RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 009196
(540 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 = 284 bits (730), Expect = 1e-93
Identities = 96/236 (40%), Positives = 132/236 (55%), Gaps = 5/236 (2%)
Query: 188 KLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQ 247
KL LAP+ V +LPFR +C+ GAD+ EM LL+G LL R+ E VQ
Sbjct: 1 KLILAPMVGVTDLPFRLLCRRYGADLVYTEMISAKALLRGNRKRLRLLTRNPEERPLIVQ 60
Query: 248 ICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATS 307
+ G+ P+TLA +++ ++ D ID+NMGCP V GAG+ LL P + I+ A
Sbjct: 61 LGGSDPETLAEAAKIV-EELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVR 119
Query: 308 GTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQC 367
V P+T+K+R G+ + + L + GASA+TVHGRTR+QRYS ADWDYI +
Sbjct: 120 EAVPIPVTVKIRLGW-DDEEETLELAKALEDAGASALTVHGRTREQRYSGPADWDYIAEI 178
Query: 368 ARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFTEIKEQRH 423
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 = 225 bits (575), Expect = 2e-69
Identities = 105/295 (35%), Positives = 151/295 (51%), Gaps = 20/295 (6%)
Query: 177 SREKKLIDFREKLYLAPLTTVGNLPFRRVCKVLGA-DVTCGEMAMCTNLLQGQASEWALL 235
+ LI+ R ++ LAP+ V +LPFRR+ + LGA D+ EM LL G+ LL
Sbjct: 1 MLKIGLIELRNRVILAPMAGVTDLPFRRLARELGAYDLLYTEMVSAKALLHGRKKFLLLL 60
Query: 236 RRHSSEDLFGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTK 295
E VQ+ G+ P+ LA ++ ++ D ID+N GCP VV GAG+ LL
Sbjct: 61 DELEEERPVAVQLGGSDPELLAEAAKIA-EELGADIIDLNCGCPSPKVVKGGAGAALLKN 119
Query: 296 PMRMKGIIEATSGTV-DKPITIKVRTGYFEGKNRIDSLIADI---GTWGASAVTVHGRTR 351
P + I++A V D P+T+K+R G+ + + + IA I GA A+TVHGRTR
Sbjct: 120 PELLAEIVKAMVEAVGDIPVTVKIRLGW-DDDDILALEIARILEDA--GADALTVHGRTR 176
Query: 352 QQRYSKLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKH--KSDCPELASCMIARGAL 409
Q Y ADWDYI + ++A + V+ NGDI S D + + MI RGAL
Sbjct: 177 AQGYLGPADWDYIKE-LKEAVPSIPVIANGDIKSLEDAKEMLEYTGA---DGVMIGRGAL 232
Query: 410 IKPWIFTEIKEQRH---WDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHFLL 461
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 (463), Expect = 5e-53
Identities = 96/288 (33%), Positives = 140/288 (48%), Gaps = 21/288 (7%)
Query: 183 IDFREKLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSED 242
I + ++ LAP+ V + PFRR+ GA +T EM ++ LL E
Sbjct: 4 IQLKSRVVLAPMAGVTDSPFRRLVAEYGAGLTVCEMVSSEAIVYDSQRTMRLLDIAEDET 63
Query: 243 LFGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGI 302
VQ+ G+ PDT+A + I+++ D IDINMGCP+ + KGAGS LL P + I
Sbjct: 64 PISVQLFGSDPDTMAEAAK-INEELGADIIDINMGCPVPKITKKGAGSALLRDPDLIGKI 122
Query: 303 IEATSGTVDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWD 362
