RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6712
(210 letters)
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 210 bits (536), Expect = 7e-67
Identities = 87/117 (74%), Positives = 104/117 (88%)
Query: 81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
+VD+LT+KM E +FTVS MHGDM QK+RD IM+EFRSG++RVLITTD+ ARGIDVQQVSL
Sbjct: 279 KVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSL 338
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
VINYDLP + E YIHRIGRSGRFGRKGVAI+FV DDI L++IE++Y+TQI+EMPM
Sbjct: 339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEMPM 395
Score = 124 bits (312), Expect = 7e-34
Identities = 49/89 (55%), Positives = 67/89 (75%)
Query: 1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
+ V+CHAC+GGT + +D+ KL G H+V GTPGRV+DMI +R LR ++K+ +LDEADEM
Sbjct: 123 LKVRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEM 182
Query: 61 LNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
L++GFK QIYDV++ LPP QV + M
Sbjct: 183 LSRGFKGQIYDVFKKLPPDVQVALFSATM 211
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 146 bits (370), Expect = 2e-41
Identities = 57/114 (50%), Positives = 83/114 (72%), Gaps = 1/114 (0%)
Query: 82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
V+ L E +R+ F V+++HGD+PQ+ERD +++F+ G RVL+ TDV ARG+D+ VS V
Sbjct: 286 VEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHV 345
Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSD-DIRILRDIEQYYSTQIDE 194
INYDLP + E Y+HRIGR+GR GRKGVAISFV + +++ L+ IE+ ++
Sbjct: 346 INYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPS 399
Score = 95.6 bits (238), Expect = 4e-23
Identities = 29/81 (35%), Positives = 45/81 (55%)
Query: 2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
++ GG ++ + + L G +V TPGR+ D+I+R L ++ LVLDEAD ML
Sbjct: 128 GLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEADRML 187
Query: 62 NKGFKEQIYDVYRYLPPATQV 82
+ GF + I + + LPP Q
Sbjct: 188 DMGFIDDIEKILKALPPDRQT 208
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 128 bits (324), Expect = 3e-38
Identities = 56/134 (41%), Positives = 81/134 (60%), Gaps = 4/134 (2%)
Query: 39 IRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSS 98
I++ VL + K+ L E L K ++ V + P +D L E +R+ V++
Sbjct: 2 IKQYVLPVEDEKLEALLE----LLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAA 57
Query: 99 MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIG 158
+HGD Q+ER+ ++K+FR G VL+ TDV ARGID+ VS+VINYDLP + Y+ RIG
Sbjct: 58 LHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIG 117
Query: 159 RSGRFGRKGVAISF 172
R+GR G+KG AI
Sbjct: 118 RAGRAGQKGTAILL 131
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 131 bits (332), Expect = 2e-36
Identities = 47/103 (45%), Positives = 66/103 (64%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
L +R+A + G+M Q +R+ +K G VL+ TDV ARGID+ VS VIN+
Sbjct: 261 LAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINF 320
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQY 187
D+P + + Y+HRIGR+GR GRKG AIS V++ D +L IE+Y
Sbjct: 321 DMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERY 363
Score = 43.8 bits (104), Expect = 3e-05
Identities = 21/60 (35%), Positives = 29/60 (48%)
Query: 10 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
GG Q +V TPGR+ I+ R ++ L+LDEAD ML+ GF + I
Sbjct: 109 GGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRMLDMGFAQDI 168
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 125 bits (317), Expect = 3e-36
Identities = 34/82 (41%), Positives = 51/82 (62%)
Query: 1 MNVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
N++ GGT++ + +RKL G H+V TPGR+ D++ R L +K LVLDEAD M
Sbjct: 96 TNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEADRM 155
Query: 61 LNKGFKEQIYDVYRYLPPATQV 82
L+ GF++QI ++ + LP Q
Sbjct: 156 LDMGFEDQIREILKLLPKDRQT 177
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 130 bits (329), Expect = 7e-36
Identities = 42/127 (33%), Positives = 77/127 (60%)
Query: 81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
+ + + + F+ ++HGD+ Q++RD ++ F + + VL+ TDV ARG+D++ +
Sbjct: 254 ECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEA 313
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGK 200
VINY+L + E+++HRIGR+GR G KG+A+S V ++++ IE Y +++ P+
Sbjct: 314 VINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSL 373
Query: 201 RSLHSYP 207
L P
Sbjct: 374 SPLSGVP 380
Score = 74.5 bits (184), Expect = 1e-15
Identities = 28/72 (38%), Positives = 42/72 (58%)
Query: 10 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
GG + + L++G H++ GTPGR+ D +R+ L + LVLDEAD ML+ GF++ I
Sbjct: 109 GGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAI 168
Query: 70 YDVYRYLPPATQ 81
+ R P Q
Sbjct: 169 DAIIRQAPARRQ 180
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 111 bits (280), Expect = 3e-32
Identities = 40/78 (51%), Positives = 57/78 (73%)
Query: 87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL 146
+ +R+ V+ +HG + Q+ER+ I+++FR+G S+VL+ TDV RGID+ V+LVINYDL
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 147 PNNRELYIHRIGRSGRFG 164
