RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9620
(453 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 276 bits (708), Expect = 2e-87
Identities = 118/214 (55%), Positives = 152/214 (71%), Gaps = 3/214 (1%)
Query: 229 QPDRQVLMWSATWPREVQKLAEDFL-DSYIQINIGSLTLSANHNIQQVVEVCAEHEKENK 287
+PDRQ LMWSATWP+EVQ LA D + + +N+GSL L+A HNI+Q V V EHEK K
Sbjct: 306 RPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGK 365
Query: 288 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFR 347
L LL I +D +K +IF ETK+ D +TK ++ GW A+ IHGDK Q+ER +VL EF+
Sbjct: 366 LKMLLQRIM-RDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFK 424
Query: 348 NGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQ 407
G++ I++ATDVA+RGLDV DVK+VINFD+PN EDY+HRIGRTGR+ G SYTF T
Sbjct: 425 TGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPD 484
Query: 408 NSRQAKDLIDVLTESNHPVDPKLSALA-SRSGGS 440
R A+DL+ VL E+ PV P+L L+ RS G+
Sbjct: 485 KYRLARDLVKVLREAKQPVPPELEKLSNERSNGT 518
Score = 257 bits (657), Expect = 7e-80
Identities = 117/243 (48%), Positives = 145/243 (59%), Gaps = 14/243 (5%)
Query: 1 TYKSSS----SGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG--RFGDRGGRG 54
T SSS S G S + YG + + YGG G G GG G
Sbjct: 4 TDGSSSNGSVSSGPSNNYNSYGPYPDSSNPYGNYQANHQDNYGGFRPGYGNYSGGYGGFG 63
Query: 55 KNS----TMGGALRAIDWG--NLPPFEKNFFHPSPSVLNRSPHEVQAFRDKHQMT-LKG- 106
NS T+G L+ IDW NL PFEKNF+ P V S EV R + ++T + G
Sbjct: 64 MNSYGSSTLGKRLQPIDWKSINLVPFEKNFYKEHPEVSALSSKEVDEIRKEKEITIIAGE 123
Query: 107 NAPNPITEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLA 166
N P P+ F +FPDY+LK +K GF PTPIQ QGWPIA+SG +M+G+A+TGSGKTLA
Sbjct: 124 NVPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLA 183
Query: 167 YMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGASK 226
++LPAIVHIN Q L+ GDGPIVLVLAPTRELA+QI+E FG+S+ +R+T YGG K
Sbjct: 184 FLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPK 243
Query: 227 GPQ 229
Q
Sbjct: 244 RGQ 246
>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 = 208 bits (532), Expect = 8e-62
Identities = 79/207 (38%), Positives = 119/207 (57%), Gaps = 5/207 (2%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGS-LTLSANHNIQQVVEVC-AEHEKENK 287
PDRQ L++SAT P ++++LA +L+ ++I + I+Q +E EK
Sbjct: 204 PDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKLEL 263
Query: 288 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFR 347
L LL D DE + I+F TKR V+++ +S++ G+ +HGD Q+ERD L++F+
Sbjct: 264 LLKLLKDE---DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFK 320
Query: 348 NGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQ 407
+G +LVATDVAARGLD+ DV VIN+D P + EDY+HRIGRTGR+ G + +F T++
Sbjct: 321 DGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEE 380
Query: 408 NSRQAKDLIDVLTESNHPVDPKLSALA 434
+ I+ E P L
Sbjct: 381 EEVKKLKRIEKRLERKLPSAVLLPLDE 407
Score = 148 bits (374), Expect = 2e-39
Identities = 51/139 (36%), Positives = 70/139 (50%), Gaps = 4/139 (2%)
Query: 92 EVQAFRDKHQMTLKGNAPNPITEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGS 151
+ H + L EFA +L+ +K GF+ PTPIQ P+ ++G
Sbjct: 8 RFVKLKSAHNVALSRGEEKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGR 67
Query: 152 NMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGS 211
+++G AQTG+GKT A++LP + I + K L+LAPTRELA QI E R G
Sbjct: 68 DVLGQAQTGTGKTAAFLLPLLQKILKSVERK---YVSALILAPTRELAVQIAEELRKLGK 124
Query: 212 STY-LRSTCVYGGASKGPQ 229
+ LR VYGG S Q
Sbjct: 125 NLGGLRVAVVYGGVSIRKQ 143
>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 = 168 bits (429), Expect = 4e-50
Identities = 51/115 (44%), Positives = 70/115 (60%), Gaps = 3/115 (2%)
Query: 115 FAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVH 174
F E +L+ + GF++PTPIQA+ P +SG +++G AQTGSGKT A+++P +
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 175 INHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGASKGPQ 229
++ DGP L+LAPTRELA QI EVAR G T L+ +YGG S Q
Sbjct: 61 LDPS---PKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQ 112
Score = 53.3 bits (129), Expect = 3e-08
Identities = 15/31 (48%), Positives = 22/31 (70%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQIN 260
DRQ L++SAT P+EV+ LA FL + ++I
Sbjct: 173 KDRQTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 168 bits (428), Expect = 4e-47
Identities = 63/211 (29%), Positives = 114/211 (54%), Gaps = 9/211 (4%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 289
RQ L++SAT+P + +++ F +++ + S I+Q + E+ L
Sbjct: 177 ARRQTLLFSATYPEGIAAISQRFQRDPVEVKVEST--HDLPAIEQRFYEVSPDERLPALQ 234
Query: 290 GLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNG 349
LL + E+ ++F TK++ ++ ++ G++A+ +HGD Q++RD VL F N
Sbjct: 235 RLLLH--HQPES-CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANR 291
Query: 350 RAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQNS 409
+LVATDVAARGLD+ ++ VIN++ + E ++HRIGRTGR+ + G + + +
Sbjct: 292 SCSVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEM 351
Query: 410 RQAKDLIDVLTESNHPVDP-KLSALASRSGG 439
++A + D L ++ L +L+ SG
Sbjct: 352 QRANAIEDYL---GRKLNWEPLPSLSPLSGV 379
Score = 67.5 bits (166), Expect = 4e-12
Identities = 35/101 (34%), Positives = 53/101 (52%), Gaps = 16/101 (15%)
Query: 113 TEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAI 172
T F+ P +L + G+ TPIQAQ P ++G +++ A+TGSGKT A+ L +
Sbjct: 4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63
Query: 173 VHINH-----QSQLKPGDGPIVLVLAPTRELAQQI-QEVAR 207
++ Q+ LVL PTRELA Q+ +E+ R
Sbjct: 64 QKLDVKRFRVQA----------LVLCPTRELADQVAKEIRR 94
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 165 bits (419), Expect = 6e-45
Identities = 110/361 (30%), Positives = 177/361 (49%), Gaps = 74/361 (20%)
Query: 113 TEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAI 172
T FA+ +L+ + G+++P+PIQA+ P ++G +++G+AQTGSGKT A+ LP +
Sbjct: 6 TTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLL 65
Query: 173 VHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCV---YGGAS---- 225
+++ +LK P +LVLAPTRELA Q+ E DF S ++R V YGG
Sbjct: 66 HNLD--PELK---APQILVLAPTRELAVQVAEAMTDF--SKHMRGVNVVALYGGQRYDVQ 118
Query: 226 -----KGPQ-----PDR------------------------------------------- 232
+GPQ P R
Sbjct: 119 LRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIP 178
Query: 233 ---QVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 289
Q ++SAT P ++++ F+ ++ I S +++ +I Q K L
Sbjct: 179 EGHQTALFSATMPEAIRRITRRFMKEPQEVRIQS-SVTTRPDISQSYWTVWGMRKNEALV 237
Query: 290 GLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNG 349
L ++D + IIF TK ++ ++++ G+ + ++GD +Q R+ L+ ++G
Sbjct: 238 RFL---EAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDG 294
Query: 350 RAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQNS 409
R IL+ATDVAARGLDV+ + V+N+D P +SE Y+HRIGRTGR+ G + F +
Sbjct: 295 RLDILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVENRER 354
Query: 410 R 410
R
Sbjct: 355 R 355
Score = 31.4 bits (71), Expect = 1.1
Identities = 17/50 (34%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 9 GSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNST 58
G RG GG + G R GG G G G R R R +ST
Sbjct: 573 GGGRGFGGERREGGRNFSGERREGGRGDGRRFS--GERREGRAPRRDDST 620
>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 = 152 bits (385), Expect = 1e-44
Identities = 54/133 (40%), Positives = 78/133 (58%), Gaps = 2/133 (1%)
Query: 271 NIQQVVEVCAEHEKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGI 330
I+Q V E EK L LL + K K +IF +K+ +D++ + ++ G +
Sbjct: 1 PIKQYVLPV-EDEKLEALLELLKEHLKKGG-KVLIFCPSKKMLDELAELLRKPGIKVAAL 58
Query: 331 HGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGR 390
HGD SQ+ER+ VLK+FR G +LVATDV ARG+D+ +V VIN+D P + Y+ RIGR
Sbjct: 59 HGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGR 118
Query: 391 TGRSDNTGTSYTF 403
GR+ GT+
Sbjct: 119 AGRAGQKGTAILL 131
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 131 bits (332), Expect = 3e-34
Identities = 70/187 (37%), Positives = 105/187 (56%), Gaps = 5/187 (2%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 289
PD QV ++SAT P E+ +L F+ +I + L+ Q V V EKE F
Sbjct: 200 PDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAV----EKEEWKF 255
Query: 290 GLLNDI-SSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRN 348
L D+ + + II+ T+RKVD +TK + + +HGD Q++RD +++EFR+
Sbjct: 256 DTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRS 315
Query: 349 GRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQN 408
G +L+ TD+ ARG+DV V VIN+D P + E+YIHRIGR+GR G + F T +
Sbjct: 316 GSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDD 375
Query: 409 SRQAKDL 415
Q K++
Sbjct: 376 IEQLKEI 382
Score = 71.4 bits (175), Expect = 2e-13
Identities = 38/125 (30%), Positives = 63/125 (50%), Gaps = 5/125 (4%)
Query: 101 QMTLKGNAPNPITEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTG 160
T++ N + F + +L+ + GF++P+ IQ +G + G + +G AQ+G
Sbjct: 16 TGTIESNYDEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSG 75
Query: 161 SGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCV 220
+GKT +++ A+ I++ L+LAPTRELAQQIQ+V G +R
Sbjct: 76 TGKTATFVIAALQLIDYDLN-----ACQALILAPTRELAQQIQKVVLALGDYLKVRCHAC 130
Query: 221 YGGAS 225
GG
Sbjct: 131 VGGTV 135
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 127 bits (320), Expect = 3e-32
Identities = 61/184 (33%), Positives = 101/184 (54%), Gaps = 4/184 (2%)
Query: 228 PQPDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENK 287
+ +RQ L++SAT+ +V LA+ + + I + A+ ++Q V A +K
Sbjct: 267 RKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENV-ASDTVEQHVYAVAGSDKYKL 325
Query: 288 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFR 347
L+ L+ + ++FA K +V +I + + G A + GD Q +R L+ FR
Sbjct: 326 LYNLVTQ---NPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFR 382
Query: 348 NGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQ 407
G+ +LVATDVA RG+ +D + VINF P + +DY+HRIGRTGR+ +G S +F +
Sbjct: 383 EGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGED 442
Query: 408 NSRQ 411
++ Q
Sbjct: 443 DAFQ 446
Score = 63.8 bits (155), Expect = 6e-11
Identities = 38/114 (33%), Positives = 56/114 (49%), Gaps = 4/114 (3%)
Query: 113 TEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAI 172
T F + N ++ + GF TPIQAQ ++G + +G AQTG+GKT A+++ I
Sbjct: 87 TRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISII 146
Query: 173 VHINH---QSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGG 223
+ + G+ P L++APTREL QI + A T L GG
Sbjct: 147 NQLLQTPPPKERYMGE-PRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGG 199
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 125 bits (316), Expect = 2e-31
Identities = 75/217 (34%), Positives = 113/217 (52%), Gaps = 11/217 (5%)
Query: 228 PQPDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENK 287
QP QVL++SAT EV+K A I I+IG+ N ++Q+ +K+ K
Sbjct: 299 SQP--QVLLFSATVSPEVEKFASSLAKDIILISIGNPN-RPNKAVKQLAIWVETKQKKQK 355
Query: 288 LFGLLNDISSKDENK--TIIFAETKRKVDKITKSIQ-NYGWAAVGIHGDKSQQERDYVLK 344
LF +L SK K ++F ++ D + +I G A+ IHG+KS +ER V+K
Sbjct: 356 LFDIL---KSKQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMK 412
Query: 345 EFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFF 404
F G ++VAT V RG+D+ V+ VI FD PN ++YIH+IGR R GT+ F
Sbjct: 413 SFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFV 472
Query: 405 TQQNSRQAKDLIDVLTESNHPVDPKLSALASRSGGSG 441
+++ +L+ +L S + +L SR GSG
Sbjct: 473 NEEDRNLFPELVALLKSSGAAIPREL--ANSRYLGSG 507
Score = 108 bits (271), Expect = 2e-25
Identities = 48/141 (34%), Positives = 78/141 (55%), Gaps = 9/141 (6%)
Query: 89 SPHEVQAFRDKHQMTLKGNA-PNPITEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIA 147
S + + R K ++ +KG A P PI F+ P +L ++ G++ PTPIQ Q P A
Sbjct: 96 SSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAA 155
Query: 148 MSGSNMVGVAQTGSGKTLAYMLPAI-----VHINHQSQLKPGDGPIVLVLAPTRELAQQI 202
+SG +++ A TGSGKT ++++P I + H S+ + P+ +VL PTREL Q+
Sbjct: 156 LSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRN---PLAMVLTPTRELCVQV 212
Query: 203 QEVARDFGSSTYLRSTCVYGG 223
++ A+ G ++ V GG
Sbjct: 213 EDQAKVLGKGLPFKTALVVGG 233
