RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020845
(320 letters)
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 93.8 bits (234), Expect = 2e-22
Identities = 56/203 (27%), Positives = 85/203 (41%), Gaps = 30/203 (14%)
Query: 69 VYEPMRHFVFAAPVNMAPALCVAACELVGGH-REQAIVAAAALHVMHAASFIHENLPLSD 127
+ E +R+ + A + P L + A +GG E A+ AAA+ ++H AS +H D
Sbjct: 6 LREALRYLLLAGGKRLRPLLVLLAARALGGPELEAALRLAAAIELLHTASLVH------D 59
Query: 128 RTSLIPKS-----KPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMV 182
++ S KPT++ F T +L D +L ELLA NP R L +
Sbjct: 60 D--VMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYP---RALELFS 114
Query: 183 EMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGA 242
E + VEGQ D + + E + K L A GA
Sbjct: 115 EAILEL-----VEGQL--------LDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGA 161
Query: 243 ILGGGSEKEIELLRRYGFYVGMI 265
+L G E+E E L+R+G +G+
Sbjct: 162 LLAGADEEEAEALKRFGRNLGLA 184
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 86.3 bits (214), Expect = 2e-19
Identities = 60/224 (26%), Positives = 88/224 (39%), Gaps = 35/224 (15%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQ----AIVA 106
I L + + +P + E MR+ + A + P L + A E +G E A+
Sbjct: 12 ARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALGIDLETGGNDALDL 71
Query: 107 AAALHVMHAASFIHENLPLSDRTSLIPKS-----KPTMYHAFKPNTELLVADAMLPFGLE 161
AAA+ ++H AS IH D L+ KPT++ F T +L DA+L E
Sbjct: 72 AAAIELIHTASLIH------DD--LMDDDDLRRGKPTVHAKFGEATAILAGDALLAAAFE 123
Query: 162 LLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEM 221
LL+ + A L + A G+ GQ D N +E
Sbjct: 124 LLSKLGSEA-------LEAI--KALAEAINGLCGGQA---------LDLAFENKPVTLEE 165
Query: 222 TYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMI 265
+ K L A A GAIL G E+ +E L YG +G+
Sbjct: 166 YLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLA 209
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 78.1 bits (193), Expect = 9e-17
Identities = 55/216 (25%), Positives = 94/216 (43%), Gaps = 16/216 (7%)
Query: 69 VYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDR 128
+ M +++ A + P L V A +G E + A A+ ++H AS +H++L + +
Sbjct: 1 LLAAMLYYLLAGGKRIRPLLVVLAARALGVEPETLLYLACAIEMIHTASLVHDDL-MDN- 58
Query: 129 TSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAM 188
S + + KPT + F +L DA+L +LLA + + + + E+ A+
Sbjct: 59 -SDLRRGKPTCHKKFGEAGAILAGDALLSRAFQLLALLGH--VRPEPKYILIS-ELANAV 114
Query: 189 GSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGS 248
G+QG V GQ +L + + D L K L GAI+ G
Sbjct: 115 GAQGEV-GQLMDL---ETEGKDITLEEYL------RIVSYKTAALFYASVQLGAIVAGAD 164
Query: 249 EKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKK 284
E++ + L +G +G+ I L T + EEL K
Sbjct: 165 EEDEKDLYDFGRDLGLAFQIQDDILDLTGDTEELGK 200
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.
Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of
class 1 isoprenoid biosynthesis enzymes which either
synthesis geranyl/farnesyl diphosphates (GPP/FPP) or
longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids,
diterpenes, ubiquinone, and archaeal ether linked
lipids; and are widely distributed among archaea,
bacteria, and eukareya. The enzymes in this family share
the same 'isoprenoid synthase fold' and include the
head-to-tail (HT) IPPS which catalyze the successive
1'-4 condensation of the 5-carbon IPP to the growing
isoprene chain to form linear, all-trans, C10-, C15-,
C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid
diphosphates. The head-to-head (HH) IPPS catalyze the
successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Isoprenoid chain
elongation reactions proceed via electrophilic
alkylations in which a new carbon-carbon single bond is
generated through interaction between a highly reactive
electron-deficient allylic carbocation and an
electron-rich carbon-carbon double bond. The catalytic
site consists of a large central cavity formed by mostly
antiparallel alpha helices with two aspartate-rich
regions located on opposite walls. These residues
mediate binding of prenyl phosphates via bridging Mg2+
ions, inducing proposed conformational changes that
close the active site to solvent, stabilizing reactive
carbocation intermediates. Mechanistically and
structurally distinct, cis-IPPS are not included in this
CD.
