RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17743
(618 letters)
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 574 bits (1482), Expect = 0.0
Identities = 247/395 (62%), Positives = 290/395 (73%), Gaps = 30/395 (7%)
Query: 121 LFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTEN 180
LFRGRGEHPK GKLKRR+ EDI IN KD+ VP PPPGHKWKEVRHDN VTWLASW EN
Sbjct: 1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKEN 60
Query: 181 VQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVAL 240
+ G +KY+ L SS LKG+ D +KYE ARKL K I+KIR++Y D KSKEM++RQRA AL
Sbjct: 61 INGSIKYVFLAASSSLKGQSDRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATAL 120
Query: 241 YFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNE 300
Y IDKLALRAGNEK ED+ADTVGCCSLRVEH+ L FDFLGKDSIRYYNE
Sbjct: 121 YLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPNKVI-----FDFLGKDSIRYYNE 175
Query: 301 VPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQ 360
V V+K+VFKNL++F++ KK DDLFDRLNTS LNKHL ELM GLTAKVFRTYNASITLQ+
Sbjct: 176 VEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQE 235
Query: 361 QLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKD 420
QL EL D + AEKILAYNRANR VA+LCNHQR+V K+H+KSM L+EKI + Q+K
Sbjct: 236 QLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKR 295
Query: 421 AERAL------KDAKKAGESKAMTD-------------------KKKTALGRLKEQLLKL 455
++ + D K+ +SK D KKK + RL+E++ KL
Sbjct: 296 LKKMILLFEMISDLKRKLKSKFERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKL 355
Query: 456 EVQETDKEENKTIALGTSKLNYLDPRISVTWLASW 490
EVQ TDKEENKT+ALGTSK+NY+DPRI+V W +
Sbjct: 356 EVQATDKEENKTVALGTSKINYIDPRITVAWCKKF 390
Score = 194 bits (494), Expect = 5e-56
Identities = 77/125 (61%), Positives = 91/125 (72%), Gaps = 9/125 (7%)
Query: 484 VTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKE 543
VTWLASW EN+ G +KY+ L SS LKG+ D +KYE ARKL K I+KIR++Y D KSKE
Sbjct: 51 VTWLASWKENINGSIKYVFLAASSSLKGQSDRKKYEKARKLKKHIDKIRKDYTKDLKSKE 110
Query: 544 MRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEE---------KDEK 594
M++RQRA ALY IDKLALRAGNEK ED+ADTVGCCSLRVEH+ L KD
Sbjct: 111 MKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLKPPNKVIFDFLGKDSI 170
Query: 595 KIYNK 599
+ YN+
Sbjct: 171 RYYNE 175
>gnl|CDD|239570 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain.
Length = 215
Score = 342 bits (880), Expect = e-115
Identities = 130/188 (69%), Positives = 154/188 (81%)
Query: 4 GGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDF 63
GK +KLS +AEE+ATFYA+M+EH+Y TKE F NF KD++K MT++E+ +I D SKCDF
Sbjct: 28 DGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIKDFSKCDF 87
Query: 64 RKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFR 123
+M AYF + EE+KAMSKEEKK IK E E + +EYG C +DGHKEK+GNFRIEPPGLFR
Sbjct: 88 TQMFAYFKAQKEEKKAMSKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFR 147
Query: 124 GRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQG 183
GRG HPK GKLKRR+ EDIIIN KD+KVP PPPGHKWKEVRHDN VTWLASWTEN+ G
Sbjct: 148 GRGAHPKTGKLKRRIMPEDIIINIGKDAKVPEPPPGHKWKEVRHDNTVTWLASWTENING 207
Query: 184 QVKYIMLN 191
+KY+MLN
Sbjct: 208 SIKYVMLN 215