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 123 bits (310), Expect = 8e-31
Identities = 59/169 (34%), Positives = 98/169 (57%), Gaps = 4/169 (2%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLF 289
RQ L++SAT+ +++ LAE L + ++I + +A+ + Q V + K L
Sbjct: 179 AKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRN-TASEQVTQHVHFVDKKRKRELLS 237
Query: 290 GLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNG 349
+ I + + ++F TK + + + + G + IHG+KSQ R L +F++G
Sbjct: 238 QM---IGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSG 294
Query: 350 RAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTG 398
+LVATD+AARGLD++++ V+N++ PN EDY+HRIGRTGR+ TG
Sbjct: 295 DIRVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATG 343
Score = 93.7 bits (233), Expect = 1e-20
Identities = 45/107 (42%), Positives = 62/107 (57%), Gaps = 1/107 (0%)
Query: 124 VLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKP 183
+L+ V QG+ PTPIQ Q P + G +++ AQTG+GKT + LP + H+ +
Sbjct: 12 ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAK 71
Query: 184 GDGPI-VLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGASKGPQ 229
G P+ L+L PTRELA QI E RD+ +RS V+GG S PQ
Sbjct: 72 GRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQ 118
Score = 28.6 bits (64), Expect = 8.5
Identities = 18/74 (24%), Positives = 22/74 (29%), Gaps = 12/74 (16%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRAIDWGNLPPFEKNFFH 80
GGGG G GGG G G R G+ G + ++ P E
Sbjct: 395 GGGG-------RGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGE----- 442
Query: 81 PSPSVLNRSPHEVQ 94
R P Q
Sbjct: 443 QQRRRRPRKPAAAQ 456
>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 = 115 bits (291), Expect = 1e-30
Identities = 42/93 (45%), Positives = 53/93 (56%), Gaps = 5/93 (5%)
Query: 137 TPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTR 196
TPIQAQ P +SG +++ A TGSGKTLA++LP + + L GP LVLAPTR
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQAL-----LPKKGGPQALVLAPTR 55
Query: 197 ELAQQIQEVARDFGSSTYLRSTCVYGGASKGPQ 229
ELA+QI E + LR + GG S Q
Sbjct: 56 ELAEQIYEELKKLFKILGLRVALLTGGTSLKEQ 88
Score = 31.5 bits (72), Expect = 0.46
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 229 QPDRQVLMWSATWPREVQKL 248
PDRQ+L+ SAT PR ++ L
Sbjct: 150 PPDRQILLLSATLPRNLEDL 169
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 121 bits (304), Expect = 1e-29
Identities = 71/202 (35%), Positives = 122/202 (60%), Gaps = 5/202 (2%)
Query: 232 RQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGL 291
RQ L++SAT V +LA + ++ ++ + + T++A ++Q + A+ EK+ L GL
Sbjct: 193 RQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAAR-VRQRIYFPADEEKQTLLLGL 251
Query: 292 LNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRA 351
L S + +T++F TK V+++ ++++ +G+ + GD Q++R+ +L F+ G+
Sbjct: 252 L---SRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQL 308
Query: 352 GILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQQNSRQ 411
ILVATDVAARGL +D VK+V N+D P ++EDY+HRIGRT R G + +F ++ +
Sbjct: 309 EILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYAMS 368
Query: 412 AKDLIDVLTESNHPVDPKLSAL 433
D I+ E PV+P + L
Sbjct: 369 LPD-IEAYIEQKIPVEPVTAEL 389
Score = 84.2 bits (208), Expect = 2e-17
Identities = 53/130 (40%), Positives = 76/130 (58%), Gaps = 8/130 (6%)
Query: 111 PITE--FAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYM 168
P+T+ F+ + +L ++ GF R TPIQA P+A+ G ++ G AQTG+GKTLA++
Sbjct: 5 PLTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL 64
Query: 169 LPAIVHINHQSQL---KPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGAS 225
+ + + + L KP D P L+LAPTRELA QI + A FG+ LR VYGG
Sbjct: 65 VAVMNRLLSRPALADRKPED-PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVD 123
Query: 226 KGPQPDRQVL 235
Q R++L
Sbjct: 124 YDKQ--RELL 131
Score = 33.4 bits (76), Expect = 0.26
Identities = 11/34 (32%), Positives = 12/34 (35%)
Query: 22 GGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGK 55
GGG G G GGG G D R +
Sbjct: 433 GGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPR 466
>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 = 107 bits (270), Expect = 9e-29
Identities = 39/76 (51%), Positives = 53/76 (69%)
Query: 318 KSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDY 377
K ++ G +HG SQ+ER+ +L++FRNG++ +LVATDVA RG+D+ DV VIN+D
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 378 PNNSEDYIHRIGRTGR 393
P N YI RIGR GR
Sbjct: 61 PWNPASYIQRIGRAGR 76
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 116 bits (294), Expect = 1e-28
Identities = 65/190 (34%), Positives = 100/190 (52%), Gaps = 31/190 (16%)
Query: 228 PQP-DRQVLMWSATWPREVQKLAEDFLDS--YIQINIGSLTLSANHNIQQVVEVCAEHE- 283
P R +++SAT V++LA + +++ Y+++ T H I++ E
Sbjct: 186 PPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKT---GHRIKE--------EL 234
Query: 284 ----KENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIH------GD 333
E K+ L I + ++ IIFA TK + ++I +G A H GD
Sbjct: 235 FYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEEI------WGHLAADGHRVGLLTGD 288
Query: 334 KSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGR 393
+Q++R +L+EF G ILVATDVAARGL + V V N+D P++ EDY+HRIGRTGR
Sbjct: 289 VAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGR 348
Query: 394 SDNTGTSYTF 403
+ +G S +
Sbjct: 349 AGASGHSISL 358
Score = 85.8 bits (213), Expect = 4e-18
Identities = 46/131 (35%), Positives = 70/131 (53%), Gaps = 11/131 (8%)
Query: 113 TEFAEANFPDY-----VLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAY 167
T E F D+ V++ ++++GF TPIQA P+ ++G ++ G AQTG+GKT+A+
Sbjct: 3 THLTEQKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAF 62
Query: 168 MLPAIVH---INHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGA 224
L A H + + + + P L++APTRELA QI A +T L+ YGG
Sbjct: 63 -LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGD 121
Query: 225 SKGPQPDRQVL 235
Q +VL
Sbjct: 122 GYDKQ--LKVL 130
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 116 bits (294), Expect = 1e-28
Identities = 57/169 (33%), Positives = 94/169 (55%), Gaps = 4/169 (2%)
Query: 232 RQVLMWSATWPRE-VQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFG 290
+Q L++SAT + VQ AE L+ +++ + I Q + E + L
Sbjct: 179 KQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP-SRRERKKIHQWYYRADDLEHKTAL-- 235
Query: 291 LLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGR 350
L + + + ++I+F T+ +V ++ ++ G + G+ Q +R+ +K +GR
Sbjct: 236 LCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGR 295
Query: 351 AGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGT 399
+LVATDVAARG+D+DDV VINFD P +++ Y+HRIGRTGR+ GT
Sbjct: 296 VNVLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGT 344
Score = 100 bits (252), Expect = 4e-23
Identities = 44/119 (36%), Positives = 72/119 (60%), Gaps = 1/119 (0%)
Query: 113 TEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAI 172
T F+E + +L+ ++ +G+ RPT IQA+ P A+ G +++G A TG+GKT A++LPA+
Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60
Query: 173 VHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGASKGPQPD 231
H+ + K G P +L+L PTRELA Q+ + AR+ T+L + GG + +
Sbjct: 61 QHLLDFPRRKSGP-PRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAE 118
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 104 bits (261), Expect = 2e-27
Identities = 35/80 (43%), Positives = 51/80 (63%)
Query: 314 DKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVI 373
+++ + ++ G +HG SQ+ER+ +L +F NG+ +LVATDVA RGLD+ V VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 374 NFDYPNNSEDYIHRIGRTGR 393
+D P + YI RIGR GR
Sbjct: 61 IYDLPWSPASYIQRIGRAGR 80
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 104 bits (261), Expect = 4e-26
Identities = 43/106 (40%), Positives = 59/106 (55%), Gaps = 7/106 (6%)
Query: 128 VKRQGFDRPTPIQAQGWPIAMSG-SNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDG 186
+++ GF+ P Q + +SG +++ A TGSGKTLA +LPA+ LK G G
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEA------LKRGKG 54
Query: 187 PIVLVLAPTRELAQQIQEVARDFGSSTYLRSTCVYGGASKGPQPDR 232
VLVL PTRELA+Q E + G S L+ +YGG SK Q +
Sbjct: 55 GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRK 100
Score = 39.4 bits (92), Expect = 0.002
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 230 PDRQVLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQV 275
+ Q+L+ SAT P E++ L E FL+ + I++G I+Q
Sbjct: 159 KNVQLLLLSATPPEEIENLLELFLNDPVFIDVGFTP---LEPIEQF 201
Score = 34.4 bits (79), Expect = 0.075
Identities = 24/115 (20%), Positives = 47/115 (40%), Gaps = 21/115 (18%)
Query: 291 LLNDISSKDENKTIIFAETK----RKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEF 346
L + + ++ T+ + +++ K + G VG++G S++E+ L++
Sbjct: 45 ALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQ---LRKL 101
Query: 347 RNGRAGILVAT------DVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSD 395
+G+ ILV T + L + +V VI D HR+ G D
Sbjct: 102 ESGKTDILVTTPGRLLDLLENDKLSLSNVDLVI-L-------DEAHRLLDGGFGD 148
>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 = 77.0 bits (190), Expect = 6e-17
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 151 SNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFG 210
+++ A TGSGKTLA +LP + L G VLVLAPTRELA Q+ E ++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPIL------ELLDSLKGGQVLVLAPTRELANQVAERLKELF 54
Query: 211 SSTYLRSTCVYGGASKGPQ 229
++ + GG S Q
Sbjct: 55 -GEGIKVGYLIGGTSIKQQ 72
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 79.6 bits (197), Expect = 7e-16
Identities = 48/191 (25%), Positives = 87/191 (45%), Gaps = 14/191 (7%)
Query: 232 RQVLMW-SATWPREVQK--LAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKL 288
++ +AT V+ + L GS +VVE E ++L
Sbjct: 166 NPPVLALTATATPRVRDDIREQLGLQDANIF-RGSFDRPNLAL--KVVEK---GEPSDQL 219
Query: 289 FGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRN 348
L + ++ II+ T++KV+++ + ++ G +A H S +ER+ V + F N
Sbjct: 220 AFLATVLPQLSKS-GIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLN 278
Query: 349 GRAGILVATDVAARGLDVD--DVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYTFFTQ 406
++VAT A G+ +D DV+FVI++D P + E Y GR GR + ++
Sbjct: 279 DEIKVMVAT--NAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSP 336
Query: 407 QNSRQAKDLID 417
++ R + LI+
Sbjct: 337 EDIRWQRYLIE 347
Score = 35.0 bits (81), Expect = 0.096
Identities = 30/97 (30%), Positives = 46/97 (47%), Gaps = 16/97 (16%)
Query: 124 VLKEV-KRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLK 182
VLK+V F RP Q + +SG + + V TG GK+L Y +PA+ L
Sbjct: 8 VLKQVFGYASF-RPG--QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL--------LL 56
Query: 183 PGDGPIVLVLAPTRELAQ-QIQEVARDFGSSTYLRST 218
G + LV++P L + Q+ ++ + YL ST
Sbjct: 57 EG---LTLVVSPLISLMKDQVDQLEAAGIRAAYLNST 90
>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 = 77.0 bits (190), Expect = 5e-15
Identities = 39/147 (26%), Positives = 71/147 (48%), Gaps = 3/147 (2%)
Query: 283 EKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYV 342
+K NK LL+ + II+A +++KV+++ + +++ G +A+ H S + R
Sbjct: 207 KKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAEN 266
Query: 343 LKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSDNTGTSYT 402
++F ++VAT+ G+D +V+FVI++D P N E Y GR GR +
Sbjct: 267 QEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPAEAIL 326
Query: 403 FFTQQNSRQAKDLIDVLTESNHPVDPK 429
++ + K I +S D K
Sbjct: 327 LYSPADIALLKRRI---EQSEADDDYK 350
Score = 28.5 bits (64), Expect = 9.5
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 12/72 (16%)
Query: 148 MSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVAR 207
+ G +++ V TG GK+L Y +PA+ L G + +V++P L + + R
Sbjct: 26 LDGRDVLVVMPTGGGKSLCYQVPAL--------LLKG---LTVVISPLISLMKDQVDQLR 74
Query: 208 DFG-SSTYLRST 218
G ++ YL ST
Sbjct: 75 AAGVAAAYLNST 86
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 76.2 bits (188), Expect = 9e-15
Identities = 48/159 (30%), Positives = 74/159 (46%), Gaps = 17/159 (10%)
Query: 268 ANHNIQQVVEVCAEHEKENKLFGLLNDISSK-DENKTIIFAETKRKVDKITKSIQN---- 322
A + + E EH K KL +L + K +++ I+F E + ++I ++
