RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 005508
(693 letters)
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 287 bits (738), Expect = 4e-93
Identities = 96/236 (40%), Positives = 132/236 (55%), Gaps = 5/236 (2%)
Query: 341 KLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQ 400
KL LAP+ V +LPFR +C+ GAD+ EM LL+G LL R+ E VQ
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 401 ICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATS 460
+ G+ P+TLA +++ ++ D ID+NMGCP V GAG+ LL P + I+ A
Sbjct: 61 LGGSDPETLAEAAKIV-EELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVR 119
Query: 461 GTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQC 520
V P+T+K+R G+ + + L + GASA+TVHGRTR+QRYS ADWDYI +
Sbjct: 120 EAVPIPVTVKIRLGW-DDEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEI 178
Query: 521 ARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFTEIKEQRH 576
K + + V+ NGDI+S D + + MI RGAL PW+F EIKE
Sbjct: 179 --KEAVSIPVIANGDIFSLEDALRCLEQT-GVDGVMIGRGALGNPWLFREIKELLE 231
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 228 bits (584), Expect = 3e-69
Identities = 105/295 (35%), Positives = 151/295 (51%), Gaps = 20/295 (6%)
Query: 330 SREKKLIDFREKLYLAPLTTVGNLPFRRVCKVLGA-DVTCGEMAMCTNLLQGQASEWALL 388
+ LI+ R ++ LAP+ V +LPFRR+ + LGA D+ EM LL G+ LL
Sbjct: 1 MLKIGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLL 60
Query: 389 RRHSSEDLFGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTK 448
E VQ+ G+ P+ LA ++ ++ D ID+N GCP VV GAG+ LL
Sbjct: 61 DELEEERPVAVQLGGSDPELLAEAAKIA-EELGADIIDLNCGCPSPKVVKGGAGAALLKN 119
Query: 449 PMRMKGIIEATSGTV-DKPITIKVRTGYFEGKNRIDSLIADI---GTWGASAVTVHGRTR 504
P + I++A V D P+T+K+R G+ + + + IA I GA A+TVHGRTR
Sbjct: 120 PELLAEIVKAMVEAVGDIPVTVKIRLGW-DDDDILALEIARILEDA--GADALTVHGRTR 176
Query: 505 QQRYSKLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKH--KSDCPELASCMIARGAL 562
Q Y ADWDYI + ++A + V+ NGDI S D + + MI RGAL
Sbjct: 177 AQGYLGPADWDYIKE-LKEAVPSIPVIANGDIKSLEDAKEMLEYTGA---DGVMIGRGAL 232
Query: 563 IKPWIFTEIKEQRH---WDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHFLL 614
PW+F +I T E L+I+++ LE++G KKG+ R L
Sbjct: 233 GNPWLFRQIDYLETGELLPPTLAEVLDILREHLELLLEYYG--KKGLRRLRKHLG 285
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 182 bits (465), Expect = 4e-52
Identities = 96/288 (33%), Positives = 140/288 (48%), Gaps = 21/288 (7%)
Query: 336 IDFREKLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSED 395
I + ++ LAP+ V + PFRR+ GA +T EM ++ LL E
Sbjct: 4 IQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDET 63
Query: 396 LFGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGI 455
VQ+ G+ PDT+A + I+++ D IDINMGCP+ + KGAGS LL P + I
Sbjct: 64 PISVQLFGSDPDTMAEAAK-INEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKI 122
Query: 456 IEATSGTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWD 515
++A VD P+T+K+R G+ + GA AVT+HGRTR Q YS A+WD
Sbjct: 123 VKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQGYSGEANWD 182
Query: 516 YI---YQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASC---MIARGALIKPWIFT 569
I Q R + V+GNGDI+S D E C MI RGAL PW+F
Sbjct: 183 IIARVKQAVR-----IPVIGNGDIFSPED----AKAMLETTGCDGVMIGRGALGNPWLFR 233
Query: 570 EIKE-----QRHWDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHF 612
+I++ + T E+L+ + + +++G K +H
Sbjct: 234 QIEQYLTTGKYKPPPTFAEKLDAILRHLQLLADYYGESKGLRIARKHI 281
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 155 bits (394), Expect = 2e-42
Identities = 93/286 (32%), Positives = 129/286 (45%), Gaps = 15/286 (5%)
Query: 344 LAPLTTVGNLPFRRVCKVLGA-DVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQIC 402
LAP+ V +LPFRR+ + GA D+ EM L+ + +L VQ+
Sbjct: 2 LAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQLG 61
Query: 403 GAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGT 462
G+ P LA +L+ D IDINMGCP V GAG+ LL P + I++A
Sbjct: 62 GSDPALLAEAAKLVADL-GADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKA 120
Query: 463 VDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQCAR 522
VD P+T+K+R G+ E + + GA A+TVHGRTR Q Y ADWD I Q +
Sbjct: 121 VDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTRAQNYEGPADWDAIKQVKQ 180
Query: 523 KASDDLQVLGNGDIYSYLDWNKH--KSDCPELASCMIARGALIKPWIFTEI----KEQRH 576
S + V+ NGDI D + + + MI RGAL PW+F E +
Sbjct: 181 AVS--IPVIANGDITDAEDAQRCLSYTGADGV---MIGRGALGNPWLFAEQHTVKTGEFD 235
Query: 577 WDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHFLLEWLSYTCR 622
E I+ + + E +G DK +H L W
Sbjct: 236 PRPPLAEEAEIVLEHLSYLEEFYGEDKGLRHARKH--LAWYLKGFP 279
>gnl|CDD|182440 PRK10415, PRK10415, tRNA-dihydrouridine synthase B; Provisional.