Score = 48.1 bits (115), Expect = 3e-06
Identities = 16/22 (72%), Positives = 20/22 (90%)
Query: 483 SVTWLASWTENVQGQVKYIMLN 504
+VTWLASWTEN+ G +KY+MLN
Sbjct: 194 TVTWLASWTENINGSIKYVMLN 215
>gnl|CDD|217286 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 339 bits (873), Expect = e-114
Identities = 113/186 (60%), Positives = 141/186 (75%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
GK + L+ +AEE+ATF+A M+E +Y TK F NF KD+RK + ++ A+I DL KCDF
Sbjct: 30 GKPVDLTPEAEEVATFFAVMLETDYATKPVFQKNFFKDFRKILKKEGGAIIKDLEKCDFT 89
Query: 65 KMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
++ YF + E++KAMSKEEKK IK+E + + + YG C +DG KEK+GNFR+EPPGLFRG
Sbjct: 90 PIYEYFEAEKEKKKAMSKEEKKAIKEEKDKLEEPYGYCLVDGRKEKVGNFRVEPPGLFRG 149
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RGEHPK GKLKRRV ED+ IN KD+ VP PPPGHKWKEVRHDN VTWLA W EN+ G
Sbjct: 150 RGEHPKTGKLKRRVMPEDVTINIGKDAPVPEPPPGHKWKEVRHDNTVTWLAMWRENINGS 209
Query: 185 VKYIML 190
KY+ML
Sbjct: 210 FKYVML 215
Score = 45.3 bits (108), Expect = 3e-05
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 483 SVTWLASWTENVQGQVKYIML 503
+VTWLA W EN+ G KY+ML
Sbjct: 195 TVTWLAMWRENINGSFKYVML 215
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 333 bits (855), Expect = e-111
Identities = 121/191 (63%), Positives = 148/191 (77%)
Query: 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSK 60
GK +KL +AEE+ATF+A M+E +Y TKE F NF KD+RK +T++E+ +I LSK
Sbjct: 25 FYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIKKLSK 84
Query: 61 CDFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPG 120
CDF ++ YF ++ E++KAMSKEEKK IK+E E + + YG C +DGHKEK+GNFRIEPPG
Sbjct: 85 CDFTPIYQYFEEEKEKKKAMSKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPG 144
Query: 121 LFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTEN 180
LFRGRGEHPKMGKLKRR+ EDI IN KD+ VP PP GHKWKEVRHDN VTWLASW EN
Sbjct: 145 LFRGRGEHPKMGKLKRRIMPEDITINIGKDAPVPEPPAGHKWKEVRHDNTVTWLASWKEN 204
Query: 181 VQGQVKYIMLN 191
+ GQ KY+ML
Sbjct: 205 INGQFKYVMLA 215
Score = 47.3 bits (113), Expect = 6e-06
Identities = 15/22 (68%), Positives = 18/22 (81%)
Query: 483 SVTWLASWTENVQGQVKYIMLN 504
+VTWLASW EN+ GQ KY+ML
Sbjct: 194 TVTWLASWKENINGQFKYVMLA 215
>gnl|CDD|238355 cd00659, Topo_IB_C, DNA topoisomerase IB, C-terminal catalytic
domain. Topoisomerase I promotes the relaxation of both
positive and negative DNA superhelical tension by
introducing a transient single-stranded break in duplex
DNA. This function is vital for the processes of
replication, transcription, and recombination. Unlike
Topo IA enzymes, Topo IB enzymes do not require a
single-stranded region of DNA or metal ions for their
function. The type IB family of DNA topoisomerases
includes eukaryotic nuclear topoisomerase I,
topoisomerases of poxviruses and bacterial versions of
Topo IB. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their C-terminal catalytic domain and the overall
reaction mechanism with tyrosine recombinases. The
C-terminal catalytic domain in topoisomerases is linked
to a divergent N-terminal domain that shows no sequence
or structure similarity to the N-terminal domains of
tyrosine recombinases.