Length = 236
Score = 67.8 bits (166), Expect = 3e-13
Identities = 55/210 (26%), Positives = 90/210 (42%), Gaps = 29/210 (13%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMY-HAFK 144
P L + +GG E A+ AAA+ ++HAAS +H++ + D S + + KPT + F
Sbjct: 3 PLLVLLLARALGGDLEAALRLAAAVELLHAASLVHDD--IVDD-SDLRRGKPTAHLRRFG 59
Query: 145 PNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS 204
+L D +L +LLA P R L + E R + +EGQ
Sbjct: 60 NALAILAGDYLLARAFQLLARLGYP------RALELFAEALREL-----LEGQA------ 102
Query: 205 QCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
D + + + ++ E + K L GA L G +++ E L+ YG +G+
Sbjct: 103 --LDLEFERDTYETLDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGL 160
Query: 265 ---IQGIVSRRLGPTEEIEELKKLAFKLRE 291
+ + L + EEL K+ LRE
Sbjct: 161 AFQLTDDL---LDVFGDAEELGKVGSDLRE 187
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 49.1 bits (117), Expect = 1e-06
Identities = 46/182 (25%), Positives = 75/182 (41%), Gaps = 30/182 (16%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKP 145
P + V A VG + AA + +H A+ +H+++ S + + K T AF
Sbjct: 49 PMIAVLAARAVGYQGNAHVTIAALIEFIHTATLLHDDVV---DESDMRRGKATANAAFGN 105
Query: 146 NTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ 205
+LV D + +++ S S ++L VM E + EG+ LQ
Sbjct: 106 AASVLVGDFIYTRAFQMMTSLG------SLKVLEVMSEAVNV-----IAEGEV--LQLMN 152
Query: 206 CDDDDRKLNGITDVEMTYETYKK----KEGRLHACGAACGAILGGGSEKEIELLRRYGFY 261
+D D +T E Y + K RL A C IL G + ++ + L+ YG Y
Sbjct: 153 VNDPD----------ITEENYMRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRY 202
Query: 262 VG 263
+G
Sbjct: 203 LG 204
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 45.5 bits (108), Expect = 2e-05
Identities = 35/134 (26%), Positives = 60/134 (44%), Gaps = 2/134 (1%)
Query: 69 VYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDR 128
V E M++ + P L A ++ G AAA+ +HA S IH++LP D
Sbjct: 32 VVEAMQYGALLGGKRLRPFLVYATGQMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDD 91
Query: 129 TSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAM 188
L + PT + F +L DA+ +L+ + P ++ R + ++ E+ A
Sbjct: 92 DDL-RRGLPTCHVKFGEANAILAGDALQTLAFSILSDAPMPEVSDRDR-ISMISELASAS 149
Query: 189 GSQGVVEGQYNELQ 202
G G+ GQ +L+
Sbjct: 150 GIAGMCGGQALDLE 163
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 43.6 bits (103), Expect = 6e-05
Identities = 57/257 (22%), Positives = 98/257 (38%), Gaps = 34/257 (13%)
Query: 34 MAMSTPNKNKSYWTSVHED---IGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCV 90
MA ++ + T + E+ + +L++ + P+ +Y +H A + PA+ +
Sbjct: 1 MATNS-----NLLTPIEEELLILEDNLKKLIGSGHPI-LYAAAKHLFSAGGKRIRPAIVL 54
Query: 91 AACELVGGHREQAI---VAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNT 147
+ GG+ E A ++H AS +H++ + D S I + PT++ F
Sbjct: 55 LVAKATGGNMEIKTSQQRLAEITEIIHTASLVHDD--VIDECS-IRRGIPTVHKIFGTKI 111
Query: 148 ELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCD 207
+L D + LA+ +N I +V+ + QG+V Q D
Sbjct: 112 AVLAGDFLFAQSSWYLANLNNLEVVKL--ISKVITDFAEGEIRQGLV----------QFD 159
Query: 208 DDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQG 267
LN I E K L A A+L EK+ YG ++G+
Sbjct: 160 TTLSILNYI-------EKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQ 212
Query: 268 IVSRRLGPTEEIEELKK 284
I+ L T E L K
Sbjct: 213 IIDDVLDITSSTESLGK 229
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 42.8 bits (101), Expect = 1e-04
Identities = 47/186 (25%), Positives = 75/186 (40%), Gaps = 32/186 (17%)
Query: 106 AAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLAS 165
A AL ++H AS +H+++ D L + +PT+ + + D + LE +
Sbjct: 68 VAVALELIHMASLVHDDV--IDDADL-RRGRPTIKSKWGNRIAMYTGDYLFAKSLETMTE 124
Query: 166 SDNPAGNNSGRIL-RVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYE 224
+P + +IL +VE+ R Q ++ +YN +
Sbjct: 125 IKDPRAH---QILSHTIVEVCRGEIEQ--IKDKYN-------------------FDQNLR 160
Query: 225 TY----KKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIE 280
TY K+K L A GAI G +E ++ L +G+YVGM I L E
Sbjct: 161 TYLRRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEE 220
Query: 281 ELKKLA 286
EL K A
Sbjct: 221 ELGKPA 226
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
phosphates via bridging Mg2+ ions, inducing proposed
conformational changes that close the active site to
solvent, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 39.4 bits (92), Expect = 0.001
Identities = 39/167 (23%), Positives = 65/167 (38%), Gaps = 25/167 (14%)
Query: 102 QAIVAAAALHVMHAASFIHENLPLSD---RTSLIPKSKPTMYHAFKPNTELLVADAMLPF 158
+A AA+ +HAAS +H D S + PT + A + +A+L
Sbjct: 11 EASRLRAAVEKLHAASLVH------DDIVDDSGTRRGLPTAHLAVAIDGL---PEAILAG 61
Query: 159 GLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITD 218
L L + + A S L ++ E + +EGQ +L+ + +
Sbjct: 62 DLLLADAFEELAREGSPEALEILAEALLDL-----LEGQLLDLKWRR--------EYVPT 108
Query: 219 VEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMI 265
+E E + K L GA L GG + +E LR+ G +G+
Sbjct: 109 LEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLA 155
>gnl|CDD|226538 COG4052, COG4052, Uncharacterized protein related to methyl
coenzyme M reductase subunit C [General function
prediction only].
