil, and id the
most abundant modified nucleoside found in all cellular
RNAs. The TruA-like proteins also exhibit a conserved
sequence with a strictly conserved aspartic acid, likely
involved in catalysis.
Length = 103
Score = 74.0 bits (182), Expect = 2e-16
Identities = 40/143 (27%), Positives = 52/143 (36%), Gaps = 40/143 (27%)
Query: 213 ACKVLVGCHDFSSFRASGCQANSPIRTLDELHVSEVVSTALFSSINQDSPVLSSIDNSSK 272
A K+ G HDFS F+ S IRT++
Sbjct: 1 AAKLYDGTHDFSGFQKQRTVQKSLIRTIES------------------------------ 30
Query: 273 LGMPNGGSNVFGIRKKHRSYEVIARARSFLYHQVRLIVGVLKAVGTGELTVSDVERILKA 332
GI + + FLYHQVR++VG L G G + V +L +
Sbjct: 31 ----------IGIERDGELLVFEIKGNGFLYHQVRIMVGALLRTGKGVHALEQVVSLLNS 80
Query: 333 KTVTAASPMAPACGLSLGFVKYD 355
K A P APA GL L V+YD
Sbjct: 81 KLRPRAPPTAPAVGLYLFHVRYD 103
Score = 44.7 bits (106), Expect = 4e-06
Identities = 23/97 (23%), Positives = 29/97 (29%), Gaps = 25/97 (25%)
Query: 62 IAVEYIGT-RFSGSQKQLNCRTVVGVLEEAFHK-------------FIGQ-------PVS 100
A Y GT FSG QKQ RTV L G +
Sbjct: 1 AAKLYDGTHDFSGFQKQ---RTVQKSLIRTIESIGIERDGELLVFEIKGNGFLYHQVRIM 57
Query: 101 ISLSSRTDAGVHAASNVCHVDVERISKRKPGEVLPPH 137
+ RT GVHA V + + + + P
Sbjct: 58 VGALLRTGKGVHALEQVVSL-LNSKLRPRAPPTAPAV 93
>gnl|CDD|173051 PRK14587, PRK14587, tRNA pseudouridine synthase ACD; Provisional.
Length = 256
Score = 60.2 bits (146), Expect = 3e-10
Identities = 76/298 (25%), Positives = 114/298 (38%), Gaps = 87/298 (29%)
Query: 60 YLIAVEYIGTRFSGSQKQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAASNVCH 119
YL + Y GT F G N ++ L F + +G+ SRTD GV A NV
Sbjct: 3 YLYRIAYDGTLFYGFTGHPN--SLEPALRRVFGEILGR------GSRTDPGVSAVGNV-- 52
Query: 120 VDVERISKRKPGEVLPPHDSSVVRRAVNHFLQSEGDIMVTDVRCVPSDFHARFRAQERTY 179
V K G V +S + R V + +E VP F+ R RA+ R Y
Sbjct: 53 --VMTSQKLPLGYV-----NSKLPRGVWAWAVAE----------VPEGFNPR-RAKRRRY 94
Query: 180 FYRILSGPEPLSVFEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSF-RASGCQANSPIR 238
Y A H E+++ AM+EA ++L G HD+SSF + G +A +
Sbjct: 95 LYV---------------APHWGEDVE--AMREAAELLAGTHDYSSFIQRRGEKATPTVT 137
Query: 239 TLDELHVSEVVSTALFSSINQDSPVLSSIDNSSKLGMPNGGSNVFGIRKKHRSYEVIARA 298
T+ E+ V G ++ +
Sbjct: 138 TVYEIGVEL------------------------------RGDLIY----------LYFVG 157
Query: 299 RSFLYHQVRLIVGVLKAVGTGELTVSDVERILKAKTVTAASPMAPACGLSLGFVKYDL 356
R F +R + + A G G L+ D+ +L+ + A P APA GL L ++YD+
Sbjct: 158 RGFRNKMIRKMAWAILAAGRGVLSRRDIAELLE-RPRPGAVPSAPAEGLVLLDIEYDV 214
>gnl|CDD|215562 PLN03078, PLN03078, Putative tRNA pseudouridine synthase;
Provisional.