Length = 218
Score = 254 bits (652), Expect = 3e-81
Identities = 118/210 (56%), Positives = 137/210 (65%), Gaps = 20/210 (9%)
Query: 201 DWQKYETARKLAKS------INKIRENYQADWKSKEM-RIRQRAVALYFIDKLALRAGNE 253
DW+KY ARKL + + KIR Y D KSK M R RQ A A+Y IDK ALR GNE
Sbjct: 1 DWKKYRKARKLKRLLAFGRALPKIRRRYTKDLKSKGMPRERQLATAVYLIDKFALRVGNE 60
Query: 254 KDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQL 313
K E + DTVG C+LR EH+ L KP VV FDFLGKDSIRY NEV VE R+FKNL+
Sbjct: 61 KYERENDTVGLCTLRKEHVTL------KPNVVRFDFLGKDSIRYENEVEVEPRLFKNLRK 114
Query: 314 FVENKKGSDDLF-----DRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLNELMDP 368
F++ G DDLF DRLN+S LN +L E MEGLTAKVFRTYNAS+T +QL +
Sbjct: 115 FLDKLPG-DDLFQYLQVDRLNSSKLNAYLREFMEGLTAKVFRTYNASLTALEQLAR-LPA 172
Query: 369 DFSEAEKILAYNRANRAVAVLCNHQRSVPK 398
S AEK AYN ANR VA+L NH ++ K
Sbjct: 173 SLSLAEKKKAYNDANREVAILLNHTPAISK 202
Score = 108 bits (273), Expect = 4e-27
Identities = 44/83 (53%), Positives = 51/83 (61%), Gaps = 7/83 (8%)
Query: 514 DWQKYETARKLAKS------INKIRENYQADWKSKEM-RIRQRAVALYFIDKLALRAGNE 566
DW+KY ARKL + + KIR Y D KSK M R RQ A A+Y IDK ALR GNE
Sbjct: 1 DWKKYRKARKLKRLLAFGRALPKIRRRYTKDLKSKGMPRERQLATAVYLIDKFALRVGNE 60
Query: 567 KDEDQADTVGCCSLRVEHIQLHE 589
K E + DTVG C+LR EH+ L
Sbjct: 61 KYERENDTVGLCTLRKEHVTLKP 83
Score = 30.7 bits (70), Expect = 2.0
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 471 GTSKLNYLDPRISVTWLASW 490
SK+NY+DPRI+V W
Sbjct: 199 AISKINYIDPRITVAWCKKE 218
>gnl|CDD|216252 pfam01028, Topoisom_I, Eukaryotic DNA topoisomerase I, catalytic
core. Topoisomerase I promotes the relaxation of DNA
superhelical tension by introducing a transient
single-stranded break in duplex DNA and are vital for
the processes of replication, transcription, and
recombination.
Length = 243
Score = 244 bits (625), Expect = 6e-77
Identities = 94/236 (39%), Positives = 132/236 (55%), Gaps = 20/236 (8%)
Query: 199 EKDWQKYETARKLAKSINKIRENYQADW-KSKEMRIRQRAVALYFIDKLALRAGNEKDED 257
+D +K+E AR+ K++ KIR+ D +S R R AVA+Y +DK ALR GNEK
Sbjct: 18 VRDEEKFERAREFGKALPKIRKRVAKDLRRSGLPRERVLAVAVYLLDKTALRVGNEKYAR 77
Query: 258 QADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317
+ TVG +LR H+ L + V+ FDFLGKD IR+ N V +KR+ KNL+ +
Sbjct: 78 ENATVGLTTLRNRHVTLEGD------VIRFDFLGKDGIRHENTVR-DKRLAKNLKRLKQK 130
Query: 318 KKGSDDLF--------DRLNTSVLNKHLSELM-EGLTAKVFRTYNASITLQQQLNELMDP 368
G D+LF DR+++S LN +L ELM EG TAK FRT+NAS+T + L +L P
Sbjct: 131 LPG-DELFQYLDDGERDRVSSSDLNAYLRELMGEGFTAKDFRTWNASVTALEALAKLGKP 189
Query: 369 DFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERA 424
S AEK A N AN+ VA+L + +V + L + I + + D +A
Sbjct: 190 L-SVAEKKKAINAANKEVAILLGNTPAVSRKSYIHPAVL-DLIYELGELIADLLKA 243
Score = 109 bits (275), Expect = 4e-27
Identities = 33/81 (40%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 512 EKDWQKYETARKLAKSINKIRENYQADW-KSKEMRIRQRAVALYFIDKLALRAGNEKDED 570
+D +K+E AR+ K++ KIR+ D +S R R AVA+Y +DK ALR GNEK
Sbjct: 18 VRDEEKFERAREFGKALPKIRKRVAKDLRRSGLPRERVLAVAVYLLDKTALRVGNEKYAR 77
Query: 571 QADTVGCCSLRVEHIQLHEEK 591
+ TVG +LR H+ L +
Sbjct: 78 ENATVGLTTLRNRHVTLEGDV 98
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the heterodimeric topo I from
Leishmania donvanni. Topo I enzymes are divided into:
topo type IA (bacterial) and type IB (eukaryotic). Topo
I relaxes superhelical tension in duplex DNA by creating
a single-strand nick, the broken strand can then rotate
around the unbroken strand to remove DNA supercoils and,
the nick is religated, liberating topo I. These enzymes
regulate the topological changes that accompany DNA
replication, transcription and other nuclear processes.