++A VD P+T+K+R G+ + GA AVT+HGRTR Q YS A+WD
Sbjct: 123 VKAVVDAVDIPVTVKIRIGWDDAHINAVEAARIAEDAGAQAVTLHGRTRAQGYSGEANWD 182
Query: 363 YI---YQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASC---MIARGALIKPWIFT 416
I Q R + V+GNGDI+S D E C MI RGAL PW+F
Sbjct: 183 IIARVKQAVR-----IPVIGNGDIFSPED----AKAMLETTGCDGVMIGRGALGNPWLFR 233
Query: 417 EIKE-----QRHWDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHF 459
+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 = 154 bits (392), Expect = 8e-43
Identities = 93/286 (32%), Positives = 129/286 (45%), Gaps = 15/286 (5%)
Query: 191 LAPLTTVGNLPFRRVCKVLGA-DVTCGEMAMCTNLLQGQASEWALLRRHSSEDLFGVQIC 249
LAP+ V +LPFRR+ + GA D+ EM L+ + +L VQ+
Sbjct: 2 LAPMAGVTDLPFRRLVREYGAGDLVVTEMVTAKAQLRPEKQRELMLPELEEPTPLAVQLG 61
Query: 250 GAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGT 309
G+ P LA +L+ D IDINMGCP V GAG+ LL P + I++A
Sbjct: 62 GSDPALLAEAAKLVADL-GADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAVVKA 120
Query: 310 VDKPITIKVRTGYFEGKNRIDSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQCAR 369
VD P+T+K+R G+ E + + GA A+TVHGRTR Q Y ADWD I Q +
Sbjct: 121 VDIPVTVKIRIGWDESHENAVEIARRVEDAGAQALTVHGRTRAQNYEGPADWDAIKQVKQ 180
Query: 370 KASDDLQVLGNGDIYSYLDWNKH--KSDCPELASCMIARGALIKPWIFTEI----KEQRH 423
S + V+ NGDI D + + + MI RGAL PW+F E +
Sbjct: 181 AVS--IPVIANGDITDAEDAQRCLSYTGADGV---MIGRGALGNPWLFAEQHTVKTGEFD 235
Query: 424 WDITSGERLNIMKDFARFGLEHWGSDKKGVETTRHFLLEWLSYTCR 469
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 (308), Expect = 3e-31
Identities = 90/256 (35%), Positives = 130/256 (50%), Gaps = 24/256 (9%)
Query: 185 FREKLYLAPLTTVGNLPFRRVCKVLGADVTCGEMAMCTNLLQGQASEWALLRRHSSE-DL 243
R +L AP+ + + PFR +C +GA +T EM M +N ++ + L H E +
Sbjct: 8 LRNRLIAAPMAGITDRPFRTLCYEMGAGLTVSEM-MSSNPQVWESDKSRLRMVHIDEPGI 66
Query: 244 FGVQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGII 303
VQI G+ P +A I+ + IDINMGCP V K AGS LL P +K I+
Sbjct: 67 RTVQIAGSDPKEMADAAR-INVESGAQIIDINMGCPAKKVNRKLAGSALLQYPDLVKSIL 125
Query: 304 EATSGTVDKPITIKVRTGYF-EGKN--RIDSLIADIGTWGASAVTVHGRTRQQRYSKLAD 360
VD P+T+K+RTG+ E +N I L D G A+T+HGRTR ++ A+
Sbjct: 126 TEVVNAVDVPVTLKIRTGWAPEHRNCVEIAQLAEDCGI---QALTIHGRTRACLFNGEAE 182
Query: 361 WDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKS----DCPELASCMIARGALIKPWIFT 416
+D I +K S + V+ NGDI + K+ D + MI R A +PWIF
Sbjct: 183 YDSIRAVKQKVS--IPVIANGDIT-----DPLKARAVLDYTGADALMIGRAAQGRPWIFR 235
Query: 417 EIKEQRHWDITSGERL 432
EI+ H+ + +GE L
Sbjct: 236 EIQ---HY-LDTGELL 247
>gnl|CDD|236713 PRK10550, PRK10550, tRNA-dihydrouridine synthase C; Provisional.
