RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14505
(1619 letters)
>1zvu_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling,
decatenation, DNA bindi topology; 3.00A {Escherichia
coli}
Length = 716
Score = 975 bits (2522), Expect = 0.0
Identities = 223/776 (28%), Positives = 387/776 (49%), Gaps = 80/776 (10%)
Query: 30 VGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDAL 89
+ RALP + DGLKPV RR+++AM E+ + F K AR VG+ +GKYHPHGD + Y+A+
Sbjct: 1 MDRALPFIGDGLKPVQRRIVYAMSELGLNASAKFKKSARTVGDVLGKYHPHGDSACYEAM 60
Query: 90 VRMAQSFSLRCTLVDGQGNFGSIDGD-SAAAMRYTECRLNKISNELLIDLDKETIDFISN 148
V MAQ FS R LVDGQGN+G+ D S AAMRYTE RL+K S LL +L + T D++ N
Sbjct: 61 VLMAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKYSELLLSELGQGTADWVPN 120
Query: 149 YDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDL 208
+DG +EP +LP R+PN+L+NG++GIAVGMAT+IPPHNL EV + ++ P+ +++ L
Sbjct: 121 FDGTLQEPKMLPARLPNILLNGTTGIAVGMATDIPPHNLREVAQAAIALIDQPKTTLDQL 180
Query: 209 IKIIPAPDFPTAG-IIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQ 267
+ I+ PD+PT II + + Y G+G V +RA E+ A++I LP+Q
Sbjct: 181 LDIVQGPDYPTEAEIITSRAEIRKIYENGRGSVRMRAVWKKED------GAVVISALPHQ 234
Query: 268 VNKKSLLEKISQLVKEKKLECISNLRDESDKSG-MRIVIELKRNEI-PEIVLNKLYKQTQ 325
V+ +LE+I+ ++ KKL + +LRDESD R+VI + N + + V+N L+ T
Sbjct: 235 VSGARVLEQIAAQMRNKKLPMVDDLRDESDHENPTRLVIVPRSNRVDMDQVMNHLFATTD 294
Query: 326 LQNTFGMNMLAL-VNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLT 384
L+ ++ +N+ + ++G+P + NL EIL +++ R++ ++RR + L K + HILEGL
Sbjct: 295 LEKSYRINLNMIGLDGRPAVKNLLEILSEWLVFRRDTVRRRLNYRLEKVLKRLHILEGLL 354
Query: 385 IALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQ 444
+A NID I+IIR+ E K ++
Sbjct: 355 VAFLNIDEVIEIIRNE---DEPKPALMSR------------------------------- 380
Query: 445 NNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIIT 504
+ L++ QA+ IL++ L+ L +E+ KI + + K+ L IL++ +++ ++
Sbjct: 381 ----FGLTETQAEAILELKLRHLAKLEEMKIRGEQSELEKERDQLQGILASERKMNNLLK 436
Query: 505 DELNIIKNKYGSHKKNIRRSEIILN--AINPSTEDLIASQDMVITLSNLGYIKSQPISEY 562
EL YG RRS + A S D++ S+ + I LS +G++
Sbjct: 437 KELQADAQAYGDD----RRSPLQEREEAKAMSEHDMLPSEPVTIVLSQMGWV-------- 484
Query: 563 RAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYWLKVWQIPQGSRNSRGK 622
R+ K + K D ++ ++ + GR Y + +P S +G+
Sbjct: 485 RSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLP--SARGQGE 542
Query: 623 PIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKTLLSNFSNPRKSGIIA 682
P+ +L + +L S+++ + M++ G ++ ++G
Sbjct: 543 PLTGKLTLPPGATVDHMLMESDDQ-------KLLMASDAGYGFVCTFNDLVARNRAGKAL 595
Query: 683 VNLSNEDFLIGAALTDGSYD-IMLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQK- 740
+ L ++ + + + D ++ + +G+ + F + + + + +G + + +
Sbjct: 596 ITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSDLPQLSK-GKGNKIINIPSAEAA 654
Query: 741 -----VIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNG 791
+ L V Q + + R + RG +G + + +
Sbjct: 655 RGEDGLAQLYVLPPQSTLTIHVGKRKIKLRPEELQKVTGERGRRGTLMRGLQRIDR 710
Score = 79.2 bits (196), Expect = 6e-15
Identities = 31/182 (17%), Positives = 73/182 (40%), Gaps = 11/182 (6%)
Query: 679 GIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSV---RAMGRSARGVIGMRL 735
+N D A + ++ +G++ + ++ R G G + L
Sbjct: 493 DAPGLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLT--L 550
Query: 736 EKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVA 795
V +L+ ++ Q +L A++ GYG + NR K +I++ N V+
Sbjct: 551 PPGATVDHMLMESDD-QKLLMASDAGYGFVCTFNDLVARNRAGKALITLPEN---AHVMP 606
Query: 796 ATLVNRYHE-IMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRLCKITM 854
++ + ++ IT G ++ VS++ ++ + G +I + + G L ++ +
Sbjct: 607 PVVIEDASDMLLAITQAGRMLMFPVSDLPQLSKGK-GNKIINIPSAEAARGEDGLAQLYV 665
Query: 855 IK 856
+
Sbjct: 666 LP 667
>3lpx_A GYRA, DNA gyrase, A subunit; topoisomraseii, ATP-binding,
isomerase, nucleo binding; HET: DNA; 2.60A {Colwellia
psychrerythraea} PDB: 2wl2_A* 2y3p_A* 3nuh_A* 1ab4_A
Length = 500
Score = 856 bits (2214), Expect = 0.0
Identities = 269/499 (53%), Positives = 375/499 (75%), Gaps = 5/499 (1%)
Query: 32 RALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIYDALVR 91
RALPDVRDGLKPVHRRVLFAM + N WN+ + K ARVVG+ +GKYHPHGD ++YD +VR
Sbjct: 2 RALPDVRDGLKPVHRRVLFAMDVLGNDWNKAYKKSARVVGDVIGKYHPHGDTAVYDTIVR 61
Query: 92 MAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNYDG 151
MAQ FSLR LVDGQGNFGS+DGDSAAAMRYTE R++KI++ +L DLDKET+DF+ NYDG
Sbjct: 62 MAQPFSLRYMLVDGQGNFGSVDGDSAAAMRYTEIRMSKIAHSILADLDKETVDFVPNYDG 121
Query: 152 KEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLIKI 211
E P+V+PTR+PNLL+NG+SGIAVGMATNIPPHNLTEVI+ L ++ N E + ++++
Sbjct: 122 TEHIPAVMPTRVPNLLVNGTSGIAVGMATNIPPHNLTEVINACLALIDNSELTFEEILEH 181
Query: 212 IPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNKK 271
IP PDFPTAGII G + + + Y TG+G++ IRA+ I+ + II+ ELPYQVNK
Sbjct: 182 IPGPDFPTAGIISGRAGIEEAYRTGRGKIKIRARASIDVHETTGKETIIVHELPYQVNKA 241
Query: 272 SLLEKISQLVKEKKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNTFG 331
L+EK+++LVK+K+LE IS LRDESDK GMR+VIE+KR E+ E+VLN LYK TQ+Q +FG
Sbjct: 242 RLIEKMAELVKDKRLEGISALRDESDKDGMRMVIEIKRGEVGEVVLNNLYKLTQMQVSFG 301
Query: 332 MNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNID 391
+NM+AL NGQPK+ N+KE+L F+LHR+EV+ RRTIFELRKAR+ AHILEGL+IAL NID
Sbjct: 302 LNMVALTNGQPKIFNIKEMLEAFVLHRREVVTRRTIFELRKARDRAHILEGLSIALANID 361
Query: 392 NFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKL 451
I++I++++ +E++ K+I W L +V+ ++ + + ++ + +Y L
Sbjct: 362 PIIEMIKNSNNRKESEEKLISQGWELGNVANMLSEAGNDAARPEWLEPEYGIR-DGLYYL 420
Query: 452 SDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIITDELNIIK 511
+ QA+ I+ + L +L+ ME KI+++Y+ ++ + +L IL+ R++E+I +EL I+
Sbjct: 421 TAEQAKAIVDLQLYKLSGMEHDKILSEYKALLDLIAELMHILATPARLMEVICEELVAIR 480
Query: 512 NKYGSHKKNIRRSEIILNA 530
+++G + RR+EI L
Sbjct: 481 DEFG----DERRTEITLEH 495
>2inr_A DNA topoisomerase 4 subunit A; topoisomerase II fold; HET: DNA;
2.80A {Staphylococcus aureus}
Length = 514
Score = 855 bits (2211), Expect = 0.0
Identities = 216/527 (40%), Positives = 328/527 (62%), Gaps = 40/527 (7%)
Query: 1 MNQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWN 60
M + ++ + + LE+ + + Y+ +I RALPDVRDGLKPV RR+L+AM+ N +
Sbjct: 21 MLEVSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHD 80
Query: 61 RPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAM 120
+ F K A+ VG+ +G+YHPHGD S+Y+A+VR++Q + LR L++ GN GSID D AAM
Sbjct: 81 KNFRKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAM 140
Query: 121 RYTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMAT 180
RYTE +L+ ++ ELL D++KET+ FI NYD EP VLP+R PNLL+NGS+GI+ G AT
Sbjct: 141 RYTEAKLSLLAEELLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYAT 200
Query: 181 NIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRV 240
+IPPHNL EVI L + NP+ ++N L+K I PDFPT GII G+ + Y +GKGR+
Sbjct: 201 DIPPHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRI 260
Query: 241 IIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSG 300
I+R+K E R R +II E+PY+VNK SL+++I +L +KK++ I +RDE+D++G
Sbjct: 261 IVRSKVEEETL-RNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTG 319
Query: 301 MRIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKE 360
+RI IELK++ E + N LYK + LQ ++ NM+A+ +G+PKL+ +++I+ ++ H+ E
Sbjct: 320 LRIAIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIE 379
Query: 361 VIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDV 420
V+ RT FEL A + HI+EGL AL+ +D I++IRS+ ++AK +IE
Sbjct: 380 VVANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEV------- 432
Query: 421 SKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYE 480
Y+ ++ QA+ I+ + L RLTN + + +++
Sbjct: 433 ----------------------------YEFTEEQAEAIVMLQLYRLTNTDIVALEGEHK 464
Query: 481 NVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEII 527
+ + L IL N ++ +I +ELN IK K+ S R S I
Sbjct: 465 ELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKSE----RLSLIE 507
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 862 bits (2229), Expect = 0.0
Identities = 259/521 (49%), Positives = 366/521 (70%), Gaps = 41/521 (7%)
Query: 8 VISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCA 67
+ + EM +S+LDYAMSVIV RALPDVRDGLKPVHRR+L+ ++E ++ + K A
Sbjct: 210 INERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSA 269
Query: 68 RVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRL 127
R+VG+ MGKYHPHGD SIY+A+VRMAQ FS R LVDGQGNFGS+DGD AAAMR+TE R+
Sbjct: 270 RIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRFTEARM 329
Query: 128 NKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNL 187
KI+ ELL D++K+TIDFI NYDG E+EPSVLP R PNLL NG+SGIAVGMATNIPPHNL
Sbjct: 330 TKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNL 389
Query: 188 TEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTH 247
TE+I+GVL + NP+ SI +L++ I PDFPTAG+I G S + Y TG+G + +R++
Sbjct: 390 TELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAV 449
Query: 248 IEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD-KSGMRIVIE 306
IEE R I++ E+P+QVNK ++EKI++LV++KK++ I++LRDE+ ++G+R+VI+
Sbjct: 450 IEE-RGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVID 508
Query: 307 LKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRT 366
++++ ++LN LYKQT LQ +FG+NM+ALVNG+PKL+NLKE L +++ H+K V++RRT
Sbjct: 509 VRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRT 568
Query: 367 IFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGF 426
+ LRKA++ AHILEGL IAL +ID I IR + T + A + +
Sbjct: 569 QYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQR------------- 615
Query: 427 NKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKV 486
+KLS+ QAQ IL M L+RLT +E+ KI +Y ++ +
Sbjct: 616 ----------------------FKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYI 653
Query: 487 IDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEII 527
+L IL++ + +++++ DEL I++++G + RR+EI
Sbjct: 654 SELETILADEEVLLQLVRDELTEIRDRFG----DDRRTEIQ 690
>2nov_A DNA topoisomerase 4 subunit A; protein, PARC, TOPO IV,
GRAM-positive bacteria, quinolone target, DNA binding,
DNA cleavage; HET: DNA; 2.67A {Streptococcus pneumoniae}
PDB: 3foe_A* 3fof_A* 3k9f_A* 3ksa_A* 3ksb_A* 3ltn_A*
3rad_A* 3rae_A* 3raf_A*
Length = 496
Score = 852 bits (2204), Expect = 0.0
Identities = 204/521 (39%), Positives = 316/521 (60%), Gaps = 40/521 (7%)
Query: 7 EVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKC 66
+ ++ LE+ M + + Y+ +I RALPD+RDGLKPV RR+L++M++ +N +++ + K
Sbjct: 3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKS 62
Query: 67 ARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECR 126
A+ VG MG +HPHGD SIYDA+VRM+Q++ R LV+ GN GS+DGD AAMRYTE R
Sbjct: 63 AKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEAR 122
Query: 127 LNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHN 186
L++I+ LL D++K+T+ F N+D EKEP+VLP PNLL+NGS+GI+ G AT+IPPHN
Sbjct: 123 LSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHN 182
Query: 187 LTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKT 246
L EVID +Y++ +P I+ L++ +P PDFPT II G + Y TGKGRV++R+KT
Sbjct: 183 LAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKT 242
Query: 247 HIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIVIE 306
IE+ + + I+I E+PY++NK +L++KI + K+ I+ +RDESD+ G+RI IE
Sbjct: 243 EIEKL-KGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIE 301
Query: 307 LKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRT 366
LK++ E+VLN L+K T LQ + NM+A+ N P+ + + IL +I HR+EVI R+
Sbjct: 302 LKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARS 361
Query: 367 IFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGF 426
F+ KA + HI+EGL ++ +D I +IR++ +AK + S
Sbjct: 362 RFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVS------------- 408
Query: 427 NKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKV 486
Y ++ QA+ I+ + L RLTN + + + + +K+
Sbjct: 409 ----------------------YDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKI 446
Query: 487 IDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEII 527
L I+ + + + ++ EL +K K+ R S +
Sbjct: 447 AMLAAIIGDERTMYNLMKKELREVKKKFA----TPRLSSLE 483
>3ilw_A DNA gyrase subunit A; DNA topology, topoisomerase, antibiotic
resistance, breakage-reunion domain, struct genomics;
HET: DNA; 1.60A {Mycobacterium tuberculosis} PDB:
3ifz_A*
Length = 470
Score = 822 bits (2127), Expect = 0.0
Identities = 239/506 (47%), Positives = 324/506 (64%), Gaps = 45/506 (8%)
Query: 27 SVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDVSIY 86
SVIVGRALP+VRDGLKPVHRRVL+AM + +R K AR V ETMG YHPHGD SIY
Sbjct: 4 SVIVGRALPEVRDGLKPVHRRVLYAMFDSGFRPDRSHAKSARSVAETMGNYHPHGDASIY 63
Query: 87 DALVRMAQSFSLRCTLVDGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFI 146
D+LVRMAQ +SLR LVDGQGNFGS D AAMRYTE RL ++ E+L ++D+ET+DFI
Sbjct: 64 DSLVRMAQPWSLRYPLVDGQGNFGSPGNDPPAAMRYTEARLTPLAMEMLREIDEETVDFI 123
Query: 147 SNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECS-- 204
NYDG+ +EP+VLP+R PNLL NGS GIAVGMATNIPPHNL E+ D V + L N +
Sbjct: 124 PNYDGRVQEPTVLPSRFPNLLANGSGGIAVGMATNIPPHNLRELADAVFWALENHDADEE 183
Query: 205 --INDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIID 262
+ ++ + PDFPTAG+I G D Y TG+G + +R +EE + RT+++I
Sbjct: 184 ETLAAVMGRVKGPDFPTAGLIVGSQGTADAYKTGRGSIRMRGVVEVEE-DSRGRTSLVIT 242
Query: 263 ELPYQVNKKSLLEKISQLVKEKKLECISNLRDE-SDKSGMRIVIELKRNEIPEIVLNKLY 321
ELPYQVN + + I++ V++ KL ISN+ D+ SD+ G+RIVIE+KR+ + ++V+N LY
Sbjct: 243 ELPYQVNHDNFITSIAEQVRDGKLAGISNIEDQSSDRVGLRIVIEIKRDAVAKVVINNLY 302
Query: 322 KQTQLQNTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFELRKAREYAHILE 381
K TQLQ +FG NMLA+V+G P+ L L +++ Y++ H+ +VI RRT + LRKA E AHIL
Sbjct: 303 KHTQLQTSFGANMLAIVDGVPRTLRLDQLIRYYVDHQLDVIVRRTTYRLRKANERAHILR 362
Query: 382 GLTIALTNIDNFIQIIRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNIS 441
GL AL +D I +IR++ T A+ +IE
Sbjct: 363 GLVKALDALDEVIALIRASETVDIARAGLIEL---------------------------- 394
Query: 442 KLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIE 501
+ +IQAQ IL M L+RL +E+++II+ + ++ DL DIL+ +R
Sbjct: 395 -------LDIDEIQAQAILDMQLRRLAALERQRIIDDLAKIEAEIADLEDILAKPERQRG 447
Query: 502 IITDELNIIKNKYGSHKKNIRRSEII 527
I+ DEL I +++G RR+ II
Sbjct: 448 IVRDELAEIVDRHGDD----RRTRII 469
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 785 bits (2030), Expect = 0.0
Identities = 198/549 (36%), Positives = 307/549 (55%), Gaps = 56/549 (10%)
Query: 1 MNQFAKE-VISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLW 59
M A + + E ++YL+YAM VI+ RALP + DGLKPV RR+++AM E+
Sbjct: 265 MTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKS 324
Query: 60 NRPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLRCTLVDGQGNFGSIDGD-SAA 118
+ K AR VG+ +GKYHPHGD + Y+A+V MAQ FS R L++GQGN+GS D S A
Sbjct: 325 SGKPKKSARTVGDVLGKYHPHGDSACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFA 384
Query: 119 AMRYTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGM 178
AMRYTE +L+ S LL +L + T ++ N+DG KEP LP R+PN+L+NG++GIAVGM
Sbjct: 385 AMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGM 444
Query: 179 ATNIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAG-IIYGLSSVHDGYYTGK 237
AT+IPPHNL EV+ G + ++ NP+ S L + IPAPD PT II + TG+
Sbjct: 445 ATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGR 504
Query: 238 GRVIIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKEKKLECISNLRDESD 297
G +RA IE + I+I ELPYQV+ ++ +I+ ++ KKL + ++RDESD
Sbjct: 505 GSYRMRAVYTIE------KNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESD 558
Query: 298 KSG-MRIVIELKRNEI-PEIVLNKLYKQTQLQNTFGMNMLAL-VNGQPKLLNLKEILYYF 354
R+VI L+ N I E V++ L+ T L++++ +N+ + +G+P++ +++ IL +
Sbjct: 559 HENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEW 618
Query: 355 ILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKIIEST 414
I RK+ + RR + L + + HIL GL IA +ID I+IIR + K ++E
Sbjct: 619 IEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREE---DQPKPVLMEH- 674
Query: 415 WNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNMEQKK 474
+ + +IQA+ IL++ L+ L +E+ +
Sbjct: 675 ----------------------------------FNIDEIQAEAILELKLRHLAKLEEME 700
Query: 475 IINKYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEIIL--NAIN 532
I ++ + + K + + L N + + +I EL K+G RRS I+ A+
Sbjct: 701 IRHEQDELSAKAAIIREQLENPESLKNLIISELKEDAKKFGDE----RRSPIVARAEAVQ 756
Query: 533 PSTEDLIAS 541
+DL+ +
Sbjct: 757 IKEQDLMPA 765
>3l6v_A GYRA, DNA gyrase subunit A; gyrase A C-terminal domain, GYRA
C-terminal domain, DNA wrapping, beta-strand-bearing
proline, ATP-binding; HET: DNA; 2.19A {Xanthomonas
campestris PV}
Length = 370
Score = 487 bits (1257), Expect = e-159
Identities = 162/347 (46%), Positives = 227/347 (65%), Gaps = 38/347 (10%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYIL 596
DLIA +D+V+TLS+ GY K QP+S YRAQ+RGGRG+ A TK+ED+I+QL++ NTHD +L
Sbjct: 2 DLIAPEDVVVTLSHAGYAKRQPVSAYRAQRRGGRGRSAASTKEEDFIDQLWLVNTHDTLL 61
Query: 597 CFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVF 656
F++ G+++WL V Q+P+ N+RG+PIIN L++ E++ +LP+ R++ N YVF
Sbjct: 62 TFTSSGKVFWLPVHQLPEAGSNARGRPIINWIPLESGERVQAVLPV----REYADNRYVF 117
Query: 657 MSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFN 716
M+T G VKKT LS F+ G IA+NL D L+G ALTDG D++LF+ +GK VRF
Sbjct: 118 MATRNGTVKKTPLSEFAFRLARGKIAINLDEGDALVGVALTDGDRDVLLFASNGKTVRFG 177
Query: 717 ENSVRAMGRSARGVIGMRLEKKQKVIALLVSNN--------------------------- 749
E++VR+MGR+A GV G+RL K ++V++L+VS
Sbjct: 178 ESTVRSMGRTATGVRGIRLAKGEEVVSLIVSERAGGVEDEVEDESAEEVVETTDGAEPAV 237
Query: 750 -------QKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVNRY 802
+LTATENGYGKRT + EY + RGT+G+I I+T +RNGK+V A L+
Sbjct: 238 IDVADNGDVAYILTATENGYGKRTPLAEYPRKGRGTQGVIGIQTTERNGKLVRAVLLGST 297
Query: 803 HEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRL 849
E+MLI+ GG L+RTR SEI ++GR+TQGV LI + KL V+RL
Sbjct: 298 DEVMLISDGGTLVRTRGSEISRVGRNTQGVTLIRLSKGEKLQAVERL 344
Score = 56.9 bits (138), Expect = 2e-08
Identities = 25/148 (16%), Positives = 58/148 (39%), Gaps = 4/148 (2%)
Query: 502 IITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMVITLSNLGYIKSQPISE 561
I+++ ++++ ++T + GY K P++E
