RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11399
(865 letters)
>4f3t_A Protein argonaute-2; hydrolase/gene regulation, RNAI, slicer,
hydrolase-RNA; 2.25A {Homo sapiens} PDB: 4ei1_A 4ei3_A*
1r4k_A 1si2_A 1si3_A
Length = 861
Score = 701 bits (1811), Expect = 0.0
Identities = 469/684 (68%), Positives = 546/684 (79%), Gaps = 24/684 (3%)
Query: 50 GAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREGRPIVLRANHFQISMPRGF 109
GA+ + G P PP P P + F P RP+ G GR I L+AN F++ +P+
Sbjct: 1 GAMYSGAG-----PALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKID 55
Query: 110 VHHYEIQIQPDKCPRKVNREIIETMVHAY-SKIFGALKPVFDGRNNLYTRDPLPIGNDRM 168
++HYE+ I+P+KCPR+VNREI+E MV + ++IFG KPVFDGR NLYT PLPIG D++
Sbjct: 56 IYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKV 115
Query: 169 ELEVTLPGEGKDRVFRVAIKWQAQVSLFALEEALEGRTRQIPFDAILALDVVMRHLPSMT 228
ELEVTLPGEGKDR+F+V+IKW + VSL AL +AL GR +PF+ I ALDVVMRHLPSM
Sbjct: 116 ELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMR 175
Query: 229 YTPVGRSFFSTPDGYYHPLGGGREVWFGFHQSVRPSQWKMMLNIDVSATAFYKSQPVIEF 288
YTPVGRSFF+ +G +PLGGGREVWFGFHQSVRPS WKMMLNIDVSATAFYK+QPVIEF
Sbjct: 176 YTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEF 235
Query: 289 MCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYRVCNVTRRPAQMQS 348
+CEVLD + + EQ+KPLTDSQRVKFTKEIKGLK+EITHCG MKRKYRVCNVTRRPA Q+
Sbjct: 236 VCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQT 295
Query: 349 FPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCI 408
FPLQ E+GQTVECTVA+YF D++K+ LR+PHLPCLQVGQE KHTYLPLEVCNIVAGQRCI
Sbjct: 296 FPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCI 355
Query: 409 KKLTDMQTSTMIKATARSAPDREREIQSLVKRADFNNDAYVHEFGLTISNSMMEVRGRVL 468
KKLTD QTSTMI+ATARSAPDR+ EI L++ A FN D YV EFG+ + + M +V GRVL
Sbjct: 356 KKLTDNQTSTMIRATARSAPDRQEEISKLMRSASFNTDPYVREFGIMVKDEMTDVTGRVL 415
Query: 469 PPPKLQYGGRMSSITAQVNSMSSQGLFASKQQALPNSGVWDMRGKQFYTGVEIRVWAIAC 528
PP + YGGR +K A P GVWDMR KQF+TG+EI+VWAIAC
Sbjct: 416 QPPSILYGGR------------------NKAIATPVQGVWDMRNKQFHTGIEIKVWAIAC 457
Query: 529 FAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPDQVEPMFRYLKSTFQAL 588
FAPQR E L+SFT+QL+KIS DAGMPI GQPCFCKYA G D VEPMFR+LK+T+ L
Sbjct: 458 FAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGL 517
Query: 589 QLVVVVLPGKTPVYAEVKRVGDTVLGMATQCVQAKNVNKTSPQTLSNLCLKINVKLGGIN 648
QLVVV+LPGKTPVYAEVKRVGDTVLGMATQCVQ KNV +T+PQTLSNLCLKINVKLGG+N
Sbjct: 518 QLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVN 577
Query: 649 SILVPSIRPKVFNEPVIFMGADVTHPPAGDNKKPSIAAVVGSMDAHPSRYAATVRVQQHR 708
+IL+P RP VF +PVIF+GADVTHPPAGD KKPSIAAVVGSMDAHP+RY ATVRVQQHR
Sbjct: 578 NILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHR 637
Query: 709 QEIIQELSSMVRLFCADKKEQSGK 732
QEIIQ+L++MVR + +
Sbjct: 638 QEIIQDLAAMVRELLIQFYKSTRF 661
Score = 229 bits (585), Expect = 1e-63
Identities = 118/148 (79%), Positives = 125/148 (84%)
Query: 718 MVRLFCADKKEQSGKSGNIPAGTTVDIGITHPTEFDFYLCSHQGIQGTSRPSHYHVLWDD 777
RLFC DK E+ GKSGNIPAGTTVD ITHPTEFDFYLCSH GIQGTSRPSHYHVLWDD
Sbjct: 714 HTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDD 773
Query: 778 NHFDADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVEKEHDSGEGSHQS 837
N F +DELQ LTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLV+KEHDS EGSH S
Sbjct: 774 NRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTS 833
Query: 838 GSSEDRTPGAMARAITVHADTKKVMYFA 865
G S R A+A+A+ VH DT + MYFA
Sbjct: 834 GQSNGRDHQALAKAVQVHQDTLRTMYFA 861
>4f1n_A Kpago; argonaute, RNAI, RNAse H, RNA binding protein-RNA complex;
3.19A {Vanderwaltozyma polyspora}
Length = 1046
Score = 494 bits (1271), Expect = e-160
Identities = 144/833 (17%), Positives = 272/833 (32%), Gaps = 193/833 (23%)
Query: 64 PNQPPQPVQPPELPMFNCPRRPNLGREGRPIVLRANHFQISM------------------ 105
QP + + R + G +G + + NH +++
Sbjct: 3 EKTVDQPKEDTHAI-YKVENRHDYGTKGTKVDILTNHILLAVGNDVPTEKIDKELVPKLD 61
Query: 106 ---PRGFVHHYEIQIQPDK--------------CPRKVNREIIETMVHAYSKIF-GALKP 147
F+ Y I +P + + E+IE ++ ++ +
Sbjct: 62 GWWKTAFIFTYHIDFKPQQKGPPRRGKPVPPQELSKPKKYELIEALLDEDEILYKYRDRI 121
Query: 148 VFDGRNNLYTRDPLP------------------------IGNDRMELEVTLPGEGKDRVF 183
F+G + +Y+ PL +++ L+ + E ++ V
Sbjct: 122 AFNGEDTIYSHVPLEEFTLFDGCWEVSNKQKKKVVPGMGAPSNKASLQKKIDPELEEMVS 181
Query: 184 RVAIKWQAQVSLFALEEALEGRTRQIP------FDAILALDVVMRHLPSMTYTPVGRS-- 235
++ +K+ +V L + + ++ D L ++ S