Length = 321
Score = 122 bits (307), Expect = 2e-30
Identities = 86/243 (35%), Positives = 123/243 (50%), Gaps = 20/243 (8%)
Query: 338 FREKLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSE-DL 396
R +L AP+ + + PFR +C +GA +T EM M +N ++ + L H E +
Sbjct: 8 LRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEM-MSSNPQVWESDKSRLRMVHIDEPGI 66
Query: 397 FGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGII 456
VQI G+ P +A I+ + IDINMGCP V K AGS LL P +K I+
Sbjct: 67 RTVQIAGSDPKEMADAAR-INVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSIL 125
Query: 457 EATSGTVDKPITIKVRTGYF-EGKN--RIDSLIADIGTWGASAVTVHGRTRQQRYSKLAD 513
VD P+T+K+RTG+ E +N I L D G A+T+HGRTR ++ A+
Sbjct: 126 TEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGI---QALTIHGRTRACLFNGEAE 182
Query: 514 WDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKS----DCPELASCMIARGALIKPWIFT 569
+D I +K S + V+ NGDI + K+ D + MI R A +PWIF
Sbjct: 183 YDSIRAVKQKVS--IPVIANGDIT-----DPLKARAVLDYTGADALMIGRAAQGRPWIFR 235
Query: 570 EIK 572
EI+
Sbjct: 236 EIQ 238
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 81.4 bits (201), Expect = 8e-17
Identities = 62/189 (32%), Positives = 94/189 (49%), Gaps = 28/189 (14%)
Query: 390 RHSSEDLFGVQICGAYPDTLA----RTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCL 445
R S L +Q+ G YP LA R VEL +D+N GCP V G G+ L
Sbjct: 58 RTPSGTLVRIQLLGQYPQWLAENAARAVELGSWG-----VDLNCGCPSKTVNGSGGGATL 112
Query: 446 LTKPMRM----KGIIEATSGTVDKPITIKVRTGYFEGKNRIDSLIAD-IGTWGASAVTVH 500
L P + K + EA + P+T+KVR G+ G+ + + IAD + GA+ + VH
Sbjct: 113 LKDPELIYQGAKAMREAVPAHL--PVTVKVRLGWDSGERKFE--IADAVQQAGATELVVH 168
Query: 501 GRTRQQRY-SKLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASC---M 556
GRT++ Y ++ +W I + ++ + + V+ NG+I+ DW + C + C M
Sbjct: 169 GRTKEDGYRAEHINWQAIGEIRQRLT--IPVIANGEIW---DWQSAQ-QCMAITGCDAVM 222
Query: 557 IARGALIKP 565
I RGAL P
Sbjct: 223 IGRGALNIP 231
>gnl|CDD|129825 TIGR00742, yjbN, tRNA dihydrouridine synthase A. This model
represents one branch of COG0042 (Predicted TIM-barrel
enzymes, possibly dehydrogenases, nifR3 family). It
represents a distinct subset by a set of shared unique
motifs, a conserved pattern of insertions/deletions
relative to other nifR3 homologs, and by subclustering
based on cross-genome bidirectional best hits. Members
are found in species as diverse as the proteobacteria, a
spirochete, a cyanobacterium, and Deinococcus
radiodurans. NifR3 itself, a protein of unknown function
associated with nitrogen regulation in Rhodobacter
capsulatus, is not a member of this branch. Members of
this family show a distant relationship to alpha/beta
(TIM) barrel enzymes such as dihydroorotate
dehydrogenase and glycolate oxidase [Protein synthesis,
tRNA and rRNA base modification].