Length = 513
Score = 39.9 bits (93), Expect = 0.002
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 12/70 (17%)
Query: 56 RIQRYLIAVEYIGTRFSGSQKQLN---CRTVVGVLEEAFHKFIG---------QPVSISL 103
R ++ ++ V Y+GT + G QKQ + T+ G LE A K G + +
Sbjct: 69 RKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWAR 128
Query: 104 SSRTDAGVHA 113
SSRTD GVH+
Sbjct: 129 SSRTDKGVHS 138
>gnl|CDD|235130 PRK03557, PRK03557, zinc transporter ZitB; Provisional.
Length = 312
Score = 34.3 bits (79), Expect = 0.077
Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 81 RTVVGVLEEAFHKFI-GQPVSIS---LSSRTDAGVHAASNVCHVDVERISKRKP-----G 131
R+ +L+E+ ++ + G PVS+ L R + NV HV V + + KP
Sbjct: 199 RSAWRLLKESVNELLEGAPVSLDIAELKRRLCREIPEVRNVHHVHVWMVGE-KPVMTLHV 257
Query: 132 EVLPPHDSSVVRRAVNHFL 150
+V+PPHD + + +L
Sbjct: 258 QVIPPHDHDALLDRIQDYL 276
>gnl|CDD|233663 TIGR01974, NDH_I_L, proton-translocating NADH-quinone
oxidoreductase, chain L. This model describes the 12th
(based on E. coli) structural gene, L, of bacterial NADH
dehydrogenase I, as well as chain 5 of the corresponding
mitochondrial complex I and subunit 5 (or F) of the
chloroplast NAD(P)H-plastoquinone dehydrogenase complex
[Energy metabolism, Electron transport].
Length = 609
Score = 31.5 bits (72), Expect = 0.87
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 295 IARARSFLYH---QVRLIVGVLKAV-----GTGELTVSDVERILKAKTVTAASPMAPACG 346
+AR S L+ +V ++ A+ T L +D++RIL T++ M A G
Sbjct: 263 VART-SPLFELSPTALYLVTIIGAITALFAATVALVQNDIKRILAYSTMSQLGYMFLALG 321
Query: 347 LS 348
+
Sbjct: 322 VG 323
>gnl|CDD|130181 TIGR01111, mtrA, N5-methyltetrahydromethanopterin:coenzyme M
methyltransferase subunit A. This model describes
N5-methyltetrahydromethanopterin: coenzyme M
methyltransferase subunit A in methanogenic archaea.
This methyltranferase is a membrane-associated enzyme
complex that uses methyl-transfer reaction to drive
sodium-ion pump. Archaea have evolved energy-yielding
pathways marked by one-carbon biochemistry featuring
novel cofactors and enzymes. This transferase (encoded
by subunit A) is involved in the transfer of 'methyl'
group from N5-methyltetrahydromethanopterin to coenzyme
M. In an accompanying reaction, methane is produced by
two-electron reduction of methyl-coenzyme M by another
enzyme, methyl-coenzyme M reductase [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 238
Score = 30.9 bits (70), Expect = 0.87
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 1 MTEFAKRISECSEQASKIPEEKEEDHQNDSVEEEEEYPEEVPETRTVT-EVMSTNKRIQR 59
M ++ EC ASK P +ED +EEE EE E + V+ E R++
Sbjct: 141 MGAITSKVKEC---ASKDPGAFDEDPMIIELEEEGGEEEEGGEVKPVSPETAVIESRMRA 197
Query: 60 YLIAVEYIG 68
++ IG
Sbjct: 198 IEARMKDIG 206
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel,
four-helix bundle structure with a large hydrophobic
patch in which 23 residues of one monomer form van der
Waals contacts with the other monomer. This CENP-B
dimer configuration may be suitable for capturing two
distant CENP-B boxes during centromeric heterochromatin
formation.
Length = 101
Score = 29.0 bits (64), Expect = 1.4
Identities = 15/54 (27%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 10 ECSEQASKIPEEKEEDHQNDSVEEEEEYPEEVPETRTVTEVMSTNKRIQRYLIA 63
E S+ S E+ +++ + D E+++E +EVP + E M+ ++RYL +
Sbjct: 10 EDSDSDSDEEEDDDDEDEEDDDEDDDEDDDEVP-VPSFGEAMAYFAMVKRYLTS 62
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 30.4 bits (68), Expect = 1.5
Identities = 16/39 (41%), Positives = 18/39 (46%)
Query: 16 SKIPEEKEEDHQNDSVEEEEEYPEEVPETRTVTEVMSTN 54
K +E E D + EEEEE EV E T STN
Sbjct: 127 KKATKEDESDEDEEEEEEEEEEEAEVEENEQGTNGTSTN 165
>gnl|CDD|224456 COG1539, FolB, Dihydroneopterin aldolase [Coenzyme metabolism].