Sbjct: 206 IVSERAGGVEDEVEDESAEEVVETTDGAEPAVIDVADNGDVAYILTATENGYGKRTPLAE 265
Query: 562 YRAQKRGGRGKKAMMTKDE-DWINQLFIANTHDYILCFSNYGRLYWLKVWQIPQGSRNSR 620
Y + RG +G + T + + + + + D ++ S+ G L + +I + RN++
Sbjct: 266 YPRKGRGTQGVIGIQTTERNGKLVRAVLLGSTDEVMLISDGGTLVRTRGSEISRVGRNTQ 325
Query: 621 GKPIINMFSLKNKEKITVILPLSNNKRD 648
G +I L EK+ + L + +
Sbjct: 326 GVTLIR---LSKGEKLQAVERLDASLEE 350
>1zi0_A DNA gyrase subunit A; beta pinwheel, topoisomerase, spiralling beta
pinwheel, DNA wrapping, isomerase, DNA bindng protein;
HET: DNA; 2.60A {Escherichia coli}
Length = 307
Score = 483 bits (1247), Expect = e-159
Identities = 157/308 (50%), Positives = 221/308 (71%), Gaps = 5/308 (1%)
Query: 542 QDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNY 601
+D+V+TLS+ GY+K QP+SEY AQ+RGG+GK A K+ED+I++L +ANTHD+ILCFS+
Sbjct: 3 EDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSR 62
Query: 602 GRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSL 661
GR+Y +KV+Q+P+ +R +RG+PI+N+ L+ E+IT ILP+ +F + VFM+T+
Sbjct: 63 GRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPV----TEFEEGVKVFMATAN 118
Query: 662 GIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVR 721
G VKKT+L+ F+ R +G +A+ L + D LIG LT G ++MLFS GK VRF E+SVR
Sbjct: 119 GTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVR 178
Query: 722 AMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGI 781
AMG + GV G+RL + KV++L+V ++LTAT+NGYGKRT + EY +R TKG+
Sbjct: 179 AMGCNTTGVRGIRLGEGDKVVSLIVP-RGDGAILTATQNGYGKRTAVAEYPTKSRATKGV 237
Query: 782 ISIKTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKS 841
ISIK +RNG VV A V+ +IM+IT G L+RTRVSEI +GR+TQGVILI
Sbjct: 238 ISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDE 297
Query: 842 KLCGVQRL 849
+ G+QR+
Sbjct: 298 NVVGLQRV 305
Score = 41.7 bits (99), Expect = 0.001
Identities = 18/102 (17%), Positives = 42/102 (41%), Gaps = 6/102 (5%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDE--DWINQLFIANTHDY 594
+ ++T + GY K ++EY + R +G ++ + + + + +
Sbjct: 202 IVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQ- 260
Query: 595 ILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKI 636
I+ ++ G L +V +I RN++G +I E +
Sbjct: 261 IMMITDAGTLVRTRVSEISIVGRNTQGVILIR---TAEDENV 299
>1suu_A DNA gyrase subunit A; topoisomerase,DNA gyrase, beta-propeller,
beta-pinwheel, ISO; HET: DNA; 1.75A {Borrelia
burgdorferi} SCOP: b.68.10.1
Length = 312
Score = 480 bits (1238), Expect = e-157
Identities = 90/317 (28%), Positives = 167/317 (52%), Gaps = 7/317 (2%)
Query: 536 EDLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYI 595
DL+ +++V+ L+ G++K +EY+ Q GG+G + D D I NTHDY+
Sbjct: 2 SDLMQKENIVVMLTKKGFLKRLSQNEYKLQGTGGKGLSSFDLNDGDEIVIALCVNTHDYL 61
Query: 596 LCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYV 655
SN G+LY + ++I SR S+G+ I + +L ++E+I I +D + Y+
Sbjct: 62 FMISNEGKLYLINAYEIKDSSRASKGQNISELINLGDQEEILTIKNS----KDLTDDAYL 117
Query: 656 FMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRF 715
++T+ G + + ++F + G+I + L+++DF+ A + ++ S G A F
Sbjct: 118 LLTTASGKIARFESTDFKAVKSRGVIVIKLNDKDFVTSAEIVFKDEKVICLSKKGSAFIF 177
Query: 716 NENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHN 775
N VR R +GV GM+L++ + +L + +L +ENGYGKR + + ++
Sbjct: 178 NSRDVRLTNRGTQGVCGMKLKEGDLFVKVLSV-KENPYLLIVSENGYGKRLNMSKISELK 236
Query: 776 RGTKGIISIK-TNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVIL 834
RG G S K ++K+ G VV A V+ EI+L++ +RT ++ + G+ +G+ +
Sbjct: 237 RGATGYTSYKKSDKKAGSVVDAIAVSEDDEILLVSKRSKALRTVAGKVSEQGKDARGIQV 296
Query: 835 ITVENKSKLCGVQRLCK 851
+ ++N S + V + K
Sbjct: 297 LFLDNDSLV-SVSKFIK 312
>3uc1_A DNA gyrase subunit A; DNA binding protein, topoisomerase,
isomerase; HET: DNA; 1.65A {Mycobacterium tuberculosis}
Length = 327
Score = 477 bits (1231), Expect = e-156
Identities = 110/312 (35%), Positives = 188/312 (60%), Gaps = 7/312 (2%)
Query: 542 QDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNY 601
+D+V+T++ GY K YR+QKRGG+G + K +D + F+ +THD IL F+
Sbjct: 3 EDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGLKQDDIVAHFFVCSTHDLILFFTTQ 62
Query: 602 GRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSL 661
GR+Y K + +P+ SR +RG+ + N+ + + +E+I ++ + R + Y+ ++T
Sbjct: 63 GRVYRAKAYDLPEASRTARGQHVANLLAFQPEERIAQVIQI----RGYTDAPYLVLATRN 118
Query: 662 GIVKKTLLSNFSNPRKSGIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNEN--S 719
G+VKK+ L++F + R GI+AVNL + D L+GA L D++L S +G+++RF+ +
Sbjct: 119 GLVKKSKLTDFDSNRSGGIVAVNLRDNDELVGAVLCSAGDDLLLVSANGQSIRFSATDEA 178
Query: 720 VRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTK 779
+R MGR+ GV GMR ++++L V + +L AT GY KRT I+EY RG K
Sbjct: 179 LRPMGRATSGVQGMRFNIDDRLLSLNVV-REGTYLLVATSGGYAKRTAIEEYPVQGRGGK 237
Query: 780 GIISIKTNKRNGKVVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVEN 839
G++++ ++R G++V A +V+ E+ +T+GG +IRT ++RK GR T+GV L+ +
Sbjct: 238 GVLTVMYDRRRGRLVGALIVDDDSELYAVTSGGGVIRTAARQVRKAGRQTKGVRLMNLGE 297
Query: 840 KSKLCGVQRLCK 851
L + R +
Sbjct: 298 GDTLLAIARNAE 309
Score = 63.7 bits (156), Expect = 1e-10
Identities = 26/121 (21%), Positives = 50/121 (41%), Gaps = 7/121 (5%)
Query: 651 KNNYVFMSTSLGIVKKTLLSNFSNPRKS----GIIAVNLSNED-FLIGAALTDGSYDIML 705
+ Y+ ++TS G K+T + + P + G++ V L+GA + D ++
Sbjct: 208 EGTYLLVATSGGYAKRTAIEEY--PVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSELYA 265
Query: 706 FSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKR 765
+ G +R VR GR +GV M L + ++A+ + + NG +
Sbjct: 266 VTSGGGVIRTAARQVRKAGRQTKGVRLMNLGEGDTLLAIARNAEESGDDNAVDANGADQT 325
Query: 766 T 766
Sbjct: 326 G 326
Score = 43.7 bits (104), Expect = 3e-04
Identities = 25/84 (29%), Positives = 40/84 (47%), Gaps = 3/84 (3%)
Query: 749 NQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLV-NRYHEIML 807
N + V+T TE GY KRT Y RG KG+ + +VA V + + I+
Sbjct: 1 NAEDVVVTITETGYAKRTKTDLYRSQKRGGKGVQGAGL--KQDDIVAHFFVCSTHDLILF 58
Query: 808 ITTGGILIRTRVSEIRKMGRSTQG 831
TT G + R + ++ + R+ +G
Sbjct: 59 FTTQGRVYRAKAYDLPEASRTARG 82
Score = 43.7 bits (104), Expect = 4e-04
Identities = 19/102 (18%), Positives = 44/102 (43%), Gaps = 6/102 (5%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDE--DWINQLFIANTHDY 594
+++ ++ ++ GY K I EY Q RGG+G +M + L + + +
Sbjct: 204 NVVREGTYLLVATSGGYAKRTAIEEYPVQGRGGKGVLTVMYDRRRGRLVGALIVDDDSE- 262
Query: 595 ILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKI 636
+ ++ G + Q+ + R ++G ++N L + +
Sbjct: 263 LYAVTSGGGVIRTAARQVRKAGRQTKGVRLMN---LGEGDTL 301
>1wp5_A Topoisomerase IV; broken beta-propeller, hairpin-invaded
beta-propeller, six- bladed beta-propeller; 1.79A
{Geobacillus stearothermophilus} SCOP: b.68.10.1
Length = 323
Score = 463 bits (1195), Expect = e-151
Identities = 82/314 (26%), Positives = 153/314 (48%), Gaps = 11/314 (3%)
Query: 538 LIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILC 597
++AS+D+++T++ GY+K + Y A KD D + + NT D +L
Sbjct: 1 MVASEDVIVTVTKDGYVKRTSLRSYAASNGQDFA-----MKDTDRLLAMLEMNTKDVLLL 55
Query: 598 FSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFM 657
F+N G + V ++P G+ I N+ + E+I +P+ DF N Y
Sbjct: 56 FTNKGNYLYCPVHELPDIRWKDLGQHIANIIPIDRDEEIIKAIPI----NDFELNGYFLF 111
Query: 658 STSLGIVKKTLLSNFSNPRKS-GIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFN 716
T G+VKKT L ++ R S + +NL N+D ++ LTDG ++ L + +G A+ F+
Sbjct: 112 VTRNGMVKKTELKHYKAQRYSKPLTGINLKNDDQVVDVHLTDGMNELFLVTHNGYALWFD 171
Query: 717 ENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNR 776
E+ V +G A GV GM L++ +++ + ++ +S++ AT+ G K+ + E+ K R
Sbjct: 172 ESEVSIVGVRAAGVKGMNLKEGDYIVSGQLITSKDESIVVATQRGAVKKMKLTEFEKATR 231
Query: 777 GTKGIISIKTNKRNGK-VVAATLVNRYHEIMLITTGGILIRTRVSEIRKMGRSTQGVILI 835
+G++ ++ K N + + I L T + +V +IR R + G ++
Sbjct: 232 AKRGVVILRELKANPHRISGFVVAQDSDTIYLQTEKSFIETIKVGDIRFSDRYSNGSFVL 291
Query: 836 TVENKSKLCGVQRL 849
E ++ V ++
Sbjct: 292 DEEENGRVISVWKV 305
>3no0_A DNA gyrase subunit A; DNA topology, topoisomerase, C-terminal DO
gyrase, DNA binding protein, isomerase; HET: DNA GOL;
1.30A {Aquifex aeolicus}
Length = 276
Score = 377 bits (970), Expect = e-120
Identities = 64/292 (21%), Positives = 116/292 (39%), Gaps = 23/292 (7%)
Query: 559 ISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSNYGRLYWLKVWQIPQGSRN 618
I+ Q + + ++ + + + + SN GR+YW+ Q QGS+
Sbjct: 3 ITVAVLQDGSIIPVEEL-PLEKAPVVNILRVPFTEGLFLVSNRGRVYWIAGSQALQGSKV 61
Query: 619 SRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKTLLSNFSNPRKS 678
S EKI F N + ++T G VKK L+ F +
Sbjct: 62 SLKSRE---------EKIVGAFIR----EKF--GNRLLLATKKGYVKKIPLAEFEY-KAQ 105
Query: 679 GIIAVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKK 738
G+ + L+ D ++ A + I+LF+ G+ RF+ V ARGV G++LEK
Sbjct: 106 GMPIIKLTEGDEVVSIASSVDETHILLFTKKGRVARFSVREVPPSTPGARGVQGIKLEKN 165
Query: 739 QKVIALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATL 798
+ L + N + +L T G K+ +E K NRG KG + + +V
Sbjct: 166 DETSGLRIW-NGEPYLLVITAKGRVKKISHEEIPKTNRGVKG---TEVSGTKDTLVDLIP 221
Query: 799 VNRYHEIMLITTGGILIRTRVSE--IRKMGRSTQGVILITVENKSKLCGVQR 848
+ E+++ T G ++++ I + + +E+ + V +
Sbjct: 222 IKEEVELLITTKNGKAFYDKINQKDIPLSTKKSIPRTRWKLEDDEIIKVVIK 273
Score = 40.2 bits (95), Expect = 0.004
Identities = 19/109 (17%), Positives = 45/109 (41%), Gaps = 7/109 (6%)
Query: 537 DLIASQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYIL 596
+ + ++ ++ G +K E RG +G + ++ +D + L +L
Sbjct: 172 RIWNGEPYLLVITAKGRVKKISHEEIPKTNRGVKGTE--VSGTKDTLVDLIPIKEEVELL 229
Query: 597 CFSNYGRLYWLKV--WQIPQGSRNSRGKPIINMFSLKNKEKITVILPLS 643
+ G+ ++ K+ IP ++ S + L++ E I V++ S
Sbjct: 230 ITTKNGKAFYDKINQKDIPLSTKKSIPRTRWK---LEDDEIIKVVIKKS 275
>3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently
linked comple supercoiling; HET: DNA PTR TSP; 2.48A
{Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A
2rgr_A*
Length = 757
Score = 369 bits (949), Expect = e-111
Identities = 98/541 (18%), Positives = 203/541 (37%), Gaps = 51/541 (9%)
Query: 1 MNQFAKEVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWN 60
+ I + + + K + ++++ + R++P+V DG KP R+VL+ + N
Sbjct: 240 GTVLDPTLKEIPISDFINKELILFSLADNI-RSIPNVLDGFKPGQRKVLYGCFKKNLKSE 298
Query: 61 RPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFSLR----CTLVDGQGNFGSIDGDS 116
+ A V E YH HG+ S+ ++ +AQ+F L +G + G
Sbjct: 299 LKVAQLAPYVSECTA-YH-HGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKD 356
Query: 117 AAAMRYTECRLNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAV 176
AAA RY LNK++ ++ D +I D K EP +P +L+NG+ GI
Sbjct: 357 AAAARYIYTELNKLTRKIFHPADDPLYKYIQE-DEKTVEPEWYLPILPMILVNGAEGIGT 415
Query: 177 GMATNIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTG 236
G +T IPP N E+I + +++++ E G + +
Sbjct: 416 GWSTYIPPFNPLEIIKNIRHLMNDEEL-------------EQMHPWFRGWTGTIEEIEPL 462
Query: 237 KGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKI-SQLVKEKKLECISNLRDE 295
+ R+ R + + + I ELP + ++ E + L K++ +E
Sbjct: 463 RYRMYGRIE-------QIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEE 515
Query: 296 SDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQ---PKLLNLKEILY 352
++ +I L E+ + Y++ +L + + + + K ++ EIL
Sbjct: 516 QHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEILS 575
Query: 353 YFILHRKEVIKRRTIFELRKAREYAHILE------------GLTIALTNIDNFIQIIRST 400
F R E ++R + + LT+ + IQ + +
Sbjct: 576 EFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENL 635
Query: 401 STPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQA--QE 458
P+ K ++++ I K + + + N + ++ +
Sbjct: 636 GFPRFNKEGKPYYGSPNDEIAEQINDVKGATSDEEDEESSHEDTENVINGPEELYGTYEY 695
Query: 459 ILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHK 518
+L M + LT +K++ + + ++ +L + +I +L + Y
Sbjct: 696 LLGMRIWSLTKERYQKLLKQKQEKETELENLLKLS-----AKDIWNTDLKAFEVGYQEFL 750
Query: 519 K 519
+
Sbjct: 751 Q 751
>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide
monophosphate kinase,, transferase; 1.75A {Escherichia
coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A*
2cmk_A* 2fem_A 2feo_A*
Length = 227
Score = 306 bits (787), Expect = 1e-95
Identities = 94/214 (43%), Positives = 142/214 (66%), Gaps = 4/214 (1%)
Query: 859 IPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILI 918
PVITIDGP+ +GKGT+ + +A L +H LDSGA+YR++ L+A+++++ + +E LV L
Sbjct: 5 APVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLA 64
Query: 919 KKLNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFP 974
L+ F+ EV L G +V+ IR ++V+N AS++A F +R+ L + Q FR+ P
Sbjct: 65 SHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELP 124
Query: 975 GLVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIR 1034
GL+ADGRDMGT VFPDA +KIFL A ++R RR QL KGFSV+ LL + +RD R
Sbjct: 125 GLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQVKGFSVNFERLLAEIKERDDR 184
Query: 1035 DKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
D+ R ++PL A +L+++ ++I QV+ + L
Sbjct: 185 DRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQ 218
>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A
{Staphylococcus aureus}
Length = 219
Score = 295 bits (758), Expect = 8e-92
Identities = 74/210 (35%), Positives = 117/210 (55%), Gaps = 1/210 (0%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
I +DGP A+GK T+A+ VAS+L Y+D+GA+YR +T + N D +
Sbjct: 4 INIALDGPAAAGKSTIAKRVASELSMIYVDTGAMYRALTYKYLKLNKTEDFAKLVDQTTL 63
Query: 920 KLNYNF-LGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVA 978
L Y G+ V L+ +VT +RN V+ + S +A + +R K Q + G+V
Sbjct: 64 DLTYKADKGQCVILDNEDVTDFLRNNDVTQHVSYVASKEPVRSFAVKKQKELAAEKGIVM 123
Query: 979 DGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTR 1038
DGRD+GT V PDA LK+++ A +++R +RRYK +G + DL ++ RD D R
Sbjct: 124 DGRDIGTVVLPDADLKVYMIASVEERAERRYKDNQLRGIESNFEDLKRDIEARDQYDMNR 183
Query: 1039 NLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
+SPL+ + A L+T+ +I +V ++IL
Sbjct: 184 EISPLRKADDAVTLDTTGKSIEEVTDEILA 213
>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase,
transferase; NMR {Streptococcus pneumoniae} SCOP:
c.37.1.1
Length = 236
Score = 295 bits (759), Expect = 1e-91
Identities = 83/214 (38%), Positives = 125/214 (58%), Gaps = 5/214 (2%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
I IDGP +SGK TVA+++A GF YLD+GA+YR T A+ N + ++ L+ L+
Sbjct: 17 IQIAIDGPASSGKSTVAKIIAKDFGFTYLDTGAMYRAATYMALKNQLGVEEVEALLALLD 76
Query: 920 KLNYNFLGKE-----VYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFP 974
+ +F E V++ V++T IR +V+N+ S IA +R++L +Q + +
Sbjct: 77 QHPISFGRSETGDQLVFVGDVDITHPIRENEVTNHVSAIAAIPEVREKLVSLQQEIAQQG 136
Query: 975 GLVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIR 1034
G+V DGRD+GT V P A LKIFL A + +R +RRYK+ + KG + L + RD +
Sbjct: 137 GIVMDGRDIGTVVLPQAELKIFLVASVDERAERRYKENIAKGIETDLETLKKEIAARDYK 196
Query: 1035 DKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
D R SPLK E A L+T+ +NI +VV +I
Sbjct: 197 DSHRETSPLKQAEDAVYLDTTGLNIQEVVEKIKA 230
>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics
center for infectious disease, ssgcid, ADP, DCMP, D
transferase; 2.00A {Mycobacterium smegmatis} PDB: 3r8c_A
4die_A*
Length = 233
Score = 292 bits (749), Expect = 2e-90
Identities = 72/221 (32%), Positives = 119/221 (53%), Gaps = 6/221 (2%)
Query: 853 TMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNEL 912
+M+ V+ +DGP +GK +V++ +A LG YLD+GA+YR+ TL+ + L +
Sbjct: 4 SMVSG-SLVVAVDGPAGTGKSSVSRGLARALGARYLDTGAMYRIATLAVLRAGADLTDPA 62
Query: 913 ELVILIKKLNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQV 968
+ +L G +V++ IR + V+ S ++ +R L IQ
Sbjct: 63 AIEKAAADAEIGVGSDPDVDAAFLAGEDVSSEIRGDAVTGAVSAVSAVPAVRTRLVDIQR 122
Query: 969 KFRKFPG-LVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLIN 1027
K G +V +GRD+GT V PDA +KIFLTA ++R +RR Q + G + +L +
Sbjct: 123 KLATEGGRVVVEGRDIGTVVLPDADVKIFLTASAEERARRRNAQNVANGLPDDYATVLAD 182
Query: 1028 LIKRDIRDKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
+ +RD D TR +SPL+ + A +++TS M+ QV+ +LD
Sbjct: 183 VQRRDHLDSTRPVSPLRAADDALVVDTSDMDQAQVIAHLLD 223
>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation,
nucleotide metab transferase; HET: C5P; 1.50A {Thermus
thermophilus} PDB: 3akc_A* 3akd_A*
Length = 208
Score = 268 bits (688), Expect = 1e-82
Identities = 71/214 (33%), Positives = 114/214 (53%), Gaps = 17/214 (7%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIK 919
++TIDGP+ASGK +VA+ VA+ LG YL SG LYR A+ + +E L+ L++
Sbjct: 3 GIVTIDGPSASGKSSVARRVAAALGVPYLSSGLLYRAAAFLALRAGVDPGDEEGLLALLE 62
Query: 920 KLNYNFL----GKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKF-P 974
L L G V +G ++T+ + +V S +A+ +R + + ++ P
Sbjct: 63 GLGVRLLAQAEGNRVLADGEDLTSFLHTPEVDRVVSAVARLPGVRAWVNRRL---KEVPP 119
Query: 975 GLVADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIR 1034
VA+GRDMGT VFP+A K +LTA + R RR ++ Q ++L +L++RD R
Sbjct: 120 PFVAEGRDMGTAVFPEAAHKFYLTASPEVRAWRRARERPQAY-----EEVLRDLLRRDER 174
Query: 1035 DKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
DK + A +L+T M +++VV +L
Sbjct: 175 DKAQ----SAPAPDALVLDTGGMTLDEVVAWVLA 204
>2khi_A 30S ribosomal protein S1; acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 115
Score = 190 bits (486), Expect = 8e-57
Identities = 65/113 (57%), Positives = 86/113 (76%), Gaps = 1/113 (0%)
Query: 1311 LKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVH 1370
+ + S G+ G W+ ++ RYP GT+L G+VTNLTDYG FVEIE+G+EGLVH
Sbjct: 1 MGSSHHHHHHSSGLVPRG-SHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVH 59
Query: 1371 ISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFS 1423
+SEMDW NKN+ PSK+V + D VE+M+L+I+EERRRISLG+KQCK NPW+ F+
Sbjct: 60 VSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFA 112
Score = 140 bits (356), Expect = 3e-39
Identities = 32/118 (27%), Positives = 64/118 (54%), Gaps = 9/118 (7%)
Query: 1398 LEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIH 1457
+ + S G+ + + W + + +G K+ G + ++TD+G F+ ++ ++GL+H
Sbjct: 1 MGSSHHHHHHSSGLVP-RGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVEGLVH 59
Query: 1458 LSDLSWT----DPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPFNNYVN 1511
+S++ WT P + GD +E ++L ID E+ RISLG+KQ + +P+ +
Sbjct: 60 VSEMDWTNKNIHPSKV----VNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAE 113
Score = 115 bits (290), Expect = 3e-30
Identities = 31/120 (25%), Positives = 62/120 (51%), Gaps = 7/120 (5%)