Length = 318
Score = 61.8 bits (150), Expect = 3e-10
Identities = 52/242 (21%), Positives = 101/242 (41%), Gaps = 18/242 (7%)
Query: 341 KLYLAPLTTVGNLPFRRVCKVLGADVTC-GEMAMCTNLLQGQASEWALLRRHSSEDLFGV 399
+ +AP+ + FR ++L EM ++ G + +L+ E +
Sbjct: 2 RFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKD--ILKFSPEESPVAL 59
Query: 400 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 459
Q+ G+ P+ LA+ ++ ++ D I++N+GCP D V N G+CL+ + ++A
Sbjct: 60 QLGGSDPNDLAKCAKIA-EKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAM 118
Query: 460 SGTVDKPITIKVRTG--YFEGKNRIDSLIADIGTWGASAVTVHGRT--------RQQRYS 509
V+ P+T+K R G + + + + G VH R ++ R
Sbjct: 119 QEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKAWLSGLSPKENREI 178
Query: 510 KLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFT 569
++ +YQ +K L + NG I + +H S + M+ R A P++
Sbjct: 179 PPLRYERVYQL-KKDFPHLTIEINGGIKNSEQIKQHLS---HVDGVMVGREAYENPYLLA 234
Query: 570 EI 571
+
Sbjct: 235 NV 236
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 44.0 bits (105), Expect = 2e-04
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 423 DFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVRTGYFEGKNRI 482
D I++N+GCP D V N G+CL+ +P + ++A V P+T+K R G +
Sbjct: 92 DEINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIGI----DDQ 147
Query: 483 DS------LIADIGTWGASAVTVHGR 502
DS + + G VH R
Sbjct: 148 DSYEFLCDFVDTVAEAGCDTFIVHAR 173
>gnl|CDD|239237 cd02911, arch_FMN, Archeal FMN-binding domain. This family of
archaeal proteins are part of the NAD(P)H-dependent
flavin oxidoreductase (oxidored) FMN-binding family that
reduce a range of alternative electron acceptors. Most
use FAD/FMN as a cofactor and NAD(P)H as electron donor.
Some contain 4Fe-4S cluster to transfer electron from
FAD to FMN. The specific function of this group is
unknown.
Length = 233
Score = 36.9 bits (86), Expect = 0.020
Identities = 37/154 (24%), Positives = 57/154 (37%), Gaps = 22/154 (14%)
Query: 423 DFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVRTGYFEGKNRI 482
++IN C +V GAG LL P R+ I+A T P+++K+R G +
Sbjct: 99 AILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKET-GVPVSVKIRAGVDVDDEEL 157
Query: 483 DSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQCARKASDDLQVLGNG---DIYSY 539
LI G A +H AD I R S +L ++GN I S
Sbjct: 158 ARLIEKAG-----ADIIHVDAMDPGNH--ADLKKI----RDISTELFIIGNNSVTTIESA 206
Query: 540 LDWNKHKSDCPELASCMIARGALIKPWIFTEIKE 573
+ + +D M++ P + E
Sbjct: 207 KEMFSYGAD-------MVSVARASLPENIEWLVE 233
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 29.8 bits (68), Expect = 0.22
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 103 LCPEVAKSGDVSSCPYKDKCRFSHDL 128
LC +++G +C Y D+C+F+H
Sbjct: 5 LCRFFSRTG---TCKYGDRCKFAHGQ 27
Score = 28.7 bits (65), Expect = 0.59
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 142 ECPFLSSEGPCPYGLACRFS 161
C F S G C YG C+F+
Sbjct: 5 LCRFFSRTGTCKYGDRCKFA 24
>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function
prediction only].