P N YI RIGR+GR G
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 109 bits (274), Expect = 3e-31
Identities = 37/82 (45%), Positives = 54/82 (65%)
Query: 83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
+ L E ++E V+ +HG + Q+ER+ I+ +F +G +VL+ TDV RG+D+ V LVI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 143 NYDLPNNRELYIHRIGRSGRFG 164
YDLP + YI RIGR+GR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 112 bits (282), Expect = 5e-29
Identities = 46/102 (45%), Positives = 70/102 (68%)
Query: 83 DWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
D+LT+++R + +HGD Q+ER ++ EF++G S ++I TDV +RG+DV+ V VI
Sbjct: 391 DFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVI 450
Query: 143 NYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDI 184
N+D PN E Y+HRIGR+GR G KG + +F+ D R+ RD+
Sbjct: 451 NFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDL 492
Score = 48.2 bits (115), Expect = 1e-06
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 6 HACI-GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKG 64
+ GG + L G ++ PGR+ D + V R + LVLDEAD ML+ G
Sbjct: 234 NTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMG 293
Query: 65 FKEQI 69
F+ QI
Sbjct: 294 FEPQI 298
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 103 bits (260), Expect = 3e-26
Identities = 41/92 (44%), Positives = 56/92 (60%)
Query: 101 GDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS 160
GD+ QK+R I++EF G +L+ TDV ARG+ + V+ V NYDLP++ E Y+HRIGR+
Sbjct: 287 GDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRT 346
Query: 161 GRFGRKGVAISFVKSDDIRILRDIEQYYSTQI 192
GR G G +IS + L IE Y I
Sbjct: 347 GRAGASGHSISLACEEYALNLPAIETYIGHSI 378
Score = 56.9 bits (138), Expect = 1e-09
Identities = 26/72 (36%), Positives = 43/72 (59%)
Query: 10 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
GG + L+ L+ G ++ GT GR+ D ++ + I+++VLDEAD M + GF + I
Sbjct: 119 GGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDEADRMFDLGFIKDI 178
Query: 70 YDVYRYLPPATQ 81
++R +PPA Q
Sbjct: 179 RWLFRRMPPANQ 190
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 102 bits (255), Expect = 2e-25
Identities = 45/115 (39%), Positives = 74/115 (64%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
L E++ + +++HG+ Q R + +F+SG RVL+ TD+ ARG+D++++ V+NY
Sbjct: 261 LAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNY 320
Query: 145 DLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNG 199
+LPN E Y+HRIGR+GR G A+S V D+ ++LRDIE+ +I + + G
Sbjct: 321 ELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRIAIPG 375
Score = 56.0 bits (135), Expect = 2e-09
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 10 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQI 69
GG +++ + KL G V+ TPGR+ D+ + ++ +++LVLDEAD ML+ GF I
Sbjct: 111 GGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDI 170
Query: 70 YDVYRYLPPATQ 81
V LP Q
Sbjct: 171 RRVLAKLPAKRQ 182
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 100 bits (250), Expect = 8e-25
Identities = 48/117 (41%), Positives = 71/117 (60%), Gaps = 1/117 (0%)
Query: 81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
+V + E++ + + + GD+PQ +R ++ FR G RVL+ TDV RGI + +S
Sbjct: 347 EVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISH 406
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQID-EMP 196
VIN+ LP + + Y+HRIGR+GR G GV+ISF DD L +IE+ +I EMP
Sbjct: 407 VINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKISCEMP 463
Score = 52.6 bits (126), Expect = 3e-08
Identities = 28/94 (29%), Positives = 50/94 (53%), Gaps = 6/94 (6%)
Query: 9 IGGTNLSEDLRKLDYGQH--VVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFK 66
+GG + + L++L+ + ++ TPGR+ D +R + ++++VLDEAD ML+ GF
Sbjct: 197 VGGMDFDKQLKQLE-ARFCDILVATPGRLLDFNQRGEVHLDMVEVMVLDEADRMLDMGFI 255
Query: 67 EQIYDVYRYLPPATQVDWLTEKMREANFTVSSMH 100
Q+ + R P + L + A FT M+
Sbjct: 256 PQVRQIIRQTPRKEERQTL---LFSATFTDDVMN 286
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 101 bits (252), Expect = 8e-25
Identities = 51/128 (39%), Positives = 82/128 (64%), Gaps = 5/128 (3%)
Query: 87 EKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDL 146
E + + ++++GDM Q R+ ++ + G +LI TDV ARG+DV+++SLV+NYD+
Sbjct: 263 EALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDI 322
Query: 147 PNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMN-----GKR 201
P + E Y+HRIGR+GR GR G A+ FV++ + R+LR+IE+ I E+ + GKR
Sbjct: 323 PMDSESYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKR 382
Query: 202 SLHSYPAR 209
L + A+
Sbjct: 383 RLEKFAAK 390
Score = 65.3 bits (159), Expect = 1e-12
Identities = 38/107 (35%), Positives = 50/107 (46%)
Query: 2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
V A GG LR L G +V GTPGR+ D ++R L + LVLDEADEML
Sbjct: 103 GVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEML 162
Query: 62 NKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKER 108
GF E + + +P Q + M EA ++ PQ+ R
Sbjct: 163 RMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVR 209
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 92.7 bits (230), Expect = 6e-22