Human topo I is the target of a diverse set of
anticancer drugs including camptothecins (CPTs). CPTs
bind to the topo I-DNA complex and inhibit re-ligation
of the single-strand nick, resulting in the accumulation
of topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 214 bits (547), Expect = 5e-66
Identities = 91/186 (48%), Positives = 127/186 (68%), Gaps = 1/186 (0%)
Query: 5 GKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFR 64
G+ ++ + EE+AT +A M EH+Y KE F NF + WR+ + +K I L CDF
Sbjct: 27 GQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWRE-ILDKRHHPIRKLELCDFT 85
Query: 65 KMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRG 124
++ + +++ E++K+ +KEEKK +K+E + + Y C DG KE++ NFR+EPPGLFRG
Sbjct: 86 PIYEWHLREKEKKKSRTKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRG 145
Query: 125 RGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQ 184
RGEHPKMGKLK+R+Q EDI IN K + +P P GHKWKEV+HDN VTWLA W + + G
Sbjct: 146 RGEHPKMGKLKKRIQPEDITINIGKGAPIPECPAGHKWKEVKHDNTVTWLAMWRDPIAGN 205
Query: 185 VKYIML 190
KY+ML
Sbjct: 206 FKYVML 211
Score = 32.2 bits (73), Expect = 0.65
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 483 SVTWLASWTENVQGQVKYIML 503
+VTWLA W + + G KY+ML
Sbjct: 191 TVTWLAMWRDPIAGNFKYVML 211
>gnl|CDD|239572 cd03490, Topoisomer_IB_N_1, Topoisomer_IB_N_1: A subgroup of the
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB. Topo IB proteins include the
monomeric yeast and human topo I and heterodimeric topo
I from Leishmania donvanni. Topo I enzymes are divided
into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topos I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I have putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 217
Score = 157 bits (399), Expect = 1e-44
Identities = 74/195 (37%), Positives = 115/195 (58%), Gaps = 4/195 (2%)
Query: 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAV-ITDLS 59
+ G+ + L + EEIAT++A+ + Y TKE F NF K + S + + + LS
Sbjct: 23 IMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFVNSFEKDHKFIRRCKLS 82
Query: 60 KCDFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPP 119
DF + + ++ E++K ++KEEK+ K E + +D +EK+ + ++EPP
Sbjct: 83 DADFSLIKNHLEEEKEKKKNLNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPP 142
Query: 120 GLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPP---PGHKWKEVRHDNQVTWLAS 176
GLF+GRGEHPK G LK R+ ED+I+N SKD+ VP GH WK++ HDN VTWLA
Sbjct: 143 GLFKGRGEHPKQGLLKSRIFPEDVILNISKDAPVPKVTNFMEGHSWKDIYHDNSVTWLAY 202
Query: 177 WTENVQGQVKYIMLN 191
+ +++ Q KY+ L+
Sbjct: 203 YKDSINDQFKYMFLS 217
>gnl|CDD|226099 COG3569, COG3569, Topoisomerase IB [DNA replication, recombination,
and repair].
Length = 354
Score = 156 bits (396), Expect = 2e-42
Identities = 78/319 (24%), Positives = 109/319 (34%), Gaps = 59/319 (18%)
Query: 41 KDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYG 100
+W R I S F K + + + K+K+
Sbjct: 94 PEWAA-----LRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAAK-------- 140
Query: 101 VCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160
VC +DG + ++GNF R G + LKR V E I K G
Sbjct: 141 VCLLDGARIRVGNF-----AYARDNGSYGLTTLLKRHVDVEGSTIRFRFKGKS-----GK 190
Query: 161 KWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRE 220
+WKE ++K L L+G+ D RKL + +++
Sbjct: 191 EWKE-------------------RLKDPRLAAI--LRGQLDLP----GRKLFQYLDEDGR 225
Query: 221 NYQADWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDG 280
+ D KS +RQ A + G E++ADTVGCCS E + L
Sbjct: 226 ERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCSEAPELVSLV----- 280
Query: 281 KPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF-VENKKGSDDLFDRLNTSVLNKHLSE 339
S R Y + +VF N + KK L DR LNK
Sbjct: 281 AAVAAVLGNTPAISRRCY----IHPQVFDNYLIGKRLPKKSGRQLRDRARLE-LNKEEQR 335
Query: 340 LMEGLTAKVFRTYNASITL 358
L+ L AKV R Y AS T+
Sbjct: 336 LLRFLEAKVRRRYRASKTM 354
Score = 58.3 bits (141), Expect = 5e-09
Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 15/105 (14%)
Query: 498 VKYIMLNPSSKLKGEKDWQKYETARKLAKS---------------INKIRENYQADWKSK 542
V+ + K K K+W++ +LA +++ + D KS
Sbjct: 175 VEGSTIRFRFKGKSGKEWKERLKDPRLAAILRGQLDLPGRKLFQYLDEDGRERRIDSKSL 234
Query: 543 EMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL 587
+RQ A + G E++ADTVGCCS E + L
Sbjct: 235 NAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCCSEAPELVSL 279
>gnl|CDD|206538 pfam14370, Topo_C_assoc, C-terminal topoisomerase domain. This
domain is found at the C-terminal of topoisomerase and
other similar enzymes.