Length = 351
Score = 33.9 bits (77), Expect = 0.25
Identities = 28/109 (25%), Positives = 36/109 (33%), Gaps = 22/109 (20%)
Query: 62 DTVKYTNERSSQQ-----HSSTLVKEKKSKRQLKRERQQEKKSASHLCPEVAKSGDVSSC 116
T Y Q H +K KK K+ + E C KSG C
Sbjct: 240 GTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEP----------CINWEKSG---YC 286
Query: 117 PYKDKCRFSHDLDGFKA--QKPDD--LEGECPFLSSEGPCPYGLACRFS 161
PY +C F H D ++ L+G C + G P G A S
Sbjct: 287 PYGLRCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPSGGAVCKS 335
Score = 32.7 bits (74), Expect = 0.57
Identities = 28/108 (25%), Positives = 44/108 (40%), Gaps = 19/108 (17%)
Query: 69 ERSSQQHSSTLVKEKKSKRQLKRERQQEK--------KSASHLCPEVAKSGDVSSCPYK- 119
+ S ++ ++ K+S E +K K+ LC + G +CPY
Sbjct: 190 KPKSGKNCTSYTLGKESDAHPHDELIYQKQEQNKPLYKTNPELCESFTRKG---TCPYWI 246
Query: 120 --DKCRFS---HDLDGFKAQKPDDLEGECPFL--SSEGPCPYGLACRF 160
KC+F+ H L+ K++K P + G CPYGL C F
Sbjct: 247 SGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPYGLRCCF 294
>gnl|CDD|227416 COG5084, YTH1, Cleavage and polyadenylation specificity factor
(CPSF) Clipper subunit and related makorin family
Zn-finger proteins [General function prediction only].
Length = 285
Score = 33.3 bits (76), Expect = 0.39
Identities = 17/61 (27%), Positives = 22/61 (36%), Gaps = 5/61 (8%)
Query: 107 VAKSGDVSSCPYKDKCRFSHDLDGFKAQKPDDLEGECPFLSSEGPCPYGLACRFSGTHRD 166
V K C C F H+ D +Q P C S +G C G +C +S D
Sbjct: 106 VCKFFLRGLCKSGFSCEFLHEYDLRSSQGP-----PCRSFSLKGSCSSGPSCGYSHIDPD 160
Query: 167 V 167
Sbjct: 161 S 161
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 32.8 bits (76), Expect = 0.58
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 399 VQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVN-KGAGSCLLTKPMRMKGIIE 457
+ G+ + A E + + VD I++N+ CP N K G T P +++
Sbjct: 96 ANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCP-----NVKHGGMAFGTDPELAYEVVK 150
Query: 458 ATSGTVDKPITIK 470
A V P+ +K
Sbjct: 151 AVKEVVKVPVIVK 163
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 32.4 bits (73), Expect = 0.68
Identities = 22/93 (23%), Positives = 31/93 (33%), Gaps = 9/93 (9%)
Query: 52 RPPPTRANQNDTVKYTNERSSQQHSSTLVKEKKSKRQLKRERQQEKKSASHLC---PEVA 108
A + R S + L K+KR K+ Q + P+V
Sbjct: 90 FERKELAEKA-----KKRRPSDDNELVLNMSGKNKRLTKQINQPTMFRDGEVIDTQPDVC 144
Query: 109 KS-GDVSSCPYKDKCRFSHDLDGFKAQKPDDLE 140
K + C Y D C+F HD FK + E
Sbjct: 145 KDYKETGYCGYGDSCKFLHDRSDFKTGWKLNQE 177
>gnl|CDD|178739 PLN03198, PLN03198, delta6-acyl-lipid desaturase; Provisional.
Length = 526
Score = 32.7 bits (74), Expect = 0.69
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 5/70 (7%)
Query: 69 ERSSQQHSSTLVKEKKSKRQLKRERQQEKKSASHLCPEVAKSGDVSSC--PYKDKCRFSH 126
+++S + + + +R +EKKS SHL EVA + C K+K +
Sbjct: 73 QKNSNSQEAAEALAESVVKPTRRRSSKEKKSKSHLLSEVAAHNKPNDCWIVIKNKV---Y 129
Query: 127 DLDGFKAQKP 136
D+ F A+ P
Sbjct: 130 DVSDFAAEHP 139
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 31.6 bits (71), Expect = 1.5
Identities = 15/72 (20%), Positives = 24/72 (33%)
Query: 15 PADSPPPQPNSTGVPVHNLTPEELVAKAIAPVKKQFLRPPPTRANQNDTVKYTNERSSQQ 74
P P Q + V N + PV+ P A Q + ++RS +Q
Sbjct: 203 PTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQPPQTEQGHKRSREQ 262
Query: 75 HSSTLVKEKKSK 86
+ +K K
Sbjct: 263 GNQEFLKMLKED 274
>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger.
Length = 27
Score = 27.6 bits (62), Expect = 1.6
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 116 CPYKDKCRFSHDL 128
CP D+C+F+H L
Sbjct: 15 CPRGDRCKFAHPL 27
>gnl|CDD|219153 pfam06733, DEAD_2, DEAD_2. This represents a conserved region
within a number of RAD3-like DNA-binding helicases that
are seemingly ubiquitous - members include proteins of
eukaryotic, bacterial and archaeal origin. RAD3 is
involved in nucleotide excision repair, and forms part
of the transcription factor TFIIH in yeast.