Identities = 45/116 (38%), Positives = 66/116 (56%)
Query: 82 VDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLV 141
V+ + + + V + GD+PQK+R+ ++ F+ G +L+ TDV ARG+ + V V
Sbjct: 270 VERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYV 329
Query: 142 INYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
NYDLP + E Y+HRIGR+ R G +G AISF L DIE Y +I P+
Sbjct: 330 YNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKIPVEPV 385
Score = 43.4 bits (102), Expect = 4e-05
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 10 GGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRR-RVLRTRNIKMLVLDEADEMLNKGFKEQ 68
GG + + L G V+ TPGR+ D +++ +V+ ++ VLDEAD M + GF +
Sbjct: 120 GGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKD 179
Query: 69 IYDVYRYLP 77
I + R +P
Sbjct: 180 IRFLLRRMP 188
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 82.7 bits (205), Expect = 4e-20
Identities = 33/84 (39%), Positives = 54/84 (64%), Gaps = 2/84 (2%)
Query: 1 MNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRRRVLRT-RNIKMLVLDEAD 58
+ ++ GGT+L E RKL G+ ++ GTPGR+ D++RR L+ +N+K+LVLDEA
Sbjct: 72 LGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAH 131
Query: 59 EMLNKGFKEQIYDVYRYLPPATQV 82
+L+ GF + + ++ LPP Q+
Sbjct: 132 RLLDMGFGDDLEEILSRLPPDRQI 155
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 86.8 bits (215), Expect = 5e-20
Identities = 45/136 (33%), Positives = 69/136 (50%), Gaps = 12/136 (8%)
Query: 63 KGFKEQIYDVY----RYLPPAT-------QVDWLTEKMREAN-FTVSSMHGDMPQKERDG 110
K K++++D+ + PPA D L + S+HG+ KER
Sbjct: 350 KQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERRE 409
Query: 111 IMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAI 170
+MK F G V++ T V RG+D+ +V VI +D+PN + YIH+IGR+ R G KG AI
Sbjct: 410 VMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAI 469
Query: 171 SFVKSDDIRILRDIEQ 186
FV +D + ++
Sbjct: 470 VFVNEEDRNLFPELVA 485
Score = 59.8 bits (145), Expect = 1e-10
Identities = 23/69 (33%), Positives = 44/69 (63%)
Query: 9 IGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQ 68
+GG + + L ++ G ++ GTPGR+ D++ + + N+ +LVLDE D ML +GF++Q
Sbjct: 231 VGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQ 290
Query: 69 IYDVYRYLP 77
+ +++ L
Sbjct: 291 VMQIFQALS 299
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 71.6 bits (176), Expect = 5e-16
Identities = 27/81 (33%), Positives = 43/81 (53%)
Query: 2 NVQCHACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEML 61
++ IGGT++ + + L +V GTPGR+ D + R L + + +L+LDEA +L
Sbjct: 57 GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL 116
Query: 62 NKGFKEQIYDVYRYLPPATQV 82
N+GF + LP QV
Sbjct: 117 NQGFGLLGLKILLKLPKDRQV 137
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 72.5 bits (178), Expect = 5e-16
Identities = 26/83 (31%), Positives = 48/83 (57%), Gaps = 1/83 (1%)
Query: 1 MNVQCHACIGGTNLSEDLRKLDYGQ-HVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADE 59
+ ++ GG + E LRKL+ G+ ++ TPGR+ D++ L N+ +++LDEA
Sbjct: 81 LGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHR 140
Query: 60 MLNKGFKEQIYDVYRYLPPATQV 82
+L+ GF +Q+ + + LP Q+
Sbjct: 141 LLDGGFGDQLEKLLKLLPKNVQL 163
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 61.9 bits (151), Expect = 2e-11
Identities = 33/102 (32%), Positives = 54/102 (52%)
Query: 81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
+V+ L E +R+ + + H + +ER+ + + F + +V++ T+ + GID V
Sbjct: 242 KVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRF 301
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
VI+YDLP + E Y GR+GR G AI +DIR R
Sbjct: 302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 57.4 bits (139), Expect = 8e-10
Identities = 39/105 (37%), Positives = 53/105 (50%), Gaps = 9/105 (8%)
Query: 103 MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YIHRIGRSG 161
M QKE+ I+ +FR G VL+ T V G+D+ +V LVI Y+ P E+ I R GR+G
Sbjct: 409 MSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFYE-PVPSEIRSIQRKGRTG 467
Query: 162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLHSY 206
R RKG + V RD YYS++ E M S+
Sbjct: 468 R-KRKGRVVVLVTEGT----RDEAYYYSSRRKEQKM--IESIRGL 505
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 56.6 bits (137), Expect = 1e-09
Identities = 34/107 (31%), Positives = 53/107 (49%), Gaps = 1/107 (0%)
Query: 81 QVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL 140
+V+ L E++ + + H + K R ++F +V++ T+ + GID V
Sbjct: 236 KVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRF 295
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD-IEQ 186
VI+YD+P N E Y GR+GR G AI DI +L+ IEQ
Sbjct: 296 VIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQ 342
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 53.9 bits (130), Expect = 1e-08
Identities = 32/131 (24%), Positives = 49/131 (37%), Gaps = 23/131 (17%)
Query: 54 LDEADEMLNKGFKE--QIYDVY------RYLPPATQVD-WLTEKMREANFTVSSMHGDMP 104
D E + + + Q Y VY L + K + V +HG M
Sbjct: 434 KDIVYEFIEEEIAKGRQAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMK 493