Query: 1222 IKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLG-GID 1280
+ ++ G + + EG + G V N+TDYG F+++ G++
Sbjct: 1 MGSSHHHHHHSSGLVP-----RGSHWVAIAKRYPEGTKLTGRVTNLTDYGCFVEIEEGVE 55
Query: 1281 GLLHITDIAW-RRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRY 1339
GL+H++++ W + HPS+++ +G + +L D+E+ R+SLG+KQ +PW + +
Sbjct: 56 GLVHVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLKQCKANPWQQFAETH 115
Score = 76.1 bits (188), Expect = 1e-16
Identities = 23/103 (22%), Positives = 46/103 (44%), Gaps = 7/103 (6%)
Query: 1485 LSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYL 1544
+ S G+ + +G+ + G + ++ T+ G +++ VEG +
Sbjct: 1 MGSSHHHHHHSSGLVPRG-SHWVAIAKRYPEGTKLTGRVTNL-TDYGCFVEIEEGVEGLV 58
Query: 1545 RISEED----NKHEKK-LKIGENIDVLTVLIDHKTRYIQLSFK 1582
+SE D N H K + +G+ ++V+ + ID + R I L K
Sbjct: 59 HVSEMDWTNKNIHPSKVVNVGDVVEVMVLDIDEERRRISLGLK 101
>3ku8_A GYRA14, DNA gyrase subunit A; alpha+beta, SH3 domain,
topoisomerase, toxin-isomerase compl; HET: DNA; 1.93A
{Escherichia coli} PDB: 1x75_A* 3kua_A*
Length = 156
Score = 174 bits (443), Expect = 3e-50
Identities = 52/148 (35%), Positives = 90/148 (60%), Gaps = 1/148 (0%)
Query: 351 LYYFILHRKEVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTPQEAKNKI 410
++ R + RRTIFELRKAR+ AHILE L +AL NID I++IR TP EAK +
Sbjct: 10 HSSGLVPRGSHMTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTAL 69
Query: 411 IESTWNLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTNM 470
+ + W L +V+ ++ + + +++ +Y L++ QAQ IL + LQ+LT +
Sbjct: 70 VANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDG-LYYLTEQQAQAILDLRLQKLTGL 128
Query: 471 EQKKIINKYENVIKKVIDLTDILSNSKR 498
E +K++++Y+ ++ ++ +L IL ++ R
Sbjct: 129 EHEKLLDEYKELLDQIAELLRILGSADR 156
>2a19_A EIF-2- alpha, eukaryotic translation initiation factor 2 alpha;
transferase, protein biosynthesis, protein synthesis
transferase complex; HET: TPO ANP; 2.50A {Saccharomyces
cerevisiae} PDB: 2a1a_A* 1q46_A
Length = 175
Score = 173 bits (440), Expect = 1e-49
Identities = 28/162 (17%), Positives = 71/162 (43%), Gaps = 8/162 (4%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
+ V V+ I + GA++ L I+G++ +++++ RR++ +++ +G++ +L
Sbjct: 14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLIRVGKNDVAVVL 73
Query: 1312 KYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHI 1371
+ D+EK + L +++ + I +Y + V ++ Y A + + +E L
Sbjct: 74 RVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSK----TVHSILRYCAE-KFQIPLEELYKT 128
Query: 1372 SEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQ 1413
K + +L+ E + I + + +K
Sbjct: 129 IAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDELKN 170
Score = 140 bits (355), Expect = 3e-38
Identities = 25/168 (14%), Positives = 65/168 (38%), Gaps = 13/168 (7%)
Query: 1338 RYPR-GTRLLGKVTNLTDYGAFVEIEK--GIEGLVHISEMDW--INKNVTPSKIVQLNDT 1392
+YP ++ V + + GA+V++ + IEG++ +SE+ I K++++
Sbjct: 11 KYPEIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRS---IQKLIRVGKN 67
Query: 1393 VEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNI 1452
++L +++E+ I L ++ ++K + + I++ + +
Sbjct: 68 DVAVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAE-----KFQIPL 122
Query: 1453 DGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQ 1500
+ L + FK E + I+ + + +K
Sbjct: 123 EELYKTIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDELKN 170
Score = 92.9 bits (231), Expect = 1e-21
Identities = 30/174 (17%), Positives = 65/174 (37%), Gaps = 22/174 (12%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIE 1481
+ + + ++ I + G ++ L NI+G+I LS+LS + I + G
Sbjct: 14 EIDDIVMVNVQQIAEMGAYVKLLEYDNIEGMILLSELSRRRIRSIQKLI----RVGKNDV 69
Query: 1482 AIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVE 1541
A++L +D EK I L +++ + K V+ I++ + +E
Sbjct: 70 AVVLRVDKEKGYIDLSKRRVSSEDIIKCEEKYQKSKTVHSILRYCAE------KFQIPLE 123
Query: 1542 GYLRISEED----NKH-EKKLKIGENIDVLTVLIDHKTRYIQLSFKKKEVIKKK 1590
+ H + K+ + + I+ ++ + K I K+
Sbjct: 124 ELYKTIAWPLSRKFGHAYEAFKLSIIDETVWEGIEPPSKDVLDEL--KNYISKR 175
>2k4k_A GSP13, general stress protein 13; cytoplasm, stress response, RNA
binding protein; NMR {Bacillus subtilis}
Length = 130
Score = 154 bits (391), Expect = 9e-44
Identities = 31/131 (23%), Positives = 58/131 (44%), Gaps = 3/131 (2%)
Query: 1250 LIETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDIST 1308
+ + G G V + YGAF+ L GL+HI+++ VK +E L++G ++
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 1309 KILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGL 1368
K+L D+EK ++SL ++ P PR + + F ++ +E
Sbjct: 61 KVLAVDEEKGKISLSIRATQAAPEK--KESKPRKPKAAQVSEEASTPQGFNTLKDKLEEW 118
Query: 1369 VHISEMDWINK 1379
+ +S + K
Sbjct: 119 IEMSNRKDLIK 129
Score = 139 bits (352), Expect = 1e-38
Identities = 34/131 (25%), Positives = 67/131 (51%), Gaps = 5/131 (3%)
Query: 1335 LSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNV-TPSKIVQLNDTV 1393
++ ++ G+ GKVT L YGAFV +++ +GLVHISE+ V ++ + + D V
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTH--GFVKDINEHLSVGDEV 58
Query: 1394 EIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNID 1453
++ +L ++EE+ +ISL ++ + P + S + K + + + F L ++
Sbjct: 59 QVKVLAVDEEKGKISLSIRATQAAPEKKES--KPRKPKAAQVSEEASTPQGFNTLKDKLE 116
Query: 1454 GLIHLSDLSWT 1464
I +S+
Sbjct: 117 EWIEMSNRKDL 127
Score = 94.0 bits (234), Expect = 2e-22
Identities = 28/132 (21%), Positives = 59/132 (44%), Gaps = 10/132 (7%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIEAI 1483
+ G G + + +G F+ LD GL+H+S+++ D E + GDE++
Sbjct: 6 EVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHL----SVGDEVQVK 61
Query: 1484 ILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGY 1543
+L++D EK +ISL I+ + P + + + + L +++E +
Sbjct: 62 VLAVDEEKGKISLSIRATQAAPEKK--ESKPRKPKAAQVSEEA-STPQGFNTLKDKLEEW 118
Query: 1544 LRISEEDNKHEK 1555
+ +S + +K
Sbjct: 119 IEMSNRKDLIKK 130
Score = 55.5 bits (134), Expect = 4e-09
Identities = 26/136 (19%), Positives = 47/136 (34%), Gaps = 10/136 (7%)
Query: 1163 LEKAMESGEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMDF 1219
+ E G + TG + G G V L + + S V VKD G +
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 1220 KVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLG-G 1278
KV+ +D ++ + LS RA +E + V + + F L
Sbjct: 61 KVLAVDEEKGKISLSIRATQAAPEKKESK------PRKPKAAQVSEEASTPQGFNTLKDK 114
Query: 1279 IDGLLHITDIAWRRVK 1294
++ + +++ K
Sbjct: 115 LEEWIEMSNRKDLIKK 130
Score = 45.1 bits (107), Expect = 1e-05
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 5/74 (6%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
GS+ G + + GA + L E +G + ISE + K L +G+ + V + +D
Sbjct: 8 GSVYTGKVTGL-QAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAVD 66
Query: 1572 HKTRYIQLSFKKKE 1585
+ I LS + +
Sbjct: 67 EEKGKISLSIRATQ 80
>1kl9_A Eukaryotic translation initiation factor 2 subuni; OB fold, helical
domain; 1.90A {Homo sapiens} SCOP: a.60.14.1 b.40.4.5
Length = 182
Score = 152 bits (385), Expect = 3e-42
Identities = 27/164 (16%), Positives = 80/164 (48%), Gaps = 10/164 (6%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
+ V V++I + GA++ L I+G++ +++++ RR++ ++++ IG++ ++
Sbjct: 14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVI 73
Query: 1312 KYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHI 1371
+ D+EK + L +++ + I ++ + + + ++ + + + E +E L
Sbjct: 74 RVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDE-QLESLFQR 132
Query: 1372 SEMDWINKNVTPSKIV------QLNDTVEIMILEINEERRRISL 1409
+ + +K P ++D + L++NE+ R + +
Sbjct: 133 TAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLI 176
Score = 131 bits (332), Expect = 3e-35
Identities = 26/172 (15%), Positives = 77/172 (44%), Gaps = 9/172 (5%)
Query: 1338 RYPR-GTRLLGKVTNLTDYGAFVEIEK--GIEGLVHISEMDWINKNVTPSKIVQLNDTVE 1394
++P ++ V ++ + GA+V + + IEG++ +SE+ + + +K++++
Sbjct: 11 KFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSR-RRIRSINKLIRIGRNEC 69
Query: 1395 IMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDG 1454
++++ +++E+ I L ++ K + + I++ + + + + ++
Sbjct: 70 VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQ-LES 128
Query: 1455 LIHLSDLSWTD----PGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLE 1502
L + + D PG FK +I+ S+D+ ++ + I +
Sbjct: 129 LFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNIN 180
Score = 93.0 bits (231), Expect = 2e-21
Identities = 23/128 (17%), Positives = 51/128 (39%), Gaps = 10/128 (7%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIE 1481
+ + + ++SI + G ++ L NI+G+I LS+LS + I + G
Sbjct: 14 EVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLI----RIGRNEC 69
Query: 1482 AIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVE 1541
+++ +D EK I L +++ + + K V I++ + +
Sbjct: 70 VVVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHV-AEVLEYTKDEQLES 128
Query: 1542 GYLRISEE 1549
+ R +
Sbjct: 129 LFQRTAWV 136
Score = 63.3 bits (154), Expect = 2e-11
Identities = 24/143 (16%), Positives = 55/143 (38%), Gaps = 10/143 (6%)
Query: 1164 EKAMESGEIITGTINGKVKGGLTV---LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMD 1218
K E +++ + + G V N ++ + S + R ++ G+
Sbjct: 10 HKFPEVEDVVMVNVRSIAEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNEC 69
Query: 1219 FKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLGG 1278
VI++D+++ + LS R V E E K + + TV +++++ + +
Sbjct: 70 VVVIRVDKEKGYIDLSKRRVSPE----EAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQ 125
Query: 1279 IDGLLHITDIAW-RRVKHPSEIL 1300
++ L T + + K P
Sbjct: 126 LESLFQRTAWVFDDKYKRPGYGA 148
Score = 45.6 bits (108), Expect = 3e-05
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 7/74 (9%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLS--NEVEGYLRISEEDNKHEKK----LKIGENIDVLTVL 1569
+V ++SI GA + L N +EG + +SE + + ++IG N V+ +
Sbjct: 16 EDVVMVNVRSI-AEMGAYVSLLEYNNIEGMILLSELSRRRIRSINKLIRIGRNECVVVIR 74
Query: 1570 IDHKTRYIQLSFKK 1583
+D + YI LS ++
Sbjct: 75 VDKEKGYIDLSKRR 88
>1q8k_A Eukaryotic translation initiation factor 2 subunit 1; NMR {Homo
sapiens} SCOP: a.60.14.1 b.40.4.5 d.58.51.1
Length = 308
Score = 153 bits (389), Expect = 3e-41
Identities = 33/198 (16%), Positives = 94/198 (47%), Gaps = 20/198 (10%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
+ V V++I + GA++ L I+G++H+++++ RR++ ++++ IG++ K++
Sbjct: 12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVI 71
Query: 1312 KYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHI 1371
+ D+EK + L +++ + I ++ + + + ++ + + + ++ +E L
Sbjct: 72 RVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTK-DEQLESLFQR 130
Query: 1372 SEMDWINKNVTPSKIV------QLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSII 1425
+ + +K P ++D + L++NE+ R + + + P
Sbjct: 131 TAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTP------- 183
Query: 1426 HKKGEKIKGIIKSITDFG 1443
+ KI+ I+ + +G
Sbjct: 184 --QAVKIRADIE-VACYG 198
Score = 106 bits (265), Expect = 6e-25
Identities = 31/198 (15%), Positives = 81/198 (40%), Gaps = 17/198 (8%)
Query: 1338 RYPR-GTRLLGKVTNLTDYGAFVEIEK--GIEGLVHISEMDW--INKNVTPSKIVQLNDT 1392
++P ++ V ++ + GA+V + + IEG++H+SE+ I +K++++
Sbjct: 9 KFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRS---INKLIRIGRN 65
Query: 1393 VEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNI 1452
+ ++ +++E+ I L ++ K + + I++ + + + + +
Sbjct: 66 ECVKVIRVDKEKGYIDLSKRRVSPEEAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQ-L 124
Query: 1453 DGLIHLSDLSWTD----PGEEIIRNFKK----GDEIEAIILSIDVEKERISLGIKQLEGD 1504
+ L + + D PG FK ++++ L+ D + I+ ++L
Sbjct: 125 ESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTPQ 184
Query: 1505 PFNNYVNINDKGSLVNGI 1522
+I GI
Sbjct: 185 AVKIRADIEVACYGYEGI 202
Score = 61.1 bits (148), Expect = 9e-10
Identities = 28/183 (15%), Positives = 68/183 (37%), Gaps = 18/183 (9%)
Query: 1164 EKAMESGEIITGTINGKVKGGLTV---LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMD 1218
K E +++ + + G V N ++ + S + R ++ G+
Sbjct: 8 HKFPEVEDVVMVNVRSIQEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNEC 67
Query: 1219 FKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLGG 1278
KVI++D+++ + LS R V E E K + + TV +++++ + +
Sbjct: 68 VKVIRVDKEKGYIDLSKRRVSPE----EAIKCEDKFTKSKTVYSILRHVAEVLEYTKDEQ 123
Query: 1279 IDGLLHITDIAW-RRVKHPSEIL--------TIGQDISTKILKYDQEKNRVSLGMKQLGI 1329
++ L T + + K P + + + L D+ + ++ ++L
Sbjct: 124 LESLFQRTAWVFDDKYKRPGYGAYDAFKHAVSDPSILDSLDLNEDEREVLINNINRRLTP 183
Query: 1330 DPW 1332
Sbjct: 184 QAV 186
Score = 42.6 bits (100), Expect = 7e-04
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 7/82 (8%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLS--NEVEGYLRISEEDNKHEKK----LKIGENIDVLTVL 1569
+V ++SI GA + L N +EG + +SE + + ++IG N V +
Sbjct: 14 EDVVMVNVRSI-QEMGAYVSLLEYNNIEGMIHLSELSRRRIRSINKLIRIGRNECVKVIR 72
Query: 1570 IDHKTRYIQLSFKKKEVIKKKK 1591
+D + YI LS ++ + K
Sbjct: 73 VDKEKGYIDLSKRRVSPEEAIK 94
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain,
coiled-coil domain, DNA and cleavage, nucleus; HET: DNA
EVP; 2.16A {Homo sapiens}
Length = 803
Score = 162 bits (411), Expect = 8e-41
Identities = 104/529 (19%), Positives = 202/529 (38%), Gaps = 54/529 (10%)
Query: 15 EEMCKSYLDYAMSVIVGRALPDVRDGLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETM 74
+ L + R++P + DG KP R+VLF + N+ + VK A++ G
Sbjct: 294 NDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFKRND---KREVKVAQLAGSVA 350
Query: 75 GK--YHPHGDVSIYDALVRMAQSFSL--RCTLVDGQGNFGSI--DGDSAAAMRYTECRLN 128
YH HG+ ++ +V +AQ+F L+ G FG+ G AA+ RY L+
Sbjct: 351 EMSAYH-HGEQALMMTIVNLAQNFVGSNNINLLQPIGQFGTRLHGGKDAASPRYIFTMLS 409
Query: 129 KISNELLIDLDKETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLT 188
++ L +D + F+ D + EP IP +LING+ GI G A +P ++
Sbjct: 410 TLARLLFPAVDDNLLKFL-YDDNQRVEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAR 468
Query: 189 EVIDGVLYVLHNPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHI 248
E+++ V +L + P++ + + Y G + + + +
Sbjct: 469 EIVNNVRRMLDGLD-------PHPMLPNYK--NFKGTIQELGQNQYAVSGEIFVVDRNTV 519
Query: 249 EEFNRENRTAIIIDELPYQVNKKSLLEKISQLV---KEKKLECISNLRDESDKSGMRIVI 305
E I ELP + + E++ + + +K IS+ ++ + ++ V+
Sbjct: 520 E-----------ITELPVRTWTQVYKEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVV 568
Query: 306 ELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPKL---LNLKEILYYFILHRKEVI 362
++ ++ + L+K +LQ T N + L + L +++IL F R
Sbjct: 569 KMTEEKLAQAEAAGLHKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYY 628
Query: 363 KRRTIFELRKAREYAHILEGLTIALTNIDNFIQ-IIRSTSTPQEAKNKIIESTWNLPDVS 421
R + + + L N FI I+ T + K +
Sbjct: 629 GLRKEWLVGMLGAESTK-------LNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYE 681
Query: 422 KIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQE----ILKMPLQRLTNMEQKKIIN 477
K + + ++ Q++D S + IL M L LT + +++I
Sbjct: 682 SDPVKAWKEAQEKAAEEDETQNQHDDSSSDSGTPSGPDFNYILNMSLWSLTKEKVEELIK 741
Query: 478 KYENVIKKVIDLTDILSNSKRIIEIITDELNIIKNKYGSHKKNIRRSEI 526
+ + ++V DL K ++ ++L + + R
Sbjct: 742 QRDAKGREVNDL-----KRKSPSDLWKEDLAAFVEELDKVESQEREDGA 785
>2khj_A 30S ribosomal protein S1; OB fold, acetylation, phosphoprotein,
ribonucleoprotein, RNA-binding; NMR {Escherichia coli}
Length = 109
Score = 135 bits (343), Expect = 2e-37
Identities = 23/108 (21%), Positives = 47/108 (43%), Gaps = 1/108 (0%)
Query: 1398 LEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIH 1457
+ + S G+ + + N+ ++KKG + G + ++ G + L ++G +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLR 60
Query: 1458 LSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDP 1505
S+ S D E+ GDE+EA +D + ISL ++ +
Sbjct: 61 ASEASR-DRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEAD 107
Score = 133 bits (337), Expect = 1e-36
Identities = 24/109 (22%), Positives = 46/109 (42%), Gaps = 1/109 (0%)
Query: 1311 LKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVH 1370
+ + S G+ G + +G + GKVT + GA VE+ G+EG +
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMFNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLR 60
Query: 1371 ISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPW 1419
SE ++ + ++ + D VE ++ + R ISL ++ +
Sbjct: 61 ASEASR-DRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEADE 108
Score = 116 bits (292), Expect = 1e-30
Identities = 33/110 (30%), Positives = 55/110 (50%), Gaps = 5/110 (4%)
Query: 1485 LSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYL 1544
+ S G+ FNN+V +N KG++V G + ++ KGA ++L++ VEGYL
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMFNNWVALNKKGAIVTGKVTAV-DAKGATVELADGVEGYL 59
Query: 1545 RISEEDNKHEKK----LKIGENIDVLTVLIDHKTRYIQLSFKKKEVIKKK 1590
R SE + L +G+ ++ +D K R I LS + K+ +K
Sbjct: 60 RASEASRDRVEDATLVLSVGDEVEAKFTGVDRKNRAISLSVRAKDEADEK 109
Score = 98.4 bits (246), Expect = 2e-24
Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 1248 QKLIETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDI 1306
+ K+G V G V + GA ++L G++G L ++ + RV+ + +L++G ++
Sbjct: 23 NNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDEV 82
Query: 1307 STKILKYDQEKNRVSLGMKQLGIDPW 1332
K D++ +SL ++
Sbjct: 83 EAKFTGVDRKNRAISLSVRAKDEADE 108
Score = 36.8 bits (86), Expect = 0.007
Identities = 25/91 (27%), Positives = 41/91 (45%), Gaps = 6/91 (6%)
Query: 1160 WLSLEKAMESGEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTTPF--EGKT 1216
+ + + G I+TG + G TV L +G++ +L S V+D T G
Sbjct: 22 FNNWVALNKKGAIVTGKVTAVDAKGATVELADGVEGYLRASEASRDRVEDATLVLSVGDE 81
Query: 1217 MDFKVIKLDRKRNNVVLSHRAVIEESMGEER 1247
++ K +DRK + LS RA E +E+
Sbjct: 82 VEAKFTGVDRKNRAISLSVRAKDEA---DEK 109
>2cqo_A Nucleolar protein of 40 kDa; S1 domain, OB-fold, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 119
Score = 135 bits (341), Expect = 3e-37
Identities = 34/114 (29%), Positives = 54/114 (47%), Gaps = 11/114 (9%)
Query: 1240 EESMGEERQKLIETLKE-GCTVKGVVKNITDYGAFIDLGGI--DGLLHITDIAWRRVKHP 1296
M R + +E L +G V +TDYGAFI + G GL+H T ++ RV P
Sbjct: 5 SSGMNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKP 64
Query: 1297 SEILTIGQDISTKILKYD--QEKNRVSLGMKQLG------IDPWIGLSFRYPRG 1342
SEI+ +G + K++ + ++ +VSL MK + +DP + P
Sbjct: 65 SEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIESGPSS 118
Score = 94.8 bits (236), Expect = 5e-23
