RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3765
(592 letters)
>3ice_A Transcription termination factor RHO; transcription, ATPase,
hexamer, helicase, RNA, RECA, OB fold ATP-binding,
hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli
k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A
Length = 422
Score = 687 bits (1776), Expect = 0.0
Identities = 247/356 (69%), Positives = 303/356 (85%), Gaps = 2/356 (0%)
Query: 8 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGE 67
IFGDG LE+L DGFGFLRS S+Y+A DDIY+SPSQIRRFNL TGD + G+IR PK GE
Sbjct: 52 IFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGE 111
Query: 68 RYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPI 127
RYFALLK+ +VN +KPE ++N+ LF+NLTPLH L +ER S E++T R++DL +PI
Sbjct: 112 RYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPI 171
Query: 128 GKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVI 187
G+GQRGL+VA PK+GK+++LQ+IA +I NH + +++V+LIDERPEEVTEMQR V+GEV+
Sbjct: 172 GRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVV 231
Query: 188 ASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGG 247
ASTFDEPA RHVQVAEMV+EKAKRLVE KKDVIILLDSITRLARAYNTV+PASGKVLTGG
Sbjct: 232 ASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGG 291
Query: 248 VDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERR 307
VD+NAL RPKRFFGAARN+EEGGSLTIIATALI+TGS+MD+VIYEEFKGTGNME+HL R+
Sbjct: 292 VDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRK 351
Query: 308 LAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLTMTSFTVSLFFIKR 363
+AEKRV+PAI+ N+SGTR+EELL ++LQK+W+LRK+++ M F I +
Sbjct: 352 IAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHP--MGEIDAMEFLINK 405
Score = 193 bits (493), Expect = 6e-56
Identities = 74/130 (56%), Positives = 91/130 (70%), Gaps = 27/130 (20%)
Query: 489 VASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA 548
VA PK+GK+++LQ+IA +I NH + +++V+LIDERPEEVTEMQR V+GEV+ASTFDEPA
Sbjct: 180 VAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPA 239
Query: 549 ---------------------------LSVMCKLARAYNTVIPASGKVLTGGVDSNALQR 581
L + +LARAYNTV+PASGKVLTGGVD+NAL R
Sbjct: 240 SRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHR 299
Query: 582 PKRFFGAARK 591
PKRFFGAAR
Sbjct: 300 PKRFFGAARN 309
Score = 156 bits (396), Expect = 4e-42
Identities = 65/113 (57%), Positives = 86/113 (76%)
Query: 388 DLEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDI 447
++ + ++ R+RKQ+++FAI K+ K GE IFGDG LE+L DGFGFLRS S+Y+A DDI
Sbjct: 23 NMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDI 82
Query: 448 YLSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVNVASPKSGKSIIL 500
Y+SPSQIRRFNL TG G+IR PK GERYFALLK+ +VN P++ ++ IL
Sbjct: 83 YVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKIL 135
>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA
capture mechanism, ATP-binding, hydrolase,
nucleotide-binding, RN binding; 2.35A {Thermotoga
maritima}
Length = 427
Score = 674 bits (1741), Expect = 0.0
Identities = 206/356 (57%), Positives = 268/356 (75%), Gaps = 5/356 (1%)
Query: 8 IFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGE 67
FG+G LE+ P+GFGFLR N + S+DDIY+SPSQIR+FNL+TGD + G IR PK GE
Sbjct: 56 FFGEGVLEIHPEGFGFLRRIEDNLLPSNDDIYISPSQIRKFNLNTGDIISGVIRKPKEGE 115
Query: 68 RYFALLKIKKVNGEKPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITGRIIDLIAPI 127
+YFA++KI+ +N E +R FDNLTP +P++ +LE + + R+IDL API
Sbjct: 116 KYFAMIKIEAINYRPVEAVNDRVNFDNLTPDYPRERFILET---DPKIYSTRLIDLFAPI 172
Query: 128 GKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVI 187
GKGQRG++VA PK+GK+ IL+ IA+ I NH + I I++LIDERPEEVT+++ S VI
Sbjct: 173 GKGQRGMIVAPPKAGKTTILKEIANGIAENHPDTIRIILLIDERPEEVTDIRESTNAIVI 232
Query: 188 ASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGG 247
A+ FD P + V+VAE+ LE AKRLVE DV+ILLDS+TRLAR YN V+P SGK+LTGG
Sbjct: 233 AAPFDMPPDKQVKVAELTLEMAKRLVEFNYDVVILLDSLTRLARVYNIVVPPSGKLLTGG 292