Length = 121
Score = 28.7 bits (65), Expect = 1.9
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 76 KQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDAGVHAAS 115
+ L +GVL+E + +GQ + L+ D A S
Sbjct: 8 ENLEFFAYIGVLDE--ERKLGQKFVVDLTLGYDLRKAAES 45
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo and
salvage pathways of DTTP synthesis. Catalytic activity:
ATP + thymidine 5'-phosphate = ADP + thymidine
5'-diphosphate [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 29.6 bits (67), Expect = 2.2
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 1/51 (1%)
Query: 193 FEKDRAWHVTEELDLRAMQEACKVLVGCHDFSSFRASGCQANSPIRTLDEL 243
F DR H+ E+ A+ E V+ + FSS G + EL
Sbjct: 70 FAADRHEHL-EDKIKPALAEGKLVISDRYVFSSIAYQGGARGIDEDLVLEL 119
>gnl|CDD|240482 cd12902, SPRY_PRY_RNF135, PRY/SPRY domain in RING finger protein
RNF135. This domain, consisting of the distinct
N-terminal PRY subdomain followed by the SPRY subdomain,
is found at the C-terminus of the RING finger protein
RNF135 (also known as Riplet/RNF135), which
ubiquitinates RIG-I (retinoic acid-inducible gene-I) to
promote interferon-beta induction during the early phase
of viral infection. Normally, RIG-I is activated by
TRIM25 in response to viral infection, leading to
activation of the RIG-I signaling pathway, thus
resulting in type I interferon production to limit viral
replication. However, RNF135, consisting of an
N-terminal RING finger domain, C-terminal SPRY and PRY
motifs and showing sequence similarity to TRIM25, acts
as an alternative factor that promotes RIG-I activation
independent of TRIM25.
Length = 168
Score = 29.0 bits (65), Expect = 2.4
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 301 FLYHQVRLIVGVLKAVGTGEL---TVSDVERILKAKTVTAASPMAPAC---GLSLG 350
FL +VGV + G L +V + ER+L V+ +SP+ PA GL G
Sbjct: 107 FLGKDKPSVVGVFLDLENGTLSFYSVDNQERLLHEFEVSFSSPLYPAFWLYGLEPG 162
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 29.7 bits (67), Expect = 2.6
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 3 EFAKRISECSEQASKIPEEKEEDHQNDSVEE---EEEYPEEVPETRTVTEV 50
E K + + E+ K +++EE+ D EE EEE E+ +T+ V E
Sbjct: 30 EVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKET 80
>gnl|CDD|227817 COG5530, COG5530, Predicted integral membrane protein [Function
unknown].
Length = 247
Score = 29.1 bits (65), Expect = 3.6
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 168 FHARFRAQERTYFYRILSGPEPLSVFEKDRAWHVTEELDLRA 209
+ AR R ER YF +IL GP+ + + WH +LR
Sbjct: 110 YRARVRQMERFYFAQIL-GPKVDAGSD----WHQLVLAELRK 146
>gnl|CDD|238298 cd00534, DHNA_DHNTPE, Dihydroneopterin aldolase (DHNA) and
7,8-dihydroneopterin triphosphate epimerase domain
(DHNTPE); these enzymes have been designated folB and
folX, respectively. Folate derivatives are essential
cofactors in the biosynthesis of purines, pyrimidines,
and amino acids, as well as formyl-tRNA. Mammalian cells
are able to utilize pre-formed folates after uptake by a
carrier-mediated active transport system. Most microbes
and plants lack this system and must synthesize folates
de novo from guanosine triphosphate. One enzyme from
this pathway is DHNA which catalyses the conversion of
7,8-dihydroneopterin to
6-hydroxymethyl-7,8-dihydropterin in the biosynthetic
pathway of tetrahydrofolate. Though it is known that
DHNTPE catalyzes the epimerization of dihydroneopterin
triphosphate to dihydromonapterin triphosphate, the
biological role of this enzyme is still unclear. It is
hypothesized that it is not an essential protein since a
folX knockout in E. coli has a normal phenotype and the
fact that folX is not present in H. influenza. In
addition both enzymes have been shown to be able to
compensate for the other's activity albeit at slower
reaction rates. The functional enzyme for both is an
octamer of identical subunits. Mammals lack many of the
enzymes in the folate pathway including, DHNA and
DHNTPE.