Sbjct: 182 QITLKFSGKVGLKDIYNDTTTQDTEVQESRMSAIDKTCLLSLLGAKFMSTDDLIFQVQGN 241
Query: 236 --FFSTPDGYYHPLGGGREVWFGFHQSVRPSQWKMMLNIDVSATAFYKSQP--------- 284
F P G + GF S+ + LN F K
Sbjct: 242 KFFIFNNFAKAIPFQIGGYLLQGFTVSLTHVYGGVALNTVSVPAPFIKHTKYLPGDPRFK 301
Query: 285 --------VIEFMCEVLD----IRDVNEQRK----------PLTDSQRVKFTKEIKGLKI 322
+++++ E IRD+ K + + +KGLK+
Sbjct: 302 NNEKEQFTLMDWIIECYHQSKAIRDIRYNPKTAPPPSVKDLNYFVEKNTDISALLKGLKV 361
Query: 323 EITHCG------------TMKRKYRVCNVTRRPAQMQSFPLQ----------LENGQTVE 360
+ + + TR A F + N + +
Sbjct: 362 YRPYINYSINKDGTPKPPRKRSSKGIVGFTRESAVSMRFNVLESSLKKNSAPKPNEKPIN 421
Query: 361 CTVAKYFLDKYKMKLRFPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCIKKLTDMQTSTMI 420
YF KY + L++P + + +G K+ +P E IV GQ+ ++ D +T I
Sbjct: 422 INTIDYFKRKYDITLKYPDMKLVNLGG--KNDVVPPECLTIVPGQKLKGQIFDTKT--YI 477
Query: 421 KATARSAPDREREIQ----SLVKRADFNNDAYVHEFGLTISNSMMEVRGRVLPPPKLQYG 476
+A ++ I +KR +++ + M V R+L P +Q+
Sbjct: 478 DFSAIRPTEKFDLISRLSMPAIKRGLTDSEKEESSAPHNSAYQFMRVPSRILDAPVVQFK 537
Query: 477 GRMSSITAQVNSMSSQGLFASKQQALPNSGVWDMRGKQFYTGVEIRVWAIACFAPQRTVR 536
+ + + + G W+M+G QF + +V A F
Sbjct: 538 ESTFEYKDK----------SYGTKHEESKGNWNMKGHQFISTPAKQVNLRAIFINNANTA 587
Query: 537 ---------EDSLRSFTQQLQKIS---NDAGMPII---GQPCFCKY-------------- 567
+ S+ F ++++ N +G PI+ P K+
Sbjct: 588 PPASMESELDISMDKFASDVKQLGVDFNVSGKPILINQFGPPIKKFQGGGRGGRGGRGSR 647
Query: 568 ----ATGPDQVEPMFR----------YLKSTFQALQLVVVVLPGK-TPVYAEVKRVGDTV 612
G P F L++ ++ V+ G + VY +K + D
Sbjct: 648 GGRGGRGAPSGPPTFETSPGEISLLNLLENIPSNTYILYVLRRGNDSAVYDRLKYITDLK 707
Query: 613 LGMATQCVQAKNVNKTSPQTLSNLCLKINVKLGGINSILVPS----IRPKVFNEPVIFMG 668
G CV N K S Q SN+ +K+N+KL G N L + K N P++ +G
Sbjct: 708 FGALNSCVVWDNFKKNSIQYNSNVVMKMNLKLLGSNHSLSIENNKLLIDKESNLPILVLG 767
Query: 669 ADVTHPPAGDNKKPSIAAVVGSMDAHPSRYAATVRVQQ-HRQEIIQELSSMVR 720
+DVTH P D + SIA++VGS D +++ +Q +EII + S++
Sbjct: 768 SDVTHYPEKD--QNSIASLVGSYDDKFTQFPGDYMLQDGPGEEIITNVGSLML 818
Score = 194 bits (494), Expect = 2e-51
Identities = 53/163 (32%), Positives = 77/163 (47%), Gaps = 9/163 (5%)
Query: 711 IIQELSSMVRLFCADKKEQS--------GKSGNIPAGTTVDIGITHPTEFDFYLCSHQGI 762
I + VR + ++ GN+ GT VD GIT FDF++ SHQ +
Sbjct: 883 IATVKRNQVRFIPIQENAKNEKGEEVAVQSMGNVMPGTVVDRGITSVAHFDFFIQSHQAL 942
Query: 763 QGTSRPSHYHVLWDDNHFDADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYH 822
+GT P HY L+D+N +D LQ + LC+ + R T SV +PAP YYA L+ RA
Sbjct: 943 KGTGVPCHYWCLYDENQSTSDYLQEICNNLCYIFGRSTTSVKVPAPVYYADLLCTRATCF 1002
Query: 823 L-VEKEHDSGEGSHQSGSSEDRTPGAMARAITVHADTKKVMYF 864
E + + + GS + T V+ + K VMY+
Sbjct: 1003 FKAGFELNMAQAPKEKGSKDQPTVSKNVLLPQVNDNIKSVMYY 1045
>1yvu_A Hypothetical protein AQ_1447; RNAse H fold, RNA binding protein,
gene regulation; 2.90A {Aquifex aeolicus} SCOP:
b.34.14.1 c.55.3.10 PDB: 2f8s_A 2f8t_A 2nub_A
Length = 706
Score = 328 bits (841), Expect = e-101
Identities = 68/631 (10%), Positives = 180/631 (28%), Gaps = 97/631 (15%)
Query: 251 REVWFGFHQ--SVRPSQWKMMLNIDVSATAFYKSQPVIEFMCEVLDIRDVNEQRKPLTDS 308
+ + F +V+ K+ L +V+ KS+ + L R Q +
Sbjct: 116 SDFYKKFRDKITVQGKNRKIALIPEVN-EKVLKSEEGYFLLHLDLKFR---IQPFETLQT 171
Query: 309 QRVKFTKEIKGLKIEITHCGTMKRKYRVCNVTRRPAQMQSFPLQLENGQTVECTVAKYFL 368
+ K ++++ + R V + + ++ ++ + +
Sbjct: 172 LLERNDFNPKRIRVKPIGIDFVGRVQDVFKAKEKGEEFFRLCMERSTHKSSKKAWEELLK 231
Query: 369 DKYKMKLRFPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAP 428
++ + F K P + V + L D + + +
Sbjct: 232 NRELREKAFL-------VVLEKGYTYPATILKPVL---TYENLEDEERNEVADIVRMEPG 281
Query: 429 DREREIQSLVKRADFNNDAYVHEFGLTISNSMMEVRGRVLPPPKLQYGGRMSSITAQVNS 488
R I+ +++R + ++G IS +G++ +
Sbjct: 282 KRLNLIRYILRRYVKA----LRDYGWYISPEEERAKGKLNFKDTVLDAK----------- 326
Query: 489 MSSQGLFASKQQALPNSGVWDMRGKQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQ 548
K + + + + + ++ I + + E F ++L
Sbjct: 327 --------GKNTKVITNLRKFLELCRPFVKKDVLSVEIISVSVYK-KLEWRKEEFLKELI 377
Query: 549 KISNDAGMPIIGQPCFCKYATGPDQVEPMFRYLKSTFQALQLVVVVLPGKTP-------- 600
+ G+ + + A ++ + + + + + LV+V L
Sbjct: 378 NFLKNKGIKLKIKGKSLILAQTREEAKEKLIPVINKIKDVDLVIVFLEEYPKVDPYKSFL 437
Query: 601 VYAEVKRVGDTVLGMATQCVQAKNVNKTSPQ-TLSNLCLKINVKLGGINSILVPSIRPKV 659
+Y VKR + +Q + + + + + L N+ ++ K G I L ++
Sbjct: 438 LYDFVKREL-LKKMIPSQVILNRTLKNENLKFVLLNVAEQVLAKTGNIPYKL-----KEI 491
Query: 660 FNEPVIFMGADVTHPPAGDNKKPSIA-AVVGSMDAHPSRYAATVRVQQHRQEIIQELSSM 718
+ F+G D++ ++A + + RY T + + + +