Sbjct: 333 ALRLLIRADESGVEHPKLEKLREILKEQLEKNGDSRVIVFTEYRDTAEEIVNFLKKIGIK 392
Query: 323 -----YGWAAVGIHGDK--SQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINF 375
G A+ GDK SQ+E+ ++ +FR G +LVAT V GLD+ +V VI +
Sbjct: 393 ARVRFIGQASRE--GDKGMSQKEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVIFY 450
Query: 376 DYPNNSE-DYIHRIGRTGRSDNTGTSYTFFTQQNSRQAK 413
+ P SE I R GRTGR G T+ +A
Sbjct: 451 E-PVPSEIRSIQRKGRTGRKRK-GRVVVLVTEGTRDEAY 487
>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 = 71.7 bits (176), Expect = 2e-13
Identities = 73/325 (22%), Positives = 123/325 (37%), Gaps = 84/325 (25%)
Query: 138 PIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRE 197
P+Q + + G + V TG GK+L Y LPA+ I LV++P
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALC-----------SDGITLVISPLIS 62
Query: 198 LAQ-QIQEVARDFGSSTYLRST-------CVYGGASKGPQ-------PDRQVLMWSATWP 242
L + Q+ ++ +T+L S+ V K + P++ S
Sbjct: 63 LMEDQVLQLKASGIPATFLNSSQSKEQQKNVLTDL-KDGKIKLLYVTPEK--CSASN--- 116
Query: 243 REVQKLAE--------------------DFLDSYIQIN----------IGSLTLSANHNI 272
R +Q L E DF Y + I +LT +A+ ++
Sbjct: 117 RLLQTLEERKGITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTATASPSV 176
Query: 273 QQVVEVC---------------------AEHEKENKLFGLLNDISSKDENKT-IIFAETK 310
++ + + L LL I + + K+ II+ ++
Sbjct: 177 REDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSR 236
Query: 311 RKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVK 370
+K +++T S+QN G AA H RD V +F+ ++VAT G++ DV+
Sbjct: 237 KKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMGINKPDVR 296
Query: 371 FVINFDYPNNSEDYIHRIGRTGRSD 395
FVI++ P + E Y GR GR
Sbjct: 297 FVIHYSLPKSMESYYQESGRAGRDG 321
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 68.4 bits (168), Expect = 3e-12
Identities = 45/124 (36%), Positives = 64/124 (51%), Gaps = 11/124 (8%)
Query: 281 EHEKENKLFGLLNDI-SSKDENKTIIFAETKRKVDKITKSIQNYGWAA---VG---IHGD 333
EH K KL ++ + +++ I+F + + +KI ++ G A VG GD
Sbjct: 345 EHPKLEKLREIVKEQLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGD 404
Query: 334 K--SQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSE-DYIHRIGR 390
K SQ+E+ +L +FR G +LV+T VA GLD+ V VI F P SE I R GR
Sbjct: 405 KGMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-FYEPVPSEIRSIQRKGR 463
Query: 391 TGRS 394
TGR
Sbjct: 464 TGRQ 467
Score = 34.8 bits (81), Expect = 0.095
Identities = 19/55 (34%), Positives = 27/55 (49%), Gaps = 8/55 (14%)
Query: 147 AMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQ 201
A+ + +V V TG GKT +L +L G VL+LAPT+ L +Q
Sbjct: 27 ALKKNTLV-VLPTGLGKTAIALLVIA------ERLHKKGGK-VLILAPTKPLVEQ 73
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 63.8 bits (156), Expect = 9e-11
Identities = 27/80 (33%), Positives = 40/80 (50%)
Query: 125 LKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPG 184
++E ++ F TP Q P SG N++ +A TGSGKT A LP I + + K
Sbjct: 12 VREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLE 71
Query: 185 DGPIVLVLAPTRELAQQIQE 204
DG L ++P + L I+
Sbjct: 72 DGIYALYISPLKALNNDIRR 91
Score = 41.1 bits (97), Expect = 0.001
Identities = 26/97 (26%), Positives = 46/97 (47%), Gaps = 1/97 (1%)
Query: 298 KDENKTIIFAETKRKVDKITKSIQNYGWAAVGIH-GDKSQQERDYVLKEFRNGRAGILVA 356
K T+IF T+ +++ ++ G + +H G S++ R V + + G +VA
Sbjct: 251 KKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVA 310
Query: 357 TDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGR 393
T G+D+ D+ VI P + ++ RIGR G
Sbjct: 311 TSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>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 = 61.3 bits (149), Expect = 5e-10
Identities = 32/129 (24%), Positives = 48/129 (37%), Gaps = 9/129 (6%)
Query: 100 HQMTLKGNAPNPITEFAEANFPDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQT 159
++ +EF E VK G +R Q + G N+V T
Sbjct: 37 RDPEIEARPGKT-SEFPELRDESLKSALVKA-GIERLYSHQVDALRLIREGRNVVVTTGT 94
Query: 160 GSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLRSTC 219
GSGKT +++LP + H+ + L+L PT LA E R+ S + T
Sbjct: 95 GSGKTESFLLPILDHLLRDPSAR------ALLLYPTNALANDQAERLRELISDLPGKVTF 148
Query: 220 -VYGGASKG 227
Y G +
Sbjct: 149 GRYTGDTPP 157
Score = 42.8 bits (101), Expect = 4e-04
Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 302 KTIIFAETKRKVDKITKSIQN--------YGWAAVGIHGDKSQQERDYVLKEFRNGRAGI 353
+T++F ++++V+ + S + A ++ER + EF+ G
Sbjct: 308 QTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLG 367
Query: 354 LVATDVAARGLDVDDVKFVINFDYPNNSE-DYIHRIGRTGRSDNTG 398
++AT+ G+D+ + VI + YP S + R GR GR
Sbjct: 368 VIATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQES 413
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 59.3 bits (144), Expect = 2e-09
Identities = 29/90 (32%), Positives = 45/90 (50%)
Query: 304 IIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARG 363
II+ ++ KV+ +Q+ G +A H R V + F+ I+VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 364 LDVDDVKFVINFDYPNNSEDYIHRIGRTGR 393
++ +V+FV++FD P N E Y GR GR
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGR 329
Score = 28.9 bits (65), Expect = 6.2
Identities = 41/163 (25%), Positives = 70/163 (42%), Gaps = 31/163 (19%)
Query: 121 PDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQ 180
VL+E G+ + P Q + +SG + + V TG GK+L Y +PA+V
Sbjct: 13 AKQVLQETF--GYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALV------- 63
Query: 181 LKPGDGPIVLVLAPTRELAQ-QIQEVARDFGSSTYLRST-------CVYGGASKGPQPDR 232
G + LV++P L + Q+ ++ + ++ L ST V G G
Sbjct: 64 -LDG---LTLVVSPLISLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTG----- 114
Query: 233 QV-LMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQ 274
Q+ L++ A P + + ++FL+ N L + H I Q
Sbjct: 115 QIKLLYIA--PERL--MMDNFLEHLAHWNPALLAVDEAHCISQ 153
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 56.7 bits (137), Expect = 1e-08
Identities = 37/153 (24%), Positives = 64/153 (41%), Gaps = 5/153 (3%)
Query: 243 REVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENK 302
+ ++ + ++ TL A + +++ A K + GLL + D K
Sbjct: 230 EDEEREYAKESARFRELLRARGTLRAENEARRIAI--ASERKIAAVRGLLLKHARGD--K 285
Query: 303 TIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAAR 362
T+IFA +I K G I G+ ++ER+ +L+ FR G +LV V
Sbjct: 286 TLIFASDVEHAYEIAKLFLAPGIVEA-ITGETPKEEREAILERFRTGGIKVLVTVKVLDE 344
Query: 363 GLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSD 395
G+D+ D +I + +I R+GR R
Sbjct: 345 GVDIPDADVLIILRPTGSRRLFIQRLGRGLRPA 377
Score = 39.3 bits (92), Expect = 0.004
Identities = 23/79 (29%), Positives = 31/79 (39%), Gaps = 13/79 (16%)
Query: 156 VAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYL 215
V TG+GKT+ AI + LVL PT+EL Q E + F
Sbjct: 61 VLPTGAGKTVVAAE-AIAEL----------KRSTLVLVPTKELLDQWAEALKKFLLLNDE 109
Query: 216 RSTCVYGGASKGPQPDRQV 234
+YGG K +P +
Sbjct: 110 IG--IYGGGEKELEPAKVT 126
>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 = 54.4 bits (131), Expect = 8e-08
Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 121 PDYVLKEVKRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQ 180
PD V+ ++ G RP QA+ +A +G ++V T SGK+LAY LP + S
Sbjct: 23 PD-VVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVL------SA 75
Query: 181 LKPGDGPIVLVLAPTRELAQ 200
L L LAPT+ LA
Sbjct: 76 LADDPRATALYLAPTKALAA 95
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 50.1 bits (120), Expect = 1e-06
Identities = 26/55 (47%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 8 GGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
G G R G GGG GG GG GGG GGG G GR G GGRG G
Sbjct: 2 MGGGFGGGR-GGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55
Score = 44.7 bits (106), Expect = 5e-05
Identities = 25/49 (51%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 8 GGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKN 56
G RG G GGGG GG R GG G G GGG GG G GG GK
Sbjct: 10 RGGGRGGGGGGGRGGGGRGGG-RGGGRGRGRGGGGGGRGGGGGGGPGKV 57
Score = 40.5 bits (95), Expect = 0.001
Identities = 22/48 (45%), Positives = 22/48 (45%), Gaps = 2/48 (4%)
Query: 7 SGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
G RG R G GGG GG G GG G GGG G RGG G
Sbjct: 5 GFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG--GGRGGGG 50
Score = 38.6 bits (90), Expect = 0.005
Identities = 21/42 (50%), Positives = 22/42 (52%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
G GG G R GG GGG GGG GGG G G G+ GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGG 42
Score = 36.6 bits (85), Expect = 0.020
Identities = 18/45 (40%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 22 GGGYGGSSRSGGYGGGYGGGS-----GGGRFGDRGGRGKNSTMGG 61
G G G GG GG GGG GG G GRG+ GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGG 45
Score = 30.5 bits (69), Expect = 1.9
Identities = 16/39 (41%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 26 GGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALR 64
G GG GGG GG GGG G G G G R
Sbjct: 2 MGGGFGGGRGGG-RGGGGGGGRGGGGRGGGRGGGRGRGR 39
Score = 28.2 bits (63), Expect = 8.3
Identities = 16/36 (44%), Positives = 16/36 (44%)
Query: 6 SSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGG 41
GG RG R G G G GG GG GGG G
Sbjct: 21 GRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 49.5 bits (118), Expect = 3e-06
Identities = 27/90 (30%), Positives = 45/90 (50%)
Query: 304 IIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARG 363
II+ ++ +K+ + +Q +G A HG +R +V K++ I+ AT G
Sbjct: 684 IIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMG 743
Query: 364 LDVDDVKFVINFDYPNNSEDYIHRIGRTGR 393
++ DV+FVI+ P + E Y GR GR
Sbjct: 744 INKPDVRFVIHHSLPKSIEGYHQECGRAGR 773
Score = 34.5 bits (79), Expect = 0.14
Identities = 23/69 (33%), Positives = 34/69 (49%), Gaps = 12/69 (17%)
Query: 148 MSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQ-QIQEVA 206
MSG ++ + TG GK+L Y LPA++ PG I LV++P L Q QI +
Sbjct: 473 MSGYDVFVLMPTGGGKSLTYQLPALI--------CPG---ITLVISPLVSLIQDQIMNLL 521
Query: 207 RDFGSSTYL 215
+ + L
Sbjct: 522 QANIPAASL 530
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 47.4 bits (113), Expect = 1e-05
Identities = 30/92 (32%), Positives = 41/92 (44%), Gaps = 12/92 (13%)
Query: 121 PDYVLKEVKRQGFD--RPTPIQAQGWPIAMSGSNMVGVAQTGSGKTL-AYMLPAIVHINH 177
D VL+ +K G D P Q +S N++ A TGSGKTL A + AI
Sbjct: 17 DDRVLEILKGDGIDELFN-PQQEAVEKGLLSDENVLISAPTGSGKTLIALL--AI----- 68
Query: 178 QSQLKPGDGPIVLVLAPTRELAQQIQEVARDF 209
S L G G +V + P + LA++ E
Sbjct: 69 LSTLLEGGGKVVYI-VPLKALAEEKYEEFSRL 99
Score = 35.4 bits (82), Expect = 0.064
Identities = 21/79 (26%), Positives = 29/79 (36%), Gaps = 16/79 (20%)
Query: 328 VGIH-GDKSQQERDYVLKEFRNGRAGILVATD------------VAARGLDVDDVKFVIN 374
V H +++R V FR G+ +LV+T V + D K I
Sbjct: 317 VAFHHAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGI- 375
Query: 375 FDYPNNSEDYIHRIGRTGR 393
D P D + GR GR
Sbjct: 376 VDIPVL--DVLQMAGRAGR 392
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 47.5 bits (114), Expect = 1e-05
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 3/75 (4%)
Query: 129 KRQGFDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPI 188
+G+ P P Q + W A+ G + + +A TGSGKTLA LP+++ + KP G
Sbjct: 8 AARGW-TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDL--AGPEKPKKGLH 64
Query: 189 VLVLAPTRELAQQIQ 203
L + P R LA I
Sbjct: 65 TLYITPLRALAVDIA 79
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 46.8 bits (111), Expect = 2e-05
Identities = 28/111 (25%), Positives = 42/111 (37%), Gaps = 14/111 (12%)
Query: 331 HGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYI----- 385
H S ++R ++ + FRN ++VAT A G+++ + VI D I
Sbjct: 292 HAGLSNEQRRFIEEMFRNRYIKVIVATPTLAAGVNL-PARLVIVRDITRYGNGGIRYLSN 350
Query: 386 ----HRIGRTGRS--DNTGTSYTFFTQQNSRQAKDLIDVLTESNHPVDPKL 430
IGR GR D G Y + S A L+ PV +
Sbjct: 351 MEIKQMIGRAGRPGYDQYGIGYIYAASPASYDAAK--KYLSGEPEPVISYM 399
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 44.8 bits (106), Expect = 2e-05
Identities = 28/62 (45%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 6 SSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRA 65
GG G G GGGGYGG SRSGG GG GG GGG G G ++ GG