Query: 248 VDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERR 307
VD AL +PKRFFGAARN EGGSLTIIATAL+ETGS+MD+VI+EEFKGTGNME+ L R+
Sbjct: 293 VDPAALYKPKRFFGAARNTREGGSLTIIATALVETGSKMDEVIFEEFKGTGNMELVLSRQ 352
Query: 308 LAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLLYSLTMTSFTVSLFFIKR 363
LA KR++PAINL SGTRREELL+ ++ L+K+W+LR++L + MT + +
Sbjct: 353 LANKRIFPAINLLLSGTRREELLLDEETLKKVWLLRRMLSA--MTEEEGLTLILNK 406
Score = 316 bits (813), Expect = e-103
Identities = 111/284 (39%), Positives = 148/284 (52%), Gaps = 80/284 (28%)
Query: 388 DLEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDI 447
L + +RK++L+FAI K +T+ FG+G LE+ P+GFGFLR N + S+DDI
Sbjct: 27 SLGIPRYTSMRKRDLIFAILKAQTESTGYFFGEGVLEIHPEGFGFLRRIEDNLLPSNDDI 86
Query: 448 YLSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVN------------------- 488
Y+SPSQIR+FNL+TG + G IR PK GE+YFA++KI+ +N
Sbjct: 87 YISPSQIRKFNLNTGDIISGVIRKPKEGEKYFAMIKIEAINYRPVEAVNDRVNFDNLTPD 146
Query: 489 ----------------------------------VASPKSGKSIILQHIAHAITTNHSEA 514
VA PK+GK+ IL+ IA+ I NH +
Sbjct: 147 YPRERFILETDPKIYSTRLIDLFAPIGKGQRGMIVAPPKAGKTTILKEIANGIAENHPDT 206
Query: 515 IMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPA-------------------------- 548
I I++LIDERPEEVT+++ S VIA+ FD P
Sbjct: 207 IRIILLIDERPEEVTDIRESTNAIVIAAPFDMPPDKQVKVAELTLEMAKRLVEFNYDVVI 266
Query: 549 -LSVMCKLARAYNTVIPASGKVLTGGVDSNALQRPKRFFGAARK 591
L + +LAR YN V+P SGK+LTGGVD AL +PKRFFGAAR
Sbjct: 267 LLDSLTRLARVYNIVVPPSGKLLTGGVDPAALYKPKRFFGAARN 310
>1a62_A RHO; transcription termination, termination, RNA binding domain,
transcription regulation, OB fold, F1-ATPase; 1.55A
{Escherichia coli BL21} SCOP: a.140.3.1 b.40.4.5 PDB:
1a63_A 2a8v_A 1a8v_A
Length = 130
Score = 155 bits (393), Expect = 4e-45
Identities = 65/118 (55%), Positives = 88/118 (74%), Gaps = 2/118 (1%)
Query: 381 LAETQTI--DLEVNSVKRLRKQELMFAIFKKKTKIGERIFGDGSLEVLPDGFGFLRSQGS 438
++E T+ ++ + ++ R+RKQ+++FAI K+ K GE IFGDG LE+L DGFGFLRS S
Sbjct: 11 VSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADS 70
Query: 439 NYMASSDDIYLSPSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVNVASPKSGK 496
+Y+A DDIY+SPSQIRRFNL TG G+IR PK GERYFALLK+ +VN P++ +
Sbjct: 71 SYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENAR 128
Score = 152 bits (387), Expect = 2e-44
Identities = 59/88 (67%), Positives = 71/88 (80%)
Query: 2 TKIGERIFGDGSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIR 61
K GE IFGDG LE+L DGFGFLRS S+Y+A DDIY+SPSQIRRFNL TGD + G+IR
Sbjct: 43 AKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIR 102
Query: 62 VPKNGERYFALLKIKKVNGEKPELSKNR 89
PK GERYFALLK+ +VN +KPE ++N+
Sbjct: 103 PPKEGERYFALLKVNEVNFDKPENARNK 130
>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*
Length = 347
Score = 104 bits (261), Expect = 1e-24
Identities = 74/269 (27%), Positives = 123/269 (45%), Gaps = 36/269 (13%)
Query: 97 PLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAIT 155
L+ + L R + + I G R ID + G GQR + A GKS +L I
Sbjct: 37 SLYAEPPDPLLRQVIDQPFILGVRAIDGLLTCGIGQRIGIFAGSGVGKSTLLGMIC---- 92
Query: 156 TNHSEA-IMIVMLIDERPEEVTE---------MQRSVRGEVIASTFDEPAYRHVQVAEMV 205
N + A I+++ LI ER EV E + + V ++ +T D PA ++ A
Sbjct: 93 -NGASADIIVLALIGERGREVNEFLALLPQSTLSKCV---LVVTTSDRPALERMKAAFTA 148
Query: 206 LEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLTGGVDSNALQR---PKRFFGA 262
A+ + K+V++++DS+TR ARA V ASG+ + P F
Sbjct: 149 TTIAEYFRDQGKNVLLMMDSVTRYARAARDVGLASGEPDV--------RGGFPPSVFSSL 200
Query: 263 ARNIE-----EGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAI 317
+ +E GS+T I T L+E ++D I +E + + + L R LAE+ +PAI
Sbjct: 201 PKLLERAGPAPKGSITAIYTVLLE-SDNVNDPIGDEVRSILDGHIVLTRELAEENHFPAI 259
Query: 318 NLNKSGTRREELLIQDDKLQKIWVLRKLL 346
++ S +R ++ + L+ +KL+
Sbjct: 260 DIGLSASRVMHNVVTSEHLRAAAECKKLI 288
Score = 40.3 bits (95), Expect = 0.001