Length = 71
Score = 70.7 bits (174), Expect = 2e-15
Identities = 27/39 (69%), Positives = 35/39 (89%)
Query: 448 LKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVTW 486
L+E++ KLE+Q DKEENKT+ALGTSK+NY+DPRI+V W
Sbjct: 1 LEERIKKLELQLKDKEENKTVALGTSKINYIDPRITVAW 39
Score = 37.2 bits (87), Expect = 0.001
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 595 KIYNKTQRAKFRWAIDMATADFVF 618
KI++KT R KF WA+D+ D+ F
Sbjct: 49 KIFSKTLREKFPWAMDV-DEDWEF 71
>gnl|CDD|238231 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal
catalytic domain. The DNA breaking-rejoining enzyme
superfamily includes type IB topoisomerases and tyrosine
recombinases that share the same fold in their catalytic
domain containing six conserved active site residues.
The best-studied members of this diverse superfamily
include human topoisomerase I, the bacteriophage lambda
integrase, the bacteriophage P1 Cre recombinase, the
yeast Flp recombinase and the bacterial XerD/C
recombinases. Their overall reaction mechanism is
essentially identical and involves cleavage of a single
strand of a DNA duplex by nucleophilic attack of a
conserved tyrosine to give a 3' phosphotyrosyl
protein-DNA adduct. In the second rejoining step, a
terminal 5' hydroxyl attacks the covalent adduct to
release the enzyme and generate duplex DNA. The enzymes
differ in that topoisomerases cleave and then rejoin the
same 5' and 3' termini, whereas a site-specific
recombinase transfers a 5' hydroxyl generated by
recombinase cleavage to a new 3' phosphate partner
located in a different duplex region. Many DNA
breaking-rejoining enzymes also have N-terminal domains,
which show little sequence or structure similarity.
Length = 164
Score = 51.3 bits (123), Expect = 1e-07
Identities = 34/191 (17%), Positives = 45/191 (23%), Gaps = 59/191 (30%)
Query: 222 YQADWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGK 281
A S R+ +AL + LR C+LR I L +
Sbjct: 6 LAAAEASTPERLY---LALLLLLATGLRISE-----------LCALRWSDIDLDK----- 46
Query: 282 PYVVCFDFLG-KDSIRYYNEVPVE-KRVFKNLQLFVENKKG-SDDLFDRL---------- 328
G K + E ++ K G + LF
Sbjct: 47 ---RVIHITGTKTKKERTVPLSEEALKLLKEYLKKRRPANGDEEYLFPSRRGGPAATLSR 103
Query: 329 -NTSVLNKHLSELM----EGLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRAN 383
N + K EGLT R AS L L+
Sbjct: 104 RNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNAGLD-------------------L 144
Query: 384 RAVAVLCNHQR 394
AV L H
Sbjct: 145 EAVQDLLGHSS 155
Score = 29.3 bits (66), Expect = 3.6
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 14/55 (25%)
Query: 535 YQADWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHE 589
A S R+ +AL + LR C+LR I L +
Sbjct: 6 LAAAEASTPERLY---LALLLLLATGLRISE-----------LCALRWSDIDLDK 46
>gnl|CDD|222985 PHA03101, PHA03101, DNA topoisomerase type I; Provisional.