Sbjct: 492 EGKVDAFVGIDISRITRDGKTVNAVAFTKIFNSKGELVRYYLTSYPAFGEKLTEKAIGDV 551
Query: 719 VRLFCADKKEQ-----------------------------------SGKSGN--IPAGTT 741
L ++ K N +
Sbjct: 552 FSLLEKLGFKKGSKIVVHRDGRLYRDEVAAFKKYGELYGYSLELLEIIKRNNPRFFSNEK 611
Query: 742 VDIGITHPTEFDFYLCSHQG--IQGTSRPSHYHVLWDDNHFDADELQCLTYQLCHTYVRC 799
G + D + + +GT +P ++ + + L L
Sbjct: 612 FIKGYFYKLSEDSVILATYNQVYEGTHQPIKVRKVYGELPV--EVLCSQILSLTLMNYSS 669
Query: 800 TRSVSIPAPAYYAHLVAFRARYHLVEKEHDS 830
+ + +PA +Y+ + + + +
Sbjct: 670 FQPIKLPATVHYSDKITKLMLRGIEPIKKEG 700
>3ho1_A Argonaute; argonaute, protein-DNA-RNA complex, nucleic acid binding
Pro RNA complex; 2.60A {Thermus thermophilus} PDB:
3dlb_A* 3dlh_A* 3f73_A* 3hm9_A 3hvr_A 3hxm_A* 3hk2_A
3hjf_A
Length = 685
Score = 316 bits (811), Expect = 1e-96
Identities = 102/788 (12%), Positives = 201/788 (25%), Gaps = 166/788 (21%)
Query: 92 RPIVLRANHFQI---SMPRGFVHHYEIQIQPDKCPRKVNREIIETMVHAYSKIFGALKPV 148
+ N F + + E+ + P +V + + G +
Sbjct: 5 GKTEVFLNRFALRPLNPEELRPWRLEVVLDPPPGREEVYPLLA----QVARRAGGVTVRM 60
Query: 149 FDGRNNLYTRDPLPIGNDRMELEVTLPGEGKDRVFRVAIKWQAQVSLFALEEALEGRTRQ 208
DG + + L LE TL G+ +R+ K + + E R
Sbjct: 61 GDGLASWSPPEVLV-------LEGTLARMGQTYAYRLYPKGRRPLDPKDPGE------RS 107
Query: 209 IPFDAIL--ALDVVMRHLPSMTYTPVGRSFFSTPDGYYHPLGGGREVWFGFHQSVRP-SQ 265
+ A+ L +R L + H G G V G +
Sbjct: 108 V-LSALARRLLQERLRRLEGVWV------EGLAVYRREHARGPGWRVLGGAVLDLWVSDS 160
Query: 266 WKMMLNIDVSATAFYKSQPVIEFMCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEIT 325
+L +D + + ++ + + +RV+ +
Sbjct: 161 GAFLLEVDPA-YRILCEMSLEAWLAQGHPL------------PKRVRNAYD--------- 198
Query: 326 HCGTMKRKYRVCNVTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQV 385
+R + + + + L L G ++ Y K +++ R
Sbjct: 199 -----RRTWELLRLGEEDPKE----LPLPGGLSL----LDYHASKGRLQGREGGRVAWVA 245
Query: 386 GQEHKHTYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREIQSLVKRADFNN 445
+ +P + ++ ++ L + + S A + +R R + +
Sbjct: 246 DPKDPRKPIP-HLTGLLVPVLTLEDLHEEEGS---LALSLPWEERRRRTREIASW----- 296
Query: 446 DAYVHEFGLTISNSMMEVRGRVLPPPKLQYGGRMSSITAQVNSMSSQGLFASKQQALPNS 505
GL + + L PKL S
Sbjct: 297 --IGRRLGLGTPE-AVRAQAYRLSIPKLMGRRA-------------------------VS 328
Query: 506 GVWDMRGKQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFC 565
D FY E A+ + E + L + +G +
Sbjct: 329 KPADALRVGFYRAQETA-LALLRLDGAQGWPEF----LRRALLRAFGASGASL-RLHTLH 382
Query: 566 KYATGPDQVEPMFRYLKSTFQALQLVVVVLPGKTP-VYAEVKRVGDTVLGMATQCVQAKN 624
+ + R K + +Q V+V+ P +K + G+ +Q +
Sbjct: 383 AHPSQGLAFREALRKAKE--EGVQAVLVLTPPMAWEDRNRLKALL-LREGLPSQILNVPL 439
Query: 625 VNKTSPQTLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMGADVTHPPAGDNKKPSI 684
+ N L + K G L + + +G D + +
Sbjct: 440 REE-ERHRWENALLGLLAKAGLQVVALSGAYP------AELAVGFDAGGRESF--RFGGA 490
Query: 685 AAVVGSMDAHPSRYAATVRVQQH-RQEIIQE-LSSMVRLFCADKKE-------------- 728
A VG H + + QE++ + L + F
Sbjct: 491 ACAVGGDGGHLLWTLPEAQAGERIPQEVVWDLLEETLWAFRRKAGRLPSRVLLLRNGRVP 550
Query: 729 ---------------------QSGKSGNI---PAGTTVDIG--ITHPTEFDFYLCSHQGI 762
KSG P + G + + L H+
Sbjct: 551 QDEFALALEALAREGIAYDLVSVRKSGGGRVYPVQGRLADGLYVPLEDKTFLLLTVHRDF 610
Query: 763 QGTSRPSHYHVLWDDNHFDADELQCLTYQLCHTYV-RCTRSVSIPAPAYYAHLVAFRARY 821
+GT RP D + L + L Y +PAP + A +
Sbjct: 611 RGTPRPLKLVHEAGDT--PLEALAHQIFHLTRLYPASGFAFPRLPAPLHLADRLVKEVGR 668
Query: 822 HLVEKEHD 829
+ +
Sbjct: 669 LGIRHLKE 676
>2yha_A Post-transcriptional gene silencing protein QDE-2; RNA binding
protein, argonaute, miRNA, siRNA; HET: GOL; 1.85A
{Neurospora crassa} PDB: 2xdy_A
Length = 388
Score = 302 bits (774), Expect = 7e-95
Identities = 92/392 (23%), Positives = 144/392 (36%), Gaps = 45/392 (11%)
Query: 511 RGKQFYT-GVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYAT 569
+ +I W + + + + N G+PI + +
Sbjct: 3 MAVKVARPCRKIEKWTYLELKGSK--ANEGVPQAMTAFAEFLNRTGIPINPRFSPGMSMS 60
Query: 570 GPDQVEPMFRYLKSTFQALQLVVVVLPG-KTPVYAEVKRVGDTVLGMATQCVQAKNVNKT 628
P + F +K + Q VVV+LP +Y VKR D G+ T C A+ T
Sbjct: 61 VPGSEKEFFAKVKELMSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLST 120
Query: 629 --SPQTLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMGADVTHPPAG-----DNKK 681
+N+ LK+N+K GG N + I P + + +G DVTHP
Sbjct: 121 KGQLGYFANVGLKVNLKFGGTNHNIKTPI-PLLAKGKTMVVGYDVTHPTNLAAGQSPASA 179
Query: 682 PSIAAVVGSMDAHPSRYAATVRVQQHRQEIIQE-LSSMVRLFCADKKEQSGKSGNIPAGT 740
PSI +V ++D H ++ A V H QE + E + + + + ++P
Sbjct: 180 PSIVGLVSTIDQHLGQWPAMVWNNPHGQESMTEQFTDKFKTRLELWRSNPANNRSLPENI 239