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 18/70 (25%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE---------MQRSVRGEV 539
A GKS +L I N + A I+++ LI ER EV E + + V +
Sbjct: 78 AGSGVGKSTLLGMIC-----NGASADIIVLALIGERGREVNEFLALLPQSTLSKCV---L 129
Query: 540 IASTFDEPAL 549
+ +T D PAL
Sbjct: 130 VVTTSDRPAL 139
>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta
structure, hydrolase; HET: ADP; 2.40A {Salmonella
typhimurium}
Length = 438
Score = 105 bits (263), Expect = 3e-24
Identities = 79/279 (28%), Positives = 121/279 (43%), Gaps = 28/279 (10%)
Query: 82 KPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPK 140
P T P +P L+R TG R I+ + +G+GQR L A
Sbjct: 113 LPAPDTLETGALITPPFNP-----LQRTPIEHVLDTGVRAINALLTVGRGQRMGLFAGSG 167
Query: 141 SGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGEVIAS 189
GKS++L +A ++ A +++V LI ER EV + RSV VIA+
Sbjct: 168 VGKSVLLGMMA-----RYTRADVIVVGLIGERGREVKDFIENILGPDGRARSV---VIAA 219
Query: 190 TFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDSITRLARAYNTVIPASGKVLT--GG 247
D +Q A A+ + + V++++DS+TR A A + A G+ G
Sbjct: 220 PADVSPLLRMQGAAYATRIAEDFRDRGQHVLLIMDSLTRYAMAQREIALAIGEPPATKGY 279
Query: 248 VDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERR 307
S + P A I GGS+T T L E G D I + + + + L RR
Sbjct: 280 PPSVFAKLPALVERAGNGIHGGGSITAFYTVLTE-GDDQQDPIADSARAILDGHIVLSRR 338
Query: 308 LAEKRVYPAINLNKSGTRREELLIQDDKLQKIWVLRKLL 346
LAE YPAI++ S +R LI + ++ + ++LL
Sbjct: 339 LAEAGHYPAIDIEASISRAMTALITEQHYARVRLFKQLL 377
Score = 38.1 bits (89), Expect = 0.008
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 19/71 (26%)
Query: 490 ASPKSGKSIILQHIAHAITTNHSEA-IMIVMLIDERPEEVTE----------MQRSVRGE 538
A GKS++L +A ++ A +++V LI ER EV + RSV
Sbjct: 164 AGSGVGKSVLLGMMA-----RYTRADVIVVGLIGERGREVKDFIENILGPDGRARSV--- 215
Query: 539 VIASTFDEPAL 549
VIA+ D L
Sbjct: 216 VIAAPADVSPL 226
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 91.1 bits (225), Expect = 3e-19
Identities = 96/616 (15%), Positives = 174/616 (28%), Gaps = 189/616 (30%)
Query: 51 HTGDFVEGEIR------VPKNGERYFALLKIKKV-NGEKPELSKNRTLFDNLTPLHPKKL 103
H DF GE + + + + K V + K LSK D++
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE--IDHI-------- 54
Query: 104 LLLERNIESKENITGRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHS---E 160
++ ++ S T R+ + + ++ + + + N+
Sbjct: 55 -IMSKDAVSG---TLRLFWTLL--------------SKQEEMVQKFVEEVLRINYKFLMS 96
Query: 161 AIMIVMLIDERPEEVTEMQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVI 220
I +P +T M R + Y QV AK V + +
Sbjct: 97 PIKTE---QRQPSMMTRMYIEQR---------DRLYNDNQVF------AKYNVSRLQPYL 138
Query: 221 ILLDSITRLARAYNTVI---PASGK-VLTGGVDSNALQRPKRFFGA----ARNIEEGGSL 272
L ++ L A N +I SGK + V + + K F +N ++
Sbjct: 139 KLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV 198
Query: 273 TIIATALIETGSRMDDVIYEEFKGTGNMEVHLE------RRLAEKRVYPAINLNKSGTRR 326
+ L+ ++D + N+++ + RRL + + Y
Sbjct: 199 LEMLQKLL---YQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE----------- 244
Query: 327 EELLIQDDKLQKIWVLR------KLLYSLTMT---SFTVSLFFIKRT-IPVE-------- 368
LL+ + +Q K+L LT T T L T I ++
Sbjct: 245 NCLLVLLN-VQNAKAWNAFNLSCKIL--LT-TRFKQVTDFLSAATTTHISLDHHSMTLTP 300
Query: 369 ---KNLL------------KDAC--MPLVLA--------ETQTID--LEVN--------- 392
K+LL ++ P L+ T D VN
Sbjct: 301 DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIE 360
Query: 393 -SVKRLRKQEL-----MFAIFKKKTKIGERIF----GDGSLEVLPD------GFGFLRSQ 436
S+ L E ++F I + D + + + Q
Sbjct: 361 SSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
Query: 437 GSNYMASSDDIYLS--PSQIRRFNLHTGILWKGEIRVPKNGERYFALLKIKKVNVASPKS 494
S IYL + LH I+ + Y + K + P
Sbjct: 421 PKESTISIPSIYLELKVKLENEYALHRSIV-----------DHY-NIPKTFDSDDLIPPY 468
Query: 495 GKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE-------MQRSVRGEVIASTFDEP 547
HI H H + + ER +++ +R + A
Sbjct: 469 LDQYFYSHIGH-----H----LKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGS 519