Query: 105 QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRS---- 160
E++ +M+EFR G +L+ T V G+DV ++++ D R G S
Sbjct: 494 SDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIED--------AERFGLSQLHQ 545
Query: 161 --GRFGRKGVA 169
GR GR
Sbjct: 546 LRGRVGRGDHQ 556
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 51.7 bits (124), Expect = 5e-08
Identities = 33/132 (25%), Positives = 58/132 (43%), Gaps = 2/132 (1%)
Query: 53 VLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKERDGIM 112
+L++ + K FK + +Y P + + +T ++ + H + RD +
Sbjct: 212 ILEDLLRFIRKEFKGKSGIIY--CPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVH 269
Query: 113 KEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRKGVAISF 172
+F+ +V++ T + GI+ V VI+Y LP + E Y GR+GR G F
Sbjct: 270 HKFQRDEIQVVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLF 329
Query: 173 VKSDDIRILRDI 184
DI LR +
Sbjct: 330 YAPADINRLRRL 341
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 51.3 bits (123), Expect = 9e-08
Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 11/110 (10%)
Query: 96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YI 154
VS+ + ++ER I EF+ G +I T+ GID+ + VI Y P L +
Sbjct: 341 VSTYRAGLHREERRRIEAEFKEGELLGVIATNALELGIDIGSLDAVIAYGYPGVSVLSFR 400
Query: 155 HRIGRSGRFGRKGVAISFVKSDDIRILRD--IEQYYSTQIDEMPMNGKRS 202
R GR+GR R ++ V +LR ++ YY +E+ G
Sbjct: 401 QRAGRAGR--RGQESLVLV------VLRSDPLDSYYLRHPEELLETGFGP 442
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 47.2 bits (112), Expect = 2e-06
Identities = 31/114 (27%), Positives = 54/114 (47%), Gaps = 4/114 (3%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
+ E+++E + HG M +R + K++ ++ T + GI+ V VI++
Sbjct: 696 VAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDVRFVIHH 755
Query: 145 DLPNNRELYIHRIGRSGRFG-RKGVAISFVKSDDIRILRDIEQYYSTQIDEMPM 197
LP + E Y GR+GR G R + + SD IR+ I Q +++ PM
Sbjct: 756 SLPKSIEGYHQECGRAGRDGQRSSCVLYYSYSDYIRVKHMISQ---GGVEQSPM 806
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 46.8 bits (112), Expect = 3e-06
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 14/84 (16%)
Query: 92 ANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRE 151
V +HG M E+D +M+ F+ G +L+ T V G+DV ++++ +
Sbjct: 506 PELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPNATVMVIEN------ 559
Query: 152 LYIHRIGRS------GRFGRKGVA 169
R G + GR GR +
Sbjct: 560 --AERFGLAQLHQLRGRVGRGDLQ 581
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 46.4 bits (111), Expect = 4e-06
Identities = 36/103 (34%), Positives = 53/103 (51%), Gaps = 9/103 (8%)
Query: 103 MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL-YIHRIGRSG 161
M QKE+ I+ +FR+G VL++T V G+D+ V LVI Y+ P E+ I R GR+G
Sbjct: 407 MSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYE-PVPSEIRSIQRKGRTG 465
Query: 162 RFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH 204
R +G + + RD Y+S++ E M K L
Sbjct: 466 R-QEEGRVVVLIAKGT----RDEAYYWSSRRKEKKM--KEELK 501
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 46.2 bits (110), Expect = 4e-06
Identities = 24/103 (23%), Positives = 49/103 (47%)
Query: 80 TQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVS 139
+V+ +++ + ++ H + R + + F+ ++++ T + GI+ V
Sbjct: 247 AKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVR 306
Query: 140 LVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILR 182
V+++D+P N E Y GR+GR G A+ F D+ LR
Sbjct: 307 FVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPADMAWLR 349
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 45.9 bits (109), Expect = 5e-06
Identities = 26/108 (24%), Positives = 51/108 (47%), Gaps = 3/108 (2%)
Query: 96 VSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIH 155
V ++ G+ P++ER+ I++ FR+G +VL+T V G+D+ ++I +R L+I
Sbjct: 309 VEAITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQ 368
Query: 156 RIGRSGR-FGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRS 202
R+GR R K ++ S E+ + + + +
Sbjct: 369 RLGRGLRPAEGKEDTLALDYSLVPD--DLGEEDIARRRRLFLIRKGYT 414
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 42.4 bits (101), Expect = 8e-05
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 99 MHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDV 135
+HG M E+D +M F++G +L+ T V G+DV
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDV 547
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 40.9 bits (95), Expect = 3e-04
Identities = 27/135 (20%), Positives = 56/135 (41%), Gaps = 7/135 (5%)
Query: 36 FDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQ--IYDVYRYLPPATQVDWLTEKMREAN 93
FD +++ +++ K+ LDE +L E+ + V + +D L + ++
Sbjct: 679 FDYLKKPLIQLSKGKLQALDE---LLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALG 735
Query: 94 FTVSSMHGDMPQKERDGIMKEFRSGTSR--VLITTDVWARGIDVQQVSLVINYDLPNNRE 151
+ G P K R ++ F + L++ G+++ VI +D N
Sbjct: 736 IKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPA 795
Query: 152 LYIHRIGRSGRFGRK 166
+ + I R+ R G+K
Sbjct: 796 VELQAIDRAHRIGQK 810
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 39.9 bits (94), Expect = 6e-04
Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
LTE ++E V +H D+ ER I+++ R G VL+ ++ G+D+ +VSLV
Sbjct: 462 LTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAIL 521
Query: 145 D------LPNNRELYIHRIGRSGR 162
D L + R L I IGR+ R
Sbjct: 522 DADKEGFLRSERSL-IQTIGRAAR 544
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 38.8 bits (90), Expect = 0.002
Identities = 22/68 (32%), Positives = 34/68 (50%)
Query: 94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY 153
F S HG + +++R + +SG R ++ T GID+ V LVI P +
Sbjct: 302 FIARSHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASG 361
Query: 154 IHRIGRSG 161
+ RIGR+G
Sbjct: 362 LQRIGRAG 369
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 38.5 bits (90), Expect = 0.002
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 100 HGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI--NYDLPNNRELYIHRI 157
HG M + E + +M EF G +VL+ T + GID+ + +I D +LY R
Sbjct: 693 HGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLR- 751
Query: 158 GRSGRFGRKGVA 169
GR GR +K A
Sbjct: 752 GRVGRSKKKAYA 763
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 37.7 bits (88), Expect = 0.003
Identities = 20/78 (25%), Positives = 36/78 (46%), Gaps = 12/78 (15%)
Query: 105 QKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL--VINYD----LPNNR------EL 152
+ + ++ +F +G + +LI T + A+G V+L V++ D P+ R +L
Sbjct: 298 KGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQL 357
Query: 153 YIHRIGRSGRFGRKGVAI 170
GR+GR G I
Sbjct: 358 LTQVAGRAGRAEDPGQVI 375
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 37.3 bits (87), Expect = 0.004
Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 7/84 (8%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINY 144
LT+ ++E V +H ++ ER I+++ R G VL+ ++ G+D+ +VSLV
Sbjct: 458 LTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAIL 517
Query: 145 D------LPNNRELYIHRIGRSGR 162
D L + R L I IGR+ R
Sbjct: 518 DADKEGFLRSERSL-IQTIGRAAR 540
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 36.9 bits (86), Expect = 0.007
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 1/66 (1%)
Query: 113 KEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSG-RFGRKGVAIS 171
+ + G + ++ T GID+ + LVI P + ++ RIGR+G R G I
Sbjct: 298 ERLKEGELKAVVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGHRLGEVSKGII 357
Query: 172 FVKSDD 177
+ D
Sbjct: 358 IAEDRD 363
Score = 28.8 bits (65), Expect = 2.5
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT 126
L E +RE V+ HGD PQ E+ ++ +LITT
Sbjct: 93 LEEPLRELGIEVAVRHGDTPQSEK----QKMLKNPPHILITT 130
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 35.9 bits (83), Expect = 0.009
Identities = 21/105 (20%), Positives = 43/105 (40%), Gaps = 14/105 (13%)
Query: 83 DWLTEKMREANFTVSSMHGDMPQKERDG----IMKEFRSGTSRVLITTDVWARGIDVQQV 138
L E + +H +K+R +++E + V++ T V +D+
Sbjct: 240 QQLKENA--PEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLDI-SA 296
Query: 139 SLVINYDLPNNRELYIHRIGRSGRFGRKGVAISFVKSDDIRILRD 183
++I P + I R+GR R+GRK ++ ++ I+
Sbjct: 297 DVMITELAPIDS--LIQRLGRLHRYGRK-----NGENFEVYIITI 334
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 34.7 bits (80), Expect = 0.023
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 83 DWLTEKMREANFTVSSMHGDMPQKER----DGIMKEFRSGTSRVLITTDVWARGIDVQQV 138
L EK E + +H +K+R ++ EF+ V++ T V +D+ V
Sbjct: 236 QQLKEKGPEEEIML--IHSRFTEKDRAKKEAELLLEFKKSEKFVIVATQVIEASLDI-SV 292
Query: 139 SLVINYDLPNNRELYIHRIGRSGRFGRK 166
++I P + I R+GR R+G K
Sbjct: 293 DVMITELAPIDS--LIQRLGRLHRYGEK 318
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 34.8 bits (80), Expect = 0.028
Identities = 31/119 (26%), Positives = 51/119 (42%), Gaps = 9/119 (7%)
Query: 49 IKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDMPQKER 108
I LV E +KG++ Q V+ Y L + + + H +P KER
Sbjct: 423 IARLVKREFSTESSKGYRGQTI-VFTYSRRRCH--ELADALTGKGLKAAPYHAGLPYKER 479
Query: 109 DGIMKEFRSGTSRVLITTDVWARGID--VQQV---SLVINYDLPNNRELYIHRIGRSGR 162
+ + F + ++TT A G+D QV SL + + + RE + +GR+GR
Sbjct: 480 KSVERAFAAQELAAVVTTAALAAGVDFPASQVIFESLAMGIEWLSVRE-FQQMLGRAGR 537
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 34.7 bits (80), Expect = 0.032
Identities = 18/71 (25%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 107 ERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELYIHRIGRSGRFGRK 166
+R + + R G + TT+ G+D+ + V+ P R + GR+GR G+
Sbjct: 317 DRRELERALRDGELLGVATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQG 376
Query: 167 GVAISFVKSDD 177
+ + V DD
Sbjct: 377 ALVV-LVARDD 386
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 33.8 bits (78), Expect = 0.054
Identities = 25/91 (27%), Positives = 38/91 (41%), Gaps = 25/91 (27%)
Query: 91 EANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNR 150
EA V+ HG M ++E + +M +F +G VL+ T + GID+ PN
Sbjct: 829 EARIAVA--HGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDI-----------PNAN 875
Query: 151 ELYIHRI------------GRSGRFGRKGVA 169
+ I R GR GR ++ A
Sbjct: 876 TIIIERADKFGLAQLYQLRGRVGRSNKQAYA 906
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 32.9 bits (75), Expect = 0.12