Length = 312
Score = 81.4 bits (201), Expect = 7e-17
Identities = 62/189 (32%), Positives = 94/189 (49%), Gaps = 28/189 (14%)
Query: 237 RHSSEDLFGVQICGAYPDTLA----RTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCL 292
R S L +Q+ G YP LA R VEL +D+N GCP V G G+ L
Sbjct: 58 RTPSGTLVRIQLLGQYPQWLAENAARAVELGSWG-----VDLNCGCPSKTVNGSGGGATL 112
Query: 293 LTKPMRM----KGIIEATSGTVDKPITIKVRTGYFEGKNRIDSLIAD-IGTWGASAVTVH 347
L P + K + EA + P+T+KVR G+ G+ + + IAD + GA+ + VH
Sbjct: 113 LKDPELIYQGAKAMREAVPAHL--PVTVKVRLGWDSGERKFE--IADAVQQAGATELVVH 168
Query: 348 GRTRQQRY-SKLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASC---M 403
GRT++ Y ++ +W I + ++ + + V+ NG+I+ DW + C + C M
Sbjct: 169 GRTKEDGYRAEHINWQAIGEIRQRLT--IPVIANGEIW---DWQSAQ-QCMAITGCDAVM 222
Query: 404 IARGALIKP 412
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 = 62.1 bits (151), Expect = 1e-10
Identities = 52/242 (21%), Positives = 101/242 (41%), Gaps = 18/242 (7%)
Query: 188 KLYLAPLTTVGNLPFRRVCKVLGADVTC-GEMAMCTNLLQGQASEWALLRRHSSEDLFGV 246
+ +AP+ + FR ++L EM ++ G + +L+ E +
Sbjct: 2 RFSVAPMLDWTDRHFRYFLRLLSKHTLLYTEMITAKAIIHGDKKD--ILKFSPEESPVAL 59
Query: 247 QICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEAT 306
Q+ G+ P+ LA+ ++ ++ D I++N+GCP D V N G+CL+ + ++A
Sbjct: 60 QLGGSDPNDLAKCAKIA-EKRGYDEINLNVGCPSDRVQNGNFGACLMGNADLVADCVKAM 118
Query: 307 SGTVDKPITIKVRTG--YFEGKNRIDSLIADIGTWGASAVTVHGRT--------RQQRYS 356
V+ P+T+K R G + + + + G VH R ++ R
Sbjct: 119 QEAVNIPVTVKHRIGIDPLDSYEFLCDFVEIVSGKGCQNFIVHARKAWLSGLSPKENREI 178
Query: 357 KLADWDYIYQCARKASDDLQVLGNGDIYSYLDWNKHKSDCPELASCMIARGALIKPWIFT 416
++ +YQ +K L + NG I + +H S + M+ R A P++
Sbjct: 179 PPLRYERVYQL-KKDFPHLTIEINGGIKNSEQIKQHLS---HVDGVMVGREAYENPYLLA 234
Query: 417 EI 418
+
Sbjct: 235 NV 236
>gnl|CDD|236991 PRK11815, PRK11815, tRNA-dihydrouridine synthase A; Provisional.
Length = 333
Score = 43.6 bits (104), Expect = 1e-04
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 10/86 (11%)
Query: 270 DFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVRTGYFEGKNRI 329
D I++N+GCP D V N G+CL+ +P + ++A V P+T+K R G +
Sbjct: 92 DEINLNVGCPSDRVQNGRFGACLMAEPELVADCVKAMKDAVSIPVTVKHRIGI----DDQ 147
Query: 330 DS------LIADIGTWGASAVTVHGR 349
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 = 36.2 bits (84), Expect = 0.031
Identities = 37/154 (24%), Positives = 57/154 (37%), Gaps = 22/154 (14%)
Query: 270 DFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVRTGYFEGKNRI 329
++IN C +V GAG LL P R+ I+A T P+++K+R G +
Sbjct: 99 AILEINAHCRQPEMVEAGAGEALLKDPERLSEFIKALKET-GVPVSVKIRAGVDVDDEEL 157
Query: 330 DSLIADIGTWGASAVTVHGRTRQQRYSKLADWDYIYQCARKASDDLQVLGNG---DIYSY 386
LI G A +H AD I R S +L ++GN I S
Sbjct: 158 ARLIEKAG-----ADIIHVDAMDPGNH--ADLKKI----RDISTELFIIGNNSVTTIESA 206
Query: 387 LDWNKHKSDCPELASCMIARGALIKPWIFTEIKE 420
+ + +D M++ P + E
Sbjct: 207 KEMFSYGAD-------MVSVARASLPENIEWLVE 233
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 32.4 bits (75), Expect = 0.57
Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 6/73 (8%)