Query: 548 ALSVMCKLARAYNTVI 563
L+ + +L + Y I
Sbjct: 520 ILNTLQQL-KFYKPYI 534
>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
A1AO, ATP synthesis, hydrogen ION transport, ION
transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
3b2q_A* 2rkw_A* 3eiu_A*
Length = 469
Score = 76.6 bits (189), Expect = 6e-15
Identities = 54/260 (20%), Positives = 91/260 (35%), Gaps = 25/260 (9%)
Query: 82 KPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPK 140
P + ++ L N ++P R TG ID + +GQ+ + ++
Sbjct: 108 GPRIVPDQLLDINGAAMNP-----YARLPPKDFIQTGISTIDGTNTLVRGQKLPIFSASG 162
Query: 141 SGKSIILQHIA-HAITTNHSEAIMIVM-LIDERPEEVTEMQRSVRGE-------VIASTF 191
+ I IA A A +V + EE V +
Sbjct: 163 LPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEKTGALERAVVFLNLA 222
Query: 192 DEPAYRHVQVAEMVLEKAKRL-VEMKKDVIILLDSITRLARAYNTVIPASGKV-----LT 245
D+PA + M L A+ L E V+++L IT A A + A +V
Sbjct: 223 DDPAVERIVTPRMALTAAEYLAYEHGMHVLVILTDITNYAEALRQMGAARNEVPGRRGYP 282
Query: 246 GGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLE 305
G + ++ +R A GS+T I + G + I + ++ +
Sbjct: 283 GYMYTDLATLYER---AGIVKGAKGSVTQIPILSMP-GDDITHPIPDLSGYITEGQIVVA 338
Query: 306 RRLAEKRVYPAINLNKSGTR 325
R L K +YP IN+ S +R
Sbjct: 339 RELHRKGIYPPINVLPSLSR 358
>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
3j0j_D*
Length = 464
Score = 74.4 bits (183), Expect = 3e-14
Identities = 50/270 (18%), Positives = 96/270 (35%), Gaps = 38/270 (14%)
Query: 82 KPELSKNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIIDLIAPIGKGQRGLLVASPK 140
P ++ + L PL+P + R + TG ID++ + +GQ+ + +
Sbjct: 103 LPPITPEKRLPITGLPLNP-----VARRKPEQFIQTGISTIDVMNTLVRGQKLPIFSGSG 157
Query: 141 SGKSIILQHIA--------HAITTNHSEAIMIVM-LIDERPEEVTE----------MQRS 181
+ I IA + E +V + E++ + RS
Sbjct: 158 LPANEIAAQIARQATVRPDLSGEGEKEEPFAVVFAAMGITQRELSYFIQEFERTGALSRS 217
Query: 182 VRGEVIASTFDEPAYRHVQVAEMVLEKAKRL-VEMKKDVIILLDSITRLARAYNTVIPAS 240
V + + D+P + M L A+ L E V+++L +T + A + A
Sbjct: 218 V---LFLNKADDPTIERILTPRMALTVAEYLAFEHDYHVLVILTDMTNYSEALREIGAAR 274
Query: 241 GKV-----LTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALIETGSRMDDVIYEEFK 295
++ G + ++ +R A + GS+T I + I +
Sbjct: 275 EEIPGRRGYPGYMYTDLATIYER---AGVVEGKKGSVTQIPILSMP-DDDRTHPIPDLTG 330
Query: 296 GTGNMEVHLERRLAEKRVYPAINLNKSGTR 325
++ L R L K +YP I+ S +R
Sbjct: 331 YITEGQIQLSRELHRKGIYPPIDPLPSLSR 360
>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis,
ATP-binding, hydrogen ION TRA hydrolase, ION transport;
2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A
3j0j_A* 1um2_C
Length = 578
Score = 59.7 bits (145), Expect = 1e-09
Identities = 54/240 (22%), Positives = 92/240 (38%), Gaps = 35/240 (14%)
Query: 116 ITG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEE 174
+TG RI+D++ P+ G + SGKS+ Q +A + +++ + ER E
Sbjct: 206 LTGMRILDVLFPVAMGGTAAIPGPFGSGKSVTQQSLAK----WSNADVVVYVGSGERGNE 261
Query: 175 VTE-----------------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKK 217
+T+ M R+V +IA+T + P + + A+ +
Sbjct: 262 MTDVLVEFPELTDPKTGGPLMHRTV---LIANTSNMPVAAREASIYVGVTIAEYFRDQGF 318
Query: 218 DVIILLDSITRLARAYNTV------IPAS-GKVLTGGVDSNALQRPKRFFGAARNIEEGG 270
V ++ DS +R A A + +PA G A +R E G
Sbjct: 319 SVALMADSTSRWAEALREISSRLEEMPAEEGYPPYLAARLAAFY--ERAGKVITLGGEEG 376
Query: 271 SLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELL 330
++TI+ G + V + G L+ LA +R +PAIN N S + L
Sbjct: 377 AVTIVGAVSPPGGDMSEPVTQSTLRIVGAFWR-LDASLAFRRHFPAINWNGSYSLFTSAL 435
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 55.8 bits (134), Expect = 4e-08
Identities = 91/535 (17%), Positives = 159/535 (29%), Gaps = 195/535 (36%)
Query: 141 SGKSIILQH--IAHAI---TTNHSEA-------IMIV------MLIDERPEEVTEM---- 178
S + + L H + H + T + A I+ D+ P E+
Sbjct: 5 STRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 179 -----------QRSVRGEVIASTFD--EPAYR-----HVQVAEMVLEKAKRLVEMKKDVI 220