Identities = 32/119 (26%), Positives = 53/119 (44%), Gaps = 11/119 (9%)
Query: 1318 NRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIE-KGIEGLVHISEMDW 1376
+ S GM + L T G+V +TDYGAF++I +GLVH + M
Sbjct: 2 SSGSSGMNSGRPETMENLP---ALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSS 58
Query: 1377 --INKNVTPSKIVQLNDTVEIMILEI--NEERRRISLGMKQCKDNPWENFSIIHKKGEK 1431
++K PS+IV + D V + ++ +R ++SL MK ++ + E
Sbjct: 59 CRVDK---PSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNVIIES 114
Score = 82.9 bits (205), Expect = 7e-19
Identities = 24/107 (22%), Positives = 46/107 (42%), Gaps = 13/107 (12%)
Query: 1405 RRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDG-NIDGLIHLSDLSW 1463
S GM + EN + +G + +TD+G FI + G GL+H + +S
Sbjct: 2 SSGSSGMNSGRPETMEN---LPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSS 58
Query: 1464 T---DPGEEIIRNFKKGDEIEAIILSIDVEKER--ISLGIKQLEGDP 1505
P E + GD++ ++ +++ +R +SL +K +
Sbjct: 59 CRVDKPSEIV----DVGDKVWVKLIGREMKNDRIKVSLSMKVVNQGT 101
>3go5_A Multidomain protein with S1 RNA-binding domains; structural genomics,
joint center for structural genomics, JCSG; HET: MSE;
1.40A {Streptococcus pneumoniae}
Length = 285
Score = 109 bits (274), Expect = 3e-26
Identities = 44/259 (16%), Positives = 86/259 (33%), Gaps = 40/259 (15%)
Query: 1253 TLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
+ G++ + D F+ G L + T+G +
Sbjct: 3 NTNLASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQH----------TVGDTVKGFA-- 50
Query: 1313 YDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNL-TDYGAFVEI-EKGIEGLVH 1370
Y K ++ L + + G+VT + D G FV+ E +V
Sbjct: 51 YTDMKQKLRLTTLE----VTA------TQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVS 100
Query: 1371 ISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGE 1430
+ + K + P K D + I LE++++ R L Q + + + +
Sbjct: 101 LDILPE-LKELWPKK----GDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQ 154
Query: 1431 KIKGIIKSITDFGIFIGL-DGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDV 1489
I+ + G F+ L + N+ G IH S E + G ++A ++
Sbjct: 155 NWPAIVYRLKLSGTFVYLPENNMLGFIHPS---------ERYAEPRLGQVLDARVIGFRE 205
Query: 1490 EKERISLGIKQLEGDPFNN 1508
++L +K + N
Sbjct: 206 VDRTLNLSLKPRSFEMLEN 224
Score = 93.1 bits (231), Expect = 1e-20
Identities = 41/272 (15%), Positives = 82/272 (30%), Gaps = 46/272 (16%)
Query: 1170 GEIITGTINGKVKGGLTVLTNGLKAFLPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRN 1229
I G I + V +G L G T+ D K+
Sbjct: 7 ASFIVGLIIDENDRFYFVQKDGQTYALAKEEGQHT--------VGDTVKGFAY-TDMKQK 57
Query: 1230 NVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLG--GIDGLLHITD 1287
+ + + + + V + D G F+D G + ++ +
Sbjct: 58 LRLTTLEVTATQ--DQ-----FGWGR-------VTEVRKDLGVFVDTGLPDKEIVVSLDI 103
Query: 1288 IAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLG 1347
+ + P + G + + L+ D++ L Q ++ +
Sbjct: 104 LPELKELWPKK----GDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYNNMQNQNWPA 158
Query: 1348 KVTNLTDYGAFVEI-EKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRR 1406
V L G FV + E + G +H SE +L ++ ++ E R
Sbjct: 159 IVYRLKLSGTFVYLPENNMLGFIHPSER---------YAEPRLGQVLDARVIGFREVDRT 209
Query: 1407 ISLGMKQCKDNPWENFSIIHKKGEKIKGIIKS 1438
++L +K EN + + I ++S
Sbjct: 210 LNLSLKPRSFEMLENDA------QMILTYLES 235
Score = 60.7 bits (147), Expect = 1e-09
Identities = 36/283 (12%), Positives = 85/283 (30%), Gaps = 41/283 (14%)
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGELEVKIGDFVSVAIESLENGFG 1145
I +I + F + D + + E + +GD V
Sbjct: 7 ASFIVGLIIDENDRFYFVQKDG--------QTYALAKEEGQHTVGDTVKG---------- 48
Query: 1146 DTILSRDKAKRLASWLSLEKAMESGEIITGTINGKVKGGLTVLTNGLKA---FLPGSLVD 1202
D ++L +LE + G + K + GL +
Sbjct: 49 --FAYTDMKQKLRL-TTLEVTATQDQFGWGRVTEVRKDLGVFVDTGLPDKEIVVSLD--I 103
Query: 1203 IRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKG 1262
+ +K+ P +G + + +++D+K L + + +
Sbjct: 104 LPELKELWPKKGDQLYIR-LEVDKKDRIWGLLAYQEDFQRLARPAYN----NMQNQNWPA 158
Query: 1263 VVKNITDYGAFIDL--GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKNRV 1320
+V + G F+ L + G +H ++ +GQ + +++ + + +
Sbjct: 159 IVYRLKLSGTFVYLPENNMLGFIHPSER--------YAEPRLGQVLDARVIGFREVDRTL 210
Query: 1321 SLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEK 1363
+L +K + + G L D + +I+
Sbjct: 211 NLSLKPRSFEMLENDAQMILTYLESNGGFMTLNDKSSPDDIKA 253
>2bh8_A 1B11; transcription, molecular evolution, unique architecture,
transcription regulation, phosphorylation; 1.9A
{Escherichia coli}
Length = 101
Score = 101 bits (252), Expect = 2e-25
Identities = 28/66 (42%), Positives = 40/66 (60%)
Query: 1400 INEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLS 1459
I + + + + ++G++++G IKSITDFGIFIGLDG IDGL+HLS
Sbjct: 33 ITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSITDFGIFIGLDGGIDGLVHLS 92
Query: 1460 DLSWTD 1465
D+SW
Sbjct: 93 DISWAQ 98
Score = 81.0 bits (200), Expect = 2e-18
Identities = 28/98 (28%), Positives = 46/98 (46%), Gaps = 7/98 (7%)
Query: 1198 GSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEG 1257
GS + + + F I D +V + A + ++G
Sbjct: 9 GSRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAG------SSGAAVRGNPQQG 62
Query: 1258 CTVKGVVKNITDYGAFIDL-GGIDGLLHITDIAWRRVK 1294
V+G +K+ITD+G FI L GGIDGL+H++DI+W + +
Sbjct: 63 DRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISWAQAE 100
Score = 71.7 bits (176), Expect = 3e-15
Identities = 19/95 (20%), Positives = 41/95 (43%), Gaps = 9/95 (9%)
Query: 1291 RRVKHPSEILTIGQDISTKILKYDQEK---------NRVSLGMKQLGIDPWIGLSFRYPR 1341
R H ++ + ++ +K + + + +
Sbjct: 2 RGSHHHHGSRLQSGKMTGIVKWFNADKGFGFITPDDGSKDVFVHFSAGSSGAAVRGNPQQ 61
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW 1376
G R+ GK+ ++TD+G F+ ++ GI+GLVH+S++ W
Sbjct: 62 GDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDISW 96
Score = 30.1 bits (68), Expect = 1.8
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 1487 IDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRI 1546
I + + + G +G V G IKSI T+ G I L ++G + +
Sbjct: 33 ITPDDGSKDVFVHFSAGSSGAAVRGNPQQGDRVEGKIKSI-TDFGIFIGLDGGIDGLVHL 91
Query: 1547 S 1547
S
Sbjct: 92 S 92
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2,
initiation factor 2 alpha subunit, initiation factor 2
beta subunit; 2.80A {Sulfolobus solfataricus} PDB: 2aho_B
3v11_B*
Length = 266
Score = 103 bits (258), Expect = 2e-24
Identities = 26/122 (21%), Positives = 58/122 (47%), Gaps = 4/122 (3%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEILTIGQDISTKIL 1311
EG + VK + DYG+++ L GG+ L ++++ + VK+ ++L + + K++
Sbjct: 10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVIVKVI 69
Query: 1312 KYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHI 1371
+ D+ K V + +K++ D + ++ + R L K+ L + + E +
Sbjct: 70 RVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQR-LDKILELVSQKLKLSEKDAWEQVAWK 128
Query: 1372 SE 1373
E
Sbjct: 129 LE 130
Score = 79.6 bits (196), Expect = 3e-16
Identities = 22/180 (12%), Positives = 68/180 (37%), Gaps = 17/180 (9%)
Query: 1338 RYPR-GTRLLGKVTNLTDYGAFVEIEK--GIEGLVHISEMDWINKNVTPSKIVQLNDTVE 1394
+ P G L+ V + DYG++V +++ G++ + SE+ +++ N V
Sbjct: 7 KLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSS-KWVKNIRDVLKENRKVI 65
Query: 1395 IMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDG 1454
+ ++ ++ + + + +K+ D+ ++ KK +++ I++ ++ D
Sbjct: 66 VKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKLSEKDAWEQV 125
Query: 1455 LIHLSD----------LSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGD 1504
L + + + +I ++ ++ + ++ G
Sbjct: 126 AWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWVKPLLEEA---SKHAEERKVKMSGL 182
Score = 71.2 bits (174), Expect = 3e-13
Identities = 22/168 (13%), Positives = 67/168 (39%), Gaps = 19/168 (11%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIE 1481
+GE + +K + D+G ++ LD G + + S++S + + + K+ ++
Sbjct: 10 SEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVL----KENRKVI 65
Query: 1482 AIILSIDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVE 1541
++ +D K + + +K++ D K ++ I++ + +E +
Sbjct: 66 VKVIRVDRRKGTVDVSLKKVTDDERRKKNLQWKKIQRLDKILELVSQKLKL-----SEKD 120
Query: 1542 GYLRISEEDNKHEKKLKIGENIDVLTVLIDHKTRYIQLSFKKKEVIKK 1589
+ +++ + K G+ I + + + + + + +K
Sbjct: 121 AWEQVAWKLEA-----KYGDPITAIEKAVKEGEKILIDAGVPEIWVKP 163
Score = 34.2 bits (78), Expect = 0.31
Identities = 26/91 (28%), Positives = 44/91 (48%), Gaps = 5/91 (5%)
Query: 1164 EKAMESGEIITGTINGKVKGGLTV---LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTMD 1218
K GEI+ T+ G V GL+AFLP S V + VK+ E + +
Sbjct: 6 SKLPSEGEILIATVKQVFDYGSYVSLDEYGGLQAFLPWSEVSSKWVKNIRDVLKENRKVI 65
Query: 1219 FKVIKLDRKRNNVVLSHRAVIEESMGEERQK 1249
KVI++DR++ V +S + V ++ ++ +
Sbjct: 66 VKVIRVDRRKGTVDVSLKKVTDDERRKKNLQ 96
>1zvt_A Topoisomerase IV subunit A; beta-pinwheel, ATPase, supercoiling,
decatenation, DNA bindi topology; 1.70A {Escherichia
coli}
Length = 256
Score = 96.0 bits (238), Expect = 8e-22
Identities = 35/253 (13%), Positives = 86/253 (33%), Gaps = 37/253 (14%)
Query: 541 SQDMVITLSNLGYIKSQPISEYRAQKRGGRGKKAMMTKDEDWINQLFIANTHDYILCFSN 600
S+ + I LS +G++ R+ K + K D ++ ++ +
Sbjct: 1 SEPVTIVLSQMGWV--------RSAKGHDIDAPGLNYKAGDSFKAAVKGKSNQPVVFVDS 52
Query: 601 YGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMSTS 660
GR Y + +P G+P+ +L + + + + M++
Sbjct: 53 TGRSYAIDPITLPSARGQ--GEPLTGKLTLPPGATVDHM-------LMESDDQKLLMASD 103
Query: 661 LGIVKKTLLSNFSNPRKSGIIAVNLS-NEDFLIGAALTDGSYDIMLFSDSGKAVRFNENS 719
G ++ ++G + L N + + D S ++ + +G+ + F +
Sbjct: 104 AGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVVIEDASDMLLAITQAGRMLMFPVSD 163
Query: 720 VRAMGRSARGVIGMRLEKKQ------KVIALLVSNNQKQSVLTATENGYGKRTL------ 767
+ + + +G + + + + L V Q + GKR +
Sbjct: 164 LPQLSK-GKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHV-----GKRKIKLRPEE 217
Query: 768 IKEYTKHNRGTKG 780
+++ RG +G
Sbjct: 218 LQKV-TGERGRRG 229
Score = 83.3 bits (205), Expect = 1e-17
Identities = 26/175 (14%), Positives = 68/175 (38%), Gaps = 3/175 (1%)
Query: 682 AVNLSNEDFLIGAALTDGSYDIMLFSDSGKAVRFNENSVRAMGRSARGVIGMRLEKKQKV 741
+N D A + ++ +G++ + ++ + + G
Sbjct: 26 GLNYKAGDSFKAAVKGKSNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGAT 85
Query: 742 IALLVSNNQKQSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNGKVVAATLVNR 801
+ ++ + Q +L A++ GYG + NR K +I++ N V + +
Sbjct: 86 VDHMLMESDDQKLLMASDAGYGFVCTFNDLVARNRAGKALITLPENAHVMPPVV--IEDA 143
Query: 802 YHEIMLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRLCKITMIK 856
++ IT G ++ VS++ ++ + +G +I + + G L ++ ++
Sbjct: 144 SDMLLAITQAGRMLMFPVSDLPQLSKG-KGNKIINIPSAEAARGEDGLAQLYVLP 197
Score = 39.7 bits (92), Expect = 0.005
Identities = 30/225 (13%), Positives = 72/225 (32%), Gaps = 17/225 (7%)
Query: 541 SQDMVITLSNLGYIKSQPISEYRAQKRGGRG-KKAMMTKDEDWINQLFIANTHDYILCFS 599
S V+ + + G + + + G + ++ + + + +L S
Sbjct: 43 SNQPVVFVDSTGRSYAIDPITLPSARGQGEPLTGKLTLPPGATVDHMLMESDDQKLLMAS 102
Query: 600 NYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFPKNNYVFMST 659
+ G + + +RN GK +I L + + + + ++ + T
Sbjct: 103 DAGYGFVCTFNDLV--ARNRAGKALIT---LPENAHVMPPVVIEDA------SDMLLAIT 151
Query: 660 SLGIVKKTLLSNFSN-PRKSGIIAVNLSNEDFLIG----AALTDGSYDIMLFSDSGKAVR 714
G + +S+ + G +N+ + + G A L L GK
Sbjct: 152 QAGRMLMFPVSDLPQLSKGKGNKIINIPSAEAARGEDGLAQLYVLPPQSTLTIHVGKRKI 211
Query: 715 FNENSVRAMGRSARGVIGMRLEKKQKVIALLVSNNQKQSVLTATE 759
RG G + Q++ + + + ++ S + E
Sbjct: 212 KLRPEELQKVTGERGRRGTLMRGLQRIDRVEIDSPRRASSGDSEE 256
>2k52_A Uncharacterized protein MJ1198; metal-binding, zinc, zinc-finger,
structural genomics, PSI-2, protein structure initiative;
NMR {Methanocaldococcus jannaschii}
Length = 80
Score = 87.3 bits (217), Expect = 7e-21
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 5/75 (6%)
Query: 1254 LKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILK 1312
++ G KGVV I YGAFI+L + GLL D+ R+++ L +G +I + +
Sbjct: 3 VEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN----LNVGDEIIVQAID 58
Query: 1313 YDQEKNRVSLGMKQL 1327
EK + L
Sbjct: 59 VRPEKREIDFKYIPL 73
Score = 82.3 bits (204), Expect = 3e-19
Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEIN 1401
G G VT + YGAF+ + + + GL+ +M + + + D + + +++
Sbjct: 6 GKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMISLRLEN-----LNVGDEIIVQAIDVR 60
Query: 1402 EERRRISLGMKQCKD 1416
E+R I +
Sbjct: 61 PEKREIDFKYIPLEH 75
Score = 75.0 bits (185), Expect = 1e-16
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 5/76 (6%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
+ G+ KG++ I +G FI L+ + GL+ D+ + N GDEI +
Sbjct: 4 EPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDMIS-----LRLENLNVGDEIIVQAID 58
Query: 1487 IDVEKERISLGIKQLE 1502
+ EK I LE
Sbjct: 59 VRPEKREIDFKYIPLE 74
Score = 49.6 bits (119), Expect = 1e-07
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKKLKIGENIDVLTVLIDHKTR 1575
G G++ I GA I L+ +V G LR + + + L +G+ I V + + + R
Sbjct: 6 GKFYKGVVTRI-EKYGAFINLNEQVRGLLRPRDMISLRLENLNVGDEIIVQAIDVRPEKR 64
Query: 1576 YIQLSFK 1582
I +
Sbjct: 65 EIDFKYI 71
>2eqs_A ATP-dependent RNA helicase DHX8; S1 domain, OB-fold, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 103
Score = 83.5 bits (207), Expect = 3e-19
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 5/101 (4%)
Query: 1331 PWIGLSFRYPRGTRLLGKVTNLTDYGAFVEIE---KGIEGLVHISEMDWINKNVTPSKIV 1387
G GKVT++ +G FV++E K EGLVHISE+ + + +V
Sbjct: 2 SSGSSGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVV 61
Query: 1388 QLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKK 1428
V++ +L + SL MK E+ + ++
Sbjct: 62 SKGQRVKVKVLSF--TGTKTSLSMKDVDQETGEDLNPNRRR 100
Score = 77.4 bits (191), Expect = 4e-17
Identities = 22/92 (23%), Positives = 42/92 (45%), Gaps = 7/92 (7%)
Query: 1246 ERQKLIETLKEGCTVKGVVKNITDYGAFIDL----GGIDGLLHITDIAW-RRVKHPSEIL 1300
E G G V +I +G F+ L +GL+HI+++ RV + ++++
Sbjct: 2 SSGSSGEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVV 61
Query: 1301 TIGQDISTKILKYDQEKNRVSLGMKQLGIDPW 1332
+ GQ + K+L + + SL MK + +
Sbjct: 62 SKGQRVKVKVLSFT--GTKTSLSMKDVDQETG 91
Score = 55.0 bits (133), Expect = 3e-09
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDG---NIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
G+ G + SI FG F+ L+G +GL+H+S+L + KG ++ +L
Sbjct: 13 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVL 72
Query: 1486 SIDVEKERISLGIKQLEGDP 1505
S + SL +K ++ +
Sbjct: 73 SFT--GTKTSLSMKDVDQET 90
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain,
transcription, RNA binding protein; 2.27A {Pseudomonas
aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5
c.55.3.13 PDB: 3bzk_A 2oce_A
Length = 785
Score = 93.0 bits (232), Expect = 4e-19
Identities = 30/77 (38%), Positives = 52/77 (67%), Gaps = 1/77 (1%)
Query: 1251 IETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSEILTIGQDISTK 1309
++ LK G ++GVV N+T++GAF+D+G DGL+HI+ ++ + VK P E++ G + K
Sbjct: 649 LKDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVK 708
Query: 1310 ILKYDQEKNRVSLGMKQ 1326
+++ D +NRV L M+
Sbjct: 709 VMEVDIPRNRVGLSMRM 725
Score = 77.6 bits (192), Expect = 2e-14
Identities = 30/75 (40%), Positives = 48/75 (64%), Gaps = 7/75 (9%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGI--EGLVHISEMDWINKNVT-PSKIVQLNDTVEIMIL 1398
G L G VTN+T++GAFV+I G+ +GLVHIS + K V P ++V+ D V++ ++
Sbjct: 655 GMVLEGVVTNVTNFGAFVDI--GVHQDGLVHISALS--EKFVKDPYEVVKAGDIVKVKVM 710
Query: 1399 EINEERRRISLGMKQ 1413
E++ R R+ L M+
Sbjct: 711 EVDIPRNRVGLSMRM 725
Score = 58.8 bits (143), Expect = 1e-08
Identities = 25/81 (30%), Positives = 48/81 (59%), Gaps = 11/81 (13%)
Query: 1427 KKGEKIKGIIKSITDFGIF--IGLDGNIDGLIHLSDLSWT---DPGEEIIRNFKKGDEIE 1481
K G ++G++ ++T+FG F IG+ + DGL+H+S LS DP E + K GD ++
Sbjct: 653 KPGMVLEGVVTNVTNFGAFVDIGV--HQDGLVHISALSEKFVKDPYEVV----KAGDIVK 706
Query: 1482 AIILSIDVEKERISLGIKQLE 1502
++ +D+ + R+ L ++ +
Sbjct: 707 VKVMEVDIPRNRVGLSMRMSD 727
>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure
initiative, midwest CENT structural genomics, MCSG; 2.79A
{Clostridium symbiosum atcc 14940}
Length = 223
Score = 87.1 bits (215), Expect = 4e-19
Identities = 35/226 (15%), Positives = 74/226 (32%), Gaps = 28/226 (12%)
Query: 853 TMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNEL 912
M K + +ITI+ SG V + +A +LG H+ D L SA+ +
Sbjct: 9 FMGNKNL-IITIEREYGSGGRIVGKKLAEELGIHFYDDDILKLASEKSAVGEQFFRLADE 67
Query: 913 ELVILIKKLNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRK 972
+ L + I + K+ +N+ K ++ + +
Sbjct: 68 KAGN-------------NLLYRLGGGRKIDLHSKPSPNDKLTSPENLFKFQSEVMRELAE 114
Query: 973 FPGLVADGRDMGTTVFP----DAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINL 1028
+ GR G + + ++IF+ D ++ +R + + + +
Sbjct: 115 SEPCIFVGRAAGYVLDQDEDIERLIRIFVYTDKVKKVQR-----VMEVDCIDEERAKRRI 169
Query: 1029 IKRDIRDKTRNLSPLKC----PEQAHL-LNTSKMNINQVVNQILDC 1069
K + K + L +NT+K+ + + I
Sbjct: 170 KKIEKERKEYYKYFTGSEWHSMKNYDLPINTTKLTLEETAELIKAY 215
>3aev_A Translation initiation factor 2 subunit alpha; proteins-rRNA complex,
16S rRNA, RNA-binding; 2.80A {Pyrococcus horikoshii} PDB:
1yz6_A
Length = 275
Score = 85.5 bits (211), Expect = 4e-18
Identities = 31/198 (15%), Positives = 72/198 (36%), Gaps = 18/198 (9%)
Query: 1243 MGEERQKLIETLKEGCTVKGVVKNITDYGAFIDL---GGIDGLLHITDIAWRRVKHPSEI 1299
M + ++ E EG V VK I +YGAF++L G + +HI+++A V++ +
Sbjct: 1 MPRKAREYPE---EGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDY 57
Query: 1300 LTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLGKVTNLTDYGAFV 1359
L GQ + K+++ D K + L ++++ + R + + +
Sbjct: 58 LKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEK---- 113
Query: 1360 EIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPW 1419
+ K E + + + I +L+ + + + + ++
Sbjct: 114 -LGKDFEAAWREVWVPLEEEWGEVYAAFEDAAKDGIEVLKGHVPDEWLPVLKEIVENY-- 170
Query: 1420 ENFSIIHKKGEKIKGIIK 1437
+ I +
Sbjct: 171 -----VEVPTVTIDAEFE 183
Score = 63.1 bits (153), Expect = 1e-10
Identities = 21/140 (15%), Positives = 53/140 (37%), Gaps = 3/140 (2%)
Query: 1429 GEKIKGIIKSITDFGIFIGLD--GNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIILS 1486
GE + +K I ++G F+ LD + +H+S+++ T I K+G ++ A ++
Sbjct: 12 GEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWV-RNIRDYLKEGQKVVAKVIR 70