Identities = 14/53 (26%), Positives = 25/53 (47%)
Query: 79 ATQVDWLTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWAR 131
A ++ L EK + + H +P KE+ M+ +G +LITT ++
Sbjct: 138 AEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLS 190
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.7 bits (70), Expect = 0.19
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 8 CIGGTNLSEDLRKL--DYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEAD----EML 61
+ LRK+ G + GT + + I L+ R +L++DEA E L
Sbjct: 38 APSLGTPKDLLRKILRALGLPLSGGTTAELLEAILDA-LKRRGRPLLIIDEAQHLSLEAL 96
Query: 62 N 62
Sbjct: 97 E 97
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 31.6 bits (72), Expect = 0.32
Identities = 27/168 (16%), Positives = 59/168 (35%), Gaps = 20/168 (11%)
Query: 35 VFDMIRRRVLRT-RNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREAN 93
VF R+ +T + +++ + + E + P ++ + L E +
Sbjct: 258 VFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLDEGASPILIPETPTSEDEELAELVLRG- 316
Query: 94 FTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGI----------DVQQVSLVIN 143
V+ H +P+++R + FR G +VL++T A G+ D ++
Sbjct: 317 --VAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGG 374
Query: 144 YDLPNNRELYIHRIGRSGRFGRKGVAISFV-----KSDDIRILRDIEQ 186
+ + GR+GR G + + + I+
Sbjct: 375 IVDIPVLD-VLQMAGRAGRPGYDDYGEAIILATSHDELEYLAELYIQS 421
>gnl|CDD|119141 pfam10621, FpoO, F420H2 dehydrogenase subunit FpoO. This is the
FpoO subunit of F420H2 dehydrogenase, an enzyme which
oxidises reduced coenzyme F420. Reduced coenzyme F420 is
a universal electron carrier in methanogens.
Length = 119
Score = 30.3 bits (68), Expect = 0.32
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 12/77 (15%)
Query: 5 CHACIGGT-----NLSEDLRKLDYGQHVVSGTPGRVF-------DMIRRRVLRTRNIKML 52
C C+ ++ + +G+ + GT +V D + V++T I +
Sbjct: 37 CEGCLDSAQKTYLESNKKVASCRFGKCDLCGTKTQVQPVEVQVPDFSKGSVVKTVKICLK 96
Query: 53 VLDEADEMLNKGFKEQI 69
L+E E + KEQI
Sbjct: 97 CLEETSESYIREKKEQI 113
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 31.3 bits (72), Expect = 0.33
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 12/72 (16%)
Query: 111 IMKEFRSGTSRVLITTDVWARGIDVQQVSLV--INYDL----PNNR------ELYIHRIG 158
++ +F G + +LI T + A+G D V+LV ++ DL P+ R +L G
Sbjct: 472 LLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAG 531
Query: 159 RSGRFGRKGVAI 170
R+GR + G +
Sbjct: 532 RAGRAEKPGEVL 543
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 30.9 bits (70), Expect = 0.41
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 106 KERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSL-VINYDLPNNRELYIHRIGRSGRFG 164
+ R ++ FR G +LITT + RG+ V + V+ + E + +I +GR G
Sbjct: 342 QHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQI--AGRVG 399
Query: 165 RK 166
R
Sbjct: 400 RS 401
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 30.8 bits (70), Expect = 0.58
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 12/72 (16%)
Query: 111 IMKEFRSGTSRVLITTDVWARGIDVQQVSLV--INYD----LPNNR------ELYIHRIG 158
++ +F +G + +LI T + A+G D V+LV ++ D P+ R +L + G
Sbjct: 526 LLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDFRASERTFQLLMQVAG 585
Query: 159 RSGRFGRKGVAI 170
R+GR G+ G +
Sbjct: 586 RAGRAGKPGEVV 597
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 30.5 bits (69), Expect = 0.68
Identities = 31/108 (28%), Positives = 52/108 (48%), Gaps = 10/108 (9%)
Query: 40 RRRVLRT--RNIKMLVLDEA--DEMLNKGFKEQIYDVYRYLPPATQV-DWLTEKMREANF 94
RR ++T R LV+ EA E+L G Q+Y +Y + + + L E + EA
Sbjct: 782 RRLAVKTFVREYDSLVVREAILREILRGG---QVYYLYNDVENIQKAAERLAELVPEARI 838
Query: 95 TVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI 142
+ HG M ++E + +M +F VL+ T + GID+ + +I
Sbjct: 839 AIG--HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTII 884
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 30.3 bits (68), Expect = 0.83
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 154 IHRIGRSGRFGRKGVAISFVKSDDIRILRDIEQYYSTQIDEMPMNGKRSLH 204
IH++ + G VA FVK ++ D E+Y T + M MN K LH
Sbjct: 378 IHKVMKPGDPVTTEVAKQFVK----KLFFDPERYDLTMVGRMKMNHKLGLH 424
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.0 bits (68), Expect = 0.92
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 100 HGDMPQKERDGIMKEFRSGTSRVLITT 126
H +P KE++ ++ SG +LITT
Sbjct: 162 HSALPTKEKEEALERIESGDFDILITT 188
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 29.9 bits (67), Expect = 1.3
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 85 LTEKMREANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVW 129
EK + + H ++ +KE++ ++ +G +L+TT +
Sbjct: 145 FCEKA-NLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQF 188
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 28.7 bits (65), Expect = 1.3
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 103 MPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQ--QVSLVI 142
+ R+ +++ F+ G +L + GID + LVI
Sbjct: 43 QGEGSREKLLERFKKGKGAILFGVGSFWEGIDFPGDALRLVI 84
>gnl|CDD|236420 PRK09229, PRK09229, N-formimino-L-glutamate deiminase; Validated.