Sbjct: 118 GGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGG--GASRPSAPAGGGFDE 175
Query: 66 ID 67
+D
Sbjct: 176 MD 177
Score = 39.4 bits (92), Expect = 0.001
Identities = 22/45 (48%), Positives = 22/45 (48%)
Query: 18 GTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
G G GG GG GGYGGG GGG GG R G G GG
Sbjct: 110 GRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGG 154
Score = 38.2 bits (89), Expect = 0.003
Identities = 26/56 (46%), Positives = 26/56 (46%), Gaps = 3/56 (5%)
Query: 9 GSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALR 64
G S G G GG G GG GGYGG G GGGR GG G GGA R
Sbjct: 112 GGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAG---GGASR 164
Score = 34.4 bits (79), Expect = 0.054
Identities = 22/40 (55%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 23 GGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
GG GGS GG GGG GG GGG G GG G S GG
Sbjct: 109 GGRGGS--GGGGGGGDEGGYGGGGGGGGGGYGGESRSGGG 146
Score = 33.6 bits (77), Expect = 0.12
Identities = 24/62 (38%), Positives = 25/62 (40%), Gaps = 11/62 (17%)
Query: 13 GTSRYGTS---------GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGAL 63
G RY T GG G G GG GGYGGG GGG G G S GG
Sbjct: 92 GQDRYSTEIVADQMQMLGGRGGSGGGGGGGDEGGYGGGGGGG--GGGYGGESRSGGGGGR 149
Query: 64 RA 65
+
Sbjct: 150 AS 151
Score = 30.1 bits (68), Expect = 1.4
Identities = 17/39 (43%), Positives = 18/39 (46%), Gaps = 3/39 (7%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGS 42
GG G SGGGG SGG GGG GGG+
Sbjct: 127 GGGGGGGGGGYGGESRSGGGGGR---ASGGGGGGAGGGA 162
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 41.9 bits (99), Expect = 6e-04
Identities = 37/124 (29%), Positives = 58/124 (46%), Gaps = 31/124 (25%)
Query: 315 KITKSIQNYGWAAVG-IHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVI 373
++ K+ Y VG +HG E++ V++EFR G ILVAT V G+DV
Sbjct: 475 RLKKAFPKY---NVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDV------- 524
Query: 374 NFDYPN-------NSEDY----IHRI-GRTGRSDNTGTSYTFFTQQN--SRQAKDLIDVL 419
PN ++E + +H++ GR GR D+ SY +N S AK + V+
Sbjct: 525 ----PNATVMVIEDAERFGLSQLHQLRGRVGRGDH--QSYCLLVYKNPKSESAKKRLRVM 578
Query: 420 TESN 423
++
Sbjct: 579 ADTL 582
Score = 30.4 bits (69), Expect = 2.5
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 14/53 (26%)
Query: 160 GSGKTL---AYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDF 209
GSGKTL ML AI G V ++APT LA+Q R+
Sbjct: 266 GSGKTLVAALAMLAAIEA-----------GYQVALMAPTEILAEQHYNSLRNL 307
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 41.1 bits (96), Expect = 7e-04
Identities = 27/58 (46%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 5 SSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGS-GGGRFGDRGGRGKNSTMGG 61
+ GGS G G +GGG GG S G GG GGGS GGG G G GK+ T G
Sbjct: 89 TGEGGSDTG----GDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEG--GSTGKSLTKEG 140
Score = 39.5 bits (92), Expect = 0.002
Identities = 18/55 (32%), Positives = 24/55 (43%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNST 58
+ G + G + G +GGG GG + G GG GGGS GG G +
Sbjct: 89 TGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGA 143
Score = 36.8 bits (85), Expect = 0.016
Identities = 25/61 (40%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 3 KSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
K GG+ G G+ GG GG + GG GGG GGSGGG G GG + + G +
Sbjct: 82 KDGDGGGTGEG----GSDTGGDTGGGNTGGGSGGGDTGGSGGG--GSDGGGSEGGSTGKS 135
Query: 63 L 63
L
Sbjct: 136 L 136
Score = 35.7 bits (82), Expect = 0.036
Identities = 21/56 (37%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 9 GSSRGTSRYGTSGGGGYGGSSRSGG--YGGGYGGGSGGGRFGDRGGRGKNSTMGGA 62
GS+ G +G GG +GG GGG GGG GG G G G S G
Sbjct: 78 GSADKDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGG-GSDGGGSEGGST 132
Score = 33.7 bits (77), Expect = 0.16
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGG 41
S GG + G+ G+ GGG GGS+ G G G
Sbjct: 105 TGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEGVGAG 144
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 41.4 bits (98), Expect = 0.001
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 311 RKVDKITKSIQN-YGWAAVG-IHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDV 366
+ +++ + +++ VG +HG E+D V++ F+ G ILVAT V G+DV
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 37.4 bits (87), Expect = 0.001
Identities = 22/42 (52%), Positives = 22/42 (52%)
Query: 7 SGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFG 48
GG G G GGG YGG GG GGGY GG GGG G
Sbjct: 48 GGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGG 89
Score = 35.9 bits (83), Expect = 0.006
Identities = 25/43 (58%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 12 RGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
G YG GGGGYGG GG GGGYGGG GG G GG G
Sbjct: 47 GGGGGYGGGGGGGYGGGGYYGG-GGGYGGGGGGYPGGGGGGYG 88
Score = 34.3 bits (79), Expect = 0.017
Identities = 22/41 (53%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGG 61
GGGGYGG GG GG GGG GG G GG G GG
Sbjct: 48 GGGGYGG----GGGGGYGGGGYYGGGGGYGGGGGGYPGGGG 84
Score = 34.0 bits (78), Expect = 0.021
Identities = 18/41 (43%), Positives = 18/41 (43%)
Query: 12 RGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGG 52
G G GGGG G GGG GG GGG G GG
Sbjct: 45 YGGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGG 85
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 39.9 bits (93), Expect = 0.002
Identities = 18/37 (48%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 10 SSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGR 46
S+ +SR +S GGG G S GGG GGG GG R
Sbjct: 565 SAIASSRRSSSSGGGGGFS------GGGSGGGGGGAR 595
Score = 35.3 bits (81), Expect = 0.067
Identities = 17/40 (42%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 15 SRYGTSGGGGYGG--SSRSGGYGGGYGGGSGGGRFGDRGG 52
SR + Y SSR GG GG SGGG G GG
Sbjct: 554 SRSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGGGGGG 593
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 39.6 bits (92), Expect = 0.003
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 15 SRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGR 46
+ G YGG R+ G G G GGG G G
Sbjct: 507 GEGISKVGQSYGGRGRTRGRGRGGGGGRGRGY 538
Score = 35.8 bits (82), Expect = 0.041
Identities = 15/36 (41%), Positives = 16/36 (44%)
Query: 10 SSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG 45
S G S+ G S GG R G GGG G G G
Sbjct: 506 SGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541
Score = 31.2 bits (70), Expect = 1.2
Identities = 14/40 (35%), Positives = 16/40 (40%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGG 41
Y + S G S+ YG G G GG G GY G
Sbjct: 502 YVNKSGEGISKVGQSYGGRGRTRGRGRGGGGGRGRGYNRG 541
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 39.8 bits (93), Expect = 0.003
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 7/46 (15%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQI 202
A TG+GKTLAY+LPA+ + +G V++ T+ L +Q+
Sbjct: 41 APTGTGKTLAYLLPALAYARE-------EGKKVIISTRTKALQEQL 79
Score = 33.2 bits (76), Expect = 0.29
Identities = 16/84 (19%), Positives = 32/84 (38%), Gaps = 5/84 (5%)
Query: 287 KLFGLLNDISSKDENKTIIFAETKRKVDKITKSI-QNYGWAAVGIHGDKSQQERDYVLKE 345
KL L +I ++ + + ++ + + V G+ ER+ +L++
Sbjct: 466 KLAAYLREILKASPGGVLVLFPSYEYLKRVAERLKDERSTLPVLTQGE---DEREELLEK 522
Query: 346 FRN-GRAGILVATDVAARGLDVDD 368
F+ G ILV G+D
Sbjct: 523 FKASGEGLILVGGGSFWEGVDFPG 546
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 38.8 bits (91), Expect = 0.003
Identities = 18/50 (36%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYG-----GGYGGGSGGGRFG 48
S S +S +S GGG S GG+G +G G GGG FG
Sbjct: 11 GSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGGLFG 60
Score = 38.1 bits (89), Expect = 0.007
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 8 GGSSRG-TSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
GGS R + + GG G GGG+G FG GG G
Sbjct: 10 GGSFRAPSRSSSSPRSSSPGGGGYYGSPGGGFGFPFLIPFFGFGGGGG 57
>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 = 39.0 bits (91), Expect = 0.004
Identities = 41/172 (23%), Positives = 66/172 (38%), Gaps = 27/172 (15%)
Query: 234 VLMWSATWPREVQKLAEDFLDSYIQ-----INIGSLTLSANHNIQQVVEVCAEHEKENKL 288
+LM SAT P FL Y + L L N + + + + L
Sbjct: 158 LLM-SATLP--------KFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSL 208
Query: 289 FGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAA--VGIHG-----DKSQQERDY 341
LL K I T + + + ++ G + IH D++++E +
Sbjct: 209 ERLLE--FIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAE- 265
Query: 342 VLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGR 393
+L EF+ ++VAT V LD+ V +I P +S I R+GR R
Sbjct: 266 LLLEFKKSEKFVIVATQVIEASLDI-SVDVMITELAPIDS--LIQRLGRLHR 314
>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 = 39.0 bits (91), Expect = 0.005
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 337 QERDYVLKEFRNGRAGILVATDVAARGLDVDDVK-FVINFDYPNNSEDYIHRI-GRTGRS 394
Q R ++ FR+G+ +L+ T + RG+ +V FV+ ++ +E + +I GR GRS
Sbjct: 342 QHRKEKVEAFRDGKITLLITTTILERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGRS 401
Query: 395 DN--TGTSYTF 403
TG F
Sbjct: 402 LERPTGDVLFF 412
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 38.9 bits (90), Expect = 0.005
Identities = 25/111 (22%), Positives = 45/111 (40%), Gaps = 10/111 (9%)
Query: 291 LLND--ISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRN 348
LL D + +K +IF++ +D + ++ G V + G + R ++ F
Sbjct: 700 LLLDKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNA 759
Query: 349 GRA--GILVATDVAARGLDVDDVKFVINFD-YPNNS-----EDYIHRIGRT 391
L++ GL++ VI FD + N + D HRIG+
Sbjct: 760 DEEEKVFLLSLKAGGLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQK 810
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 39.0 bits (92), Expect = 0.005
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 323 YGWAAVG-IHGDKSQQERDYVLKEFRNGRAGILVATDV 359
+ VG +HG E+D V+ F+ G ILVAT V
Sbjct: 503 FPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTV 540
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 38.6 bits (90), Expect = 0.007
Identities = 36/177 (20%), Positives = 64/177 (36%), Gaps = 33/177 (18%)
Query: 234 VLMWSATWPREVQKLAEDFLDSYIQIN-IGSLTLSANHNI---QQVVEVCAEHEKENKLF 289
+LM SAT P + ++ L + + + E +
Sbjct: 374 LLM-SATLPPFL----KEKLKKALGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEE 428
Query: 290 GLLNDISSKDENK--TIIFAETKRKVDKITKSIQNYGWAAVGIHG-----DKSQQERDYV 342
+ E K +I T + ++ + ++ G + +H D+ ++ER+ +
Sbjct: 429 LIELISEEVKEGKKVLVIV-NTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERE-L 486
Query: 343 LKEFRNGRAGILVATDVAARGLDVDDVKFVINFDY------PNNSEDYIHRIGRTGR 393
K F+ I+VAT V G+D+D FD P +S I R GR R
Sbjct: 487 KKLFKQNEGFIVVATQVIEAGVDID-------FDVLITELAPIDS--LIQRAGRVNR 534
Score = 37.4 bits (87), Expect = 0.017
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFG 210
A TG GKT A ++ A K V+ + P R + + + A++
Sbjct: 221 APTGYGKTEASLILA----LALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIF 270
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 37.7 bits (88), Expect = 0.007
Identities = 20/57 (35%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGY-GGSSRSGGYGGGYGGGS---GGGRFGDRGGRG 54
+ S G G G GS SGG GGG GG GGG G G G
Sbjct: 213 FGRSLYLGRQPDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG 269
Score = 36.2 bits (84), Expect = 0.025
Identities = 17/33 (51%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 3 KSSSSGGSSRGTSRYGTSGGGG-YGGSSRSGGY 34
S SGGS G+S G SGGGG GG SG +
Sbjct: 239 GSGGSGGSGGGSSGGGFSGGGGSSGGGGASGSW 271
Score = 36.2 bits (84), Expect = 0.028
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 1 TYKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGR 46
+ SS G S G+ GGG G SGG GG GGG G
Sbjct: 233 RRRRSSGSGGSGGS-------GGGSSGGGFSGG-GGSSGGGGASGS 270
Score = 32.7 bits (75), Expect = 0.29
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 11 SRGTSRYGTSGGGGYGGSSRSGGYGGGYG--GGSGGGRF 47
R G+ G GG GG S GG+ GG G GG G
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASGS 270
>gnl|CDD|240430 PTZ00473, PTZ00473, Plasmodium Vir superfamily; Provisional.