Query: 741 TVDIGITHPTEFDFYL----------CSHQGIQG------------TSRPSHYHVLWD-- 776
+ +F + C G S +HY VL D
Sbjct: 240 LIFRDGVSEGQFQMVIKDELPLVRAACKLVYPAGKLPRITLIVSVKGSGSAHYTVLVDEI 299
Query: 777 ----DNHFDADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVEKEHDSGE 832
+ AD L+ LT+ +C+ + R T++VSI PAYYA LV RAR H E E
Sbjct: 300 FRADYGNKAADTLEQLTHDMCYLFGRATKAVSICPPAYYADLVCDRARIHQKELFDALDE 359
Query: 833 GSHQSGSSEDRTPGAMARAITVHADTKKVMYF 864
R + VH + + MY+
Sbjct: 360 NDSVKTDDFAR----WGNSGAVHPNLRNSMYY 387
>1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ,
RISC, slicer, RNAse H hydrolase-gene regulation complex;
2.25A {Pyrococcus furiosus} SCOP: b.34.14.1 c.55.3.10
PDB: 1z25_A 1z26_A
Length = 771
Score = 218 bits (555), Expect = 3e-60
Identities = 70/677 (10%), Positives = 174/677 (25%), Gaps = 120/677 (17%)
Query: 243 YYHPLGGGR-EVWFGFHQSVRPSQWKMMLNIDVSATAFYKSQPVIEFMCEVLDIRDVNEQ 301
+ P G +V SV L I + ++ I+ M + ++ + + +
Sbjct: 114 FRKPKTFGDYKVIPSVEMSVIKHDEDFYLVIHII----HQ----IQSMKTLWELVNKDPK 165
Query: 302 RKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYRVCNVTRRPAQMQSFPLQLENGQTVEC 361
+F K + +K Y+ C ++
Sbjct: 166 ELE-------EFLMTHKENLMLKDIASPLKTVYKPCFEEYTKKPKLDHNQEIVKYWYNYH 218
Query: 362 TVAKYFLDKYKMKLRF----------PHLPCLQVGQEHKHT----YLPLEVCNIVAGQRC 407
+Y+ + P + + K+ YL ++
Sbjct: 219 IE-RYWNTPEAKLEFYRKFGQVDLKQPAILAKFASKIKKNKNYKIYLLPQLVVPTYNA-- 275
Query: 408 IKKLTDMQTSTMIKATARSAPDREREIQSLVKRADFNNDAY------VHEFGLTISNSMM 461
++L +++ T +R+ +++++ D + V + + N +
Sbjct: 276 -EQLESDVAKEILEYTKLMPEERKELLENILAEVDSDIIDKSLSEIEVEKIAQELENKIR 334
Query: 462 EVRGRVLPPPKLQYGGRMSSITAQVNSMSSQGLFASKQQALPNSGVWDMRGKQFYTGVEI 521
+ P Q + S + N + + + ++ +
Sbjct: 335 VRDDKGNSVPISQLNVQKSQLLLWTNYSRKYPVILPYEVPEKFRKIREIPMFIILDSGLL 394
Query: 522 RVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGP---------- 571
R + + S ++ ++ A F +
Sbjct: 395 ADIQNFATNEFRELVKSMYYSLAKKYNSLAKKARSTNEIGLPFLDFRGKEKVITEDLNSD 454
Query: 572 DQVEPMFRYLKSTFQALQLVVVVLPGKTP----VYAEVKRVGDTVLGMATQCVQAKNVNK 627
+ + + S + +L + + + + E+KR L + +Q V +
Sbjct: 455 KGIIEVVEQVSSFMKGKELGLAFIAARNKLSSEKFEEIKRRLFN-LNVISQVVNEDTLKN 513
Query: 628 TS---------PQTLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMGADVTHPPAGD 678
NL ++ KLG +L +G DV
Sbjct: 514 KRDKYDRNRLDLFVRHNLLFQVLSKLGVKYYVLDYRF------NYDYIIGIDVAPMKR-S 566
Query: 679 NKKPSIAAVVGSMDAHPSRYAATVRVQQHRQEIIQELSSMVRLFCADKKEQSG------- 731
+AV+ + + +Q + + +++ + KE +
Sbjct: 567 EGYIGGSAVMFDSQGYIRKIVPIKIGEQRGESV--DMNEFFKEMVDKFKEFNIKLDNKKI 624
Query: 732 ---------------------------------KSGNI----PAGTTVDIG---ITHPTE 751
K+ + ++G P +
Sbjct: 625 LLLRDGRITNNEEEGLKYISEMFDIEVVTMDVIKNHPVRAFANMKMYFNLGGAIYLIPHK 684
Query: 752 FDFYLCSHQGIQGTSRPSHYHVLWDDNHFDADELQCLTYQLCHTYVRCTRSVSIPAPAYY 811
+ I+ + + + ++ + Y + + +PAP +Y
Sbjct: 685 LKQAKGTPIPIKLAKKRIIKNGKVEKQSITRQDVLDIFILTRLNYGSISADMRLPAPVHY 744
Query: 812 AHLVAFRARYHLVEKEH 828
AH A R KE
Sbjct: 745 AHKFANAIRNEWKIKEE 761
>2yhb_A QDE-2, post-transcriptional gene silencing protein QDE-2; RNA
binding protein, argonaute, miRNA, siRNA; 3.65A
{Neurospora crassa}
Length = 437
Score = 202 bits (515), Expect = 2e-57
Identities = 54/237 (22%), Positives = 90/237 (37%), Gaps = 13/237 (5%)
Query: 511 RGKQFYT-GVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYAT 569
+ +I W + + + + N G+PI + +
Sbjct: 3 MAVKVARPCRKIEKWTYLELKGSK--ANEGVPQAMTAFAEFLNRTGIPINPRFSPGMSMS 60
Query: 570 GPDQVEPMFRYLKSTFQALQLVVVVLPG-KTPVYAEVKRVGDTVLGMATQCVQAKNVNKT 628
P + F +K + Q VVV+LP +Y VKR D G+ T C A+ T
Sbjct: 61 VPGSEKEFFAKVKELMSSHQFVVVLLPRKDVAIYNMVKRAADITFGVHTVCCVAEKFLST 120
Query: 629 SP--QTLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMGADVTHPPA-----GDNKK 681
+N+ LK+N+K GG N + I P + + +G DVTHP
Sbjct: 121 KGQLGYFANVGLKVNLKFGGTNHNIKTPI-PLLAKGKTMVVGYDVTHPTNLAAGQSPASA 179
Query: 682 PSIAAVVGSMDAHPSRYAATVRVQQHRQEIIQE-LSSMVRLFCADKKEQSGKSGNIP 737
PSI +V ++D H ++ A V H QE + E + + + + ++P
Sbjct: 180 PSIVGLVSTIDQHLGQWPAMVWNNPHGQESMTEQFTDKFKTRLELWRSNPANNRSLP 236
Score = 196 bits (500), Expect = 2e-55
Identities = 55/160 (34%), Positives = 78/160 (48%), Gaps = 10/160 (6%)
Query: 711 IIQELSSMVRLFCADKKEQSGKSGNIPAGTTVDIGITHPTEFDFYLCSHQGIQGTSRPSH 770
I+ R F D K KS + GT VD G+T+ +DF+L +H +QGT+R +H
Sbjct: 281 IVSVKRHQTRFFPTDPKHIHFKSKSPKEGTVVDRGVTNVRYWDFFLQAHASLQGTARSAH 340
Query: 771 YHVLWDD------NHFDADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLV 824