Length = 456
Score = 29.0 bits (66), Expect = 2.0
Identities = 17/55 (30%), Positives = 21/55 (38%), Gaps = 22/55 (40%)
Query: 6 HACIGGTNLSEDLRKLDYGQHVVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEM 60
H I +L E+LR L+YGQ R R RN VL A +
Sbjct: 324 HVSI---DLVEELRLLEYGQ---------------RLRDRRRN----VLAAAAQP 356
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.7 bits (65), Expect = 2.3
Identities = 7/36 (19%), Positives = 17/36 (47%)
Query: 91 EANFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITT 126
+ H + +KE++ ++ + G +L+TT
Sbjct: 151 GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTT 186
>gnl|CDD|204660 pfam11479, Suppressor_P21, RNA silencing suppressor P21. P21 is
produced by Beet yellows virus to suppress the antiviral
silencing response mounted by the host. P21 acts by
binding directly to siRNA which is a mediator in the
process. P21 has an octameric ring structure with a
large central cavity.
Length = 177
Score = 28.2 bits (62), Expect = 2.3
Identities = 19/78 (24%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 32 PGRVFDMIR--RRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKM 89
P R+ +M++ R L+ R + + + A + LN + Y + + D L EKM
Sbjct: 75 PSRIGEMLKEIRAFLKVRVVTPMHKETASDTLNA-----FLEEYCRITGLAREDALREKM 129
Query: 90 REANFTVSSMHGDMPQKE 107
R+ V H ++ + E
Sbjct: 130 RKVKSVVLFHHSELLKFE 147
>gnl|CDD|184200 PRK13640, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 282
Score = 28.6 bits (64), Expect = 2.3
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 12/54 (22%)
Query: 50 KMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLTEKMREANFTVSSMHGDM 103
K+++LDE+ ML+ KEQI + R L ++ N TV S+ D+
Sbjct: 163 KIIILDESTSMLDPAGKEQILKLIRKL------------KKKNNLTVISITHDI 204
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 28.4 bits (64), Expect = 2.7
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 6/67 (8%)
Query: 101 GDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNREL--YIHRIG 158
GD + E ++ S + A G+D ++ +V N D + EL + +G
Sbjct: 51 GDPSKSE----ERKLLSREEVLENAKAQLACGLDPEKSEIVNNSDWLEHLELAWLLRDLG 106
Query: 159 RSGRFGR 165
R
Sbjct: 107 NHFSLNR 113
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 28.4 bits (64), Expect = 3.1
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 8/68 (11%)
Query: 141 VINYDLPNNRELYIHRIGRSGRFGRK-----GVAISFVKSDDIRILRDIEQYYSTQIDEM 195
V+NYD P R L R F RK GV FVK+ I I ++ IDE+
Sbjct: 217 VLNYDDPRTRSLAKKAKARVIFFSRKSLLEEGV---FVKNGKIVISLGGKEEEVIDIDEI 273
Query: 196 PMNGKRSL 203
+ G+ +L
Sbjct: 274 FIPGEHNL 281
>gnl|CDD|182700 PRK10752, PRK10752, sulfate transporter subunit; Provisional.
Length = 329
Score = 28.2 bits (63), Expect = 3.1
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 6/42 (14%)
Query: 112 MKEFRSGTSRVLITTDVWARGIDVQQVSLVINYDLPNNRELY 153
M ++ G + +L T V A+ I + VS YD P RELY
Sbjct: 1 MNKWGVGLTLLLAATSVMAKDIQLLNVS----YD-P-TRELY 36
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 26.1 bits (58), Expect = 3.8
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 3/40 (7%)
Query: 159 RSGRFGRKGVAI-SFVKSDDIRILRDIEQYYSTQIDEMPM 197
+ R R GVA +V+ DD L I++Y + ++D PM
Sbjct: 28 KRARLVRPGVAEVVYVRKDDA--LTAIDKYNNRELDGQPM 65
>gnl|CDD|241219 cd12775, RRM2_HuB, RNA recognition motif 2 in vertebrate Hu-antigen
B (HuB). This subgroup corresponds to the RRM2 of HuB,
also termed ELAV-like protein 2 (ELAV-2), or ELAV-like
neuronal protein 1, or nervous system-specific
RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal
members of the Hu family. The neuronal Hu proteins play
important roles in neuronal differentiation, plasticity
and memory. HuB is also expressed in gonads. It is
up-regulated during neuronal differentiation of
embryonic carcinoma P19 cells. Like other Hu proteins,
HuB contains three RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). RRM1 and RRM2 may cooperate
in binding to an AU-rich RNA element (ARE). RRM3 may
help to maintain the stability of the RNA-protein
complex, and might also bind to poly(A) tails or be
involved in protein-protein interactions. .
Length = 90
Score = 26.7 bits (58), Expect = 4.1
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 89 MREANFTVSSMHGDMPQKERDGIMKEF-RSGTSRVLI 124
+R+AN VS + M QKE + + ++ R TSR+L+
Sbjct: 3 IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 39
>gnl|CDD|222032 pfam13299, CPSF100_C, Cleavage and polyadenylation factor 2
C-terminal. This family lies at the C-terminus of many
fungal and plant cleavage and polyadenylation
specificity factor subunit 2 proteins. The exact
function of the domain is not known, but is likely to
function as a binding domain for the protein within the
overall CPSF complex.