Query: 1487 IDVEKERISLGIKQLEGDPFNNYVNINDKGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRI 1546
+D K I L ++++ + + +++ G + +
Sbjct: 71 VDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLRLAAEKLGKDFEAAWREVWVPLE 130
Query: 1547 SEEDNKHEKKLKIGENIDVL 1566
E + ++ +
Sbjct: 131 EEWGEVYAAFEDAAKDGIEV 150
Score = 35.4 bits (81), Expect = 0.13
Identities = 25/161 (15%), Positives = 55/161 (34%), Gaps = 12/161 (7%)
Query: 1163 LEKAMESGEIITGTINGKVKGGLTV---LTNGLKAFLPGSLVDIRPVKDTTPF--EGKTM 1217
+ E GE + T+ G + G +AF+ S V V++ + EG+ +
Sbjct: 5 AREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKV 64
Query: 1218 DFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLG 1277
KVI++D ++ ++ LS R V ++ + Q+ K + +++ + +
Sbjct: 65 VAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQE----FKRAQKAENLLRLAAEK---LGKD 117
Query: 1278 GIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKN 1318
+ ++LK
Sbjct: 118 FEAAWREVWVPLEEEWGEVYAAFEDAAKDGIEVLKGHVPDE 158
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 83.0 bits (205), Expect = 6e-16
Identities = 14/97 (14%), Positives = 34/97 (35%), Gaps = 6/97 (6%)
Query: 1232 VLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAW 1290
L + + GE +T +G + V+ ++ +++ A
Sbjct: 885 PLQGDEIFQSLTGES----EKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAG 940
Query: 1291 RRVKHPS-EILTIGQDISTKILKYDQEKNRVSLGMKQ 1326
+++ P+ EI IG+ K++ D + +
Sbjct: 941 AQLRRPANEIYEIGKTYPAKVIYIDYANITAEVSLLD 977
Score = 72.2 bits (177), Expect = 1e-12
Identities = 7/74 (9%), Positives = 23/74 (31%), Gaps = 4/74 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVT--PSKIVQLNDTVEIMILE 1399
G+ + +V +E +V+ + ++I ++ T ++
Sbjct: 906 GSIIPVRVERFWHNDIICTTNSEVECVVNAQRH--AGAQLRRPANEIYEIGKTYPAKVIY 963
Query: 1400 INEERRRISLGMKQ 1413
I+ + +
Sbjct: 964 IDYANITAEVSLLD 977
Score = 64.1 bits (156), Expect = 4e-10
Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 6/77 (7%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLS---WTDPGEEIIRNFKKGDEIEAI 1483
KG I ++ I + ++ +++ + P EI ++ G A
Sbjct: 904 FKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEI---YEIGKTYPAK 960
Query: 1484 ILSIDVEKERISLGIKQ 1500
++ ID + +
Sbjct: 961 VIYIDYANITAEVSLLD 977
Score = 39.1 bits (91), Expect = 0.014
Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 1515 KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH-----EKKLKIGENIDVLTVL 1569
KGS++ ++ + I ++EVE + + +IG+ +
Sbjct: 905 KGSIIPVRVERF-WHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIY 963
Query: 1570 IDHKTRYIQLSFKKKEVIKKKK 1591
ID+ ++S +V ++
Sbjct: 964 IDYANITAEVSLLDHDVKQQYV 985
Score = 31.0 bits (70), Expect = 4.3
Identities = 20/113 (17%), Positives = 35/113 (30%), Gaps = 18/113 (15%)
Query: 1137 IESLENGFGDTILSRDKAKRLASW-----LSLE--KAMESGEIITGTINGKVKGGLTV-L 1188
+ L +GF + R+ L L+ E K G II + +
Sbjct: 869 VLELLDGFEEL---RNDFHPLQGDEIFQSLTGESEKTFFKGSIIPVRVERFWHNDIICTT 925
Query: 1189 TNGLKAFLPGSLVDIRPVKDTTPFE-----GKTMDFKVIKLDRKRNNVVLSHR 1236
+ ++ + ++ P GKT KVI +D +S
Sbjct: 926 NSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIYIDYANITAEVSLL 976
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 82.2 bits (203), Expect = 1e-15
Identities = 10/78 (12%), Positives = 28/78 (35%), Gaps = 2/78 (2%)
Query: 1251 IETLKEGCTVKGVVKNITDYGAFIDLG-GIDGLLHITDIAWRRVKHPSE-ILTIGQDIST 1308
+T +G + V+ ++ +++ A +++ P+ I IG+
Sbjct: 897 EKTFFKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPA 956
Query: 1309 KILKYDQEKNRVSLGMKQ 1326
K++ D + +
Sbjct: 957 KVIYIDYANITAEVSLLD 974
Score = 71.8 bits (176), Expect = 2e-12
Identities = 7/73 (9%), Positives = 23/73 (31%)
Query: 1341 RGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEI 1400
+G+ + +V +E +V+ ++I ++ T ++ I
Sbjct: 902 KGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIYI 961
Query: 1401 NEERRRISLGMKQ 1413
+ + +
Sbjct: 962 DYANITAEVSLLD 974
Score = 63.0 bits (153), Expect = 8e-10
Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 6/77 (7%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLS---WTDPGEEIIRNFKKGDEIEAI 1483
KG I ++ I + ++ +++ + P EI ++ G A
Sbjct: 901 FKGSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRRPANEI---YEIGKTYPAK 957
Query: 1484 ILSIDVEKERISLGIKQ 1500
++ ID + +
Sbjct: 958 VIYIDYANITAEVSLLD 974
Score = 39.5 bits (92), Expect = 0.010
Identities = 13/82 (15%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 1515 KGSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKH-----EKKLKIGENIDVLTVL 1569
KGS++ ++ + I ++EVE + + +IG+ +
Sbjct: 902 KGSIIPVRVERF-WHNDIICTTNSEVECVVNAQRHAGAQLRRPANEIYEIGKTYPAKVIY 960
Query: 1570 IDHKTRYIQLSFKKKEVIKKKK 1591
ID+ ++S +V ++
Sbjct: 961 IDYANITAEVSLLDHDVKQQYV 982
Score = 32.2 bits (73), Expect = 1.9
Identities = 12/73 (16%), Positives = 22/73 (30%), Gaps = 8/73 (10%)
Query: 1170 GEIITGTINGKVKGGLTV-LTNGLKAFLPGSLVDIRPVKDTTPFE-----GKTMDFKVIK 1223
G II + + + ++ + ++ P GKT KVI
Sbjct: 903 GSIIPVRVERFWHNDIICTTNSEVECVVNAQRHAGAQLRR--PANEIYEIGKTYPAKVIY 960
Query: 1224 LDRKRNNVVLSHR 1236
+D +S
Sbjct: 961 IDYANITAEVSLL 973
>4aid_A Polyribonucleotide nucleotidyltransferase; transferase-peptide
complex; 2.60A {Caulobacter vibrioides} PDB: 4aim_A
4am3_A
Length = 726
Score = 77.9 bits (193), Expect = 2e-14
Identities = 27/100 (27%), Positives = 53/100 (53%), Gaps = 6/100 (6%)
Query: 1237 AVIEESMGEERQKLIETL----KEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWR 1291
+ + + + I+++ + G G V + D+GAF++ G DGL+H++ I+
Sbjct: 614 SASDGAKIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNE 673
Query: 1292 RVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDP 1331
RV PS++L GQ + K+L +D ++ + L MK + +
Sbjct: 674 RVAKPSDVLKEGQMVKVKLLGFD-DRGKTKLSMKVVDQET 712
Score = 71.4 bits (176), Expect = 2e-12
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 6/75 (8%)
Query: 1346 LGKVTNLTDYGAFVEIEKGIEGLVHISEMDW--INKNVTPSKIVQLNDTVEIMILEINEE 1403
GKV + D+GAFV +GLVH+S++ + K PS +++ V++ +L ++
Sbjct: 642 DGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAK---PSDVLKEGQMVKVKLLGF-DD 697
Query: 1404 RRRISLGMKQCKDNP 1418
R + L MK
Sbjct: 698 RGKTKLSMKVVDQET 712
Score = 50.2 bits (121), Expect = 6e-06
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSW--TDPGEEIIRNFKKGDEIEAIILS 1486
G+ G + + DFG F+ G DGL+H+S +S +++ K+G ++ +L
Sbjct: 638 GKIYDGKVVKVVDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVL---KEGQMVKVKLLG 694
Query: 1487 IDVEKERISLGIKQLEGDP 1505
D ++ + L +K ++ +
Sbjct: 695 FD-DRGKTKLSMKVVDQET 712
Score = 35.2 bits (82), Expect = 0.24
Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 8/80 (10%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
G + +G + + + GA + +G + +S+ N+ K LK G+ + V + D
Sbjct: 638 GKIYDGKVVKV-VDFGAFVNFFGAKDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFD 696
Query: 1572 HKTRYIQLSFKKKEVIKKKK 1591
+ + +LS K V ++
Sbjct: 697 DRGK-TKLS--MKVVDQETG 713
>3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation,
kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A
Length = 723
Score = 77.5 bits (192), Expect = 2e-14
Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 6/97 (6%)
Query: 1240 EESMGEERQKLIETL----KEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDIAWRRVK 1294
+ + + IE + + G G V I D+GAF+ GG +GL+HI+ IA +RV+
Sbjct: 607 DGEKAKHAIRRIEEITAEIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVE 666
Query: 1295 HPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDP 1331
++ L +GQ++ K+L+ D + R+ L +K+
Sbjct: 667 KVTDYLQMGQEVPVKVLEVD-RQGRIRLSIKEATEQS 702
Score = 73.3 bits (181), Expect = 4e-13
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 6/79 (7%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDW--INKNVTPSKIVQLNDTVEIMILE 1399
G GKVT + D+GAFV I G EGLVHIS++ + K + +Q+ V + +LE
Sbjct: 628 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEK---VTDYLQMGQEVPVKVLE 684
Query: 1400 INEERRRISLGMKQCKDNP 1418
+ + + RI L +K+ +
Sbjct: 685 V-DRQGRIRLSIKEATEQS 702
Score = 49.8 bits (120), Expect = 7e-06
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRN----FKKGDEIEAII 1484
G G + I DFG F+ + G +GL+H+S ++ + + + G E+ +
Sbjct: 628 GRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIAD-----KRVEKVTDYLQMGQEVPVKV 682
Query: 1485 LSIDVEKERISLGIKQLEGDP 1505
L +D + RI L IK+
Sbjct: 683 LEVD-RQGRIRLSIKEATEQS 702
Score = 32.5 bits (75), Expect = 1.3
Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 1516 GSLVNGIIKSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKK----LKIGENIDVLTVLID 1571
G + G + I + GA + + EG + IS+ +K +K L++G+ + V + +D
Sbjct: 628 GRVYTGKVTRI-VDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVD 686
Query: 1572 HKTRYIQLSFKKKEVIKKKK 1591
+ R I+LS KE ++ +
Sbjct: 687 RQGR-IRLS--IKEATEQSQ 703
>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 = 76.8 bits (188), Expect = 4e-14
Identities = 88/622 (14%), Positives = 199/622 (31%), Gaps = 149/622 (23%)
Query: 144 DFISNYDGKEKE---PSVLPTR-IPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLH 199
F+ N+D K+ + S+L I +++++ + T + L L
Sbjct: 28 AFVDNFDCKDVQDMPKSILSKEEIDHIIMSKD------------AVSGTLRLFWTL--LS 73
Query: 200 NPECSINDLIKIIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAI 259
E + ++ + ++ + +S + + ++ + +IE+ +R
Sbjct: 74 KQEEMVQKFVEEVLRINYK-----FLMSPIKTEQ---RQPSMMT-RMYIEQRDRLYNDNQ 124
Query: 260 IIDELPYQVNKKSLLEKISQLVKEKKLE----------C------ISNLRDESDKSGM-- 301
+ Y V++ K+ Q + E + + + M
Sbjct: 125 VFA--KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF 182
Query: 302 RIV-IELKRNEIPEIV---LNKLYKQ-----TQLQNTFGMNMLALVNGQPKLLNL----- 347
+I + LK PE V L KL Q T + L + + Q +L L
Sbjct: 183 KIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKP 242
Query: 348 -------------KEILYYF-----ILHRKEVIKR-RTIFELRKAREYAHI-LEGLTIAL 387
+ F IL + R + + + A HI L+ ++ L
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNLSCKIL----LTTRFKQVTDFLSAATTTHISLDHHSMTL 298
Query: 388 TNIDN---FIQI--IRSTSTPQEAKNKIIESTWNLPDVSKIIGFNKKNYNTISKINNISK 442
T + ++ R P+E P II + ++ ++ +N
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPREVL-TTN------PRRLSIIAESIRDG--LATWDNWKH 349
Query: 443 LQNNDMYKLSDIQAQEILKMPLQRLTNMEQKK------IINKYENVIKKVIDLTDIL--S 494
+ + KL+ I++ L L E +K + ++ ++ ++
Sbjct: 350 VNCD---KLT-----TIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL---SLIWFD 398
Query: 495 NSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMVITLSNLGYI 554
K + ++ ++L +KY +K + S I + +I ++ + L N +
Sbjct: 399 VIKSDVMVVVNKL----HKYSLVEKQPKESTISIPSI---------YLELKVKLENEYAL 445
Query: 555 KSQPISEYRAQKRGGRGKKAMMTKDEDWIN----QLFIANTHDYILCFSN-YGRLYWLKV 609
+ Y K D+ + + L + + F + +L+
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQ 505
Query: 610 WQIPQGSRNSRGKPIINMFS-LKN-KEKITVILPLSNNKRDFPKNNYVFMSTSLGIVKKT 667
+ + I+N LK K I +N + + + I +
Sbjct: 506 KIRHDSTAWNASGSILNTLQQLKFYKPYIC------DNDPKYERLVNAILDFLPKIEENL 559
Query: 668 LLSNFSNPRKSGIIAVNLSNED 689
+ S +++ ++ + L ED
Sbjct: 560 ICSKYTD-----LLRIALMAED 576
Score = 72.6 bits (177), Expect = 9e-13
Identities = 96/677 (14%), Positives = 198/677 (29%), Gaps = 217/677 (32%)
Query: 1006 KRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTRNLSPLKCPEQAHLLNTSKMNINQVVNQ 1065
+ +YK ++ V + N +D++D +++ L E H++ + V+
Sbjct: 15 QYQYKDILS----VFEDAFVDNFDCKDVQDMPKSI--LSKEEIDHIIMSK-----DAVSG 63
Query: 1066 ILDCFATLFKESLLRHDMRSGEVISAEVIG--LDRNFVIINADLKSEAFIP--------- 1114
L F TL + E + + + L N+ + + +K+E P
Sbjct: 64 TLRLFWTL---------LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIE 114
Query: 1115 -IEEFKNDN---GELEVKIGDFVSVAIESLEN-------------GFGDTILS----RDK 1153
+ NDN + V ++L G G T ++
Sbjct: 115 QRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSY 174
Query: 1154 AKRLAS-----WLSLEKAMESGEIIT------------GTINGKVKGGLTVLTNGLKAFL 1196
+ WL+L+ ++ T + + + ++A L
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 1197 ---------PGSLVDIRPVKDTTPFEGKTMDF--KVIKLDRKRNNV------VLSHRAVI 1239
L+ + V++ + + K++ R + +H ++
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAW--NAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292
Query: 1240 EESMG-EERQKL----------IETL-KEGCTVKGVVKNITDYGAFIDLGGIDGLLHITD 1287
SM + + L +E T +I I DGL
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI--IAESI----RDGLAT--- 343
Query: 1288 IAWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDPWIGLSFRYPRGTRLLG 1347
W KH + D+ + + L P R +
Sbjct: 344 --WDNWKH---------------VNCDKLTTIIESSLNVL-----------EPAEYRKM- 374
Query: 1348 KVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQL--NDTVEIMILEINEERR 1405
+ HI P+ ++ L D ++ ++ + +
Sbjct: 375 -------FDRLSVFPPS----AHI-----------PTILLSLIWFDVIKSDVMVVVNKLH 412
Query: 1406 RISLGMKQCKDNPWENFSI------IHKKGEKIKGIIKSITD-FGIFIGLDGN------I 1452
+ SL KQ K++ SI + K E + +SI D + I D + +
Sbjct: 413 KYSLVEKQPKES---TISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469
Query: 1453 DGLI------HLSDLSWTDPGEEIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEGDPF 1506
D HL + I + ++ + L +++I
Sbjct: 470 DQYFYSHIGHHLKN----------IEHPERMTLFRMVFLDFRFLEQKIR----------- 508
Query: 1507 NNYVNINDKGSLVNGII------KSIDTNKGAIIQLSNEVEGYLRISEEDNKHEKKLKIG 1560
++ N GS++N + I N +L N + +L K E+ L
Sbjct: 509 HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLP------KIEENLICS 562
Query: 1561 ENIDVLTVLIDHKTRYI 1577
+ D+L + + + I
Sbjct: 563 KYTDLLRIALMAEDEAI 579
Score = 66.0 bits (160), Expect = 9e-11
Identities = 81/525 (15%), Positives = 164/525 (31%), Gaps = 152/525 (28%)
Query: 752 QSVLTATENGYGKRTLIKEYTKHNRGTKGIISIKTNKRNG--KVVAATLVNRYHEIMLIT 809
+S+L+ E +I + + ++ + + K V L Y +M
Sbjct: 43 KSILSKEE----IDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM--- 95
Query: 810 TGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCG---------VQRLCKITMIKKYI- 859
S I+ R + + +E + +L V RL +++ +
Sbjct: 96 ----------SPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALL 145
Query: 860 -----PVITIDGPTASGKGTVAQLVASKLGFH-YLDSGALYRLVTLSAINNNIQLDNELE 913
+ IDG SGK VA V +D + + L ++
Sbjct: 146 ELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFW--LNLK------NCNSPET 197
Query: 914 LVILIKKLNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKF 973
++ +++KL Y + R++ SN +I + + L K + +
Sbjct: 198 VLEMLQKLLYQI----------DPNWTSRSDHSSNIKLRIHSIQAELRRLLKS----KPY 243
Query: 974 PG--LVADG-RDMGTTVFPDAFL---KIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLIN 1027
LV ++ + +AF KI LT T R+K ++D L
Sbjct: 244 ENCLLVLLNVQN--AKAW-NAFNLSCKILLT------T--RFK---------QVTDFLSA 283
Query: 1028 LIKRDIR--DKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILDCFATLFKESLLRHDMRS 1085
I + L+P E LL K LDC + L ++ +
Sbjct: 284 ATTTHISLDHHSMTLTP---DEVKSLL--LK---------YLDC-----RPQDLPREVLT 324
Query: 1086 GEVISAEVIGLDRNFVIINADLKSEAFIPIEEFKNDNGELEVKIGDFVSVAIESLENG-- 1143
+ + + I ++ + + +K+ N + K+ + ++ LE
Sbjct: 325 ---TNPRRLSI------IAESIR-DGLATWDNWKHVNCD---KLTTIIESSLNVLEPAEY 371
Query: 1144 ---FGD-TILSRD---KAKRLAS-WLSLEKAMESGEIITGTINGKVKGGLTVLTNGLKAF 1195
F ++ L+ W + K ++ +
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIK--SDVMVV------------------VNKL 411
Query: 1196 LPGSLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIE 1240
SLV+ +P + T ++ K K N HR++++
Sbjct: 412 HKYSLVEKQPKESTISIPSIYLELK-----VKLENEYALHRSIVD 451
Score = 64.9 bits (157), Expect = 2e-10
Identities = 84/692 (12%), Positives = 197/692 (28%), Gaps = 186/692 (26%)
Query: 442 KLQNNDMYK------LSDIQAQEILKMPLQRLTNMEQKKIINKYENVIKKVIDLTDIL-S 494
+ Q D+ + + +++ MP L+ E II ++ + + L L S
Sbjct: 15 QYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMS-KDAVSGTLRLFWTLLS 73
Query: 495 NSKRIIEIITDELNIIKNKYGSHKKNIRRSEIILNAINPSTEDLIASQDMVITLSNLGYI 554
+ +++ +E+ ++ Y +++ I M I + Y
Sbjct: 74 KQEEMVQKFVEEV--LRINYK----------FLMSPIKTEQRQPSMMTRMYIEQRDRLYN 121
Query: 555 KSQPISEY---RAQK----R-----------------GGRGKKAMMTKDEDWINQLFIAN 590
+Q ++Y R Q R G GK + +
Sbjct: 122 DNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALD---------VCL 172
Query: 591 THDYILCFSNYGRLYWLKVWQIPQGSRNSRGKPIINMFSLKNKEKITVILPLSNNKRDFP 650
++ +++WL + + NS + + L + I P ++ D
Sbjct: 173 SYKVQCKMDF--KIFWLNL-----KNCNSPETVLEMLQKL-----LYQIDPNWTSRSDHS 220
Query: 651 KNNYVFMSTSLGIVKKTLLSNFSNPRKSGIIAVNLSN----EDFLIGAA--LTDGSYDIM 704
N S+ + LL + ++ +N+ N F + LT +
Sbjct: 221 S-NIKLRIHSIQAELRRLLKSKPYEN-CLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVT 278
Query: 705 LFSDSGKAVRFNENSVR-------AMGRSARGVIGMRLEK----KQKVIALLVSNNQKQS 753
F + + + + + R + +S
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEVKSLLLK-YLDCRPQDLPREVLTTNPRRLS------ 331
Query: 754 VLTATENGYGKRTLIKEYTKHNRGT-KGIISIKTNKRNGKVVAATLVN-------RYHEI 805
+I E + T + +K ++ ++L + +
Sbjct: 332 -------------IIAESIRDGLATWDNWKHVNCDKLT-TIIESSLNVLEPAEYRKMFDR 377
Query: 806 MLITTGGILIRTRVSEIRKMGRSTQGVILITVENKSKLCGVQRLCKITMIKK-------Y 858
+ + I T + + V+++ V +L K ++++K
Sbjct: 378 LSVFPPSAHIPTILLSLIWFDVIKSDVMVV----------VNKLHKYSLVEKQPKESTIS 427
Query: 859 IPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILI 918
IP I ++ L + AL+R + + N D++ + +
Sbjct: 428 IPSIYLE-----------------LKVKLENEYALHRSI-VDHYNIPKTFDSDDLIPPYL 469
Query: 919 KKLNYNFLGKEVY-LNGVNVTTLIRNEKVSNNASKIAKFKNIRKEL-FKIQVKFRKFPGL 976
+ Y+ +G + L K + ++ F+ + + F ++ K R
Sbjct: 470 DQYFYSHIG---HHL------------KNIEHPERMTLFRMVFLDFRF-LEQKIRH-DST 512
Query: 977 VADGRDMGTTVFPDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDK 1036
+ + YK + + + L+N I +
Sbjct: 513 AWNASGSILNTLQQL---------------KFYKPYICD--NDPKYERLVNAILDFLPKI 555
Query: 1037 TRNL--SPLKCPEQAHLLNTSKMNINQVVNQI 1066
NL S + L+ + + Q+
Sbjct: 556 EENLICSKYTDLLRIALMAEDEAIFEEAHKQV 587
Score = 60.6 bits (146), Expect = 5e-09
Identities = 72/471 (15%), Positives = 145/471 (30%), Gaps = 144/471 (30%)
Query: 39 DGLKPVHRRVLFAMHEMNNLW-NRPFVKCARVVGETMGKYHPHGDVSIYDALVRMAQSFS 97
D + R+ E+ L ++P+ C V+ +V +A + +F+
Sbjct: 218 DHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL----------NV--QNA--KAWNAFN 263
Query: 98 LRC-TLV---DGQGNFGSIDGDSAAAMRYTECRLNKISNELLIDLDKETIDFISNYDGKE 153
L C L+ Q D +A T L+ S L E + Y
Sbjct: 264 LSCKILLTTRFKQ------VTDFLSAATTTHISLDHHSMTL---TPDEVKSLLLKY---- 310
Query: 154 KEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPE--CSINDL-IK 210
+ P +L P + N +