Y VL D+ + AD L+ LT+ +C+ + R T++VSI PAYYA LV RAR H
Sbjct: 341 YTVLVDEIFRADYGNKAADTLEQLTHDMCYLFGRATKAVSICPPAYYADLVCDRARIHQK 400
Query: 825 EKEHDSGEGSHQSGSSEDRTPGAMARAITVHADTKKVMYF 864
E E R + VH + + MY+
Sbjct: 401 ELFDALDENDSVKTDDFAR----WGNSGAVHPNLRNSMYY 436
>2w42_A PIWI, putative uncharacterized protein; RNAI, RISC, argonaute, PIWI
domain, protein/DNA complex; 1.90A {Archaeoglobus
fulgidus} PDB: 1ytu_A 2bgg_A 1w9h_A
Length = 427
Score = 175 bits (445), Expect = 5e-48
Identities = 50/422 (11%), Positives = 116/422 (27%), Gaps = 89/422 (21%)
Query: 495 FASKQQALPNSGVWDMRG---KQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKIS 551
+ ++ ++G Y ++ IA + + Q+
Sbjct: 15 IGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQF--SSLINQLKSQISSKI 72
Query: 552 NDAGMPIIGQPCFCKYATGPDQVEPMFRYLKSTF-QALQLVVVVLPG-KTPVYAEVKRVG 609
++ Y + + + + + + +++VLP TP+Y ++K
Sbjct: 73 DEVWHIHNINISEFIYDS--PHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSY- 129
Query: 610 DTVLGMATQCVQAKNVNKTSPQ-TLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMG 668
+ + +Q ++ ++ + + NL ++ KLGG IL ++ P+ ++ +I G
Sbjct: 130 -LINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWIL--NVDPEKGSDIII--G 184
Query: 669 ADVTHPPAGDNKKPSIAAVVGSMDAHPSRYAAT--------------------------- 701
T + A V D +
Sbjct: 185 TGATRI--DNVNLFCFAMVF-KKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSN 241
Query: 702 -------------VRVQQHRQEIIQELSSMVRLFCADKKEQ------------------- 729
+ + + + L V +
Sbjct: 242 PDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVM 301
Query: 730 --SGKSGNIPAGTTVDIGITHPTEF---DFYLCSHQGIQGTSRPSHYHVLWDDNHFD--- 781
+ GT V + + + + +P ++ D+ +
Sbjct: 302 GDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYY 361
Query: 782 --ADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFR-ARYHLVEKEHDSGEGSHQSG 838
E+ Y L R RS ++P Y LVA A + + EG+
Sbjct: 362 HNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQ 421
Query: 839 SS 840
++
Sbjct: 422 TN 423
>1vyn_A Argonaute2; nucleic acid binding, RNA interference; NMR {Drosophila
melanogaster} SCOP: b.34.14.1
Length = 143
Score = 165 bits (420), Expect = 7e-48
Identities = 45/148 (30%), Positives = 70/148 (47%), Gaps = 11/148 (7%)
Query: 282 SQPVIEFMCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMK---RKYRVCN 338
+ P+IE++ +N D R ++G+ + T + + R YRV
Sbjct: 4 AMPMIEYLERFSLKAKINNT--TNLDYSRRFLEPFLRGINVVYTPPQSFQSAPRVYRVNG 61
Query: 339 VTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHKHTYLPLEV 398
++R PA ++F +G+ V T+A YF + L+FP L CL VG K LP+E+
Sbjct: 62 LSRAPASSETFE---HDGKKV--TIASYFHSRN-YPLKFPQLHCLNVGSSIKSILLPIEL 115
Query: 399 CNIVAGQRCIKKLTDMQTSTMIKATARS 426
C+I GQ +K Q + MIK A S
Sbjct: 116 CSIEEGQALNRKDGATQVANMIKYAATS 143
>3luc_A Protein argonaute-2; MID domain, ribonucleoprotein, RNA-binding,
RNA-mediated GEN silencing, translation regulation, RNA
binding protein; 1.69A {Homo sapiens} PDB: 3lud_A*
3lug_A 3luh_A 3luj_A* 3luk_A 3qx8_A* 3qx9_A*
Length = 138
Score = 164 bits (415), Expect = 2e-47
Identities = 109/136 (80%), Positives = 122/136 (89%)
Query: 513 KQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPD 572
KQF+TG+EI+VWAIACFAPQR E L+SFT+QL+KIS DAGMPI GQPCFCKYA G D
Sbjct: 3 KQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGAD 62
Query: 573 QVEPMFRYLKSTFQALQLVVVVLPGKTPVYAEVKRVGDTVLGMATQCVQAKNVNKTSPQT 632
VEPMFR+LK+T+ LQLVVV+LPGKTPVYAEVKRVGDTVLGMATQCVQ KNV +T+PQT
Sbjct: 63 SVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQT 122
Query: 633 LSNLCLKINVKLGGIN 648
LSNLCLKINVKLGG+N
Sbjct: 123 LSNLCLKINVKLGGVN 138
>4g0o_A Protein argonaute 5; MID domain, small RNA 5' nucleotide
recognition, gene regula; 2.19A {Arabidopsis thaliana}
Length = 139
Score = 157 bits (399), Expect = 4e-45
Identities = 44/139 (31%), Positives = 72/139 (51%), Gaps = 2/139 (1%)
Query: 513 KQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPD 572
K+ G ++ W F+ + + + F +QL + GM QP + P+
Sbjct: 3 KKMVNGAKVTSWTCVSFSTR--IDRGLPQEFCKQLIGMCVSKGMEFKPQPAIPFISCPPE 60
Query: 573 QVEPMFRYLKSTFQALQLVVVVLPGKTPVYAEVKRVGDTVLGMATQCVQAKNVNKTSPQT 632
+E + LQL++V+LP T Y ++KR+ +T LG+ +QC Q + VNK + Q
Sbjct: 61 HIEEALLDIHKRAPGLQLLIVILPDVTGSYGKIKRICETELGIVSQCCQPRQVNKLNKQY 120
Query: 633 LSNLCLKINVKLGGINSIL 651
+ N+ LKINVK GG N++L
Sbjct: 121 MENVALKINVKTGGRNTVL 139
>3mj0_A Protein argonaute-2; argonaut, PAZ domain, 3'-END 2'-O-methylated