Length = 420
Score = 38.3 bits (89), Expect = 0.007
Identities = 21/65 (32%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 1 TYKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGG----YGGGSGGGRFGDRGGRGKN 56
S++ GGSS GTS+ T YG S GG GG + GG G +
Sbjct: 344 YDSSTTYGGSSYGTSQ--TDSTSTYGSRSTFDSSTGGGSQSGGGSTYGGSSTFDGSSRGS 401
Query: 57 STMGG 61
S G
Sbjct: 402 SDSFG 406
Score = 29.4 bits (66), Expect = 4.2
Identities = 20/51 (39%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 1 TYKSSSS-GGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDR 50
TY S S+ S+ G S+ G GG YGGSS G G G FG +
Sbjct: 365 TYGSRSTFDSSTGGGSQSG--GGSTYGGSSTFDGSSRGSSDSFGVSYFGPQ 413
>gnl|CDD|221210 pfam11759, KRTAP, Keratin-associated matrix. The major
structural proteins of mammalian hair are the hair
keratin intermediate filaments (KIFs) and the
keratin-associated proteins (KRTAPs). In the hair
cortex, hair keratins are embedded in an
inter-filamentous matrix consisting of KRTAPs which are
essential for the formation of a rigid and resistant
hair shaft as a result of disulfide bonds between
cysteine residues. There are essentially three groups
of KRTAPs, viz: the high-sulfur (HS) and
ultra-high-sulfur (UHS) KRTAPs (cysteine content: 16-30
and >30 mol%, respectively) and the
high-glycine/tyrosine (HGT: 35-60 mol% glycine and
tyrosine) KRTAPs.
Length = 61
Score = 34.7 bits (80), Expect = 0.007
Identities = 20/53 (37%), Positives = 23/53 (43%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
Y + GG G +G G G G G GGGYG GSG G +G R
Sbjct: 3 YYGNYYGGLGYGCGGFGGLGCGYGCGCGLGYGSGGGYGCGSGYGGYGYGCCRP 55
Score = 29.7 bits (67), Expect = 0.38
Identities = 21/47 (44%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 15 SRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGG 61
YG GG G GG G GYG G G G +G GG G S GG
Sbjct: 2 CYYGNYYGGLGYGCGGFGGLGCGYGCGCGLG-YGSGGGYGCGSGYGG 47
Score = 29.3 bits (66), Expect = 0.53
Identities = 15/31 (48%), Positives = 16/31 (51%)
Query: 17 YGTSGGGGYGGSSRSGGYGGGYGGGSGGGRF 47
G GGGYG S GGYG G S GR+
Sbjct: 31 LGYGSGGGYGCGSGYGGYGYGCCRPSCYGRY 61
>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 = 38.2 bits (89), Expect = 0.008
Identities = 34/171 (19%), Positives = 65/171 (38%), Gaps = 18/171 (10%)
Query: 234 VLMWSATWPREVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLLN 293
+LM SAT P+ +++ AE Y++ N + + L
Sbjct: 159 LLM-SATLPKFLKEYAEKIG--YVEFNEPLDLKEERRFERHRFIKIESDKVGE--ISSLE 213
Query: 294 DI--SSKDENKTIIFAETKRKVDKITKSIQNYG--WAAVGIHG-----DKSQQERDYVLK 344
+ K K I T + + + ++ + +H D++++E + +L+
Sbjct: 214 RLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAE-LLE 272
Query: 345 EFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGRTGRSD 395
E + ++VAT V LD+ +I P +S I R+GR R
Sbjct: 273 EMKKNEKFVIVATQVIEASLDI-SADVMITELAPIDS--LIQRLGRLHRYG 320
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 38.3 bits (89), Expect = 0.008
Identities = 18/51 (35%), Positives = 24/51 (47%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
SS++ S+ + + S GG GGG+GG GGG G GG G
Sbjct: 53 SSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGG 103
Score = 34.8 bits (80), Expect = 0.10
Identities = 20/70 (28%), Positives = 27/70 (38%), Gaps = 1/70 (1%)
Query: 1 TYKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMG 60
S+S+ S+ +S + G S+ + GGG GGG GG G GG G
Sbjct: 45 CSASASASSSATSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Query: 61 G-ALRAIDWG 69
LR
Sbjct: 105 RFWLRLFAPA 114
Score = 34.4 bits (79), Expect = 0.13
Identities = 18/62 (29%), Positives = 23/62 (37%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGAL 63
SSS+ + G ++ GG GG+GG GGG GGG G
Sbjct: 57 SSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGWRFWLRLFAPADA 116
Query: 64 RA 65
A
Sbjct: 117 HA 118
>gnl|CDD|226808 COG4371, COG4371, Predicted membrane protein [Function unknown].
Length = 334
Score = 38.0 bits (88), Expect = 0.008
Identities = 26/54 (48%), Positives = 27/54 (50%), Gaps = 13/54 (24%)
Query: 8 GGSSRGTSRY--GTSGGGGYGGSSRSGGY-GGGYG----------GGSGGGRFG 48
GGS R S Y G SGGG GG GGY GGG+G GG GG FG
Sbjct: 55 GGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPFIIPGGGGGGGFGGIFG 108
Score = 33.4 bits (76), Expect = 0.20
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 6 SSGGSSRGTSRYGTSGGGGYGGSSRSGG--YGGGYGGGSGGGRF 47
S G G+ R + GY G SGG GGGY GG G F
Sbjct: 49 SGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFGFPF 92
Score = 30.3 bits (68), Expect = 1.8
Identities = 20/49 (40%), Positives = 21/49 (42%), Gaps = 9/49 (18%)
Query: 9 GSSRGTSRYGTSGGGGY--GGSSRSGGY------GGGYGGGS-GGGRFG 48
S +R G GGG S S GY GGGY GG GG FG
Sbjct: 41 LSVAAAARSGGRIGGGSFRAPSGYSRGYSGGGPSGGGYSGGGYSGGGFG 89
>gnl|CDD|221784 pfam12810, Gly_rich, Glycine rich protein. This family of proteins
is greatly expanded in Trichomonas vaginalis. The
proteins are composed of several glycine rich motifs
interspersed through the sequence. Although many
proteins have been annotated by similarity in the family
these annotations given the biased composition of the
sequences these are unlikely to be functionally
relevant.
Length = 248
Score = 37.6 bits (88), Expect = 0.009
Identities = 24/55 (43%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 1 TYKSSSSGGSSRGTSRYGTSGGGG---YGGSSRSGGYGGGYGGGSGGGRFGDRGG 52
+ ++S+GG+ +SGG G YGGS GG GGGY GG GG G GG
Sbjct: 138 SNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGGGGGGGYFGGGGGHYAGGGGG 192
Score = 32.6 bits (75), Expect = 0.35
Identities = 21/58 (36%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 8 GGSSRGTSRYGTSG----GGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGG 61
GG T G GG S +GG+G G G GGG G GG G + GG
Sbjct: 133 GGGGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGGGGGGGYFGGGGGHYAGGG 190
Score = 32.2 bits (74), Expect = 0.41
Identities = 21/44 (47%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG 45
S +GG G S G GGGGY G G GG Y GG GGG
Sbjct: 155 ASSGGNGGFGYGGSGNGGGGGGGYFG-----GGGGHYAGGGGGG 193
Score = 30.2 bits (69), Expect = 1.6
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 10 SSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGS 42
+S G GGG GG+ S G G GGG+
Sbjct: 62 NSSNNMVKGGYNGGGDGGNDNSSNDGSGSGGGA 94
Score = 30.2 bits (69), Expect = 1.6
Identities = 13/38 (34%), Positives = 13/38 (34%)
Query: 8 GGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG 45
GG S GG GG G GSGGG
Sbjct: 56 GGKGEDNSSNNMVKGGYNGGGDGGNDNSSNDGSGSGGG 93
Score = 30.2 bits (69), Expect = 1.7
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 20 SGGGGYGGSSRSGGYGGGYGGGSG-------GGRFGDRGGRGKNSTMGG 61
GGG + SGG+GGG GG G G GG G +S G
Sbjct: 113 GGGGSGNYNGGSGGFGGGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNG 161
Score = 29.9 bits (68), Expect = 2.2
Identities = 27/79 (34%), Positives = 28/79 (35%), Gaps = 25/79 (31%)
Query: 8 GGSSRGTSRYGTSGGG------------GYGGSSRSGGYGG--------GYGG-----GS 42
GGS G GGG GG+ SGG G GYGG G
Sbjct: 115 GGSGNYNGGSGGFGGGLVGGGGTSNGNNSTGGTQTSGGEGASSGGNGGFGYGGSGNGGGG 174
Query: 43 GGGRFGDRGGRGKNSTMGG 61
GGG FG GG GG
Sbjct: 175 GGGYFGGGGGHYAGGGGGG 193
Score = 29.5 bits (67), Expect = 3.6
Identities = 23/73 (31%), Positives = 27/73 (36%), Gaps = 22/73 (30%)
Query: 7 SGGSSRGTSRYGTSGGG-------------------GYGGSSRSGGYGGGYGGGSGGGRF 47
GG+ ++ SGGG G GGS G GG+GGG G
Sbjct: 77 DGGNDNSSNDGSGSGGGATDIRLNENSLKSRIIVAGGGGGSGNYNGGSGGFGGGLVG--- 133
Query: 48 GDRGGRGKNSTMG 60
G G NST G
Sbjct: 134 GGGTSNGNNSTGG 146
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 35.5 bits (82), Expect = 0.022
Identities = 18/40 (45%), Positives = 18/40 (45%)
Query: 18 GTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNS 57
G GGGG GG GG G G GG R GG G S
Sbjct: 118 GEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFS 157
Score = 32.9 bits (75), Expect = 0.19
Identities = 14/45 (31%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 5 SSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGD 49
GG G GGG +G S S G G GG D
Sbjct: 118 GEGGGGGGG---GDDGGGGDFGSSGPSRGGPRPASSGGGGNFSRD 159
Score = 31.3 bits (71), Expect = 0.57
Identities = 18/52 (34%), Positives = 21/52 (40%)
Query: 23 GGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRAIDWGNLPPF 74
G G GG G GGG G RGG S+ GG + D + PF
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSRDMDDDIPF 166
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 35.4 bits (82), Expect = 0.032
Identities = 23/52 (44%), Positives = 27/52 (51%), Gaps = 10/52 (19%)
Query: 3 KSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
++S GG G GGGG+GG GG GGG GGG GGG G G +
Sbjct: 119 RASRGGG--------GGGGGGGFGGGG--GGSGGGGGGGGGGGAPGGGGAQA 160
Score = 31.9 bits (73), Expect = 0.45
Identities = 22/54 (40%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 19 TSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRAIDWGNLP 72
S GGG GG GGG+GGG GG G GG G + GG +A + P
Sbjct: 120 ASRGGGGGGG------GGGFGGGGGGSGGGGGGGGGGGAPGGGGAQASAPADDP 167
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 33.7 bits (78), Expect = 0.033
Identities = 22/93 (23%), Positives = 34/93 (36%), Gaps = 21/93 (22%)
Query: 156 VAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQ-----IQEVARDFG 210
V TGSGKTL I + + VL + P ++L +Q I E
Sbjct: 24 VMATGSGKTLTAAA-LIARLAKGKK-------KVLFVVPRKDLLEQALVIIIDEAHH-SS 74
Query: 211 SSTYLRSTCVYGGASKGPQPDRQVLMWSATWPR 243
+ T Y + +P + + +AT R
Sbjct: 75 AKTK------YRKILEKFKPAFLLGL-TATPER 100
>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 = 35.8 bits (83), Expect = 0.039
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 12/77 (15%)
Query: 334 KSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKF--VINFDYPNNSEDY------- 384
+ + +L +F NG+A IL+ T + A+G +V V++ D +S D+
Sbjct: 296 SRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGF 355
Query: 385 --IHRI-GRTGRSDNTG 398
+ ++ GR GR+++ G
Sbjct: 356 QLLTQVAGRAGRAEDPG 372
>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 = 36.1 bits (84), Expect = 0.041
Identities = 25/114 (21%), Positives = 51/114 (44%), Gaps = 6/114 (5%)
Query: 288 LFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFR 347
L + +++E + ++ TK+ + +T ++ G +H + ER ++++ R
Sbjct: 431 LLSEIRQRVARNE-RVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLR 489
Query: 348 NGRAGILVATDVAARGLDVDDVKFVINFD-----YPNNSEDYIHRIGRTGRSDN 396
G +LV ++ GLD+ +V V D + + I IGR R+ N
Sbjct: 490 LGEFDVLVGINLLREGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVN 543
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 35.8 bits (83), Expect = 0.044
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQI--QEVAR 207
AQTG GKT Y+LP + + Q Q ++V PT+ L QI +EV
Sbjct: 271 AQTGIGKTYGYLLPLLAQ-SDQRQ--------IIVSVPTKILQDQIMAEEVKA 314
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 36.1 bits (83), Expect = 0.046
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 4/87 (4%)
Query: 331 HGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDYIHRIGR 390
HG S+++R + ++G +VAT G+D+ V VI P + + RIGR
Sbjct: 308 HGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRIGR 367
Query: 391 TGRSDNTGTSYTFFTQQNSRQAKDLID 417
G + FF R +DL+D
Sbjct: 368 AGHQVGGVSKGLFF----PRTRRDLVD 390
Score = 28.4 bits (63), Expect = 9.7
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 156 VAQTGSGKTLAYMLPAIVHINHQ-----SQLKPGDGPIVLVLAPTRELAQQIQ 203
+A TGSGKTLA L A+ + + + +L ++P + L +Q
Sbjct: 2 IAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQ 54
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 35.9 bits (83), Expect = 0.047
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 8/48 (16%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQE 204
A TG+GKTL Y+LPA+ V++ T+ L Q+ E
Sbjct: 271 APTGTGKTLGYLLPAL------YYAITEKP--VVISTNTKVLQSQLLE 310
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 35.7 bits (83), Expect = 0.056
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARD 208
A TG+GK+LAY+LPA + + +P V++ T +L QQ+ E +D
Sbjct: 283 AGTGTGKSLAYLLPAAYFA-KKKE-EP-----VVISTYTIQLQQQLLE--KD 325
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 35.3 bits (82), Expect = 0.066
Identities = 32/149 (21%), Positives = 66/149 (44%), Gaps = 18/149 (12%)
Query: 264 LTLSANHNIQQVV----------EV-CAEHEKENKLFGLLNDISSKDENKTIIFAETKRK 312
L S + ++Q++ EV + + ++ L + +K+E + ++ TK+
Sbjct: 401 LEQSGGNVVEQIIRPTGLLDPEIEVRPTKGQVDD-LLSEIRKRVAKNE-RVLVTTLTKKM 458
Query: 313 VDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFV 372
+ +T+ ++ G +H D ER ++++ R G +LV ++ GLD+ +V V
Sbjct: 459 AEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLV 518
Query: 373 INFD-----YPNNSEDYIHRIGRTGRSDN 396
D + + I IGR R+ N
Sbjct: 519 AILDADKEGFLRSERSLIQTIGRAARNVN 547
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 34.3 bits (79), Expect = 0.10
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 16 RYGTSGG-GGYGGSSRSGGYGGGYGGGSGGGRFGD 49
+YG +G GG+GG G GG+ G G G F D
Sbjct: 67 QYGAAGANGGFGGG---AGGFGGFDGSGGFGGFED 98
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 34.8 bits (80), Expect = 0.10
Identities = 16/64 (25%), Positives = 29/64 (45%)
Query: 302 KTIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVATDVAA 361
+TI+F ++R+ ++ ++ G A H +ER V + F +V T A
Sbjct: 442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALA 501
Query: 362 RGLD 365
G+D
Sbjct: 502 AGVD 505
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 34.2 bits (79), Expect = 0.13
Identities = 40/187 (21%), Positives = 79/187 (42%), Gaps = 34/187 (18%)
Query: 273 QQVVEVCAEHEKENKLF-GLLNDISSKDENKTIIFAETKR-KVDKITKSIQNYGWAAVGI 330
Q+ ++ H K NK L ++ K EN ++F + K + + ++ +
Sbjct: 317 QEEIKYITSHTKRNKWIANLALKLAKKGENTFVMFKYVEHGKP--LYEMLKKVYDKVYYV 374
Query: 331 HGDKSQQERDYVLKEFRNGRAGILVAT-DVAARGLDVDDVKFVINFDYPNNSE----DYI 385
G+ ++R+ + K G+ I+VA+ V + G+ + ++ VI F +P+ S+ I
Sbjct: 375 SGEVDTEDRNEMKKIAEGGKGIIIVASYGVFSTGISIKNLHHVI-FAHPSKSKIIVLQSI 433
Query: 386 HRIGRTGRSDNTGTSYTFFTQQNSRQAKDLIDVLTESNHPVDPKLSALASRSGGSGGGYQ 445
R+ R S + T + D+ID L ++ +S + Y
Sbjct: 434 GRVLRKHGSKSIATVW------------DIIDDL------------SVKPKSANAKKKYV 469
Query: 446 VLHYSLK 452
L+Y+LK
Sbjct: 470 HLNYALK 476
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 34.4 bits (80), Expect = 0.14
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 343 LKEFRNGRAGILVATDVAARGLDVDDVKFV--INFDYPNNSEDY---------IHRI-GR 390
L +F G A IL+ T + A+G D +V V ++ D S D+ + ++ GR
Sbjct: 473 LAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDFRASERTFQLLTQVAGR 532
Query: 391 TGRSDNTG 398
GR++ G
Sbjct: 533 AGRAEKPG 540
>gnl|CDD|147458 pfam05268, GP38, Phage tail fibre adhesin Gp38. This family
contains several Gp38 proteins from T-even-like phages.