Sbjct: 311 --------------------------LDCRPQDL-------------PREVLTTNPRRLS 331
Query: 211 IIPAPDFPTAGIIYGLSSVHDGYYTGKGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNK 270
II S+ DG + + N D+L + +
Sbjct: 332 IIAE-------------SIRDG------------LATWDNWKHVN-----CDKLT-TIIE 360
Query: 271 KSLLEKISQLVKEKKLECISNLRDESDKSGMRIVI---ELKRNEIPEIVLNKLYKQTQLQ 327
S L + K + +S + + + + ++ +++ +V+NKL+K +
Sbjct: 361 SS-LNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSD-VMVVVNKLHKYS--- 415
Query: 328 NTFGMNMLALVNGQPKLLNLKEILYYFILHRKEVIKRRTIFEL-RKAREYAHILEGL--- 383
LV QPK + + ++ + +K + L R ++ +I +
Sbjct: 416 ---------LVEKQPK----ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 384 TIALTNIDNFI--QIIRSTSTPQEAKNKIIESTWNLPDVS----KIIGFNKKNYNTISKI 437
+ +D + I + + + L D KI + +N I
Sbjct: 463 DLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFL-DFRFLEQKIR-HDSTAWNASGSI 520
Query: 438 NNISKLQNNDMYK----LSDIQAQEILKMPLQRLTNMEQKKIINKYENVIK 484
N LQ YK +D + + ++ L L +E+ I +KY ++++
Sbjct: 521 LNT--LQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
>1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase,
ATP-GTP diphosphotransferase RNA processing, RNA
degradation; 2.5A {Streptomyces antibioticus} SCOP:
a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1
d.101.1.1 PDB: 1e3h_A
Length = 757
Score = 70.7 bits (174), Expect = 3e-12
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 1342 GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNV---TPSKIVQLNDTVEIMIL 1398
G R+LG V T +GAFV + G +GL+HIS++ + ++ + V++ I
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 1399 EINEERRRISLGMKQCKDNP 1418
EI + R ++SL +
Sbjct: 728 EI-DSRGKLSLIPVIEGEEA 746
Score = 69.9 bits (172), Expect = 5e-12
Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 12/103 (11%)
Query: 1240 EESMGEERQKLIETL------KEGCTVKGVVKNITDYGAFID-LGGIDGLLHITDI---- 1288
+ E + I + + G + G V T +GAF+ L G DGLLHI+ I
Sbjct: 645 DGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLA 704
Query: 1289 AWRRVKHPSEILTIGQDISTKILKYDQEKNRVSLGMKQLGIDP 1331
+RV++ ++L +GQ + +I + D + ++SL G +
Sbjct: 705 GGKRVENVEDVLGVGQKVQVEIAEID-SRGKLSLIPVIEGEEA 746
Score = 51.4 bits (124), Expect = 3e-06
Identities = 21/80 (26%), Positives = 36/80 (45%), Gaps = 4/80 (5%)
Query: 1429 GEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIR---NFKKGDEIEAIIL 1485
GE+I G + T FG F+ L DGL+H+S + G+ + G +++ I
Sbjct: 668 GERILGSVVKTTTFGAFVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIA 727
Query: 1486 SIDVEKERISLGIKQLEGDP 1505
ID + ++SL +
Sbjct: 728 EID-SRGKLSLIPVIEGEEA 746
>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 = 70.5 bits (172), Expect = 5e-12
Identities = 103/605 (17%), Positives = 184/605 (30%), Gaps = 209/605 (34%)
Query: 7 EVISILLEEEMCKSYLDYAMSVIVGRALPDVRDGLK--------------PVHRRV--LF 50
E + E+ +L Y S++ + L +H L
Sbjct: 53 EPTTPA---ELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 51 AMHEMNNLWNRPFVKC---ARVV-GETMGKYHPHGDVSIYDALVRMAQSFSLRCTLV-DG 105
++ + + +K AR++ K AL R + + + G
Sbjct: 110 QENDTTLVKTKELIKNYITARIMAKRPFDKKSNS-------ALFRAVGEGNAQLVAIFGG 162
Query: 106 QGNFGSIDGDSAAAMRY-TECR-LNKISNELLIDLDKETIDFISNYDGKEKEPSVLPTRI 163
QGN Y E R L + + L+ DL I F +
Sbjct: 163 QGN----------TDDYFEELRDLYQTYHVLVGDL----IKFSA---------------- 192
Query: 164 PNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLHNPECSINDLIKIIPAPD------- 216
L + T+ ++ +L L NP PD
Sbjct: 193 -ETLSELIRT-----TLDAEKV-FTQGLN-ILEWLENPS----------NTPDKDYLLSI 234
Query: 217 ---FPTAGII----YGLSSVHDGYYTGKGRVIIRAKT-HI---------------EEFNR 253
P G+I Y +++ G+ G+ R ++ T H E F
Sbjct: 235 PISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFV 294
Query: 254 ENRTAIII---------DELPYQVNKKSLLEKISQLVKEKKLECISNLRDESDKSGMRIV 304
R AI + + P SL I + + + N +E S M +
Sbjct: 295 SVRKAITVLFFIGVRCYEAYP----NTSLPPSILE-------DSLEN--NEGVPSPMLSI 341
Query: 305 IELKRNEIPEIV--LNK-LYKQTQLQNTFGMNMLALVNGQPKLLNLK---EILYYFILH- 357
L + ++ + V N L Q++ ++LVNG K L + + LY L
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVE-------ISLVNG-AKNLVVSGPPQSLYGLNLTL 393
Query: 358 RK-----EVIKRRTIFELRKAREYAHILEGLTIALTNIDNFIQIIRSTSTP------QEA 406
RK + + R F RK + F+ + ++P A
Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSN--------------RFLPV----ASPFHSHLLVPA 435
Query: 407 KNKIIESTWNLPDVSKI-IGFNKKN-----YNTISKINNISKLQNNDMYKLSDIQAQEIL 460
+ I + D+ K + FN K+ Y+T + L+ I I+
Sbjct: 436 SDLINK------DLVKNNVSFNAKDIQIPVYDTFDGSD----LRVLSGSISERI-VDCII 484
Query: 461 KMPL--QRLTNMEQKKII-------NKYENVIKKVIDLTDILSNSKRIIEIITDELNIIK 511
++P+ + T + I+ + + + D T + R+I T ++N
Sbjct: 485 RLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV-----RVIVAGTLDIN-PD 538
Query: 512 NKYGS 516
+ YG
Sbjct: 539 DDYGF 543
Score = 69.3 bits (169), Expect = 9e-12
Identities = 106/576 (18%), Positives = 186/576 (32%), Gaps = 196/576 (34%)
Query: 865 DGPTASGKGTVAQLVASKLGF--HYLDSGALYRLVTLSAINNNIQLDNELELVILIKKLN 922
D PT A+LV LG+ ++ + Q D L L L
Sbjct: 52 DEPTT-----PAELVGKFLGYVSSLVEPSKVG------------QFDQVLNLC-----LT 89
Query: 923 YNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIR-----KELFKIQVKFRKFPGL- 976
F + YL G ++ L N+ + + + I+ + + K + L
Sbjct: 90 E-F--ENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF 146
Query: 977 --VADGRDMGTTVF-----PDAFLK----IFLTADIKQRTKRRYKQLMQKGFSVSMSDLL 1025
V +G +F D + + ++ T Y L+ ++ L
Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT----------YHVLVGD-LIKFSAETL 195
Query: 1026 INLIKRDIRDK---TRNL-------SPLKCPEQAHLLNT--SKMNINQVVNQILDCFATL 1073
LI+ + + T+ L +P P++ +LL+ S + V+ Q L +
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS-CPLIGVI-Q-LAHYVVT 252
Query: 1074 FKESLLRH-DMR---------SGEVISAEVIGLDRNFVIINADLKS-EAFIPIEEFKNDN 1122
K ++R S +++A I A+ S E+F F +
Sbjct: 253 AKLLGFTPGELRSYLKGATGHSQGLVTAVAI----------AETDSWESF-----FVSVR 297
Query: 1123 GELEV--KIG-----DFVSVAI------ESLENGFGDT--ILS-RDKAKRLASWLSLEKA 1166
+ V IG + + ++ +SLEN G +LS + L+ E+
Sbjct: 298 KAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN--------LTQEQ- 348
Query: 1167 MESGEIITGTINGKVKGGLTV---LTNGLKAF----LPGSLV----DIRPVK-----D-- 1208
++ + + T N + G V L NG K P SL +R K D
Sbjct: 349 VQ--DYVNKT-NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQS 405
Query: 1209 ------------------TTPFEGKTMD--FKVIKLDRKRNNVVLSHRA----VIEESMG 1244
+PF + +I D +NNV + + V + G
Sbjct: 406 RIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG 465
Query: 1245 EERQKLIETLKEG---CTVKGVV--KNITDYGA--FIDLG-----GIDGLLH-ITDIAWR 1291
+ + L ++ E C ++ V + T + A +D G G+ L H D
Sbjct: 466 SDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGV 525
Query: 1292 RVKHPSEILTIGQDISTKILKYDQEKNRVS-LGMKQ 1326
RV I+ + N G KQ
Sbjct: 526 RV----------------IVAGTLDINPDDDYGFKQ 545
Score = 58.5 bits (141), Expect = 2e-08
Identities = 56/361 (15%), Positives = 107/361 (29%), Gaps = 151/361 (41%)
Query: 170 GSSGIAVGMATNIPPHNLTEVIDGVL-----YVLHNPECSINDLIKIIPAPDFPTAGIIY 224
GS GM ++ + ++ V + SI D++ + P I+
Sbjct: 1625 GSQ--EQGMGMDL--YKTSKAAQDVWNRADNHFKDTYGFSILDIVI-----NNPVNLTIH 1675
Query: 225 GLSSVHDGYYTG-KGRVIIRAKTHIEEFNRENRTAIIIDELPYQVNKKSLLEKISQLVKE 283
+ G KG+ I REN +A+I + + + K EKI + + E
Sbjct: 1676 ---------FGGEKGKRI-----------RENYSAMIFETIV---DGKLKTEKIFKEINE 1712
Query: 284 KKLECISNLRDESDKSGMRIVIELKRNEIPEIVLNKLYKQTQLQNTFGMNMLALVNGQPK 343
+ +L+ TQ T QP
Sbjct: 1713 HSTSYTF--------------------RSEKGLLS----ATQ--FT-----------QPA 1735
Query: 344 LLNLKEILYYFILHRKEVIKRRTIFELRKAR------EYAHILEGLTIALT------NID 391
L L E + E +K + + EYA AL +I+
Sbjct: 1736 LT-LMEKAAF------EDLKSKGLIPADATFAGHSLGEYA--------ALASLADVMSIE 1780
Query: 392 NFIQIIR------------------------------STSTPQEAKNKIIE-----STW- 415
+ ++++ + S QEA ++E + W
Sbjct: 1781 SLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWL 1840
Query: 416 ------NLPDVSKIIGFNKKNYNTISKINNISKLQNNDMYKLSDIQAQEILKMPLQRLTN 469
N+ + + + + +T++ + N KLQ D+ +L + L+ +
Sbjct: 1841 VEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQK-------SLSLEEVEG 1893
Query: 470 M 470
Sbjct: 1894 H 1894
Score = 50.4 bits (120), Expect = 6e-06
Identities = 75/459 (16%), Positives = 141/459 (30%), Gaps = 153/459 (33%)
Query: 1103 INAD-LKSEAFI-----PIEEFKNDN-----GELEVKIGDFVSVAIESLENGFGDTILSR 1151
A L+ E F P E F D+ EL K +VS +E + G D +L
Sbjct: 28 FIASQLQ-EQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVL-- 84
Query: 1152 DKAKRLASWLSLEKA-MESGEI--ITGTINGKVKGGLTVLTNGLKAFLPGSLVDIRPVKD 1208
E +E +I + + + L +K ++ ++ RP
Sbjct: 85 -----NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDK 139
Query: 1209 TTP---FE----------------GKTMDFKVIKLD--RKRNNVVLSHRAVIEESMGEER 1247
+ F G T D+ + R ++ ++ + +
Sbjct: 140 KSNSALFRAVGEGNAQLVAIFGGQGNTDDY----FEELRDLYQ---TYHVLVGDLIKFSA 192
Query: 1248 QKLIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDIS 1307
+ L E ++ + V + +++ + W +++PS T +D
Sbjct: 193 ETLSELIRTTLDAEKV------FTQGLNI-----------LEW--LENPSN--TPDKDYL 231
Query: 1308 TKILKYDQEKNRVSLGMKQLGIDPWIGL-SF-RYPRGTRLLGKVTNLTDYGAFVEIEKGI 1365
I +S P IG+ Y +LLG G KG
Sbjct: 232 LSIP--------ISC--------PLIGVIQLAHYVVTAKLLGF-----TPGELRSYLKGA 270
Query: 1366 EGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSII 1425
G + + + + D+ WE+F
Sbjct: 271 TGHS---------QGLVTAVAIAETDS--------------------------WESF--- 292
Query: 1426 HKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDE-IEAII 1484
+ K+IT FIG+ + + T I+ + + +E + + +
Sbjct: 293 ------FVSVRKAIT-VLFFIGVRC------YEA-YPNTSLPPSILEDSLENNEGVPSPM 338
Query: 1485 LSI-DVEKERISLGIKQLEGD-PFNNYVNINDKGSLVNG 1521
LSI ++ +E++ + + P V I SLVNG
Sbjct: 339 LSISNLTQEQVQDYVNKTNSHLPAGKQVEI----SLVNG 373
Score = 50.0 bits (119), Expect = 8e-06
Identities = 54/335 (16%), Positives = 105/335 (31%), Gaps = 131/335 (39%)
Query: 1199 SLVDIRPVKDTTPFEGKTMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGC 1258
S++DI V + P T+ F K R R N + A+I E++ + + K + KE
Sbjct: 1660 SILDI--VINN-PVN-LTIHFGGEKGKRIREN----YSAMIFETIVDGKLKTEKIFKE-- 1709
Query: 1259 TVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSEILTIGQDISTKILKYDQEKN 1318
+ ++ T Y GLL T P+ + + +
Sbjct: 1710 ----INEHSTSY----TFRSEKGLLSATQFT-----QPA-LTL----MEKAAFED----- 1746
Query: 1319 RVSLGMKQLGIDPWI----GLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISE- 1373
+K G+ P G S LG +Y A L +++
Sbjct: 1747 -----LKSKGLIPADATFAGHS---------LG------EYAA----------LASLADV 1776
Query: 1374 MDWINKNVTPSKIVQLNDTVEI--------MILEINEERRRISLGMKQCKDNPWENFSII 1425
M + VE+ + +E R + GM NP +
Sbjct: 1777 MS-------------IESLVEVVFYRGMTMQVAVPRDELGRSNYGM--IAINPGR----V 1817
Query: 1426 HKKG--EKIKGIIKSI---TDF----------G--IFIGLDGNIDGLIHLSDLSWTDPGE 1468
E ++ +++ + T + G++ L ++
Sbjct: 1818 AASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAA--GDLRALDTVT--------- 1866
Query: 1469 EIIRNFKKGDEIEAIILSIDVEKERISLGIKQLEG 1503
++ K + ID+ + + SL ++++EG
Sbjct: 1867 NVLNFIK--------LQKIDIIELQKSLSLEEVEG 1893
Score = 48.5 bits (115), Expect = 2e-05
Identities = 54/294 (18%), Positives = 91/294 (30%), Gaps = 98/294 (33%)
Query: 983 MGTTVF--PDAFLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDI-RDKTRN 1039
MG ++ A ++ AD K Y GFS+ DI + N
Sbjct: 1631 MGMDLYKTSKAAQDVWNRAD--NHFKDTY------GFSIL-----------DIVINNPVN 1671
Query: 1040 LSPLKCPEQAHLL--NTSKMNINQVVNQILDCFATLFKESLLRHDMRSGEVI---SAEVI 1094
L+ E+ + N S M +V+ L +FKE + S ++
Sbjct: 1672 LTIHFGGEKGKRIRENYSAMIFETIVDGKLK-TEKIFKEI----NEHSTSYTFRSEKGLL 1726
Query: 1095 GLDRN-----FVI---INADLKSEAFIPIEEFKNDN-------GE------------LE- 1126
+ ++ DLKS+ IP D GE +E
Sbjct: 1727 SATQFTQPALTLMEKAAFEDLKSKGLIP-----ADATFAGHSLGEYAALASLADVMSIES 1781
Query: 1127 -VKI----GDFVSVAIESLENGFGDTILSRDKAKRLASWLSLEK--------AMESGE-- 1171
V++ G + VA+ E G + + R+A+ S E +G
Sbjct: 1782 LVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVGKRTGWLV 1841
Query: 1172 ------------IITGTINGKVKGGLTVLTNGLKAFLPGSLVDIRPVKDTTPFE 1213
+ G + L +TN L F+ +DI ++ + E
Sbjct: 1842 EIVNYNVENQQYVAAGDLR-----ALDTVTNVLN-FIKLQKIDIIELQKSLSLE 1889
Score = 41.2 bits (96), Expect = 0.003
Identities = 28/171 (16%), Positives = 49/171 (28%), Gaps = 53/171 (30%)
Query: 25 AMSVIVGRALPDVRD-GLKPVHRRVLFAMHEMNNLWNRPFVKCARVVGETMGKYHPHGDV 83
M L + GL P FA H +GE
Sbjct: 1738 LMEKAAFEDL---KSKGLIPAD--ATFAGHS---------------LGE----------- 1766
Query: 84 SIYDALVRMAQSFSLR--CTLVDGQGNF--GSIDGDSAAAMRYTECRLN--KISNELLID 137
Y AL +A S+ +V +G ++ D Y +N +++ +
Sbjct: 1767 --YAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824
Query: 138 LDKETIDFISNYDGKEKEPSVLPTRIPNLLINGS----SG--IAVGMATNI 182
+ ++ + G E V N + +G A+ TN+
Sbjct: 1825 ALQYVVERVGKRTGWLVEI-V------NYNVENQQYVAAGDLRALDTVTNV 1868
>1wi5_A RRP5 protein homolog; S1 domain, OB-fold, structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Homo sapiens} SCOP: b.40.4.5
Length = 119
Score = 62.3 bits (151), Expect = 1e-11
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 3/79 (3%)
Query: 1251 IETLKEGCTVKGVVKNITDYGAFIDLG--GIDGLLHITDI-AWRRVKHPSEILTIGQDIS 1307
E LK G + G V ++ D+G +D+G G L + + R K+ L +GQ ++
Sbjct: 16 AEALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLN 75
Query: 1308 TKILKYDQEKNRVSLGMKQ 1326
+ K VSL +
Sbjct: 76 CIVEKVKGNGGVVSLSVGH 94
Score = 47.7 bits (113), Expect = 2e-06
Identities = 13/95 (13%), Positives = 37/95 (38%), Gaps = 6/95 (6%)
Query: 1342 GTRLLGKVTNLTDYGAFVEI-EKGIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEI 1400
G L G V++L D+G V+I G + + + + +++ + ++ ++
Sbjct: 22 GMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKV 81
Query: 1401 NEERRRISLGMKQ-----CKDNPWENFSIIHKKGE 1430
+SL + +++++ + G
Sbjct: 82 KGNGGVVSLSVGHSEVSTAIATEQQSWNLNNLSGP 116
Score = 43.5 bits (102), Expect = 5e-05
Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 1427 KKGEKIKGIIKSITDFGIF--IGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAII 1484
K G + G + S+ D G IG+DG + L + K G + I+
Sbjct: 20 KPGMLLTGTVSSLEDHGYLVDIGVDG-TRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIV 78
Query: 1485 LSIDVEKERISLGIKQ 1500
+ +SL +
Sbjct: 79 EKVKGNGGVVSLSVGH 94
Score = 40.0 bits (93), Expect = 8e-04
Identities = 20/109 (18%), Positives = 44/109 (40%), Gaps = 10/109 (9%)
Query: 1507 NNYVNIND--KGSLVNGIIKSIDTNKGAIIQLS-NEVEGYLRISEEDNKH-----EKKLK 1558
N ++ G L+ G + S++ + G ++ + + +L + + KLK
Sbjct: 11 NRVLSAEALKPGMLLTGTVSSLE-DHGYLVDIGVDGTRAFLPLLKAQEYIRQKNKGAKLK 69
Query: 1559 IGENIDVLTVLIDHKTRYIQLSFKKKEVIKKK-KLLTSINANTISGTTN 1606
+G+ ++ + + + LS EV S N N +SG ++
Sbjct: 70 VGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQSWNLNNLSGPSS 118
>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG,
PRK04182 class ME structural genomics, protein structure
initiative; 2.20A {Eubacterium ventriosum}
Length = 201
Score = 52.7 bits (126), Expect = 2e-07
Identities = 27/217 (12%), Positives = 63/217 (29%), Gaps = 35/217 (16%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVILIKK 920
+I I SG VA+ +A L + A + + ++++
Sbjct: 8 IIAIGREFGSGGHLVAKKLAEHYNIPLYSKELLDEV----AKDGRYSKE-------VLER 56
Query: 921 LNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVADG 980
+ + TT+ + ++ + + + V G
Sbjct: 57 FDEKPMNFAFIPVPAGGTTISLEQDIAIRQFNFIR-----------KKANEEKESFVIVG 105
Query: 981 RDMGTTVFPDA--FLKIFLTADIKQRTKRRYKQLMQKGFSVSMSDLLINLIKRDIRDKTR 1038
R + D + F+ D +TKR + + V L + K D K
Sbjct: 106 R-CAEEILSDNPNMISAFILGDKDTKTKR-----VMEREGVDEKTALNMMKKMDKMRKVY 159
Query: 1039 NLSPLKC----PEQAHL-LNTSKMNINQVVNQILDCF 1070
+ + + + K++++ + I+
Sbjct: 160 HNFYCESKWGDSRTYDICIKIGKVDVDTATDMIIKYI 196
>4ayb_E DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_E
4b1o_E 4b1p_T 2waq_E 2wb1_E 2pmz_E 3hkz_E
Length = 180
Score = 50.7 bits (121), Expect = 5e-07
Identities = 27/138 (19%), Positives = 65/138 (47%), Gaps = 15/138 (10%)
Query: 1377 INKNVTPSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGII 1436
+ + + L + I+ ++ +EE + + ++ + + E ++G +
Sbjct: 30 LRQQYQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEV 89
Query: 1437 KSITDFGIFIGLDGNIDGLIHLSDLSWT----DP------GEEIIRNFKKGDEIEAIILS 1486
+ ++G+F+ L G +DGL+H+S ++ D GE+ + +KGD++ A ++S
Sbjct: 90 LQVDNYGVFVNL-GPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVIS 148
Query: 1487 IDVEKE----RISLGIKQ 1500
+ RI+L ++Q
Sbjct: 149 VASTVTGRLPRIALTMRQ 166
Score = 49.1 bits (117), Expect = 2e-06
Identities = 26/144 (18%), Positives = 60/144 (41%), Gaps = 24/144 (16%)
Query: 1212 FEGKTMD-----FKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKN 1266
++ K + ++ + +++ + + + ++E V+G V
Sbjct: 34 YQEKILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQE--VVEGEVLQ 91
Query: 1267 ITDYGAFIDLGGIDGLLHITDIAWRRVKHPSE-----------ILTIGQDISTKILKYDQ 1315
+ +YG F++LG +DGL+HI+ I +K+ + ++ G + +++
Sbjct: 92 VDNYGVFVNLGPMDGLVHISQITDDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVAS 151
Query: 1316 EKN----RVSLGMKQ--LGIDPWI 1333
R++L M+Q LG WI
Sbjct: 152 TVTGRLPRIALTMRQPYLGKLEWI 175
Score = 42.2 bits (99), Expect = 4e-04
Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 19/98 (19%)
Query: 1332 WIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMD------------WINK 1379
+ +++ + G+V + +YG FV + ++GLVHIS++ +
Sbjct: 72 FDMITYVPVVQEVVEGEVLQVDNYGVFVNLG-PMDGLVHISQITDDTLKYDNVRGIIFGE 130
Query: 1380 NVTPSKIVQLNDTVEIMILEINEERR----RISLGMKQ 1413
K++Q D V ++ + RI+L M+Q
Sbjct: 131 K--SKKVIQKGDKVRARVISVASTVTGRLPRIALTMRQ 166
>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 = 49.1 bits (118), Expect = 1e-05
Identities = 10/73 (13%), Positives = 28/73 (38%), Gaps = 12/73 (16%)
Query: 1347 GKVTNLTDYGAFVEI-EKGIEGLVHISEMDWINKNVTPS-----------KIVQLNDTVE 1394
++ +++ G V + + G + + + + S + ++ D ++
Sbjct: 566 AEIVDISRGGMRVRLVDNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVID 625
Query: 1395 IMILEINEERRRI 1407
+ I E+ E R I
Sbjct: 626 VTIAEVRMETRSI 638
Score = 47.5 bits (114), Expect = 3e-05
Identities = 14/75 (18%), Positives = 25/75 (33%), Gaps = 16/75 (21%)
Query: 1434 GIIKSITDFGIFIGLDGN-IDGLIHLSDLSWTDPGEEIIRN-------------FKKGDE 1479
I I+ G+ + L N I L +E++ + +K D
Sbjct: 566 AEIVDISRGGMRVRLVDNGAIAFIPAPFL--HAVRDELVCSQENGTVQIKGETVYKVTDV 623
Query: 1480 IEAIILSIDVEKERI 1494
I+ I + +E I
Sbjct: 624 IDVTIAEVRMETRSI 638
Score = 30.2 bits (69), Expect = 6.7
Identities = 4/29 (13%), Positives = 10/29 (34%), Gaps = 2/29 (6%)
Query: 1262 GVVKNITDYGAFIDLG--GIDGLLHITDI 1288