ssRNA, RNA-RNA protein complex; HET: OMU; 2.31A
{Drosophila melanogaster} PDB: 1t2r_A 1t2s_A
Length = 124
Score = 145 bits (367), Expect = 5e-41
Identities = 39/131 (29%), Positives = 62/131 (47%), Gaps = 11/131 (8%)
Query: 282 SQPVIEFMCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMK---RKYRVCN 338
S P+IE++ +N D R ++G+ + T + + R YRV
Sbjct: 2 SMPMIEYLERFSLKAKINNT--TNLDYSRRFLEPFLRGINVVYTPPQSFQSAPRVYRVNG 59
Query: 339 VTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHKHTYLPLEV 398
++R PA ++F +G+ V T+A YF + L+FP L CL VG K LP+E+
Sbjct: 60 LSRAPASSETFE---HDGKKV--TIASYFHSRN-YPLKFPQLHCLNVGSSIKSILLPIEL 113
Query: 399 CNIVAGQRCIK 409
C+I GQ +
Sbjct: 114 CSIEEGQALNR 124
>4g0m_A Protein argonaute 2; MID domain, small RNA 5' nucleotide
recognition, gene regula; 2.31A {Arabidopsis thaliana}
Length = 150
Score = 144 bits (364), Expect = 3e-40
Identities = 37/149 (24%), Positives = 58/149 (38%), Gaps = 11/149 (7%)
Query: 513 KQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGM----PIIGQPCFCKYA 568
K G ++ WA+ F + F L GM PI+ + +
Sbjct: 3 KGVTRGSIVKHWAVLDFTASERFNKM-PNDFVDNLIDRCWRLGMQMEAPIVYKTSRMETL 61
Query: 569 TGPDQVEPMFRYL------KSTFQALQLVVVVLPGKTPVYAEVKRVGDTVLGMATQCVQA 622
+ + +E + R + K LV+ + K Y +K + +T LG+ TQC
Sbjct: 62 SNGNAIEELLRSVIDEASRKHGGARPTLVLCAMSRKDDGYKTLKWIAETKLGLVTQCFLT 121
Query: 623 KNVNKTSPQTLSNLCLKINVKLGGINSIL 651
K Q +NL LK+N K+GG N L
Sbjct: 122 GPATKGGDQYRANLALKMNAKVGGSNVEL 150
>4g0x_A Protein argonaute 1; MID domain, small RNA 5' nucleotide
recognition, gene regula; 1.35A {Arabidopsis thaliana}
PDB: 4g0q_A* 4g0p_A 4g0y_A* 4g0z_A*
Length = 147
Score = 138 bits (349), Expect = 2e-38
Identities = 45/147 (30%), Positives = 80/147 (54%), Gaps = 10/147 (6%)
Query: 513 KQFYTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPD 572
K+ G + W F+ Q V+++ R+F Q+L ++ +GM +P + P+
Sbjct: 3 KKMINGGTVNNWICINFSRQ--VQDNLARTFCQELAQMCYVSGMAFNPEPVLPPVSARPE 60
Query: 573 QVEPMFRYLKSTFQA-------LQLVVVVLPGK-TPVYAEVKRVGDTVLGMATQCVQAKN 624
QVE + + + + L++V+LP +Y ++KR+ +T LG+ +QC K+
Sbjct: 61 QVEKVLKTRYHDATSKLSQGKEIDLLIVILPDNNGSLYGDLKRICETELGIVSQCCLTKH 120
Query: 625 VNKTSPQTLSNLCLKINVKLGGINSIL 651
V K S Q ++N+ LKINVK+GG N++L
Sbjct: 121 VFKMSKQYMANVALKINVKVGGRNTVL 147
>2xfm_A MIWI, PIWI-like protein 1; RNA-protein complex, differentiation,
RNA interference; HET: OMU; NMR {Mus musculus}
Length = 150
Score = 77.7 bits (191), Expect = 6e-17
Identities = 27/166 (16%), Positives = 59/166 (35%), Gaps = 25/166 (15%)
Query: 281 KSQPVIEFMCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYRVCNVT 340
+S+ V++FM + ++ + + +KE+ GL + + + YRV ++
Sbjct: 1 RSETVLDFMFNLY--------QQTEEHKFQEQVSKELIGLIVLTKYN---NKTYRVDDID 49
Query: 341 RRPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCL---------QVGQEHKH 391
+F +G V + +Y+ +Y ++ P L G
Sbjct: 50 WDQNPKSTFKK--ADGSEV--SFLEYYRKQYNQEITDLKQPVLVSQPKRRRGPGGTLPGP 105
Query: 392 TYLPLEVCNIVAGQRCIKKLTDMQTSTMIKATARSAPDREREIQSL 437
L E+C + ++ + T + R+RE+ L
Sbjct: 106 AMLIPELCYLTGLTDKMRN-DFNVMKDLAVHTRLTPEQRQREVGRL 150
>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 = 71.0 bits (173), Expect = 1e-12
Identities = 82/611 (13%), Positives = 182/611 (29%), Gaps = 200/611 (32%)
Query: 280 YKSQPVIEFMCEV----LDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYR 335
Y+ + ++ + D +DV + K + + + I K ++ R
Sbjct: 16 YQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEI---DHIIMSKDAVS------GTLR 66
Query: 336 V--CNVTRRPAQMQSFPLQLENGQTVECTVAK-Y-FL-DKYKMKLRFPHLPCLQVGQEHK 390
+ ++++ +Q F VE + Y FL K + R P + ++
Sbjct: 67 LFWTLLSKQEEMVQKF---------VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRD 117
Query: 391 HTY------LPLEVC---NIVAGQRCIKKLTDMQT-----------STMIKATARSAPDR 430
Y V + ++ + +L + + + S
Sbjct: 118 RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS---- 173
Query: 431 EREIQSLVKRADFNNDAYVHEFGLTISNS--------MMEVRGRVLPPPKLQYGGRMSSI 482
+ + DF + F L + N M++ + P S+I
Sbjct: 174 ----YKVQCKMDFK----I--FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI 223
Query: 483 TAQVNSMSSQ--GLFASKQQALPNS-----GVWDMRGKQFYTGVEIRVWAIACFAPQRTV 535
+++S+ ++ L SK N V + + + ++C + +
Sbjct: 224 KLRIHSIQAELRRLLKSKP--YENCLLVLLNVQNAK--------AWNAFNLSC----KIL 269
Query: 536 REDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATG--PDQVEPMF-RYLKSTFQALQLVV 592
T + +++++ ++ PD+V+ + +YL Q
Sbjct: 270 -------LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQD----- 317