Length = 310
Score = 31.7 bits (72), Expect = 0.41
Identities = 19/44 (43%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 242 AILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKL 285
+ GG E + E + YVG I G VS RL EEI L KL
Sbjct: 162 VVTGGPEEIDTEDVPGADLYVGNI-GRVSHRLRRGEEIRALDKL 204
>gnl|CDD|236959 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE;
Provisional.
Length = 234
Score = 31.0 bits (71), Expect = 0.58
Identities = 20/64 (31%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 219 VEMTYETYKKKEGRLHACGAACGAIL------GGGSEKEIELLRRYGFYVGMIQGIVSRR 272
+E K +L A G +L GG S +EIELLR GF
Sbjct: 156 LEELLPADLKAGLKLVLHPEAGGKVLLLIGPEGGFSPEEIELLREAGF--------TPVS 207
Query: 273 LGPT 276
LGP
Sbjct: 208 LGPR 211
>gnl|CDD|197850 smart00738, NGN, In Spt5p, this domain may confer affinity for
Spt4p. It possesses a RNP-like fold. In Spt5p, this
domain may confer affinity for Spt4p.Spt4p.
Length = 106
Score = 29.6 bits (67), Expect = 0.79
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 11/79 (13%)
Query: 247 GSEKE-IELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFN-------DE 298
G EK E L R +G+ IVS + PTEE++E+++ K+ E F D
Sbjct: 10 GQEKRVAENLERKAEALGLEDKIVSILV-PTEEVKEIRRGKKKVVERKLFPGYIFVEADL 68
Query: 299 NAEVIFSLVDDNITHVLGF 317
EV ++ V GF
Sbjct: 69 EDEVWTAI--RGTPGVRGF 85
>gnl|CDD|224303 COG1385, COG1385, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 246
Score = 30.3 bits (69), Expect = 1.2
Identities = 15/32 (46%), Positives = 15/32 (46%), Gaps = 8/32 (25%)
Query: 245 GGGSEKEIELLRRYGFYVGMIQGIVSRRLGPT 276
GG SE EIELLR GF LGP
Sbjct: 202 GGFSEDEIELLREAGF--------TPVSLGPR 225
>gnl|CDD|129157 TIGR00046, TIGR00046, RNA methyltransferase, RsmE family. Members
of this protein family, previously called conserved
hypothetical protein TIGR00046, include the YggJ protein
of E. coli, which has now been shown to methylate U1498
in 16S rRNA [Protein synthesis, tRNA and rRNA base
modification].
Length = 240
Score = 28.5 bits (64), Expect = 3.9
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 245 GGGSEKEIELLRRYGFY 261
GG SEKEI+LL+ GF
Sbjct: 195 GGFSEKEIQLLKEKGFT 211
>gnl|CDD|190632 pfam03431, RNA_replicase_B, RNA replicase, beta-chain. This family
is of Leviviridae RNA replicases. The replicase is also
known as RNA dependent RNA polymerase.
Length = 540
Score = 29.0 bits (65), Expect = 4.0
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 38 TPNKNKSYWT-SVHEDIGAHLRQAVVVKEPVEVYEPMR 74
TPN K++ + E G H V V P + P+
Sbjct: 355 TPNLKKTFTSGPFRESCGKHYFAGVDVT-PFYIKRPIV 391
>gnl|CDD|218092 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA
methyltransferases modify nucleotides during ribosomal
RNA maturation in a site-specific manner. The
Escherichia coli member is specific for U1498
methylation.
Length = 224
Score = 28.0 bits (63), Expect = 5.3
Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 245 GGGSEKEIELLRRYGFYVGMIQGIVSRRLGPT 276
GG S KEIELL+ GF VS LGP
Sbjct: 184 GGFSPKEIELLKEAGFT------PVS--LGPR 207
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
0.319 0.134 0.390
Gapped
Lambda K H
0.267 0.0698 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,600,384
Number of extensions: 1623958
Number of successful extensions: 1562
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1548
Number of HSP's successfully gapped: 26
Length of query: 320
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 223
Effective length of database: 6,635,264
Effective search space: 1479663872
Effective search space used: 1479663872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (26.6 bits)