Length = 314
Score = 39.2 bits (92), Expect = 0.005
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 8/111 (7%)
Query: 248 LRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRV 307
+R G K + +TVG +L+ +HI + +K + F+GKD + + V R+
Sbjct: 130 IRTGKMKYLKENETVGLLTLKNKHITISNDK------ILIKFVGKDKVSHEFVVHKSNRL 183
Query: 308 FKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITL 358
+K L ++ D LF++L+ + K + G+ K RTY + T
Sbjct: 184 YKPLLKLIDKTNPDDFLFNKLSERKVYKFMK--QFGIRLKDLRTYGVNYTF 232
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 33.7 bits (78), Expect = 0.37
Identities = 20/108 (18%), Positives = 45/108 (41%), Gaps = 5/108 (4%)
Query: 358 LQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQ 417
+Q QL+ L EAE L + +A+L R + LK++++ +
Sbjct: 41 VQAQLDALNKQKLLEAEDKLVQQDLEQTLALLDKIDRQ-----KEETEQLKQQLAQAPAK 95
Query: 418 VKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEEN 465
++ A+ L+ K + + +L +L+ +L + Q + + +
Sbjct: 96 LRQAQAELEALKDDNDEETRETLSTLSLRQLESRLAQTLDQLQNAQND 143
>gnl|CDD|221794 pfam12825, DUF3818, Domain of unknown function in PX-proteins
(DUF3818). This domain is found on proteins carrying a
PX domain. Its function is unknown.
Length = 340
Score = 32.7 bits (75), Expect = 0.52
Identities = 41/193 (21%), Positives = 77/193 (39%), Gaps = 31/193 (16%)
Query: 282 PYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELM 341
PY V K +R+ N + + K + L LF+ G L R+ + VLN L E
Sbjct: 62 PYTVL-----KQILRFTNPMAIMKGM---LDLFLAQPFGGRSLLQRIFSMVLNDDLKEFE 113
Query: 342 EGLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHD 401
+ + A I + +K+ + A+ + + +V + D
Sbjct: 114 KEIKE-----LEAKIDDYPVI----------CQKLKNFVEADEDIKDAI-REEAVKEDED 157
Query: 402 KSM-----GNLKEKIS-NKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKL 455
+ L K+S + ++V ++ A K+A ++ ++ LK QLL+L
Sbjct: 158 LLLAILRSSRLAPKLSKEQLQEVIESYTAWKNAVESEPVDEEESEEAELYSNLK-QLLQL 216
Query: 456 EVQETDKEENKTI 468
++E DK+ K +
Sbjct: 217 YLRERDKDLMKKL 229
>gnl|CDD|225821 COG3283, TyrR, Transcriptional regulator of aromatic amino acids
metabolism [Transcription / Amino acid transport and
metabolism].
Length = 511
Score = 32.0 bits (73), Expect = 1.0
Identities = 30/87 (34%), Positives = 40/87 (45%), Gaps = 16/87 (18%)
Query: 260 DTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVF----KNLQLFV 315
D +G S R++ L DG F +G+D +EV V+ RV NL V
Sbjct: 300 DEIGEMSPRLQAKLLRFLNDG-----TFRRVGED-----HEVHVDVRVICATQVNLVELV 349
Query: 316 ENKKGSDDLFDRLNTSVLNKHLSELME 342
+ K +DLF RLN VL +L L E
Sbjct: 350 QKGKFREDLFYRLN--VLTLNLPPLRE 374
>gnl|CDD|225347 COG2733, COG2733, Predicted membrane protein [Function unknown].
Length = 415
Score = 30.8 bits (70), Expect = 2.4
Identities = 29/181 (16%), Positives = 63/181 (34%), Gaps = 17/181 (9%)
Query: 289 FLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGS---DDLFDRLNTSVLNKHLSELMEGLT 345
+ + IR EV + + L+ + + D L DRL +LN + E + +
Sbjct: 150 VIKRAVIRAIAEVYLGPTAGRVLESLTADDRHQALLDKLIDRLIRWLLNDKVREFIAAVI 209
Query: 346 AKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMG 405
+ + ++ + D S+A V +H+ + K D+ +
Sbjct: 210 VRYLEEEHPLFAPIIIVSLVGKRDISDAVNSFL-----DEVRRDPDHK--MRKDFDRFLF 262
Query: 406 NLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEEN 465
+L + + + AE K+ TA G + L + ++ + E++
Sbjct: 263 DLIDDLYHDPGMAARAEAIKSYLKEDEA-------IATAAGDMWTSLSEWLKEDYESEDS 315
Query: 466 K 466
Sbjct: 316 M 316
>gnl|CDD|164495 CHL00091, apcE, phycobillisome linker protein.