Query: 593 VVLPGKTPVYAEVKRVGDTVLGMATQCVQAKNVNKTSPQTLSNLCLKINV-KLGGI--NS 649
LP EV L + A+++ + T N +N KL I +S
Sbjct: 318 --LP------REVLTTNPRRLSII-----AESI-RDGLATWDNW-KHVNCDKLTTIIESS 362
Query: 650 I--LVPSIRPKVFNEPVIFMGADVTHPPAGDNKKPSIAAVVGSMDAH-PSRYAATVRVQQ 706
+ L P+ K+F+ +F PP AH P+ + +
Sbjct: 363 LNVLEPAEYRKMFDRLSVF-------PP----------------SAHIPTILLSLIWFDV 399
Query: 707 HRQEIIQELSSMVRLFCADKKEQSGKSGNIPAGTTVDIGITHPTEFDFYLCSHQGIQGTS 766
+ +++ ++ + + +K P E +
Sbjct: 400 IKSDVMVVVNKLHKYSLVEK---------------------QPKESTISI---------- 428
Query: 767 RPSHYHVLWDDNHFDADELQCL------TYQLCHTYVRCTRSVSIPAP-AY-YAHLVAFR 818
++ + + L Y + T+ + + P Y Y+H+
Sbjct: 429 -----PSIYLELKVKLENEYALHRSIVDHYNIPKTF--DSDDLIPPYLDQYFYSHIG--- 478
Query: 819 ARYHLVEKEHD 829
+HL EH
Sbjct: 479 --HHLKNIEHP 487
Score = 44.8 bits (105), Expect = 1e-04
Identities = 51/342 (14%), Positives = 101/342 (29%), Gaps = 113/342 (33%)
Query: 115 IQIQPDKCPRKVNREIIETMVHAYSKIFGALKPVFDGRNNLYTRDPLPIGNDRME--LEV 172
+ +P PR+V + I + + + D++ +E
Sbjct: 311 LDCRPQDLPREVLT--TNPRRLS---IIAESIRDGLATWDNWKH----VNCDKLTTIIES 361
Query: 173 TL----PGEGKDR-----VFR--VAIK-------WQAQV--------------SLFALEE 200
+L P E + VF I W + SL +E+
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSL--VEK 419
Query: 201 ALEGRTRQIPFDAILALDVVMRHLPSM------TYTPVGRSF----FSTP--DGYYHPLG 248
+ T IP L L V + + ++ Y ++F P D Y++
Sbjct: 420 QPKESTISIP-SIYLELKVKLENEYALHRSIVDHYNIP-KTFDSDDLIPPYLDQYFY--- 474
Query: 249 GGREVWF-GFHQSVRPSQWKMMLNIDVSATAFYKSQPVIEFMCEVLDIRDVNEQRKPLTD 307
G H + NI+ + + F LD R + ++K D
Sbjct: 475 -----SHIGHH----------LKNIE-------HPERMTLFRMVFLDFRFL--EQKIRHD 510
Query: 308 SQRVKFTKEIKGLKIEITHCGTMKRKYR--VCNVTRRPAQMQSFPLQLENGQTVECTVAK 365
S + I ++ + Y+ +C+ + ++ + + +
Sbjct: 511 STAWNASGSILNTLQQL-------KFYKPYICDNDPKYERLVN---AILD---------- 550
Query: 366 YFLDKYKMKL-RFPHLPCLQVGQEHKHTYLPLEVCNIVAGQR 406
FL K + L + L++ + + E V QR
Sbjct: 551 -FLPKIEENLICSKYTDLLRIALMAEDEAIFEEAHKQV--QR 589
Score = 39.5 bits (91), Expect = 0.006
Identities = 45/325 (13%), Positives = 86/325 (26%), Gaps = 84/325 (25%)
Query: 537 EDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPDQVEPMFRYL-----KSTFQALQLV 591
+D +S +S + II D V R K + V
Sbjct: 39 QDMPKSI------LSKEEIDHIIMSK---------DAVSGTLRLFWTLLSKQEEMVQKFV 83
Query: 592 VVVLPGKTP-VYAEVKRVGDTVLGMATQCVQAKNVNKTSPQTLSNLCLKINV----KLGG 646
VL + + +K M ++ ++ Q + K NV
Sbjct: 84 EEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFA----KYNVSRLQPYLK 139
Query: 647 INSILVPSIRPKVFNEPVIF---MGADVTHPPAGDNKKPSIAAVV----GSMDAHPSR-Y 698
+ L+ +RP + + +G K +A V + +
Sbjct: 140 LRQALL-ELRP----AKNVLIDGVLG------SG---KTWVALDVCLSYKVQCKMDFKIF 185
Query: 699 AATVRVQQHRQEIIQELSSMVRLFCADKKEQSGKSGNIPAGTTVDIGITHPTEFDFYLCS 758
++ + +++ L ++ + +S S NI I E L S
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL-RIHSI----QAELRRLLKS 240
Query: 759 HQGIQGTSRPSHYHVL---WDDNHFDADELQC---LTYQLCHTYVRCTRSVSIPAPAYYA 812
+ VL + ++A L C LT TR +
Sbjct: 241 KP------YENCLLVLLNVQNAKAWNAFNLSCKILLT----------TRFKQV------T 278
Query: 813 HLVAFRARYHLVEKEHDSGEGSHQS 837
++ H+ H +
Sbjct: 279 DFLSAATTTHISLDHHSMTLTPDEV 303
>1r6z_P Chimera of maltose-binding periplasmic protein AN argonaute 2;
deviant OB fold, RNAI, gene regulation; HET: MAL; 2.80A
{Escherichia coli} SCOP: b.34.14.1 c.94.1.1
Length = 509
Score = 67.6 bits (165), Expect = 7e-12
Identities = 42/139 (30%), Positives = 65/139 (46%), Gaps = 7/139 (5%)
Query: 273 DVSATAFYKSQPVIEFMCEV-LDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMK 331
D+S +F S P+IE++ L + N + F + I + +
Sbjct: 375 DISHKSFPISMPMIEYLERFSLKAKINNTTNLDYSRRFLEPFLRGINVVYTPPQSFQSAP 434
Query: 332 RKYRVCNVTRRPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHKH 391
R YRV ++R PA ++F +G+ V T+A YF + L+FP L CL VG K
Sbjct: 435 RVYRVNGLSRAPASSETFEH---DGKKV--TIASYFHSR-NYPLKFPQLHCLNVGSSIKS 488
Query: 392 TYLPLEVCNIVAGQRCIKK 410
LP+E+C+I GQ +K
Sbjct: 489 ILLPIELCSIEEGQALNRK 507
>3o7v_X PIWI-like protein 1; PIWI, RNA silencing, PI-RNA, HIWI1, HILI, PAZ
domain, RNA BI protein; HET: OMU; 2.10A {Homo sapiens}
PDB: 2l5c_A 2l5d_A 3o3i_X 3o6e_X*
Length = 124
Score = 57.2 bits (138), Expect = 5e-10
Identities = 26/145 (17%), Positives = 50/145 (34%), Gaps = 31/145 (21%)
Query: 282 SQPVIEFMCEVLDIRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYRVCNVTR 341
S+ V++FM + + + +KE+ GL + + + YRV ++