Query: 246 VQICGAYPDTLARTVELIDQQCTVDFIDINMGCPIDIVVN-KGAGSCLLTKPMRMKGIIE 304
+ G+ + A E + + VD I++N+ CP N K G T P +++
Sbjct: 96 ANVAGSTEEEYAEVAEKLSKAPNVDAIELNISCP-----NVKHGGMAFGTDPELAYEVVK 150
Query: 305 ATSGTVDKPITIK 317
A V P+ +K
Sbjct: 151 AVKEVVKVPVIVK 163
>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 = 29.5 bits (66), Expect = 3.6
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 269 VDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIEATSGTVDKPITIKVR 319
D I+IN C + G G LL +K + ++KPI +K+R
Sbjct: 93 ADIIEINAHCRQPEITEIGIGQELLKNKELLKEFLTKMK-ELNKPIFVKIR 142
>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 = 5.1
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 5/73 (6%)
Query: 246 VQICGAYPDTLARTVELIDQQC-TVDFIDINMGCPIDIVVNKGAGSCLLTKPMRMKGIIE 304
+ G+ + A E +++ VD ++N+ CP KG G + P +++
Sbjct: 95 ASVYGSSVEEFAEVAEKLEKAPPYVDAYELNLSCP----HVKGGGIAIGQDPELSADVVK 150
Query: 305 ATSGTVDKPITIK 317
A D P+ K
Sbjct: 151 AVKDKTDVPVFAK 163
>gnl|CDD|178275 PLN02670, PLN02670, transferase, transferring glycosyl groups.
Length = 472
Score = 29.1 bits (65), Expect = 6.3
Identities = 23/84 (27%), Positives = 32/84 (38%), Gaps = 19/84 (22%)
Query: 437 DFARFGLEHWGSDKKGVETTRHFLLEWLS-----YTCRYIPVGLLDVIPQRLNWRPPAYS 491
D RFG GSD + ++ F EW Y IP+G L PP
Sbjct: 203 DSVRFGFAIGGSDVVIIRSSPEFEPEWFDLLSDLYRKPIIPIGFL----------PPVIE 252
Query: 492 GRDDLETLMASDSAADWIRISEML 515
++ +T+ W+RI E L
Sbjct: 253 DDEEDDTI----DVKGWVRIKEWL 272
>gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt).
This entry represents 77 residues of an 80 amino acid
(240 nucleotide) tandem repeat, found in a variable
number of copies in an immunodominant outer membrane
protein of Ehrlichia chaffeensis, a tick-borne obligate
intracellular pathogen.
Length = 707
Score = 28.8 bits (63), Expect = 7.9
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 11/82 (13%)
Query: 98 GDSVDESECSPCVPEENNIVNDRPLKKAKSENVENCCSVEGDNGVSVLEEDTRNNTADTQ 157
+ V ES E V L+ A ++E+ S G EE ++ ++
Sbjct: 167 DEIVSESSKEEFTAE----VKAEDLQPAVDGSIEHSSSEVG-------EEVSKTEKEESN 215
Query: 158 PAAKIDDILPETDGSLKTHSRE 179
P K +D+ P D + H E
Sbjct: 216 PEVKAEDLQPAVDDDVAHHESE 237
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 27.2 bits (61), Expect = 9.6
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 411 KPWIFTEIKEQRHWDITSGERLNIMKDFAR 440
K +++ + WD +G+ + I+ DF +
Sbjct: 31 KDSVYSRNPDDDFWDGYTGQPVVIIDDFGQ 60
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
0.317 0.134 0.408
Gapped
Lambda K H
0.267 0.0420 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,076,093
Number of extensions: 2609692
Number of successful extensions: 1726
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1701
Number of HSP's successfully gapped: 18
Length of query: 540
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 438
Effective length of database: 6,413,494
Effective search space: 2809110372
Effective search space used: 2809110372
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 (28.1 bits)