+ +V+ E Y H A+++ E LV+ K++I
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVK-TKELI 123
Query: 221 ILLDSITRLARAYNTVIPASGKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATALI 280
+ Y T + + +S AL F A G+ ++A
Sbjct: 124 ----------KNYITARIMAKRPFDKKSNS-AL------FRAVGE----GNAQLVAI--- 159
Query: 281 ETGSRMDDVIYEEFKGTGNMEVHLE--RRLAEKRVYPAIN---LNKSGTRREELLIQDDK 335
F G GN + + E R L + Y + + S EL+
Sbjct: 160 -------------FGGQGNTDDYFEELRDLYQ--TYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 336 LQKI---------WVLRK------LLYSLTMTSFTVSLFFIK-----------RTI---P 366
+K+ W L Y + S +S I + + P
Sbjct: 205 AEKVFTQGLNILEW-LENPSNTPDKDY---LLSIPISCPLIGVIQLAHYVVTAKLLGFTP 260
Query: 367 VE-KNLL-------KDACMPLVLAETQTID-LEVNSVKRLRKQELMFAIFKKKTKIGER- 416
E ++ L + + +AET + + V+ K + ++F IG R
Sbjct: 261 GELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI---TVLF-------FIGVRC 310
Query: 417 --IFGDGSLE--VLPD----GFGFLRSQGSNYMASSDDIYLSPSQ----IRRFNLHTGIL 464
+ + SL +L D G + M S + L+ Q + + N H
Sbjct: 311 YEAYPNTSLPPSILEDSLENNEG-----VPSPMLSISN--LTQEQVQDYVNKTNSH---- 359
Query: 465 WKGEIRVPKNGERYFALLKIKKVN------VA-SPKS--GKSIILQHIAHAITTNHSEAI 515
+P + +L VN V+ P+S G ++ L+ + S
Sbjct: 360 ------LPAGKQVEISL-----VNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408
Query: 516 MIVMLIDERPEEVTEMQRSVRGEVIA----STFDEPALSVMCKLARAYNTVIPAS 566
ER + S R +A S PA ++ K N A
Sbjct: 409 F-----SERKLKF-----SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAK 453
Score = 46.2 bits (109), Expect = 3e-05
Identities = 40/248 (16%), Positives = 78/248 (31%), Gaps = 64/248 (25%)
Query: 164 IVMLIDERPEEVTEMQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILL 223
I+ ++ P +T +G+ I + + + ++ EK + +
Sbjct: 1661 ILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFR 1720
Query: 224 DSITRLARAYNTVIPASGKVLT------------GGVDSNALQRPKRFF-G--------- 261
L+ T PA + G + ++A F G
Sbjct: 1721 SEKGLLSATQFTQ-PA---LTLMEKAAFEDLKSKGLIPADA------TFAGHSLGEYAAL 1770
Query: 262 AAR----NIEEG-------GSLTIIATALIETGS---RMDDVIYEEFKGTGNMEV--HLE 305
A+ +IE G +A E G M + + + E ++
Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVV 1830
Query: 306 RRLAEKR---VYPAINLNK-------SGTRR--EEL--LIQDDKLQKIWVLRKLLYSLTM 351
R+ ++ V N N +G R + + ++ KLQKI + +L SL++
Sbjct: 1831 ERVGKRTGWLVEIV-NYNVENQQYVAAGDLRALDTVTNVLNFIKLQKI-DIIELQKSLSL 1888
Query: 352 TSFTVSLF 359
LF
Sbjct: 1889 EEVEGHLF 1896
Score = 43.5 bits (102), Expect = 2e-04
Identities = 46/252 (18%), Positives = 73/252 (28%), Gaps = 109/252 (43%)
Query: 4 IGER---IFGDGSLE--VLPD----GFGFLRSQGSNYMASSDDIYLSPSQ----IRRFNL 50
IG R + + SL +L D G + M S + L+ Q + + N
Sbjct: 306 IGVRCYEAYPNTSLPPSILEDSLENNEG-----VPSPMLSISN--LTQEQVQDYVNKTNS 358
Query: 51 HTGDFVEGEIRVP-KNGERYF--------------ALLKIKKVNG----------EKPEL 85
H ++ + NG + L K K +G K +
Sbjct: 359 HLPA--GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKF 416
Query: 86 SKNRTLFDNLT-PLHPKKLL----------LLERNI---------------------ESK 113
S NR F + P H LL L++ N+
Sbjct: 417 S-NR--FLPVASPFH-SHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLS 472
Query: 114 ENITGRIIDLIA--PI----------------GKGQR---GLLVASPKSGK--SIILQHI 150
+I+ RI+D I P+ G G G+L K G +I +
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVI---V 529
Query: 151 AHAITTNHSEAI 162
A + N +
Sbjct: 530 AGTLDINPDDDY 541
Score = 39.6 bits (92), Expect = 0.003
Identities = 53/309 (17%), Positives = 94/309 (30%), Gaps = 92/309 (29%)
Query: 14 LEVLPDGF--GFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPK-----NG 66
+ VL F G +R + Y +S L PS + D +E VP +
Sbjct: 300 ITVL---FFIG-VRCYEA-YPNTS----LPPSILE-------DSLENNEGVPSPMLSISN 343
Query: 67 ERYFALLK-IKKVNGEKPELSKNRTLFDNL--TPLH------PKKLLLLERNIESKENIT 117
+ + K N P + + +L + P+ L L + +
Sbjct: 344 LTQEQVQDYVNKTNSHLPA---GKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK--- 397
Query: 118 GRIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTN-HSEAIMIVMLIDERPEEVT 176