Length = 877
Score = 31.0 bits (70), Expect = 2.5
Identities = 29/127 (22%), Positives = 56/127 (44%), Gaps = 22/127 (17%)
Query: 311 LQLFVENKKGSD---DLFDRL--------NTSVLNKHLSELMEGLTAKVFRTY-NASITL 358
L +F E+ +G + + FD + T + K S ++GL ++ + Y A +
Sbjct: 201 LSIFTEDIEGQELVKEYFDVVISEFEAPALTDKVRKRSSTDLQGL--RLPQIYSQAGV-- 256
Query: 359 QQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQV 418
+ +M P+ S EK R + +R + K++ S+ L+ K+ N + +
Sbjct: 257 -SKPRFVMKPNLSSTEKNQVIKACYRQI-----FERDIAKAYGLSLSELESKVKNGQISI 310
Query: 419 KDAERAL 425
K+ RAL
Sbjct: 311 KEFIRAL 317
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 30.4 bits (69), Expect = 3.5
Identities = 27/111 (24%), Positives = 53/111 (47%), Gaps = 8/111 (7%)
Query: 357 TLQQQLNELMDPDFSEAEKILAYNRANRAV-AVLCNHQRSVPKSHDKSMGNLKEKISNKR 415
LQ+Q +L + S ++I N + L + ++ + + +G+LK++
Sbjct: 837 ELQEQRIDLKEQIKSIEKEIENLNGKKEELEEELEELEAAL-RDLESRLGDLKKERDELE 895
Query: 416 KQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENK 466
Q+++ ER K E +A +KK+ L LK +L LE + ++ E+ K
Sbjct: 896 AQLRELER------KIEELEAQIEKKRKRLSELKAKLEALEEELSEIEDPK 940
>gnl|CDD|132934 cd07023, S49_Sppa_N_C, Signal peptide peptidase A (SppA), a serine
protease, has catalytic Ser-Lys dyad. Signal peptide
peptidase A (SppA; Peptidase S49; Protease IV): SppA is
found in all three domains of life and is involved in
the cleavage of signal peptides after their removal from
the precursor proteins by signal peptidases. This
subfamily contains members with either a single domain
(sometimes referred to as 36K type), such as sohB
peptidase, protein C and archaeal signal peptide
peptidase, or an amino-terminal domain in addition to
the carboxyl-terminal protease domain that is conserved
in all the S49 family members (sometimes referred to as
67K type), similar to E. coli and Arabidopsis thaliana
SppA peptidases. Site-directed mutagenesis and sequence
analysis have shown these SppAs to be serine proteases.
The predicted active site serine for members in this
family occurs in a transmembrane domain. Mutagenesis
studies also suggest that the catalytic center comprises
a Ser-Lys dyad and not the usual Ser-His-Asp catalytic
triad found in the majority of serine proteases.
Interestingly, the single membrane spanning E. coli SppA
carries out catalysis using a Ser-Lys dyad with the
serine located in the conserved carboxy-terminal
protease domain and the lysine in the non-conserved
amino-terminal domain.
Length = 208
Score = 29.4 bits (67), Expect = 4.2
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 47 MTEKERAVITDLSKCDFRKMHAYFVQKSEERKAMSKEEKKKIKD 90
+TE+ERA++ L ++ FV E + MS E K+ D
Sbjct: 140 LTEEERAILQALVD----DIYDQFVDVVAEGRGMSGERLDKLAD 179
>gnl|CDD|215618 PLN03184, PLN03184, chloroplast Hsp70; Provisional.
Length = 673
Score = 29.8 bits (67), Expect = 4.6
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 5/86 (5%)
Query: 371 SEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRK-QVKDAERALKDAK 429
EAEK ++ R N SV +K + L +K+ K +V+ + LKDA
Sbjct: 549 QEAEKFAKEDKEKRDAVDTKNQADSVVYQTEKQLKELGDKVPADVKEKVEAKLKELKDAI 608
Query: 430 KAGESKAMTDKKKTALGRLKEQLLKL 455
+G ++ M K A+ L ++++++
Sbjct: 609 ASGSTQKM----KDAMAALNQEVMQI 630
>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein.
Length = 122
Score = 28.0 bits (63), Expect = 6.3
Identities = 23/108 (21%), Positives = 51/108 (47%), Gaps = 12/108 (11%)
Query: 359 QQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQV 418
+++L EL E + L+ + + A L N+Q + + D+++ ++++ KQV
Sbjct: 18 EEKLEELQQ-YRLEYRQQLSGSGQGISAAELRNYQAFI-SALDEAIAQQQQELEQAEKQV 75
Query: 419 KDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENK 466
+ A ++A + ++ L +L E+ K E +E ++ E K
Sbjct: 76 EQAREQWQEANQ----------ERKKLEKLLEREKKKEQKEENRREQK 113
>gnl|CDD|172390 PRK13870, PRK13870, transcriptional regulator TraR; Provisional.