Gp38, together with a second phage protein, gp57,
catalyzes the organisation of gp37 but is absent from
the phage particle. Gp37 is responsible for receptor
recognition.
Length = 261
Score = 33.6 bits (77), Expect = 0.16
Identities = 26/74 (35%), Positives = 29/74 (39%), Gaps = 14/74 (18%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGG--GSGGGRFGDRGGRGKNSTMGG 61
S S S S GG G G + YGGG GG G+ GGR GG G G
Sbjct: 186 KSGSHMSGGNASLTAPGGGSGTGSA-----YGGGNGGNVGAAGGRAW--GGNGYEYGGGA 238
Query: 62 ALRAI-----DWGN 70
A A+ W N
Sbjct: 239 AGYAVIGSAPTWQN 252
Score = 32.1 bits (73), Expect = 0.42
Identities = 19/44 (43%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 20 SGGGGYGGSSRSGGYGGGYGGGSGGGR-FGDRGGRGKNSTMGGA 62
GGGG GG+S + G G GGGR FG G G + + G A
Sbjct: 153 GGGGGGGGASLKNSWRGNGVCGGGGGRPFGAGGKSGSHMSGGNA 196
Score = 29.4 bits (66), Expect = 4.0
Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSR--SGGYGGGYGGGSGGGRFGDRGGRGKN 56
GG R G SG GG++ + G G G G GGG G+ G G
Sbjct: 169 GNGVCGGGGGRPFGAGGKSGSHMSGGNASLTAPGGGSGTGSAYGGGNGGNVGAAGGR 225
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 33.9 bits (78), Expect = 0.16
Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 7/77 (9%)
Query: 8 GGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRAID 67
G + +S YG+ G G G + G GG+ G FG R +
Sbjct: 228 GPGAGPSSGYGSGGTRSGQGGWGPGFWTGLGAGGALGYLFGSRRNNNSSYGRS------- 280
Query: 68 WGNLPPFEKNFFHPSPS 84
+G+ P + S
Sbjct: 281 YGSGSPSYSPSSSSNSS 297
Score = 31.2 bits (71), Expect = 1.0
Identities = 23/67 (34%), Positives = 25/67 (37%), Gaps = 16/67 (23%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGG----------------SSRSGGYGGGYGGGSGGGRF 47
GG + YG GGGG GG SS YG G G SG G
Sbjct: 181 GGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPPPGFKSSFPPPYGPGAGPSSGYGSG 240
Query: 48 GDRGGRG 54
G R G+G
Sbjct: 241 GTRSGQG 247
>gnl|CDD|213562 TIGR00810, secG, protein translocase, SecG subunit. This family
of proteins forms a complex with SecY and SecE. SecA
then recruits the SecYEG complex to form an active
protein translocation channel [Protein fate, Protein
and peptide secretion and trafficking].
Length = 73
Score = 30.9 bits (71), Expect = 0.17
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 28 SSRSGGYGGGYGGGSGGGRFGDRG 51
S + GG GG +GGG+ FG RG
Sbjct: 23 SGKGGGLGGAFGGGASQSLFGSRG 46
>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 = 33.9 bits (78), Expect = 0.18
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 4/88 (4%)
Query: 326 AAVGI-HGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDY 384
A + I HG ++ E + V+ EF G +LV T + G+D+ + +I
Sbjct: 687 ARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQ 746
Query: 385 IHRI-GRTGRSDNTGTSYTFFTQQNSRQ 411
++++ GR GRS Y + + +
Sbjct: 747 LYQLRGRVGRSKKKA--YAYLLYPHQKA 772
>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
present in several RNA-processing factors such as Pcf11
and Nrd1. Pcf11 is a conserved and essential subunit of
the yeast cleavage factor IA, which is required for
polyadenylation-dependent 3'-RNA processing and
transcription termination. Nrd1 is implicated in
polyadenylation-independent 3'-RNA processing. CID binds
tightly to the carboxy-terminal domain (CTD) of RNA
polymerase (Pol) II. During transcription, Pol II
synthesizes eukaryotic messenger RNA. Transcription is
coupled to RNA processing through the CTD, which
consists of up to 52 repeats of the sequence Tyr 1-Ser
2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
alpha-helices in a right-handed superhelical
arrangement, which closely resembles that of the VHS
domains and ARM (Armadillo) repeat proteins, except for
its two amino-terminal helices.
Length = 114
Score = 31.8 bits (73), Expect = 0.22
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 18/80 (22%)
Query: 258 QINIGSLTLSANHNIQ---QVVEVCAEHEK----ENKLFGL--LNDIS--SKDENKTI-- 304
Q +I +LT A N + ++VE+ +H K E KL L L+ I + K
Sbjct: 18 QPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFS 77
Query: 305 -----IFAETKRKVDKITKS 319
+F + KVD+ T+
Sbjct: 78 EFLVPLFLDAYEKVDEKTRK 97
>gnl|CDD|236966 PRK11747, dinG, ATP-dependent DNA helicase DinG; Provisional.
Length = 697
Score = 33.3 bits (77), Expect = 0.29
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 157 AQTGSGKTLAYMLPAI 172
A TG GKTL+Y+L I
Sbjct: 56 AGTGVGKTLSYLLAGI 71
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 33.1 bits (76), Expect = 0.37
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 14/69 (20%)
Query: 343 LKEFRNGRAGILVATDVAARGLDVDDVKFVI---------NFDYPNNSEDYIHRI----G 389
L +F NG A IL+ T + A+G D +V V + D+ SE + G
Sbjct: 527 LDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGLGSPDF-RASERTFQLLMQVAG 585
Query: 390 RTGRSDNTG 398
R GR+ G
Sbjct: 586 RAGRAGKPG 594
Score = 30.0 bits (68), Expect = 3.0
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 9/58 (15%)
Query: 159 TGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARD-FGSSTYL 215
TGSGKT Y L AI + L G VLVL P L Q+ + FG+ +
Sbjct: 226 TGSGKTEVY-LEAIAKV-----LAQGKQ--VLVLVPEIALTPQLLARFKARFGAKVAV 275
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 32.8 bits (74), Expect = 0.37
Identities = 23/61 (37%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGAL 63
S G R S G GGGG GG GG S G DR GR K T G A
Sbjct: 171 SFDQGRQGRYPSGGGAFGGGGGGGGGGERRSGG--FRDSPGADDSDRWGRKKVETFGSAF 228
Query: 64 R 64
Sbjct: 229 G 229
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 33.1 bits (76), Expect = 0.39
Identities = 25/157 (15%), Positives = 64/157 (40%), Gaps = 32/157 (20%)
Query: 232 RQVLMWSATWPREVQKLAEDFLD---------SY-IQINIGSLTLSANHNIQQVVEVCAE 281
+ ++M SAT + ++ + F + +Y ++I + + +V
Sbjct: 197 KLIIM-SAT--LDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYILLDAIVAAVDI 253
Query: 282 HEKENKLFGLLNDISSKDENKTI-IF----AETKRKVDKITKSIQNYGWAAVGIHGDKSQ 336
H ++ + +I +F E +R + + K+ + ++G S
Sbjct: 254 H--------------LREGSGSILVFLPGQREIERTAEWLEKAELGDDLEILPLYGALSA 299
Query: 337 QERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVI 373
+E+ V + G+ +++AT++A L + +++VI
Sbjct: 300 EEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRYVI 336
>gnl|CDD|237655 PRK14279, PRK14279, chaperone protein DnaJ; Provisional.
Length = 392
Score = 32.4 bits (74), Expect = 0.42
Identities = 19/60 (31%), Positives = 22/60 (36%), Gaps = 16/60 (26%)
Query: 13 GTSRYGTSGGGGYGGSSRSGGYGGGY--------GGGSGGGRFGD-------RGGRGKNS 57
G GGGG+GG +GG G + G GGG GD RGG
Sbjct: 82 GFGGRRFDGGGGFGG-FGTGGDGAEFNLNDLFDAAGRGGGGGIGDLFGGLFNRGGGSARP 140
Score = 28.5 bits (64), Expect = 7.7
Identities = 17/51 (33%), Positives = 19/51 (37%), Gaps = 4/51 (7%)
Query: 14 TSRYGTSGGGGYGGSSRSGGYGG-GYGGGSGGGRFGD---RGGRGKNSTMG 60
T R GG G GG+GG G GG D GRG +G
Sbjct: 74 TRRLFAGGGFGGRRFDGGGGFGGFGTGGDGAEFNLNDLFDAAGRGGGGGIG 124
>gnl|CDD|226728 COG4278, COG4278, Uncharacterized conserved protein [Function
unknown].
Length = 269
Score = 32.2 bits (73), Expect = 0.43
Identities = 19/53 (35%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
+K SG S G +G+ G G GG+ GG G GGG G GG
Sbjct: 214 FKKWMSGCGSYGGKNFGSPSGVGDMYFHGCGGHTGGDGSFCGGG-CGGFGGDP 265
>gnl|CDD|217757 pfam03840, SecG, Preprotein translocase SecG subunit.
Length = 74
Score = 29.8 bits (68), Expect = 0.50
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 28 SSRSGGYGGGYGGGSGGGRFGDRGGRG 54
S + G GG +GGG+ FG RG R
Sbjct: 23 SGKGAGLGGAFGGGASQSLFGSRGARN 49
>gnl|CDD|165387 PHA03108, PHA03108, poly(A) polymerase small subunit; Provisional.
Length = 300
Score = 32.0 bits (73), Expect = 0.54
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 370 KFVINFDYPNNSEDYIH 386
K V+NFDYPN D+ H
Sbjct: 246 KIVLNFDYPNQEYDFFH 262
>gnl|CDD|235881 PRK06870, secG, preprotein translocase subunit SecG; Reviewed.