+ +I+ G + L G + +
Sbjct: 566 AEIVDISRGGMRVRLVDNGAIAFIPAPFL 594
>2c35_B Human RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transcription, nucleotidyltransferase; 2.70A {Homo
sapiens} SCOP: b.40.4.5 d.230.1.1
Length = 172
Score = 45.3 bits (107), Expect = 3e-05
Identities = 14/81 (17%), Positives = 27/81 (33%), Gaps = 12/81 (14%)
Query: 1426 HKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDL-----------SWTDPGEEIIRNF 1474
KGE + ++ + G+F + G + I + +
Sbjct: 79 PFKGEVVDAVVTQVNKVGLFTEI-GPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVI 137
Query: 1475 KKGDEIEAIILSIDVEKERIS 1495
++ DEI I+ V+K I
Sbjct: 138 QQDDEIRLKIVGTRVDKNDIF 158
Score = 34.5 bits (79), Expect = 0.13
Identities = 13/91 (14%), Positives = 29/91 (31%), Gaps = 14/91 (15%)
Query: 1250 LIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSE----------- 1298
++ +G V VV + G F ++G + + I P+
Sbjct: 75 IVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDED 134
Query: 1299 -ILTIGQDISTKIL--KYDQEKNRVSLGMKQ 1326
++ +I KI+ + D+ +
Sbjct: 135 IVIQQDDEIRLKIVGTRVDKNDIFAIGSLMD 165
Score = 33.7 bits (77), Expect = 0.22
Identities = 12/79 (15%), Positives = 27/79 (34%), Gaps = 12/79 (15%)
Query: 1341 RGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMD-----------WINKNVTPSKIVQL 1389
+G + VT + G F EI + + + K + ++Q
Sbjct: 81 KGEVVDAVVTQVNKVGLFTEIGP-MSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQ 139
Query: 1390 NDTVEIMILEINEERRRIS 1408
+D + + I+ ++ I
Sbjct: 140 DDEIRLKIVGTRVDKNDIF 158
>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding,
exonucle binding, mitochondrion, rRNA processing; 3.00A
{Saccharomyces cerevisiae}
Length = 977
Score = 47.5 bits (113), Expect = 4e-05
Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 20/86 (23%)
Query: 1347 GKVTNLTDYGAFVEI-EKGIEGLVHISEMD----------------WINKNVTPSKIVQL 1389
G V + + G V + + G+EGL+ + + ++ N + V +
Sbjct: 892 GYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYV 951
Query: 1390 NDTVEIMILEINEE---RRRISLGMK 1412
D VE+ + + + +R+ L +K
Sbjct: 952 FDKVEVQVRSVMDPITSKRKAELLLK 977
Score = 42.8 bits (101), Expect = 0.001
Identities = 15/110 (13%), Positives = 35/110 (31%), Gaps = 30/110 (27%)
Query: 1403 ERR-----RISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGN-IDGLI 1456
R R S+ + ++ G + + + GI + + ++GLI
Sbjct: 864 HRNAQFAGRASIEYYVGQ--------VMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLI 915
Query: 1457 HLSDLS----------------WTDPGEEIIRNFKKGDEIEAIILSIDVE 1490
L +L+ + + R+ D++E + S+
Sbjct: 916 RLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDP 965
>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA
degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A
{Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5
b.40.4.5 b.40.4.16
Length = 760
Score = 47.4 bits (113), Expect = 4e-05
Identities = 16/86 (18%), Positives = 35/86 (40%), Gaps = 20/86 (23%)
Query: 1347 GKVTNLTDYGAFVEI-EKGIEGLVHISEMD----------------WINKNVTPSKIVQL 1389
G V + + G V + + G+EGL+ + + ++ N + V +
Sbjct: 675 GYVIKVFNNGIVVLVPKFGVEGLIRLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYV 734
Query: 1390 NDTVEIMILEINEE---RRRISLGMK 1412
D VE+ + + + +R+ L +K
Sbjct: 735 FDKVEVQVRSVMDPITSKRKAELLLK 760
Score = 42.7 bits (101), Expect = 0.001
Identities = 15/110 (13%), Positives = 35/110 (31%), Gaps = 30/110 (27%)
Query: 1403 ERR-----RISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGN-IDGLI 1456
R R S+ + ++ G + + + GI + + ++GLI
Sbjct: 647 HRNAQFAGRASIEYYVGQ--------VMRNNESTETGYVIKVFNNGIVVLVPKFGVEGLI 698
Query: 1457 HLSDLS----------------WTDPGEEIIRNFKKGDEIEAIILSIDVE 1490
L +L+ + + R+ D++E + S+
Sbjct: 699 RLDNLTEDPNSAAFDEVEYKLTFVPTNSDKPRDVYVFDKVEVQVRSVMDP 748
>3h0g_G DNA-directed RNA polymerase II subunit RPB7; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 172
Score = 43.8 bits (103), Expect = 9e-05
Identities = 14/119 (11%), Positives = 41/119 (34%), Gaps = 13/119 (10%)
Query: 1393 VEIMILEINEERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNI 1452
++ ++I++ R G + + + +GE + I+ ++ G F + G +
Sbjct: 50 LDSNTIDIDKGRVVPGQGFAEFEVK-YRAVLWRPFRGEVVDAIVTTVNKMGFFANI-GPL 107
Query: 1453 DGLIHLSDL---------SWTDPGEEIIRNFKKGDEIEAIILSIDVEKERIS--LGIKQ 1500
+ + + + + +KG + I+ + I +K+
Sbjct: 108 NVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGSNVRLKIVGTRTDATEIFAIATMKE 166
Score = 34.5 bits (79), Expect = 0.11
Identities = 13/84 (15%), Positives = 29/84 (34%), Gaps = 12/84 (14%)
Query: 1255 KEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDIAWRRVKHPSE----------ILTIGQ 1304
G V +V + G F ++G ++ + + P+ ++ G
Sbjct: 83 FRGEVVDAIVTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQVIEKGS 142
Query: 1305 DISTKI--LKYDQEKNRVSLGMKQ 1326
++ KI + D + MK+
Sbjct: 143 NVRLKIVGTRTDATEIFAIATMKE 166
Score = 32.6 bits (74), Expect = 0.61
Identities = 13/86 (15%), Positives = 25/86 (29%), Gaps = 16/86 (18%)
Query: 1341 RGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMD-----------WINKNVTPSKIVQL 1389
RG + VT + G F I + V + ++++
Sbjct: 84 RGEVVDAIVTTVNKMGFFANI-GPLNVFVSSHLVPPDMKFDPTANPPNYSG--EDQVIEK 140
Query: 1390 NDTVEIMILEINEERRRIS--LGMKQ 1413
V + I+ + I MK+
Sbjct: 141 GSNVRLKIVGTRTDATEIFAIATMKE 166
>1go3_E DNA-directed RNA polymerase subunit E; transferase, transferase,
transcription; 1.75A {Methanococcus jannaschii} SCOP:
b.40.4.5 d.230.1.1
Length = 187
Score = 43.0 bits (101), Expect = 2e-04
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIH----LSDLSWTDP------GEEIIRNFKKG 1477
E I+G + + +FG F+ L G +DGLIH + D DP G+E + + G
Sbjct: 81 MYELIEGEVVDVVEFGSFVRL-GPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIG 139
Query: 1478 DEIEAIILSIDVEKERI 1494
D + A I++I ++ ER
Sbjct: 140 DYVRARIVAISLKAERK 156
Score = 36.4 bits (84), Expect = 0.035
Identities = 31/143 (21%), Positives = 60/143 (41%), Gaps = 21/143 (14%)
Query: 1212 FEGK---TMDFKVIKLDRKRNNVVLSHRAVIEESMGEERQKLIETLKEGCTVKGVVKNIT 1268
+EG+ + F + +D K + L+ + ++G V ++
Sbjct: 34 YEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVV 93
Query: 1269 DYGAFIDLGGIDGLLHITDIAWRRV-----------KHPSEILTIGQDISTKILKYDQEK 1317
++G+F+ LG +DGL+H++ I V K ++L IG + +I+ +
Sbjct: 94 EFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKA 153
Query: 1318 NR-----VSLGMKQ--LGIDPWI 1333
R ++L M+Q LG WI
Sbjct: 154 ERKRGSKIALTMRQPYLGKLEWI 176
Score = 34.9 bits (80), Expect = 0.10
Identities = 22/99 (22%), Positives = 47/99 (47%), Gaps = 20/99 (20%)
Query: 1332 WIGLSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMD------------WINK 1379
+ L + + G+V ++ ++G+FV + ++GL+H+S++ I K
Sbjct: 72 FETLVYIPEMYELIEGEVVDVVEFGSFVRLGP-LDGLIHVSQIMDDYVSYDPKREAIIGK 130
Query: 1380 NVTPSKIVQLNDTVEIMILEINEERRR-----ISLGMKQ 1413
K++++ D V I+ I+ + R I+L M+Q
Sbjct: 131 E--TGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQ 167
>2b8k_G B16, DNA-directed RNA polymerase II 19 kDa polypeptide; DNA-dependent
RNA polymerase, cellular RNA polymerase; 4.15A
{Saccharomyces cerevisiae} SCOP: b.40.4.5 d.230.1.1
Length = 215
Score = 42.4 bits (99), Expect = 5e-04
Identities = 11/79 (13%), Positives = 21/79 (26%), Gaps = 10/79 (12%)
Query: 1426 HKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDL---------SWTDPGEEIIRNFKK 1476
KGE + G + S + G + + G + + + S +
Sbjct: 81 PFKGEVVDGTVVSCSQHGFEVQV-GPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITI 139
Query: 1477 GDEIEAIILSIDVEKERIS 1495
I I + I
Sbjct: 140 KSRIRVKIEGCISQVSSIH 158
>1y14_B B16, RPB7, DNA-directed RNA polymerase II 19 kDa polypeptide;
transferase; 2.30A {Saccharomyces cerevisiae} SCOP:
b.40.4.5 d.230.1.1 PDB: 1nt9_G 1wcm_G 1pqv_G 1y1v_G
1y1w_G 1y1y_G 1y77_G* 2b63_G* 2ja5_G* 2ja6_G* 2ja7_G*
2ja8_G* 2r7z_G 2r92_G 2r93_G 2vum_G* 3fki_G 3h3v_H
3hou_G* 3hov_G* ...
Length = 171
Score = 41.4 bits (97), Expect = 6e-04
Identities = 11/86 (12%), Positives = 22/86 (25%), Gaps = 10/86 (11%)
Query: 1419 WENFSIIHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDL---------SWTDPGEE 1469
+ KGE + G + S + G + + G + + + S +
Sbjct: 74 YRAVVFKPFKGEVVDGTVVSCSQHGFEVQV-GPMKVFVTKHLMPQDLTFNAGSNPPSYQS 132
Query: 1470 IIRNFKKGDEIEAIILSIDVEKERIS 1495
I I + I
Sbjct: 133 SEDVITIKSRIRVKIEGCISQVSSIH 158
>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2, structure
initiative, northeast structural genomics consort NESG;
1.80A {Deinococcus radiodurans R1} SCOP: b.40.4.5
b.40.4.16 PDB: 2r7f_A
Length = 469
Score = 42.7 bits (101), Expect = 0.001
Identities = 6/64 (9%), Positives = 17/64 (26%), Gaps = 15/64 (23%)
Query: 1347 GKVTNLTDYGAFVEIEK-GIEGLVHISEMDWINKNVTPSKIVQLNDTVEIMILEINEERR 1405
V + A + I + V+ +++ +I+ +
Sbjct: 409 AVVVDRRGAQATLLIPDLAFDVQVNTP--------------AAPGTALQVQFADIDLPQM 454
Query: 1406 RISL 1409
R+
Sbjct: 455 RVRA 458
Score = 39.2 bits (92), Expect = 0.011
Identities = 5/71 (7%), Positives = 17/71 (23%), Gaps = 15/71 (21%)
Query: 1427 KKGEKIKGIIKSITDFGIFIGLDGN-IDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAIIL 1485
+ ++ + + D ++ G ++
Sbjct: 402 QPERVWDAVVVDRRGAQATLLIPDLAFDVQVNTPAA--------------PGTALQVQFA 447
Query: 1486 SIDVEKERISL 1496
ID+ + R+
Sbjct: 448 DIDLPQMRVRA 458
>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta
protein., structural genomics, PSI-2, protein structure
initiative; HET: G3D; 2.20A {Bacillus subtilis} PDB:
2axp_A*
Length = 173
Score = 40.1 bits (94), Expect = 0.002
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 859 IPVITIDGPTASGKGTVAQLVASKLGFHYLD 889
+ +I ++GP K TVA ++ +L + +
Sbjct: 1 MTLIILEGPDCCFKSTVAAKLSKELKYPIIK 31
>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A
{Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A
1ko5_A* 1ko8_A* 1kof_A*
Length = 175
Score = 40.4 bits (94), Expect = 0.002
Identities = 13/59 (22%), Positives = 26/59 (44%)
Query: 853 TMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNE 911
+ + + G + SGK VA VA +L +LD L+ + + + L+++
Sbjct: 2 STTNHDHHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDFLHPRRNIEKMASGEPLNDD 60
>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure
initiati YORK structural genomics research consortium,
nysgrc; 2.20A {Sinorhizobium meliloti}
Length = 202
Score = 39.3 bits (91), Expect = 0.004
Identities = 12/56 (21%), Positives = 30/56 (53%)
Query: 856 KKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNE 911
+++ I + G + SGK +V + +A G+ +++ AL+ + ++ I L ++
Sbjct: 15 RRFPGSIVVMGVSGSGKSSVGEAIAEACGYPFIEGDALHPPENIRKMSEGIPLTDD 70
>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate
hydrolases fold, S genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.70A {Chloroflexus
aurantiacus}
Length = 193
Score = 38.4 bits (89), Expect = 0.009
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
+I + G A+GK T++Q +A+ L L A
Sbjct: 7 LIIVTGHPATGKTTLSQALATGLRLPLLSKDAFKE 41
>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural
genomics, PSI, protein struc initiative; 3.20A
{Agrobacterium tumefaciens str} SCOP: c.37.1.25
Length = 191
Score = 37.0 bits (85), Expect = 0.027
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 11/76 (14%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLG-----------FHYLDSGALYRLVTLSAINNNIQL 908
++ + G SGK T+A+ +A+ G + Y+ G + + S N + +
Sbjct: 10 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDLWGYIKHGRIDPWLPQSHQQNRMIM 69
Query: 909 DNELELVILIKKLNYN 924
++ K Y
Sbjct: 70 QIAADVAGRYAKEGYF 85
>2ckz_B C25, DNA-directed RNA polymerase III 25 KD polypeptide; multiprotein
complex, nucleotidyltransferase, nuclear protein,
hypothetical protein; 3.2A {Saccharomyces cerevisiae}
Length = 218
Score = 36.6 bits (84), Expect = 0.037
Identities = 15/73 (20%), Positives = 23/73 (31%), Gaps = 13/73 (17%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTD-------------PGEEIIRNF 1474
GE + G I T GI + L G D + ++ + EE F
Sbjct: 81 LGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDEETKLYF 140
Query: 1475 KKGDEIEAIILSI 1487
++I I
Sbjct: 141 DVNEKIRFRIERE 153
Score = 30.1 bits (67), Expect = 4.6
Identities = 15/76 (19%), Positives = 30/76 (39%), Gaps = 3/76 (3%)
Query: 1335 LSFRYPRGTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSK--IVQLNDT 1392
+ F+ G + G ++ T G V + + + M + TP + + D
Sbjct: 75 VVFKPFLGEIVTGWISKCTAEGIKVSLLGIFDDIFIPQNMLFEGCYYTPEESAWIWPMDE 134
Query: 1393 VEIMILEINEE-RRRI 1407
+ ++NE+ R RI
Sbjct: 135 ETKLYFDVNEKIRFRI 150
>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function
initiative, EFI, STRU genomics, transferase; 1.60A
{Janibacter SP}
Length = 200
Score = 36.6 bits (84), Expect = 0.039
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 854 MIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGAL 893
M + + + G + SGK T+A VA + G + ++ A
Sbjct: 24 MTGEPTRHVVVMGVSGSGKTTIAHGVADETGLEFAEADAF 63
>2vli_A Antibiotic resistance protein; transferase, tunicamycin,
phosphotransferase; 1.95A {Deinococcus radiodurans}
Length = 183
Score = 36.1 bits (83), Expect = 0.041
Identities = 31/217 (14%), Positives = 65/217 (29%), Gaps = 63/217 (29%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLG----FHYLDSGALYRLVTLSAINNNIQLDNELELV 915
P+I I+GP GK A + +L F + G R +T + + + L+
Sbjct: 6 PIIWINGPFGVGKTHTAHTLHERLPGSFVFEPEEMGQALRKLTPGFSGDPQEHPMWIPLM 65
Query: 916 I-LIKKLNYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFP 974
+ ++ + G + V + S A+ + + L + F
Sbjct: 66 LDALQYASREAAGPLI---------------VPVSISDTARHRRLMSGLKDRGLSVHHF- 109
Query: 975 GLVADGRDMGTTVFPDAFLKIFLTAD---IKQRTKRRYKQLMQKGFSVSMSDLLINLIKR 1031
L A + +R +R + +
Sbjct: 110 ---------------------TLIAPLNVVLERLRRDGQ------------------PQV 130
Query: 1032 DIRDKTRNLSPLKCPEQAHLLNTSKMNINQVVNQILD 1068
++ L+ L+ + ++T+ + QV QI
Sbjct: 131 NVGTVEDRLNELRGEQFQTHIDTAGLGTQQVAEQIAA 167
>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins
(A/B), protein binding, transferase, phosphotransferase;
HET: ADP; 1.76A {Homo sapiens} PDB: 3iik_A 3iil_A*
3iim_A* 1rkb_A
Length = 180
Score = 35.0 bits (80), Expect = 0.084
Identities = 18/83 (21%), Positives = 34/83 (40%)
Query: 852 ITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNE 911
+ +P I + G GK T+ + +ASK G Y++ G L R L +
Sbjct: 4 GSPEFMLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPI 63
Query: 912 LELVILIKKLNYNFLGKEVYLNG 934
L+ ++ +L+ V ++
Sbjct: 64 LDEDRVVDELDNQMREGGVIVDY 86
>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein
struct initiative, northeast structural genomics
consortium, NESG, function; 2.40A {Bacillus halodurans}
SCOP: c.37.1.25
Length = 189
Score = 34.9 bits (80), Expect = 0.098
Identities = 12/56 (21%), Positives = 21/56 (37%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLSAINNNIQLDNELELVI 916
+ I GP GK T + +A++L G + + + + D L L
Sbjct: 4 LYIITGPAGVGKSTTCKRLAAQLDNSAYIEGDIINHMVVGGYRPPWESDELLALTW 59
>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI,
protein structure initiative; 1.90A {Geobacillus
stearothermophilus} SCOP: c.37.1.6
Length = 201
Score = 35.0 bits (81), Expect = 0.12
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 861 VITIDGPTASGKGTVAQLVASKLG 884
V+ IDG + SGK T+A ++ L
Sbjct: 24 VLGIDGLSRSGKTTLANQLSQTLR 47
>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate
kinase); nucleoside monophosphate kinase, NMP kinase;
HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP:
c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*
Length = 194
Score = 34.0 bits (79), Expect = 0.21
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 854 MIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
M K V+ + G SGKGT + G+ +L +G L R
Sbjct: 1 MEKSKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLR 42
>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG,
structural genomics, midwest center for structural
genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB:
3h0k_A
Length = 179
Score = 32.9 bits (75), Expect = 0.44
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
VI I G SGK A+L+ + G + + R
Sbjct: 3 VILITGMPGSGKSEFAKLLK-ERGAKVIVMSDVVR 36
>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system
kinase, STRU genomics, joint center for structural
genomics, JCSG; 1.95A {Silicibacter SP}
Length = 208
Score = 33.2 bits (76), Expect = 0.45
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 13/40 (32%)
Query: 861 VITIDGPTASGKGTVAQLVASKL-------------GFHY 887
++ + G SGK T++ +A+ L GFH
Sbjct: 24 LVALSGAPGSGKSTLSNPLAAALSAQGLPAEVVPMDGFHL 63
>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase,
transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens}
PDB: 1z83_A* 3adk_A
Length = 196
Score = 32.9 bits (76), Expect = 0.48
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 857 KYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
K +I + G SGKGT + + K G+ +L +G L R
Sbjct: 7 KKTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLR 45
>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP
phosphotransferase, myokinase, structural genomics,
structural genomics consortium, SGC; 1.48A {Homo
sapiens} PDB: 2ak3_A*
Length = 227
Score = 32.9 bits (76), Expect = 0.55
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G SGKGTV+ + + +L SG L R
Sbjct: 14 GAPGSGKGTVSSRITTHFELKHLSSGDLLR 43
>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces
cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*
Length = 203
Score = 32.9 bits (76), Expect = 0.59
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 853 TMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
+ VI + G +GKGT + + F +L +G L R
Sbjct: 9 AFSPDQVSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAGDLLR 51
>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding,
human, structura genomics, structural genomics
consortium, SGC, transferase; HET: GP5; 2.05A {Homo
sapiens} PDB: 2ar7_A* 3ndp_A
Length = 246
Score = 33.0 bits (76), Expect = 0.60
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP SGKGTV Q +A G +L SG R
Sbjct: 34 GPPGSGKGTVCQRIAQNFGLQHLSSGHFLR 63
>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1,
nicotinic acid riboside kinase activity, NAD
biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB:
2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*
Length = 207
Score = 32.5 bits (74), Expect = 0.65