Length = 234
Score = 28.8 bits (64), Expect = 7.4
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 9/87 (10%)
Query: 5 GKEMKLSQDAEEIA-----TFYARM-IEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDL 58
G E L +IA T YA + I+H + T TN+ ++W+ +K+ + +
Sbjct: 16 GDECILKTGLADIADHFGFTGYAYLHIQHRHITAV---TNYHREWQSVYFDKKFDALDPV 72
Query: 59 SKCDFRKMHAYFVQKSEERKAMSKEEK 85
K + H + +ER +SK+E+
Sbjct: 73 VKRARSRKHIFTWSGEQERPRLSKDER 99
>gnl|CDD|235600 PRK05771, PRK05771, V-type ATP synthase subunit I; Validated.
Length = 646
Score = 29.1 bits (66), Expect = 7.4
Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 47 MTEKERA--VITDLSKCDFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKE 98
+ KE + V +L K F ++ E KEE ++I+ E E++ +E
Sbjct: 184 VVLKELSDEVEEELKKLGFERLELEEEGTPSELIREIKEELEEIEKERESLLEE 237
>gnl|CDD|222589 pfam14199, DUF4317, Domain of unknown function (DUF4317). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 225 and 451 amino
acids in length. There is a single completely conserved
residue P that may be functionally important.
Length = 370
Score = 29.1 bits (66), Expect = 7.6
Identities = 17/40 (42%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 80 MSKEE----KKKIKDENEAITKEYGVCTIDGHKEKIGNFR 115
M+K+E +K+ K +N AIT+ G C +DG KE I F+
Sbjct: 1 MNKKEIAEIRKRFKPDNCAITRICG-CYVDGEKEIITEFK 39
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 28.9 bits (65), Expect = 8.0
Identities = 13/66 (19%), Positives = 29/66 (43%)
Query: 406 NLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEEN 465
+L E + +++ ++ ++A + ++K + L RL+ QL E + EE
Sbjct: 243 DLDEYLKKLNQELAKLAAEIERVQEALKESPKSEKAQNKLNRLQMQLEAFEERIALIEEV 302
Query: 466 KTIALG 471
+A
Sbjct: 303 IVLAGI 308
>gnl|CDD|180907 PRK07251, PRK07251, pyridine nucleotide-disulfide oxidoreductase;
Provisional.
Length = 438
Score = 28.9 bits (65), Expect = 9.3
Identities = 21/91 (23%), Positives = 33/91 (36%), Gaps = 15/91 (16%)
Query: 67 HAYFVQKSEERKAMSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRG 126
+ F Q + ++ +++ +N A+ GV D + N IE
Sbjct: 61 NLSFEQVMATKNTVTS----RLRGKNYAMLAGSGVDLYDAEAHFVSNKVIEVQA------ 110
Query: 127 EHPKMGKLKRRVQAEDIIINCSKDSKVPPPP 157
G K + AE I+IN S V P P
Sbjct: 111 -----GDEKIELTAETIVINTGAVSNVLPIP 136
>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase;
Provisional.
Length = 330
Score = 28.6 bits (65), Expect = 9.8
Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 44 RKSMTEKERAVITDLSKC--DFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKE 98
++ ++K +T+L++ + ++ + +E KA K +KKK K E +A +
Sbjct: 31 QRKKSQKGELEVTNLNEQYKEMKEELKAALLDKKELKAWHKAQKKKEKQEAKAAKAK 87
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 28.2 bits (63), Expect = 10.0
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 4/70 (5%)
Query: 327 RLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQL---NELMDPDFSEAEKILAYNRAN 383
+L++ L K ++E++EG K R + ++ LQ L + D FS + K+ + N
Sbjct: 3 KLSSEALRKAIAEILEGSEEKK-RKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPN 61
Query: 384 RAVAVLCNHQ 393
V VL +
Sbjct: 62 LKVCVLGDAV 71
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 0.130 0.375
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,214,401
Number of extensions: 3038771
Number of successful extensions: 4062
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3970
Number of HSP's successfully gapped: 142
Length of query: 618
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 515
Effective length of database: 6,369,140
Effective search space: 3280107100
Effective search space used: 3280107100
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 (21.5 bits)
S2: 62 (27.5 bits)