Length = 168
Score = 30.4 bits (69), Expect = 1.8
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 1/71 (1%)
Query: 98 KSASHLCPEVAKSGDVSSCPYKDKCRFSHDLDGFKAQKPDDLEGECPFLSSEGPCPYGLA 157
+ + C E+ +SG SCP+ + L D+E + G CPY +
Sbjct: 49 EDINEKCKELKRSGKRESCPFYNNLEDLKKLKDLLGNGVYDIEDLVEYGKKLGLCPYYSS 108
Query: 158 CRFSGTHRDVV 168
R D++
Sbjct: 109 -REMLKDADII 118
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.4 bits (71), Expect = 2.3
Identities = 15/55 (27%), Positives = 17/55 (30%)
Query: 9 SESRVLPADSPPPQPNSTGVPVHNLTPEELVAKAIAPVKKQFLRPPPTRANQNDT 63
+ES LP D P P P P+ P RP P A D
Sbjct: 2895 TESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDP 2949
>gnl|CDD|218660 pfam05620, DUF788, Protein of unknown function (DUF788). This
family consists of several eukaryotic proteins of
unknown function.
Length = 166
Score = 30.0 bits (68), Expect = 2.6
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 68 NERSSQQHSSTLVKEKKSKRQLKRERQQEK 97
+ SSQ + E KSKRQ K E++ EK
Sbjct: 140 SLPSSQGAET---NETKSKRQEKLEKRGEK 166
>gnl|CDD|129819 TIGR00736, nifR3_rel_arch, TIM-barrel protein, putative. Members
of this family show a distant relationship by PSI-BLAST
to alpha/beta (TIM) barrel enzymes such as
dihydroorotate dehydrogenase and glycolate oxidase. At
least two closely related but well-separable families
among the bacteria, the nifR3/yhdG family and the yjbN
family, share a more distant relationship to this family
of shorter, exclusively archaeal proteins [Unknown
function, General].
Length = 231
Score = 29.9 bits (67), Expect = 3.9
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 422 VDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVR 472
D I+IN C + G G LL +K + ++KPI +K+R
Sbjct: 93 ADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTKMK-ELNKPIFVKIR 142
>gnl|CDD|227577 COG5252, COG5252, Uncharacterized conserved protein, contains
CCCH-type Zn-finger protein [General function prediction
only].
Length = 299
Score = 29.7 bits (66), Expect = 5.0
Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 59 NQNDTVKYTNERSSQQHSSTLVKEKKSKRQLKRERQQEK---KSASHLCPEVAKSGDVSS 115
N++ V+ ++ + +++K+ R ++ R+ EK ++ V +
Sbjct: 36 NRSTKVQAIIKQIETLNLKEQLEKKEKMRMEEKRREPEKQVIRAGVDPKTVVCALFLNKT 95
Query: 116 CPYKDKCRFSHDLD-GFKAQKPD 137
C D C+F+H + K +KPD
Sbjct: 96 CAKGDACKFAHGKEEARKTEKPD 118
>gnl|CDD|202837 pfam03980, Nnf1, Nnf1. NNF1 is an essential yeast gene that is
necessary for chromosome segregation. It is associated
with the spindle poles and forms part of a kinetochore
subcomplex called MIND.
Length = 108
Score = 28.0 bits (63), Expect = 5.5
Identities = 10/44 (22%), Positives = 16/44 (36%), Gaps = 7/44 (15%)
Query: 6 TELSESRVLPADSPPPQPNSTGVPVHNLTPEELVAKAIAPVKKQ 49
E ++ R P +LTPEEL+ + P +
Sbjct: 43 IEEAKERKEDGGDDP-------AWRDSLTPEELIRSHLVPYLLK 79
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 29.3 bits (66), Expect = 6.0
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 399 VQICGAYPDTLARTVELIDQQC-TVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIE 457
+ G+ + A E +++ VD ++N+ CP KG G + P +++
Sbjct: 95 ASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCP----HVKGGGIAIGQDPELSADVVK 150
Query: 458 ATSGTVDKPITIK 470
A D P+ K
Sbjct: 151 AVKDKTDVPVFAK 163
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
0.315 0.132 0.401
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 34,363,898
Number of extensions: 3310172
Number of successful extensions: 2735
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2707
Number of HSP's successfully gapped: 32
Length of query: 693
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 589
Effective length of database: 6,324,786
Effective search space: 3725298954
Effective search space used: 3725298954
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: 62 (27.6 bits)