Length = 152
Score = 26.8 bits (60), Expect = 5.6
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 18 LRKLDYGQHVVSGTPGRVFDMIRR 41
+RK G+ V+ GT + +R+
Sbjct: 123 VRKSATGRIVIEGTLSPSYYEVRK 146
>gnl|CDD|178324 PLN02723, PLN02723, 3-mercaptopyruvate sulfurtransferase.
Length = 320
Score = 27.5 bits (61), Expect = 6.0
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 78 PATQVDWLTEKMREANFTVSSMHGDMPQKERDGI 111
P VDWL +RE + V MP ++R+ I
Sbjct: 22 PVVSVDWLHANLREPDVKVLDASWYMPDEQRNPI 55
>gnl|CDD|241218 cd12774, RRM2_HuD, RNA recognition motif 2 in vertebrate Hu-antigen
D (HuD). This subgroup corresponds to the RRM2 of HuD,
also termed ELAV-like protein 4 (ELAV-4), or
paraneoplastic encephalomyelitis antigen HuD, one of the
neuronal members of the Hu family. The neuronal Hu
proteins play important roles in neuronal
differentiation, plasticity and memory. HuD has been
implicated in various aspects of neuronal function, such
as the commitment and differentiation of neuronal
precursors as well as synaptic remodeling in mature
neurons. HuD also functions as an important regulator of
mRNA expression in neurons by interacting with AU-rich
RNA element (ARE) and stabilizing multiple transcripts.
Moreover, HuD regulates the nuclear processing/stability
of N-myc pre-mRNA in neuroblastoma cells and also
regulates the neurite elongation and morphological
differentiation. HuD specifically binds poly(A) RNA.
Like other Hu proteins, HuD contains three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). RRM1 and
RRM2 may cooperate in binding to an ARE. RRM3 may help
to maintain the stability of the RNA-protein complex,
and might also bind to poly(A) tails or be involved in
protein-protein interactions. .
Length = 81
Score = 25.8 bits (56), Expect = 6.0
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 90 REANFTVSSMHGDMPQKERDGIMKEF-RSGTSRVLI 124
R+AN VS + M QKE + + ++ R TSR+L+
Sbjct: 1 RDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILV 36
>gnl|CDD|235619 PRK05826, PRK05826, pyruvate kinase; Provisional.
Length = 465
Score = 27.0 bits (61), Expect = 8.0
Identities = 7/18 (38%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 168 VAISFVKS-DDIRILRDI 184
+A+SFV+S +D+ R +
Sbjct: 190 IAVSFVRSAEDVEEARRL 207
>gnl|CDD|181534 PRK08671, PRK08671, methionine aminopeptidase; Provisional.
Length = 291
Score = 27.1 bits (61), Expect = 8.0
Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 22/89 (24%)
Query: 27 VVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVDWLT 86
VV G ++ ++R R +R L A ++L E+I + Y LP A + WL
Sbjct: 195 VVEGPEVEIYSLLRNRPVR--------LPAARKLL-----EEIEEEYNTLPFAER--WLE 239
Query: 87 EKMREANFTVSSMHGDMPQKERDGIMKEF 115
E ++ + + G + +
Sbjct: 240 GLFGE-------DKLELRRLLKAGALYGY 261
>gnl|CDD|239875 cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B
(NDPk7B): The nm23-H7 class of nucleoside diphosphate
kinase (NDPk7) consists of an N-terminal DM10 domain
and two functional catalytic NDPk modules, NDPk7A and
NDPk7B. The function of the DM10 domain, which also
occurs in multiple copies in other proteins, is
unknown. NDPk7 is predominantly expressed in testes,
although appreciable amount are also found in liver,
heart, brain, ovary, small intestine and spleen. The
nm23-H7 gene is located in or near the hereditary
prostrate cancer susceptibility locus. Nm23-H7 may be
involved in the development of colon and gastric
carcinoma, the latter possibly in a type-specific
manner.
Length = 134
Score = 26.1 bits (58), Expect = 8.3
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 7/48 (14%)
Query: 27 VVSGTPGRVFDMIRRRVLRTRNIKMLVLDEADEMLNKGFKEQIYDVYR 74
V G G + I ++M L A+ E+ +VY+
Sbjct: 12 VSHGLLGEILQQILDEGFEITALQMFNLTRAN-------AEEFLEVYK 52
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 27.1 bits (60), Expect = 9.2
Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 11/108 (10%)
Query: 87 EKMREA-NFTVSSMHGDMPQKERDGIMKEFRSGTSRVLITTDVWARGIDVQQVSLVI--- 142
EK+++A V+ H + + ER I FR G +V+ T + GI++ ++I
Sbjct: 288 EKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDT 347
Query: 143 ----NYDLPNNRELYIHR-IGRSGR--FGRKGVAISFVKSDDIRILRD 183
N+ + L I + +GR+GR + G AI +++ L +
Sbjct: 348 KRYSNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLME 395
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
0.322 0.138 0.409
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,121,978
Number of extensions: 1062638
Number of successful extensions: 1124
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1111
Number of HSP's successfully gapped: 108
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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 (21.9 bits)
S2: 57 (25.6 bits)