Length = 76
Score = 29.4 bits (67), Expect = 0.62
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 28 SSRSGGYGGGYGGGSGGGRFGDRG 51
S + G GG +GGG+ FG RG
Sbjct: 24 SGKGAGLGGSFGGGASSTLFGARG 47
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 32.2 bits (74), Expect = 0.65
Identities = 25/114 (21%), Positives = 44/114 (38%), Gaps = 28/114 (24%)
Query: 326 AAVGI-HGDKSQQERDYVLKEFRNGRAGILVATDVAARGLDVDDVKFVINFDYPNNSEDY 384
A + + HG ++E + V+ +F NG +LV T + G+D+ PN +
Sbjct: 830 ARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDI-----------PNANTII 878
Query: 385 IHRI------------GRTGRSDNTGTSYTFFTQQN---SRQAKDLIDVLTESN 423
I R GR GRS+ +Y F + A+ ++ +
Sbjct: 879 IERADKFGLAQLYQLRGRVGRSNKQAYAY-FLYPPQKALTEDAEKRLEAIASFT 931
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 30.8 bits (70), Expect = 0.69
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 160 GSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARD 208
G+GKT LP +V +L+ LVLAPTR + +++E R
Sbjct: 12 GAGKTRKV-LPELVRECIDRRLR------TLVLAPTRVVLAEMEEALRG 53
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 32.1 bits (73), Expect = 0.69
Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 19/86 (22%)
Query: 243 REVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENK 302
+E +K +D L+SY NI L A+ + + +L LL ++DEN
Sbjct: 804 KENKKNNQDLLNSY---NILIQKLEAH-----------TEKNDEELKQLLQKFPTEDENL 849
Query: 303 TI-----IFAETKRKVDKITKSIQNY 323
+ F E + VD I K I+N
Sbjct: 850 NLKELEKEFNENNQIVDNIIKDIENM 875
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
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;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 31.8 bits (72), Expect = 0.70
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 15/57 (26%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQ----IQEVARDF 209
A TG+GKTLA++ P + + K + L PT L + I+E D
Sbjct: 21 APTGAGKTLAWLTPLL-----HGENK------AIALYPTNALIEDQTEAIKEFVDDA 66
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 31.7 bits (72), Expect = 0.83
Identities = 17/49 (34%), Positives = 21/49 (42%), Gaps = 10/49 (20%)
Query: 18 GTSGGGGYGGS--------SRSGGYGGGYGGGSGG--GRFGDRGGRGKN 56
G +GGGG+ G S G GG+GGG GG G G +
Sbjct: 77 GAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGGFGGFGGFGGGGSQQRVF 125
Score = 31.7 bits (72), Expect = 0.87
Identities = 21/67 (31%), Positives = 26/67 (38%), Gaps = 16/67 (23%)
Query: 15 SRYGTSGGGGYGGSSRSGGYGGG--------------YGGGSGGGRFGDRGGRGKNSTMG 60
SRY G G GG++ GG+ G +GG GG FG GG G +
Sbjct: 65 SRYDQFGHAGVGGAAGGGGFSGEGMSMEDIFSMFGDIFGGHGGG--FGGFGGFGGGGSQQ 122
Query: 61 GALRAID 67
R D
Sbjct: 123 RVFRGSD 129
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 30.1 bits (68), Expect = 0.95
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 17 YGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGG 52
+G GG G+G GG+ G GG GG + + GG
Sbjct: 73 WGNGGGRGWGNGGSGGGWVNGGGGWGNGG-WVNGGG 107
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 31.8 bits (73), Expect = 0.99
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 133 FDRPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAI 172
F TP Q P+ G N++ + TGSGKTLA L I
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAII 69
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.9 bits (65), Expect = 1.1
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 146 IAMSGSNMVGV-AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQE 204
A SG ++ V G+GKT A I + L G VLV+APT A++++E
Sbjct: 5 AAASGRSLFVVDGGPGTGKT-ATAAAIIARL-----LAAGRS--VLVVAPTGRAARRLRE 56
Query: 205 VARDFG 210
Sbjct: 57 RLAALD 62
>gnl|CDD|115660 pfam07020, Orthopox_C10L, Orthopoxvirus C10L protein. This
family consists of several Orthopoxvirus C10L proteins.
C10L viral protein can play an important role in
vaccinia virus evasion of the host immune system. It
may consist in the blockade of IL-1 receptors by the
C10L protein, a homologue of the IL-1 Ra.
Length = 83
Score = 28.9 bits (64), Expect = 1.2
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 5 SSSGGSSRGTSRYGTSGGGGYGGSSRS---GGYGGGYGGGSGGGRFGDRGG 52
GG+ + Y + GGG +GG + GG GG+ GGS G + G GG
Sbjct: 21 HGPGGAVKRPKTYSSGGGGMWGGLEKRMCVGGGSGGFWGGSSGVKGGVNGG 71
>gnl|CDD|219481 pfam07596, SBP_bac_10, Protein of unknown function (DUF1559). A
large family of paralogous proteins apparently unique to
planctomycetes.
Length = 255
Score = 30.9 bits (70), Expect = 1.2
Identities = 21/63 (33%), Positives = 24/63 (38%), Gaps = 2/63 (3%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGAL 63
S SG + T SGG G G + G GG G + GG G G NS
Sbjct: 99 SDPSGDTGASTGPSTGSGGAGAGAGAAGGSGGGTDSGTNAGGPSSTNGMFGPNSKTR--F 156
Query: 64 RAI 66
R I
Sbjct: 157 RDI 159
>gnl|CDD|112992 pfam04202, Mfp-3, Foot protein 3. Mytilus foot protein-3 (Mfp-3)
is a highly polymorphic protein family located in the
byssal adhesive plaques of blue mussels.
Length = 71
Score = 28.8 bits (64), Expect = 1.2
Identities = 17/35 (48%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGK 55
GGG Y G +R Y GYGG G RG RGK
Sbjct: 39 GGGYYNGYNR---YARGYGGNKGWNNGWKRGRRGK 70
>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 = 30.2 bits (69), Expect = 1.3
Identities = 8/34 (23%), Positives = 15/34 (44%)
Query: 335 SQQERDYVLKEFRNGRAGILVATDVAARGLDVDD 368
+ R+ +L+ F+ G+ IL G+D
Sbjct: 44 GEGSREKLLERFKKGKGAILFGVGSFWEGIDFPG 77
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 31.0 bits (70), Expect = 1.3
Identities = 32/152 (21%), Positives = 45/152 (29%), Gaps = 23/152 (15%)
Query: 81 PSPSVLNRSPHEVQAFRDKHQMTLKGNAPNPITEFAEANFPDYVLKEVKRQGFDRPTPIQ 140
P+ V P A D TL A A V R +
Sbjct: 518 PAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPVVAPRPPRASASGLPDMF 577
Query: 141 AQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQ 200
WP + + G+AQ LA QS+L +G V + P LA+
Sbjct: 578 DGDWPALAARLPVRGLAQ-----QLA----------RQSELAGVEGDTVRLRVPVPALAE 622
Query: 201 -----QIQEVARD-FGSSTYLRSTCVYGGASK 226
++Q + FG +R C G
Sbjct: 623 AEVVERLQAALTEHFG--QPVRVVCEVGAVGA 652
>gnl|CDD|132156 TIGR03112, 6_pyr_pter_rel, 6-pyruvoyl tetrahydropterin
synthase-related domain. Members of this family are
small proteins, or small domains of larger proteins,
that occur in certain Firmicutes in the same regions as
members of families TIGR03110 and TIGR03111. Members of
TIGR03110 resemble exosortase, a proposed protein
sorting transpeptidase (see TIGR02602). TIGR03111
represents a small clade among the group 2
glycosyltransferases. Members of the current protein
family resemble eukaryotic known and prokaryotic
predicted 6-pyruvoyl tetrahydropterin synthases.
Length = 113
Score = 29.3 bits (66), Expect = 1.5
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 297 SKDENKTIIFAETKRKVDKITKSIQN 322
K E+K I+F + ++KV+K K QN
Sbjct: 34 IKKEDKFILFNDVEKKVEKYLKPYQN 59
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 31.1 bits (71), Expect = 1.5
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 135 RPTPIQAQGWPIAMSGSNMVGVAQTGSGKTLAYMLPAIVH 174
R +Q G +SG + QTG GKTL LPA
Sbjct: 103 RHFDVQLMGGLALLSG--RLAEMQTGEGKTLTATLPAGTA 140
>gnl|CDD|132561 TIGR03522, GldA_ABC_ATP, gliding motility-associated ABC
transporter ATP-binding subunit GldA. Members of this
protein family are exclusive to the Bacteroidetes phylum
(previously Cytophaga-Flavobacteria-Bacteroides). GldA
is an ABC transporter ATP-binding protein (pfam00005)
linked to a type of rapid surface gliding motility found
in certain Bacteroidetes, such as Flavobacterium
johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA
abolish the gliding phenotype. Gliding motility appears
closely linked to chitin utilization in the model
species Flavobacterium johnsoniae. Bacteroidetes with
members of this protein family appear to have all of the
genes associated with gliding motility.
Length = 301
Score = 30.5 bits (69), Expect = 1.6
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 19/116 (16%)
Query: 243 REVQKLAEDFLDSYIQINIGSLTLS------ANHNIQQVVEVCAEHEKENKLFGLLNDIS 296
+EV+ + D I IN G + + N +QV+EV E + + +LF L +IS
Sbjct: 193 QEVEAIC----DRVIIINKGKIVADKKLDELSAANKKQVIEVEFEEQIDLQLFETLEEIS 248
Query: 297 S---KDENKTIIFAETKRKVDK-ITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRN 348
S N + ET I K Q G + + QQ + + FR
Sbjct: 249 SVKNTGGNTWKLTFETPNDTRPEIFKLAQQKGLKLISL-----QQNEKNLEQVFRE 299
>gnl|CDD|197548 smart00157, PRP, Major prion protein. The prion protein is a
major component of scrapie-associated fibrils in
Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler
syndrome and bovine spongiform encephalopathy.
Length = 218
Score = 30.2 bits (68), Expect = 1.7
Identities = 19/56 (33%), Positives = 21/56 (37%), Gaps = 5/56 (8%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGY-----GGSSRSGGYGGGYGGGSGGGRFGDRGGRG 54
S G S G +RY GGG G GG G GG G G G+G
Sbjct: 15 SRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQG 70
Score = 29.1 bits (65), Expect = 4.0
Identities = 24/59 (40%), Positives = 29/59 (49%), Gaps = 12/59 (20%)
Query: 8 GGSSRGTSRY---GTSGG------GGYGGSSRSGGYGGGYGGGSG---GGRFGDRGGRG 54
GG + G SRY G+ GG GG G GG+G +GGG G GG +G G G
Sbjct: 8 GGWNTGGSRYPGQGSPGGNRYPPQGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGG 66
>gnl|CDD|220915 pfam10961, DUF2763, Protein of unknown function (DUF2763). This
eukaryotic family of proteins has no known function.
Length = 91
Score = 28.5 bits (64), Expect = 2.0
Identities = 13/45 (28%), Positives = 13/45 (28%), Gaps = 2/45 (4%)
Query: 19 TSGGGGYGGSSRSGGYGGGYGGGSGGGRFG--DRGGRGKNSTMGG 61
R G GG G GG R G GG M G
Sbjct: 46 KRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRPPMAG 90
Score = 27.8 bits (62), Expect = 3.2
Identities = 16/45 (35%), Positives = 16/45 (35%)
Query: 5 SSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGD 49
SS G G GG G G R G GG GG S G
Sbjct: 47 RYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRPPMAGG 91
Score = 27.4 bits (61), Expect = 5.5
Identities = 8/43 (18%), Positives = 11/43 (25%)
Query: 3 KSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG 45
+ +S R+ GG G GGG
Sbjct: 44 VTKRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRP 86
Score = 27.0 bits (60), Expect = 7.5
Identities = 15/44 (34%), Positives = 17/44 (38%)
Query: 2 YKSSSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGG 45
Y+ +SS G R G GG R GG GG GG
Sbjct: 48 YRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRPPMAGG 91
>gnl|CDD|152063 pfam11627, HnRNPA1, Nuclear factor hnRNPA1. This family of
proteins represents hnRNPA1, a nuclear factor that
binds to Pol II transcripts. The family of hnRNP
proteins are involved in numerous RNA-related
activities.
Length = 37
Score = 26.8 bits (59), Expect = 2.3
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 5 SSSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGG 37
+ G S+ S YG GG +GG SG YGGG
Sbjct: 5 NDFGNYSQQQSNYGPMKGGNFGGGRSSGPYGGG 37
>gnl|CDD|237657 PRK14281, PRK14281, chaperone protein DnaJ; Provisional.
Length = 397
Score = 30.2 bits (68), Expect = 2.4
Identities = 21/63 (33%), Positives = 22/63 (34%), Gaps = 14/63 (22%)
Query: 16 RYGTSGGGGYGGSSRSGGYGGGYGGG--------------SGGGRFGDRGGRGKNSTMGG 61
RY G G G S+ SGG G GGG GG R G G GG
Sbjct: 64 RYDQFGHAGVGSSAASGGGPGYGGGGGDFNDIFSAFNDMFGGGARRGGGSPFGFEDVFGG 123
Query: 62 ALR 64
R
Sbjct: 124 GGR 126
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 30.3 bits (68), Expect = 2.5
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 157 AQTGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDF 209
A TG+GKTLA++ P + + + L PT L + E ++F
Sbjct: 21 APTGAGKTLAWLTPLL-----HGEND------TIALYPTNALIEDQTEAIKEF 62
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 30.2 bits (68), Expect = 2.7
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 1/55 (1%)
Query: 303 TIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVAT 357
T++ +T K++ + N V H + ++E++ L+ NG ILV T
Sbjct: 132 TLLVKQTVEKIESFCEKA-NLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTT 185
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 30.0 bits (68), Expect = 2.9
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 159 TGSGKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFG 210
TG+GKTL L A + + L +LV+ P + L Q A FG
Sbjct: 33 TGTGKTLT-ALAAASKLYEKIGLLV-----LLVVCPYQHLVDQWAREAEKFG 78
>gnl|CDD|165250 PHA02940, PHA02940, hypothetical protein; Provisional.