AP G Q + P S + + + + + HS ++ +
Sbjct: 398 -------APSGLDQSRI----PFSERKLKFSNRFLPVASPFHSH-LL---------VPAS 436
Query: 177 EM--QRSVRGEVI--ASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVI-ILLDSITRLAR 231
++ + V+ V A P Y L + + ++D I RL
Sbjct: 437 DLINKDLVKNNVSFNAKDIQIPVY-DT-------FDGSDLRVLSGSISERIVDCIIRL-P 487
Query: 232 AY---NTVIPASGKVLTGGVDSNALQRPKRFFG----AARNIEEGGSLTIIATALIETGS 284
T A+ +L G P G RN + G I+A L +
Sbjct: 488 VKWETTTQFKAT-HILDFG--------PGGASGLGVLTHRNKDGTGVRVIVAGTL--DIN 536
Query: 285 RMDDVIYEE 293
DD +++
Sbjct: 537 PDDDYGFKQ 545
>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop,
phenylalanine mutant, hydrolase; 2.35A {Pyrococcus
horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A
3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A
3sdz_A
Length = 588
Score = 54.0 bits (130), Expect = 9e-08
Identities = 60/292 (20%), Positives = 100/292 (34%), Gaps = 55/292 (18%)
Query: 72 LLKIKKVNGEKPELS--------KNRTLFDNLTPLHPKKLLLLERNIESKENITG-RIID 122
+ K+K +GE EL R + L P P ITG R+ID
Sbjct: 174 IAKVKTPSGEIKELKMYQRWPVRVKRPYKEKLPPEVPL--------------ITGQRVID 219
Query: 123 LIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTE----- 177
P KG + SGK++ +A ++I + ER E+T+
Sbjct: 220 TFFPQAKGGTAAIPGPAGSGKTVTQHQLAKWSDAQ----VVIYIGCGERGNEMTDVLEEF 275
Query: 178 ------------MQRSVRGEVIASTFDEPAYRHVQVAEMVLEKAKRLVEMKKDVIILLDS 225
M+R+V +IA+T + P + A+ +M DV ++ DS
Sbjct: 276 PKLKDPKTGKPLMERTV---LIANTSNMPVAAREASIYTGITIAEYFRDMGYDVALMADS 332
Query: 226 ITRLARAYNTV------IP-ASGKVLTGGVDSNALQRPKRFFGAARNIEEGGSLTIIATA 278
+R A A + +P G + GS+++I
Sbjct: 333 TSRWAEALREISGRLEEMPGEEGYPAYLASKLAEFYERAGRVVTLGSDYRVGSVSVIGAV 392
Query: 279 LIETGSRMDDVIYEEFKGTGNMEVHLERRLAEKRVYPAINLNKSGTRREELL 330
G + V+ + L+ LA +R +PAIN S + + +
Sbjct: 393 SPPGGDFSEPVVQNTLRVVKVFWA-LDADLARRRHFPAINWLTSYSLYVDAV 443
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay,
RNR family, hydrolase; 2.35A {Escherichia coli} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A*
2ix1_A
Length = 644
Score = 34.1 bits (79), Expect = 0.15
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 10/57 (17%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFNLHTGDFVEGEIRVPKNGER 68
G ++ GFGFL ++ P Q+++ +H GD + + ER
Sbjct: 24 GVVKATEKGFGFLEVDA------QKSYFIPPPQMKKV-MH-GDRI--IAVIHSEKER 70
Score = 29.8 bits (68), Expect = 2.7
Identities = 8/36 (22%), Positives = 15/36 (41%), Gaps = 6/36 (16%)
Query: 421 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRR 456
G ++ GFGFL ++ P Q+++
Sbjct: 24 GVVKATEKGFGFLEVDA------QKSYFIPPPQMKK 53
>1nlf_A Regulatory protein REPA; replicative DNA helicase structural
changes, replication; 1.95A {Escherichia coli} SCOP:
c.37.1.11 PDB: 1g8y_A 1olo_A
Length = 279
Score = 32.4 bits (73), Expect = 0.39
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 130 GQRGLLVASPKSGKSIILQHIAHAITT 156
G G LV+ +GKS++ +A I
Sbjct: 30 GTVGALVSPGGAGKSMLALQLAAQIAG 56
>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA,
national P protein structural and functional analyses;
HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8
Length = 190
Score = 31.1 bits (71), Expect = 0.58
Identities = 20/105 (19%), Positives = 36/105 (34%), Gaps = 19/105 (18%)
Query: 133 GLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEEVTEMQRSVRGEVIASTFD 192
G ++ PK + I I H I N + V+++D + + RGE+ D
Sbjct: 55 GFMMGLPKEVQERIKDEIVHFIEDNAKNIDVAVLVVDGKAAPEIIKRWEKRGEIPI---D 111
Query: 193 EPAYRHVQVAEMVLEKAKRLVEMKKDVIILL---DSITRLARAYN 234
+ + L E+ I+ + D I + N
Sbjct: 112 V------EFYQF-------LRELDIPTIVAVNKLDKIKNVQEVIN 143
>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP
ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11
PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A*
1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A*
2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...