Identities = 11/44 (25%), Positives = 16/44 (36%)
Query: 841 SKLCGVQRLCKITMIKKYIPVITIDGPTASGKGTVAQLVASKLG 884
S + +I I G T SGK T+A+ + L
Sbjct: 3 SSHHHHHHSSGLVPRGSKTFIIGISGVTNSGKTTLAKNLQKHLP 46
>1hh2_P NUSA, N utilization substance protein A; transcription regulation,
termination; 2.1A {Thermotoga maritima} SCOP: b.40.4.5
d.52.3.1 d.52.3.1 d.202.1.1 PDB: 1l2f_A
Length = 344
Score = 33.2 bits (77), Expect = 0.68
Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 10/68 (14%)
Query: 1425 IHKKGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDLSWTDPGEEIIRNFKKGDEIEAII 1484
KG + + I + G ++ + + PGE K GD ++ I
Sbjct: 131 SELKGTVTTAEVIRVMGEWADIRI-GKLETRLPKKEWI---PGE----EIKAGDLVKVYI 182
Query: 1485 LSIDVEKE 1492
+ DV K
Sbjct: 183 I--DVVKT 188
Score = 31.7 bits (73), Expect = 1.8
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 1084 RSGEVISAEVIGLDRNFVIINADLKSEAFIPIEE 1117
G V +AEVI + + I K E +P +E
Sbjct: 133 LKGTVTTAEVIRVMGEWADIRIG-KLETRLPKKE 165
>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET:
AMP; 2.3A {Homo sapiens}
Length = 199
Score = 32.5 bits (75), Expect = 0.72
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 857 KYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
+ +I I G SGKGT + + K GF +L +G L R
Sbjct: 10 RKCKIIFIIGGPGSGKGTQCEKLVEKYGFTHLSTGELLR 48
>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase;
HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A*
2jas_A*
Length = 205
Score = 32.3 bits (73), Expect = 0.92
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 862 ITIDGPTASGKGTVAQLVASKLGFHYL 888
I I G +GK T++ ++ KLG+
Sbjct: 3 IAIFGTVGAGKSTISAEISKKLGYEIF 29
>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A
{Coxiella burnetii}
Length = 185
Score = 31.8 bits (73), Expect = 1.0
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 854 MIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDS 890
M K + I G +GK +V +A DS
Sbjct: 1 MKKNLTNIYLI-GLMGAGKTSVGSQLAKLTKRILYDS 36
>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase,
antibiotic resistance, phosphorylation, mononucleoti
binding fold; HET: ATP; 2.50A {Streptomyces venezuelae}
SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A*
1qhy_A*
Length = 178
Score = 31.7 bits (71), Expect = 1.1
Identities = 7/28 (25%), Positives = 17/28 (60%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYL 888
+I ++G +++GK + + + S L +L
Sbjct: 5 MIILNGGSSAGKSGIVRCLQSVLPEPWL 32
>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET:
AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1
Length = 222
Score = 31.8 bits (73), Expect = 1.2
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G ASGKGT +L+ +K ++ +G L R
Sbjct: 12 GAPASGKGTQCELIKTKYQLAHISAGDLLR 41
>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid
biosynthesis, P-loop kinase, metal- binding, shikimate
pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis}
SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A*
2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A*
1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A*
3baf_A*
Length = 184
Score = 31.8 bits (73), Expect = 1.2
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYLDS 890
P + G SGK T+ + +A LG LD+
Sbjct: 3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDT 33
>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein
inhibitors, nucleotide-binding, transferase; HET: AP5;
1.60A {Cryptosporidium parvum iowa II}
Length = 217
Score = 31.7 bits (73), Expect = 1.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G SGKGT + + + G +L +G + R
Sbjct: 12 GAPGSGKGTQCEFIKKEYGLAHLSTGDMLR 41
>1y63_A LMAJ004144AAA protein; structural genomics, protein structure
initiative, PSI, SGPP structural genomics of pathogenic
protozoa consortium; HET: ADP; 1.70A {Leishmania major}
SCOP: c.37.1.1
Length = 184
Score = 31.6 bits (71), Expect = 1.4
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 853 TMIKKYIPVITIDGPTASGKGTVAQLVASKL-GFHYLDSGAL 893
+M + I I G +GK ++A+++A++L GF +L+ G L
Sbjct: 4 SMEQPKGINILITGTPGTGKTSMAEMIAAELDGFQHLEVGKL 45
>3tlx_A Adenylate kinase 2; structural genomics, structural genomics
consortium, SGC, RO fold, transferase, ATP binding,
phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium
falciparum}
Length = 243
Score = 31.8 bits (73), Expect = 1.4
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 2/62 (3%)
Query: 834 LITVENKSKLCGVQRLCKITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYLDSGAL 893
L L ++R + K I + G SGKGT + + + +L +G L
Sbjct: 6 LENFSTIDLLNELKRRYA-CLSKPDGRYIFL-GAPGSGKGTQSLNLKKSHCYCHLSTGDL 63
Query: 894 YR 895
R
Sbjct: 64 LR 65
>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide
biosynthesis, nucleotide-BIND transferase, structural
genomics; 2.10A {Burkholderia pseudomallei 1710B}
Length = 230
Score = 31.8 bits (73), Expect = 1.4
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G +GKGT A + K G + +G + R
Sbjct: 15 GAPGAGKGTQANFIKEKFGIPQISTGDMLR 44
>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P;
2.25A {Thermus thermophilus} PDB: 3asy_A*
Length = 211
Score = 31.4 bits (72), Expect = 1.6
Identities = 15/24 (62%), Positives = 17/24 (70%)
Query: 861 VITIDGPTASGKGTVAQLVASKLG 884
VI I G TASGK T+AQ +A LG
Sbjct: 8 VIGIAGGTASGKTTLAQALARTLG 31
>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD,
transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP:
c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*
Length = 252
Score = 31.7 bits (72), Expect = 1.7
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLS 900
+I + G TASGK +V + LG + +D ++V LS
Sbjct: 24 LIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQ-KQVVILS 62
>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway,
P-loop protein, transferase; 1.8A {Erwinia chrysanthemi}
SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*
Length = 173
Score = 31.0 bits (71), Expect = 1.9
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDS 890
G G TV + +A LG+ ++D+
Sbjct: 9 GARGCGMTTVGRELARALGYEFVDT 33
>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase,
transferase (phosphotransferase); HET: AP5; 1.63A
{Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB:
2aky_A* 3aky_A* 1dvr_A*
Length = 220
Score = 31.4 bits (72), Expect = 1.9
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A + + +L +G + R
Sbjct: 11 GPPGAGKGTQAPNLQERFHAAHLATGDMLR 40
>3ayh_B DNA-directed RNA polymerase III subunit RPC8; transcription; 2.19A
{Schizosaccharomyces pombe}
Length = 203
Score = 31.2 bits (70), Expect = 2.0
Identities = 17/78 (21%), Positives = 26/78 (33%), Gaps = 19/78 (24%)
Query: 1428 KGEKIKGIIKSITDFGIFIGLDGNIDGLIHLSDL------------------SWTDPGEE 1469
+GE + G IKS ++ GI + + D + D+ D E
Sbjct: 81 RGEVMLGKIKSCSEEGIRVTI-SFFDDIFIPKDMLFDPCVFRPDERAWVWKIEGEDGSEG 139
Query: 1470 IIRNFKKGDEIEAIILSI 1487
F +EI I S
Sbjct: 140 TELYFDIDEEIRFQIESE 157
Score = 29.7 bits (66), Expect = 5.7
Identities = 7/39 (17%), Positives = 17/39 (43%)
Query: 1250 LIETLKEGCTVKGVVKNITDYGAFIDLGGIDGLLHITDI 1288
+I G + G +K+ ++ G + + D + D+
Sbjct: 75 IIFRPFRGEVMLGKIKSCSEEGIRVTISFFDDIFIPKDM 113
>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein,
feedback inhibition, deoxyribonucleoside kinase, salvage
pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP:
c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A*
2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A*
1zm7_A* 1zmx_A*
Length = 230
Score = 31.2 bits (70), Expect = 2.2
Identities = 8/38 (21%), Positives = 11/38 (28%), Gaps = 1/38 (2%)
Query: 851 KITMIKKYIPVITIDGPTASGKGTVAQLVASKLGFHYL 888
K + + I+G SGK T L
Sbjct: 13 KYAEGTQPF-TVLIEGNIGSGKTTYLNHFEKYKNDICL 49
>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region,
conformational changes, transferase; 2.10A {Homo
sapiens} SCOP: c.37.1.1
Length = 196
Score = 31.0 bits (71), Expect = 2.5
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYR 895
V+ + G +GKGT + K G+ +L +G L R
Sbjct: 5 VVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELLR 39
>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding,
nucleoside kinase, nucleotide-binding; 2.50A {Homo
sapiens} PDB: 2uvq_A*
Length = 245
Score = 30.9 bits (70), Expect = 2.5
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHYLDSGALYRLVTLS 900
+I + G TASGK TV + + LG + ++ ++V LS
Sbjct: 27 LIGVSGGTASGKSTVCEKIMELLGQNEVEQRQ-RKVVILS 65
>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC,
cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo
sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B*
2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A*
2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A*
2zi7_B* 2zia_A* 3kfx_A* ...
Length = 263
Score = 31.0 bits (69), Expect = 2.6
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 856 KKYIPVITIDGPTASGKGTVAQLVASKLG 884
I I+I+G A+GK T ++
Sbjct: 21 GTRIKKISIEGNIAAGKSTFVNILKQLCE 49
>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase;
HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A*
3l0p_A*
Length = 223
Score = 31.1 bits (71), Expect = 2.7
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP SGKGT LV K +++SG ++R
Sbjct: 7 GPNGSGKGTQGNLVKDKYSLAHIESGGIFR 36
>1ujc_A Phosphohistidine phosphatase SIXA; alpha-beta fold, hydrolase;
1.90A {Escherichia coli} PDB: 1ujb_A
Length = 161
Score = 30.4 bits (69), Expect = 2.7
Identities = 16/86 (18%), Positives = 29/86 (33%), Gaps = 10/86 (11%)
Query: 140 KETIDFISNYDGKEKEPSVLPTRIPNLLINGSSGIAVGMATNIPPHNLTEVIDGVLYVLH 199
++T++ + + VLP P G G+ + + VL + H
Sbjct: 57 EQTLEEVGDCLNLPSSAEVLPELTPC----GDVGLVSAYLQALTNEG----VASVLVISH 108
Query: 200 NPECS--INDLIKIIPAPDFPTAGII 223
P + +L P F T+ I
Sbjct: 109 LPLVGYLVAELCPGETPPMFTTSAIA 134
>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase,
phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1
g.41.2.1 PDB: 2ak2_A 2c9y_A*
Length = 233
Score = 31.0 bits (71), Expect = 2.8
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A +A +L +G + R
Sbjct: 23 GPPGAGKGTQAPKLAKNFCVCHLATGDMLR 52
>2rgx_A Adenylate kinase; transferase(phosphotransferase), ATP-binding,
nucleo binding, transferase; HET: AP5; 1.90A {Aquifex
aeolicus} PDB: 2rh5_A
Length = 206
Score = 30.6 bits (70), Expect = 2.8
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
GP +GKGT A+ +A + GF ++ +G + R
Sbjct: 7 GPPGAGKGTQAKRLAKEKGFVHISTGDILR 36
>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding,
nucleotide-binding, transferase; HET: AP5; 2.00A
{Marinibacillus marinus}
Length = 216
Score = 30.6 bits (70), Expect = 3.0
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G +GKGT A+ + K ++ +G ++R
Sbjct: 7 GLPGAGKGTQAEQIIEKYEIPHISTGDMFR 36
>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP;
2.37A {Humulus lupulus}
Length = 339
Score = 31.1 bits (70), Expect = 3.0
Identities = 5/25 (20%), Positives = 13/25 (52%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLG 884
++ + G T +GK ++ +A+
Sbjct: 41 KLLVLMGATGTGKSRLSIDLAAHFP 65
>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A
{Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A*
1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*
Length = 214
Score = 30.6 bits (70), Expect = 3.2
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G +GKGT AQ + K G + +G + R
Sbjct: 7 GAPVAGKGTQAQFIMEKYGIPQISTGDMLR 36
>2ba0_A Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation,
exoribonuclease, S1domain, KH domain, archaeal; 2.70A
{Archaeoglobus fulgidus} SCOP: b.40.4.5 b.84.4.2 d.51.1.1
Length = 229
Score = 30.4 bits (68), Expect = 3.5
Identities = 26/132 (19%), Positives = 52/132 (39%), Gaps = 11/132 (8%)
Query: 1332 WIGLSFRY-PR-GTRLLGKVTNLTDYGAFVEIEKGIEGLVHISEMDWINKNVTPSKIVQL 1389
I L RY P G ++G + + G V+I + + +SE + N P++++ +
Sbjct: 46 VIPLKGRYTPSVGDVVIGIIREVAANGWAVDIYSPYQAFLPVSENPEMKPNKKPNEVLDI 105
Query: 1390 NDTVEIMILEINE---------ERRRISLGMKQCKDNPWENFSIIHKKGEKIKGIIKSIT 1440
D + +L I+ +R + + + K + ++KS
Sbjct: 106 GDAIIAKVLNIDPKMKVTLTMKDRICRPIRFGRIVAINPARVPRVIGKKGSMIKLLKSEL 165
Query: 1441 DFGIFIGLDGNI 1452
D I +G +G I
Sbjct: 166 DVQIVVGQNGLI 177
>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination,
ATP-binding, cytoplasm, metal-binding, nucleotide
biosynthesis, nucleotide-binding; HET: AP5; 1.58A
{Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A*
2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A*
1s3g_A*
Length = 216
Score = 30.6 bits (70), Expect = 3.7
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDSGALYR 895
G +GKGT + + K G ++ +G ++R
Sbjct: 7 GLPGAGKGTQGERIVEKYGIPHISTGDMFR 36
>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex,
transferase; HET: DTP; 2.80A {Homo sapiens} SCOP:
c.37.1.1
Length = 241
Score = 30.5 bits (68), Expect = 3.9
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 861 VITIDGPTASGKGTVAQLVASKLG 884
++I+G A GK T +L+
Sbjct: 4 RLSIEGNIAVGKSTFVKLLTKTYP 27
>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding,
nucleotide-binding, nucleotidyltransferase, tRNA
processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A
3crr_A
Length = 323
Score = 30.6 bits (70), Expect = 4.0
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLG 884
P I + GPTA+GK +A +A L
Sbjct: 6 PAIFLMGPTAAGKTDLAMALADALP 30
>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the
strand order 23145, walker A motif, cholesterol
biosynthesis, lipid synthesis; 1.76A {Homo sapiens}
Length = 202
Score = 30.4 bits (68), Expect = 4.1
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 861 VITIDGPTASGKGTVAQLVASKLGFHY 887
V+ G SGK V + + S+LG
Sbjct: 13 VLLFSGKRKSGKDFVTEALQSRLGADV 39
>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter
sphaeroides} SCOP: c.37.1.6
Length = 290
Score = 30.4 bits (68), Expect = 4.1
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 854 MIKKYIPVITIDGPTASGKGTVAQLVASKLG 884
M KK+ P+I++ G + +G TV
Sbjct: 1 MSKKH-PIISVTGSSGAGTSTVKHTFDQIFR 30
>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2; 2.70A
{Staphylococcus epidermidis atcc 12228}
Length = 340
Score = 30.6 bits (70), Expect = 4.9
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 854 MIKKYIPVITIDGPTASGKGTVAQLVASKLG 884
M K +I I GPTASGK ++ VA K
Sbjct: 4 MTKP--FLIVIVGPTASGKTELSIEVAKKFN 32
>2vdv_E TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl-L-methionine,
phosphorylation, M7G, spout MT, tRNA processing; HET:
SAM; 2.30A {Saccharomyces cerevisiae} PDB: 2vdu_E
Length = 246
Score = 30.1 bits (68), Expect = 4.9
Identities = 21/101 (20%), Positives = 30/101 (29%), Gaps = 23/101 (22%)
Query: 922 NYNFLGKEVYLNGVNVTTLIRNEKVSNNASKIAKFKNIRKELFKIQVKFRKFPGLVADGR 981
LG E+ + N R + NN + F+NI L +
Sbjct: 73 EDLILGMEIRVQVTN-YVEDRIIALRNNTASKHGFQNIN--------------VLRGNAM 117
Query: 982 DMGTTVFPDAFL-KIFLT-AD--IKQR-TKRRYKQLMQKGF 1017
F L K+F D KQR K R ++
Sbjct: 118 KFLPNFFEKGQLSKMFFCFPDPHFKQRKHKAR---IITNTL 155
>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A
Length = 322
Score = 30.2 bits (69), Expect = 5.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 859 IPVITIDGPTASGKGTVAQLVASKLG 884
++ I GPTA GK + ++A +L
Sbjct: 3 EKLVAIVGPTAVGKTKTSVMLAKRLN 28
>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside
modification, isopentenyl-tRNA transferase,
transferase-RNA complex; 2.50A {Escherichia coli k-12}
PDB: 2zxu_A* 2zm5_A
Length = 316
Score = 30.2 bits (69), Expect = 5.8
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 860 PVITIDGPTASGKGTVAQLVASKLGFHYL--DSGALYR 895
I + GPTASGK +A + L + DS +Y+
Sbjct: 11 KAIFLMGPTASGKTALAIELRKILPVELISVDSALIYK 48
>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI,
protein structure initiative; 2.05A {Escherichia coli}
SCOP: c.37.1.2
Length = 173
Score = 29.4 bits (67), Expect = 5.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDS 890
GP +GK T+ + +A +L + DS
Sbjct: 11 GPMGAGKSTIGRQLAQQLNMEFYDS 35
>2w0i_A Twinfilin-2; cytoskeleton, actin-binding, actin binding,
cofilin-like, phosphoprotein, phosphorylation,
transferase, protein tyros kinase-9; 1.8A {Homo sapiens}
Length = 135
Score = 29.1 bits (65), Expect = 6.4
Identities = 7/34 (20%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 1463 WTDPGEEIIRNFKKGDEIEAIILSIDVEKERISL 1496
+ ++ K+ + I + +D+E+E I L
Sbjct: 4 LQPEAQRALQQLKQK-MVNYIQMKLDLERETIEL 36
>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A
{Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A
3n2e_A*
Length = 168
Score = 29.1 bits (66), Expect = 7.0
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDS 890
G SGK ++AQ + L LD+
Sbjct: 14 GFMGSGKSSLAQELGLALKLEVLDT 38
>2ho3_A Oxidoreductase, GFO/IDH/MOCA family; streptococcus pneumonia
reductive methylation, structural genomics, PSI-2,
protein initiative; HET: MLY; 2.00A {Streptococcus
pneumoniae} PDB: 2ho5_A
Length = 325
Score = 30.0 bits (68), Expect = 7.2
Identities = 12/98 (12%), Positives = 24/98 (24%), Gaps = 7/98 (7%)
Query: 1328 GIDPWIGLSFRYPRGTRLL--GKVTNLTDYGAFVEIEKG---IEGLVHISEMDWINKNVT 1382
ID YP + GK ++ + G + + HI + +
Sbjct: 206 SIDLNGDGILFYPDYQVHIKAGKNIT-SNLPCEIYTTDGTLTLNTIEHIRSAIFTDHQGN 264
Query: 1383 PSKIVQLNDTVEIMILEINEERRRISLGMKQCKDNPWE 1420
++ + M E+ I
Sbjct: 265 QVQL-PIQQAPHTMTEEVAAFAHMIQQPDLNLYQTWLY 301
>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A
{Campylobacter jejuni} SCOP: c.37.1.2
Length = 175
Score = 29.1 bits (66), Expect = 8.7
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 866 GPTASGKGTVAQLVASKLGFHYLDS 890
G SGK T+A+ +A L +LDS
Sbjct: 11 GFMGSGKSTLARALAKDLDLVFLDS 35
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
0.318 0.137 0.384
Gapped
Lambda K H
0.267 0.0529 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 24,842,809
Number of extensions: 1624773
Number of successful extensions: 4242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3936
Number of HSP's successfully gapped: 265
Length of query: 1619
Length of database: 6,701,793
Length adjustment: 107
Effective length of query: 1512
Effective length of database: 3,714,246
Effective search space: 5615939952
Effective search space used: 5615939952
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.9 bits)