Length = 315
Score = 29.5 bits (66), Expect = 3.1
Identities = 19/130 (14%), Positives = 40/130 (30%), Gaps = 33/130 (25%)
Query: 243 REVQKLAEDFLDSYIQINIG---------------SLTLSANHNIQQVV----EVCAEH- 282
+ L + S+I+ ++ L A +Q V A
Sbjct: 110 AAINALLR-LIRSFIKPEPTLTTPLFIDFTQKAKDTVILLAGRYVQDVKKDDRRTIANKL 168
Query: 283 -----------EKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAAVGI- 330
E E L +I + E K + T + + + ++ + W + +
Sbjct: 169 SKELSWTIDYQENEPDLESDFKEIEEELEEKDDLSRGTYKVLKRALDLMKEHYWKGIRLA 228
Query: 331 HGDKSQQERD 340
+ K+ +RD
Sbjct: 229 NEAKAMIKRD 238
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 29.7 bits (68), Expect = 3.5
Identities = 19/43 (44%), Positives = 22/43 (51%), Gaps = 10/43 (23%)
Query: 32 GGYGGGYGGGSG-GGRFGD---------RGGRGKNSTMGGALR 64
GG GGG+GGG G G FGD RGG + + G LR
Sbjct: 77 GGGGGGFGGGGGFGDIFGDIFGDIFGGGRGGGRQRARRGADLR 119
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 29.6 bits (67), Expect = 3.6
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 16/61 (26%)
Query: 361 ARGLDVDDVKFVINFDYPNNSE--DYIHRIGRTGR--------------SDNTGTSYTFF 404
A GLD + + V N D+ + E + +G N G S F
Sbjct: 76 ACGLDPEKSEIVNNSDWLEHLELAWLLRDLGNHFSLNRMLQFKDVKKRLKQNPGISLGEF 135
Query: 405 T 405
T
Sbjct: 136 T 136
>gnl|CDD|221477 pfam12235, FXR1P_C, Fragile X-related 1 protein C terminal. This
domain family is found in eukaryotes, and is typically
between 126 and 160 amino acids in length. The family
is found in association with pfam05641, pfam00013. This
family is the C terminal region of the fragile X
related 1 protein FXR1P. FXR1P contains two KH domains
and a RGG box that are characteristic motifs in
RNA-binding proteins as well as nuclear localization
and export signals. FXR1P is thought to regulate mRNA
transport and translation.
Length = 79
Score = 27.4 bits (61), Expect = 3.6
Identities = 15/47 (31%), Positives = 20/47 (42%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGALRAID 67
G G SR G GY GGR GG+G ++++ L D
Sbjct: 19 GAGSRPPPSRPGDKEKGYLTDDSGGRGRGGGGKGNSNSISSVLDDPD 65
>gnl|CDD|147988 pfam06120, Phage_HK97_TLTM, Tail length tape measure protein. This
family consists of the tail length tape measure protein
from bacteriophage HK97 and related sequences from
Escherichia coli O157:H7.
Length = 311
Score = 29.4 bits (65), Expect = 4.0
Identities = 33/145 (22%), Positives = 57/145 (39%), Gaps = 18/145 (12%)
Query: 243 REVQKLAEDFLDSYIQINIGSLTLSANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENK 302
+E+Q+L ED D I + I + +Q ++E+ EH + ++L GL N + + +
Sbjct: 161 KEIQQLIEDIEDQAIDL-IRNKAAEMAGAVQSLLEMNGEHAEFDRLLGLGNKLLAARQG- 218
Query: 303 TIIFAETKRKVDKITKSIQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGIL--VATDVA 360
+I V D +++D + K R+ L A +A
Sbjct: 219 --------------LANIPMKYAGPVIPAADLDNKQKDAIEKAQRDLELSGLKGEAKAIA 264
Query: 361 ARGLDVDDVKFVINFDYPNNSEDYI 385
D DD+ + Y NN E I
Sbjct: 265 QAEFDADDLGLPADPQYQNNREALI 289
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 29.3 bits (66), Expect = 5.0
Identities = 27/88 (30%), Positives = 34/88 (38%), Gaps = 21/88 (23%)
Query: 131 QGFD-RPTPIQAQG---------WPIAMSGSNMVGVAQTGSGKTLAYMLPAIVHINHQSQ 180
F TP QAQ P+AM + + G GKT M A + + + Q
Sbjct: 595 DSFPFETTPDQAQAINAVLSDMCQPLAM---DRLVCGDVGFGKTEVAMRAAFLAVENHKQ 651
Query: 181 LKPGDGPIVLVLAPTRELAQQIQEVARD 208
V VL PT LAQQ + RD
Sbjct: 652 --------VAVLVPTTLLAQQHYDNFRD 671
>gnl|CDD|144813 pfam01358, PARP_regulatory, Poly A polymerase regulatory subunit.
Length = 295
Score = 29.0 bits (65), Expect = 5.1
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 370 KFVINFDYPNNSEDYIH 386
K V NFDYPN DY H
Sbjct: 243 KIVNNFDYPNQEYDYFH 259
>gnl|CDD|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4;
Provisional.
Length = 144
Score = 28.1 bits (62), Expect = 5.4
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 20 SGGGGYGGSSRSGGYGGGYGGGSG 43
+ GGG G S GGYGGG GG G
Sbjct: 120 AYGGGGGYSGGGGGYGGGGDGGGG 143
Score = 27.7 bits (61), Expect = 6.9
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 6 SSGGSSRGTSRYGTSGGGGYGGSSRSGGYGGGY 38
S + G + GGGGYGG G GGG+
Sbjct: 115 PSAPRAYGGGGGYSGGGGGYGG---GGDGGGGF 144
Score = 27.7 bits (61), Expect = 7.3
Identities = 14/26 (53%), Positives = 14/26 (53%)
Query: 20 SGGGGYGGSSRSGGYGGGYGGGSGGG 45
S YGG G GGGYGGG GG
Sbjct: 116 SAPRAYGGGGGYSGGGGGYGGGGDGG 141
>gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 1. Members
identified as glutathione-dependent formaldehyde
dehydrogenase(FDH), a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. FDH converts formaldehyde and NAD(P) to formate
and NAD(P)H. The initial step in this process the
spontaneous formation of a S-(hydroxymethyl)glutathione
adduct from formaldehyde and glutathione, followed by
FDH-mediated oxidation (and detoxification) of the
adduct to S-formylglutathione. MDH family uses NAD(H)
as a cofactor in the interconversion of alcohols and
aldehydes, or ketones. Like many zinc-dependent alcohol
dehydrogenases (ADH) of the medium chain alcohol
dehydrogenase/reductase family (MDR), these FDHs form
dimers, with 4 zinc ions per dimer. The medium chain
alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 386
Score = 29.0 bits (66), Expect = 5.8
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 17 YGTSGGGGYGGSSRSGGYGGG 37
YG +G G +G S +GGY GG
Sbjct: 117 YGHAGAGIFGYSHLTGGYAGG 137
>gnl|CDD|221518 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 28.2 bits (63), Expect = 6.0
Identities = 23/63 (36%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 7 SGGSSRGTS---RYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMGGAL 63
GG G S +G GGY G GGG GGG GGG G G + T+ G +
Sbjct: 61 PGGDGGGFSDSDLADVAGDGGYKPDK---GKGGGGGGGGGGGTDGGPEGGAETGTIAGIV 117
Query: 64 RAI 66
A+
Sbjct: 118 SAV 120
>gnl|CDD|185378 PRK15481, PRK15481, transcriptional regulatory protein PtsJ;
Provisional.
Length = 431
Score = 28.9 bits (65), Expect = 6.3
Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 162 GKTLAYMLPAIVHINHQSQLKPGDGPIVLVLAPTRELAQQIQEVARDFGSSTYLR 216
GKT + +I + +L+PGD L P RELA ++ V R+ ++ Y R
Sbjct: 4 GKTANEIFDSIRQLIQAGRLRPGD-----SLPPVRELASEL-GVNRNTVAAAYKR 52
>gnl|CDD|237662 PRK14292, PRK14292, chaperone protein DnaJ; Provisional.
Length = 371
Score = 28.7 bits (64), Expect = 6.4
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 8/44 (18%)
Query: 16 RYGTSGGGGYGGSSRSGGYGGG--------YGGGSGGGRFGDRG 51
R+GT+ G G G GG G +GG GG G RG
Sbjct: 65 RFGTAPGAGMPGGDPFGGMGFDPMDIFEQLFGGAGFGGGRGRRG 108
>gnl|CDD|221759 pfam12764, Gly-rich_Ago1, Glycine-rich region of argonaut. This
domain is often found at the very N-terminal of
argonaut-like proteins.
Length = 102
Score = 27.2 bits (60), Expect = 6.5
Identities = 15/28 (53%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGGRFG 48
G G GG + GG GG GGG GGG G
Sbjct: 7 QGRGRGGPPQQGG-RGGGGGGRGGGSTG 33
>gnl|CDD|217818 pfam03964, Chorion_2, Chorion family 2. The chorion genes of
Drosophila are amplified in response to developmental
signals in the follicle cells of the ovary.
Length = 96
Score = 27.2 bits (60), Expect = 6.7
Identities = 18/36 (50%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 17 YGTSGGGGYGGSSR-SGGYGGGYGGGSGGGRFGDRG 51
YG G GGY + +G YG GYG G G G +G RG
Sbjct: 2 YGGVGVGGYAYQVQPAGYYGPGYGRGRGRGGYGRRG 37
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 28.3 bits (63), Expect = 7.3
Identities = 23/46 (50%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGG-GRFGDRGGRGKNSTMGGALRA 65
GGGGYGG GG GGG GGG G G G +GG G MG +
Sbjct: 186 GGGGYGGGG--GGMGGGGGGGMGEMGGMGPQGGGGGYGGMGAPGQG 229
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 28.9 bits (64), Expect = 7.5
Identities = 14/52 (26%), Positives = 22/52 (42%)
Query: 9 GSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRGGRGKNSTMG 60
SS G + ++GG G G+ +G G G G + G + +T G
Sbjct: 392 SSSIGGNANSSTGGNGAAGAGGAGAAGKGGGSAAARATVGGVAEENELNTFG 443
>gnl|CDD|204270 pfam09579, Spore_YtfJ, Sporulation protein YtfJ (Spore_YtfJ).
Proteins in this family are encoded by bacterial
genomes if, and only if, the species is capable of
endospore formation. YtfJ was confirmed in spores of B.
subtilis; it appears to be expressed in the forespore
under control of SigF.
Length = 81
Score = 26.7 bits (60), Expect = 7.9
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 21 GGGGYGGSSRSGGYGGGYGGGSGGG 45
G G GG + G+GGG G G
Sbjct: 17 GFGAGGGEGKDKKGKTGFGGGGGAG 41
>gnl|CDD|233507 TIGR01648, hnRNP-R-Q, heterogeneous nuclear ribonucleoprotein R, Q
family. Sequences in this subfamily include the human
heterogeneous nuclear ribonucleoproteins (hnRNP) R , Q
and APOBEC-1 complementation factor (aka APOBEC-1
stimulating protein). These proteins contain three RNA
recognition domains (rrm: pfam00076) and a somewhat
variable C-terminal domain.
Length = 578
Score = 28.8 bits (64), Expect = 8.0
Identities = 13/43 (30%), Positives = 18/43 (41%)
Query: 9 GSSRGTSRYGTSGGGGYGGSSRSGGYGGGYGGGSGGGRFGDRG 51
G RG + +GG GY YG YG G++ D+
Sbjct: 370 GRGRGGAPSRAAGGRGYPPYGYEAYYGDYYGYHDYRGKYEDKY 412
>gnl|CDD|107383 cd06388, PBP1_iGluR_AMPA_GluR4, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR4 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR4 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 371
Score = 28.5 bits (63), Expect = 9.0
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 1/64 (1%)
Query: 268 ANHNIQQVVEVCAEHEKENKLFGLLNDISSKDENKTIIFAETKRKVDKITKSIQNYGWAA 327
A N QV +C E+ + LL D+ + E K +I E +R + I + I + G
Sbjct: 147 AGQNGWQVSAICVENFNDASYRRLLEDLDRRQEKKFVIDCEIER-LQNILEQIVSVGKHV 205
Query: 328 VGIH 331
G H
Sbjct: 206 KGYH 209
>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 = 28.6 bits (64), Expect = 9.1
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 8/59 (13%)
Query: 303 TIIFAETKRKVDKITKS----IQNYGWAAVGIHGDKSQQERDYVLKEFRNGRAGILVAT 357
T++ + K+ + + N G H +E+ ++ NG IL+ T
Sbjct: 131 TLLVIQVAEKISSLAEKAGVGTVNIGA----YHSRLPTKEKKEFMERIENGDFDILITT 185
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 28.5 bits (63), Expect = 9.2
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 4 SSSSGGSSRGTSRYGTSGGGGYGGSSRS--GGYGGGYGGGSGGGRFGDR 50
+SSS G S+ +++ G+ +G S+ S G S G G
Sbjct: 144 ASSSDGKSKASAKSGSKSASKHGESNSSDESATDSGKASASVAGIVGAD 192
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
0.314 0.134 0.396
Gapped
Lambda K H
0.267 0.0630 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,302,042
Number of extensions: 2283470
Number of successful extensions: 3534
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2844
Number of HSP's successfully gapped: 295
Length of query: 453
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 353
Effective length of database: 6,502,202
Effective search space: 2295277306
Effective search space used: 2295277306
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 61 (27.5 bits)