Length = 510
Score = 31.9 bits (73), Expect = 0.67
Identities = 31/141 (21%), Positives = 59/141 (41%), Gaps = 34/141 (24%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKS------IILQHIAHAITTNHSEAIMI----- 164
TG + +D + PIG+GQR L++ ++GK+ II Q + T + I
Sbjct: 148 TGIKAVDSLVPIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIG 207
Query: 165 -----VMLIDERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRL 212
V + +R + M+ ++ V+++T + A Y + E +
Sbjct: 208 QKRSTVAQLVKRLTDADAMKYTI---VVSATASDAAPLQYLAPYSGCSMGEYFRDNG--- 261
Query: 213 VEMKKDVIILLDSITRLARAY 233
K +I+ D +++ A AY
Sbjct: 262 ----KHALIIYDDLSKQAVAY 278
>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase,
single analysis, thermoalkaliphilic, hydrolase; 3.06A
{Bacillus SP} PDB: 1sky_B
Length = 502
Score = 31.1 bits (71), Expect = 1.2
Identities = 50/191 (26%), Positives = 78/191 (40%), Gaps = 51/191 (26%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIMIVMLI 168
ID + PIG+GQR L++ ++GK+ II Q I AI S +V
Sbjct: 153 IDSMIPIGRGQRELIIGDRQTGKTTIAIDTIINQKGQDVICIYVAIGQKQSTVAGVV--- 209
Query: 169 DERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVII 221
E + + ++ V+ ++ EPA Y + E + K K ++
Sbjct: 210 -ETLRQHDALDYTI---VVTASASEPAPLLYLAPYAGCAMGEYFMYKG-------KHALV 258
Query: 222 LLDSITRLARAYNTVI-----PASGKVLTGGV---DSNALQRPKRFFGAARNIEE--GGS 271
+ D +++ A AY + P + G V S L+R AA+ +E GGS
Sbjct: 259 VYDDLSKQAAAYRELSLLLRRPPGREAYPGDVFYLHSRLLER------AAKLSDEKGGGS 312
Query: 272 LTIIATALIET 282
LT A IET
Sbjct: 313 LT--ALPFIET 321
>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability,
potential tentoxin binding hydrolase; 3.20A {Spinacia
oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*
Length = 507
Score = 30.7 bits (70), Expect = 1.3
Identities = 32/132 (24%), Positives = 58/132 (43%), Gaps = 33/132 (25%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIMIVMLI 168
ID + P+G+GQR L++ ++GK+ I+ Q + AI S +V
Sbjct: 154 IDAMIPVGRGQRELIIGDRQTGKTAVATDTILNQQGQNVICVYVAIGQKASSVAQVV--- 210
Query: 169 DERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVII 221
+E M+ ++ V+A T D PA Y +AE + + + +I
Sbjct: 211 -TNFQERGAMEYTI---VVAETADSPATLQYLAPYTGAALAEYFMYRE-------RHTLI 259
Query: 222 LLDSITRLARAY 233
+ D +++ A+AY
Sbjct: 260 IYDDLSKQAQAY 271
>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for
structural genomics, JCSG, protein structure initiative
ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima
MSB8}
Length = 515
Score = 30.7 bits (70), Expect = 1.6
Identities = 30/132 (22%), Positives = 55/132 (41%), Gaps = 33/132 (25%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIMIVMLI 168
ID + PIG+GQR L++ ++GK+ II Q I AI S I+
Sbjct: 166 IDSMIPIGRGQRELIIGDRQTGKTAIAIDTIINQKGQGVYCIYVAIGQKKSAIARII--- 222
Query: 169 DERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVII 221
++ + M+ + V+ ++ +PA Y + E +D ++
Sbjct: 223 -DKLRQYGAMEYTT---VVVASASDPASLQYIAPYAGCAMGEYFAYSG-------RDALV 271
Query: 222 LLDSITRLARAY 233
+ D +++ A AY
Sbjct: 272 VYDDLSKHAVAY 283
>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC
F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1
b.49.1.1 c.37.1.11
Length = 473
Score = 30.4 bits (69), Expect = 1.7
Identities = 37/129 (28%), Positives = 62/129 (48%), Gaps = 18/129 (13%)
Query: 117 TG-RIIDLIAPIGKGQRGLLVASPKSGKSIILQHIAHAITTNHSEAIMIVMLIDERPEE- 174
TG +++DL+AP KG + L GK++++Q + H I H I + + ER E
Sbjct: 137 TGIKVVDLLAPYIKGGKIGLFGGAGVGKTVLIQELIHNIAQEHG-GISVFAGVGERTREG 195
Query: 175 ---VTEMQRSVRGEVIAST------FDEPAYRHVQVAEMVLEKAK--RLVEMKKDVIILL 223
EM+ S VI+ T +EP ++VA L A+ R + +D ++ +
Sbjct: 196 NDLYHEMKDS---GVISKTAMVFGQMNEPPGARMRVALTGLTMAEYFRDEQ-GQDGLLFI 251
Query: 224 DSITRLARA 232
D+I R +A
Sbjct: 252 DNIFRFTQA 260
>1x65_A UNR protein; cell-free protein synthesis, beta-barrel,
translational REGU RNA chaperone, RNA/DNA binding, QB
fold, greek-KEY topology protein; NMR {Homo sapiens}
Length = 89
Score = 28.3 bits (63), Expect = 1.9
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 8/70 (11%)
Query: 12 GSLEVLPDGFGFLRSQGSNYMASSDDIYLSPSQIRRFN-LHTGDFVEGEIRV-PKNGERY 69
G + + DGFGF++ + ++ S+I N LH D VE + + +R
Sbjct: 11 GVIAAMRDGFGFIKCVDRD-----VRMFFHFSEILDGNQLHIADEVEFTVVPDMLSAQRN 65
Query: 70 FALLKIKKVN 79
A ++IKK+
Sbjct: 66 HA-IRIKKLP 74
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 2.0
Identities = 5/24 (20%), Positives = 11/24 (45%), Gaps = 8/24 (33%)
Query: 304 LERRLAEKRVY-----PAINLNKS 322
L+ L ++Y PA+ + +
Sbjct: 25 LQASL---KLYADDSAPALAIKAT 45
Score = 28.4 bits (62), Expect = 4.0
Identities = 8/30 (26%), Positives = 18/30 (60%), Gaps = 6/30 (20%)
Query: 523 ERPEEVTEMQRSVRGEVIASTFDE-PALSV 551