Length = 118
Score = 27.2 bits (61), Expect = 6.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 76 KQLNCRTVVGVLEEAFHKFIGQPVSISLSSRTDA 109
K L T+ GV EE + +GQ + L+ D
Sbjct: 7 KGLRFYTIHGVFEEE--RLLGQKFVVDLTLWYDL 38
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 28.8 bits (64), Expect = 6.7
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 12 SEQASKIPEEKEEDHQNDSVEEEEEYPEEVP 42
SE+ + EE+EE+ + + EEEEE E P
Sbjct: 863 SEEEEEEEEEEEEEEEEEEEEEEEEEENEEP 893
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 28.4 bits (64), Expect = 7.9
Identities = 22/134 (16%), Positives = 44/134 (32%), Gaps = 31/134 (23%)
Query: 12 SEQASKIPEEKEEDHQNDSVEEEEEYPEEVPETRTVTEVMSTNKRI----------QRYL 61
+ ++ ++ + P T + Q+ L
Sbjct: 390 IQPSAPKTKQAATTPSPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLNLEELWQQIL 449
Query: 62 IAVEYIGTR--FSGSQKQL----NCRTVVGV--------------LEEAFHKFIGQPVSI 101
+E TR S Q +L + R V+ V LE+AF K +G+ + +
Sbjct: 450 AKLELPSTRMLLS-QQAELVSLDSNRAVIAVSPNWLGMVQSRKPLLEQAFAKVLGRSIKL 508
Query: 102 SLSSRTDAGVHAAS 115
+L S++ + + A
Sbjct: 509 NLESQSGSASNTAK 522
>gnl|CDD|238071 cd00124, MYSc, Myosin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Myosins are actin-dependent molecular
motors that play important roles in muscle contraction,
cell motility, and organelle transport. The head domain
is a molecular motor, which utilizes ATP hydrolysis to
generate directed movement toward the plus end along
actin filaments. A cyclical interaction between myosin
and actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 679
Score = 28.4 bits (64), Expect = 8.3
Identities = 20/89 (22%), Positives = 36/89 (40%), Gaps = 12/89 (13%)
Query: 72 SGSQKQLNCRTVVGVLEEAFHK-----FIGQPVSISLSSRTDAGVHAASNVCHVDVERIS 126
S LN TV+ L + + K + G P+ I+++ D + + R
Sbjct: 5 LASLPHLNEATVLNNLRQRYKKDLIYTYAG-PILIAVNPYKDLPNYG------PETIRKY 57
Query: 127 KRKPGEVLPPHDSSVVRRAVNHFLQSEGD 155
+ K LPPH ++ RA + L+ +
Sbjct: 58 RGKSRSELPPHVFAIADRAYRNMLRDRRN 86
>gnl|CDD|132031 TIGR02986, restrict_Alw26I, type II restriction endonuclease,
Alw26I/Eco31I/Esp3I family. Members of this family are
type II restriction endonucleases of the
Alw26I/Eco31I/Esp3I family. Characterized specificities
of three members are GGTCTC, CGTCTC, and the shared
subsequence GTCTC [DNA metabolism,
Restriction/modification].
Length = 424
Score = 28.2 bits (63), Expect = 8.6
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 321 LTVSDVERILKAKTVTAASPMAPACGLSLGFVKYDLPEDDQT 362
LT+SDV+ +++ + T S + C +K+D+ DD
Sbjct: 290 LTLSDVKTLIEYENRTGESVASWQCRAIWDSIKHDVSNDDTL 331
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 0.131 0.374
Gapped
Lambda K H
0.267 0.0664 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,231,629
Number of extensions: 1852296
Number of successful extensions: 2122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2061
Number of HSP's successfully gapped: 59
Length of query: 382
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 283
Effective length of database: 6,546,556
Effective search space: 1852675348
Effective search space used: 1852675348
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: 60 (27.0 bits)