E+ + + ++Q S++ + A D PAL++
Sbjct: 18 EK-QALKKLQASLK--LYAD--DSAPALAI 42
>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase,
hydrolase-transport PROT complex; HET: ANP ADP; 3.26A
{Escherichia coli DH1} PDB: 2a7u_A
Length = 513
Score = 29.2 bits (66), Expect = 4.9
Identities = 32/132 (24%), Positives = 56/132 (42%), Gaps = 33/132 (25%)
Query: 121 IDLIAPIGKGQRGLLVASPKSGKS------IILQH------IAHAITTNHSEAIMIVMLI 168
+D + PIG+GQR L++ ++GK+ II Q I AI S +V
Sbjct: 153 VDSMIPIGRGQRELIIGDRQTGKTALAIDAIINQRDSGIKCIYVAIGQKASTISNVV--- 209
Query: 169 DERPEEVTEMQRSVRGEVIASTFDEPA-------YRHVQVAEMVLEKAKRLVEMKKDVII 221
+ EE + ++ V+ +T E A Y + E ++ +D +I
Sbjct: 210 -RKLEEHGALANTI---VVVATASESAALQYLAPYAGCAMGEYFRDRG-------EDALI 258
Query: 222 LLDSITRLARAY 233
+ D +++ A AY
Sbjct: 259 IYDDLSKQAVAY 270
>2hk9_A Shikimate dehydrogenase; shikimate pathway, drug design,
oxidoreductase; HET: ATR SKM NAP; 2.20A {Aquifex
aeolicus} PDB: 2hk8_A 2hk7_A
Length = 275
Score = 28.3 bits (64), Expect = 6.1
Identities = 19/92 (20%), Positives = 35/92 (38%), Gaps = 35/92 (38%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG----GVDSNALQRPKRFFGAARNIEE 268
K+++I LLD + A+ A NTV +GK G G ++++
Sbjct: 76 KEEIIPLLDYVEDTAKEIGAVNTVKFENGK-AYGYNTDW------------IGFLKSLKS 122
Query: 269 ---------------GGSLTIIATALIETGSR 285
GG+ + AL++ G++
Sbjct: 123 LIPEVKEKSILVLGAGGASRAVIYALVKEGAK 154
>3jyo_A Quinate/shikimate dehydrogenase; enzyme-cofactor complex,
amino-acid biosynthesis, aromatic A biosynthesis, NAD,
oxidoreductase; HET: NAD; 1.00A {Corynebacterium
glutamicum} PDB: 3jyp_A* 3jyq_A* 2nlo_A
Length = 283
Score = 28.3 bits (64), Expect = 6.3
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG 246
K+ V+ LLD ++ A A NTV+ + TG
Sbjct: 73 KQAVLPLLDEVSEQATQLGAVNTVVIDATGHTTG 106
>1nvt_A Shikimate 5'-dehydrogenase; structural genomics, PSI, protein
structure initiative; HET: NAP; 2.35A
{Methanocaldococcus jannaschii} SCOP: c.2.1.7 c.58.1.5
Length = 287
Score = 28.3 bits (64), Expect = 7.4
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG 246
K +++ LD I + A+ A NT+ GK G
Sbjct: 75 KIEIMKYLDEIDKDAQLIGAVNTIKIEDGK-AIG 107
>3tnl_A Shikimate dehydrogenase; structural genomics, center for structural
genomics of infec diseases, csgid; HET: NAD SKM; 1.45A
{Listeria monocytogenes} PDB: 3toz_A*
Length = 315
Score = 28.4 bits (64), Expect = 7.8
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG 246
K ++ LD ++ A A NTV+ G LTG
Sbjct: 101 KTNIHKYLDKLSPAAELVGAVNTVVNDDGV-LTG 133
>3t4e_A Quinate/shikimate dehydrogenase; structural genomics, center for
structural genomics of infec diseases, csgid; HET: NAD;
1.95A {Salmonella enterica subsp} PDB: 1npd_A* 1o9b_A*
1vi2_A*
Length = 312
Score = 28.0 bits (63), Expect = 8.2
Identities = 16/62 (25%), Positives = 23/62 (37%), Gaps = 20/62 (32%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG----GVDSNALQRPKRFFGAARNIEE 268
K+ +D +T A+ A NT++ G L G G G R I+E
Sbjct: 95 KQLACEYVDELTPAAKLVGAINTIVNDDGY-LRGYNTDGT------------GHIRAIKE 141
Query: 269 GG 270
G
Sbjct: 142 SG 143
>2d5c_A AROE, shikimate 5-dehydrogenase; substrate, dimer, structural
genomics, NPPSFA, Na project on protein structural and
functional analyses; HET: SKM; 1.65A {Thermus
thermophilus} PDB: 1wxd_A* 2cy0_A* 2ev9_A*
Length = 263
Score = 27.9 bits (63), Expect = 8.7
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 10/79 (12%)
Query: 216 KKDVIILLDSITRLAR---AYNTVIPASGKVLTG------GVDSNALQRPKRFFGAARNI 266
K+ + LD ++ A+ A NTV+ G+ L G G G A +
Sbjct: 64 KEAALAHLDWVSPEAQRIGAVNTVLQVEGR-LFGFNTDAPGFLEALKAGGIPLKGPALVL 122
Query: 267 EEGGSLTIIATALIETGSR 285
GG+ +A AL E G
Sbjct: 123 GAGGAGRAVAFALREAGLE 141
>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox
sensor, atomic resolution, transferase; HET: FAD; 1.04A
{Azotobacter vinelandii}
Length = 120
Score = 27.1 bits (61), Expect = 8.8
Identities = 8/29 (27%), Positives = 11/29 (37%), Gaps = 5/29 (17%)
Query: 459 LHTGILWKGEI---RVPKNGERYFALLKI 484
L W G + R K+ Y A L +
Sbjct: 70 LAQKKPWSGVLVNRR--KDKTLYLAELTV 96
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.136 0.379
Gapped
Lambda K H
0.267 0.0769 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 9,187,408
Number of extensions: 602269
Number of successful extensions: 1063
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1034
Number of HSP's successfully gapped: 59
Length of query: 592
Length of database: 6,701,793
Length adjustment: 99
Effective length of query: 493
Effective length of database: 3,937,614
Effective search space: 1941243702
Effective search space used: 1941243702
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)