Sbjct: 1 SETVLDFMFNFY--------HQTEEHKFQEQVSKELIGLVVLTKY---NNKTYRVDDIDW 49
Query: 342 RPAQMQSFPLQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQV---------GQEHKHT 392
+F +G E + +Y+ +Y ++ P L G
Sbjct: 50 DQNPKSTFKK--ADGS--EVSFLEYYRKQYNQEITDLKQPMLVSQPKRRRGPGGTLPGPA 105
Query: 393 YLPLEVCNIVAGQRCIKKLTDMQTS 417
L E+C + G LTD +
Sbjct: 106 MLIPELCYL-TG------LTDKMRN 123
>3qir_A PIWI-like protein 2; structural genomics consortium, SGC, PAZ
domain, RNAI, RNA B RNA binding protein; 2.45A {Homo
sapiens} PDB: 3o7x_A
Length = 148
Score = 52.0 bits (124), Expect = 5e-08
Identities = 26/155 (16%), Positives = 53/155 (34%), Gaps = 22/155 (14%)
Query: 292 VLD-IRDVNEQRKPLTDSQRVKFTKEIKGLKIEITHCGTMKRKYRVCNVTRRPAQMQSFP 350
VLD + + +Q K + + + TK + G + + R YR+ +V SF
Sbjct: 5 VLDVMHAIYQQNK---EHFQDECTKLLVGNIVITRY---NNRTYRIDDVDWNKTPKDSFT 58
Query: 351 LQLENGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHK----------HTYLPLEVCN 400
+ +G+ E T +Y+ Y + ++ P L + L E+
Sbjct: 59 M--SDGK--EITFLEYYSKNYGITVKEEDQPLLIHRPSERQDNHGMLLKGEILLLPELSF 114
Query: 401 IVAGQRCIKKLTDMQTSTMIKATARSAPDREREIQ 435
+ +KK + + S ++
Sbjct: 115 MTGIPEKMKK-DFRAMKDLAQQINLSPKQHHSALE 148
>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 = 52.0 bits (124), Expect = 8e-07
Identities = 112/702 (15%), Positives = 192/702 (27%), Gaps = 267/702 (38%)
Query: 92 RPIVLRANH----FQISMPRGFVHHYE------IQIQPDKCPRKVNREIIETMVHAYSKI 141
RP+ L +H + +P +I P+ + T K
Sbjct: 7 RPLTL--SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKF 64
Query: 142 FGALKPVFDGRNNLYT---RDPLPIGNDRMELEVTLPG------EGKDRVFRVAIKWQAQ 192
G Y +P +G L + L EG D + +A
Sbjct: 65 LG------------YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGND-IHALA------ 105
Query: 193 VSLFALEEALEGRTRQIP---FDAILALDVVMRHLPSMTYTPVGRS--FFSTPDG---YY 244
L + +T+++ A R + + S F + +G
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITA--------RIMAKRPFDKKSNSALFRAVGEGNAQLV 157
Query: 245 HPLGG-G-REVWFGFHQSVRPSQWKMMLNIDVSATAFYKS--QPVIEFMCEVLDIRDVNE 300
GG G + +F + +R D+ T Y +I+F E L +E
Sbjct: 158 AIFGGQGNTDDYF---EELR----------DLYQT--YHVLVGDLIKFSAETL-----SE 197
Query: 301 QRKPLTDSQRVKFTKEIKGLKIE--ITHCGTMKRKYRVCNVTRRPAQMQSFPL----QLE 354
+ D+++V FT+ GL I + + K + ++ P S PL QL
Sbjct: 198 LIRTTLDAEKV-FTQ---GLNILEWLENPSNTPDKDYLLSI---PI---SCPLIGVIQL- 246
Query: 355 NGQTVECTVAKYFLDKYKMKLRFPHLPCLQVGQEHKHTYLPLEVCNIVAGQRCIKKLTDM 414
A Y + +G + P E+ + + G +
Sbjct: 247 ---------AHYVVT------------AKLLG------FTPGELRSYLKG--ATGHSQGL 277
Query: 415 QTSTMIKATARSAPDREREIQSLVK-------RADFNNDAYVH------------EFGLT 455
T+ I A S ++ + R +AY + E
Sbjct: 278 VTAVAI-AETDSWESFFVSVRKAITVLFFIGVRC---YEAYPNTSLPPSILEDSLENNEG 333
Query: 456 ISNSMMEVRGRVLPPPKLQYGGRMSSITAQVNSMSSQGLFASKQQ--ALPNSGVWDMRGK 513
+ + M+ + L ++Q + N L A KQ +L N K
Sbjct: 334 VPSPMLSISN--LTQEQVQ------DYVNKTN----SHLPAGKQVEISLVNGA------K 375
Query: 514 QF-YTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGM---------------- 556
+G PQ SL L+K +G+
Sbjct: 376 NLVVSG-----------PPQ------SLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSN 418
Query: 557 ---PIIGQPCFCKY-ATGPDQVEPMFRYLKSTFQALQLVVVVLPGKTPVYAEVKRVGDTV 612
P + P D + +F A + + PVY DT
Sbjct: 419 RFLP-VASPFHSHLLVPASDLINKDLVKNNVSFNAKDI-------QIPVY-------DTF 463
Query: 613 LGMATQCVQAKNVNKTSPQTLSNLCLKINVKLGGINSILVPSIRPKVFNEPVIFMGA--- 669
G S+L ++ + I + PV +
Sbjct: 464 DG-------------------SDLR--------VLSGSISERIVDCIIRLPVKWETTTQF 496
Query: 670 DVTH----PPAG---------DNKKPSIAAVV--GSMDAHPS 696
TH P G NK + V+ G++D +P
Sbjct: 497 KATHILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTLDINPD 538
Score = 44.3 bits (104), Expect = 2e-04
Identities = 37/198 (18%), Positives = 64/198 (32%), Gaps = 78/198 (39%)
Query: 64 PNQ--PPQPVQ--------PPELPMFNCPRRPNLGREG-RPIVLRAN-------HFQISM 105
PN PP ++ P PM + NL +E + V + N +IS+
Sbjct: 315 PNTSLPPSILEDSLENNEGVPS-PMLSIS---NLTQEQVQDYVNKTNSHLPAGKQVEISL 370
Query: 106 ---PRGFV--------HHYEIQIQPDKCP------------RK---VNR----------- 128
+ V + + ++ K P RK NR
Sbjct: 371 VNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSH 430
Query: 129 ------EIIETMVHAYSKIFGA--LK-PVFDGRNNLYTRDPLPIGNDRMELEVTLPGEGK 179
++I + + F A ++ PV+D T D G+D L ++
Sbjct: 431 LLVPASDLINKDLVKNNVSFNAKDIQIPVYD------TFD----GSDLRVLSGSISERIV 480
Query: 180 DRVFRVAIKWQAQVSLFA 197
D + R+ +KW+ A
Sbjct: 481 DCIIRLPVKWETTTQFKA 498
Score = 30.8 bits (69), Expect = 2.4
Identities = 42/294 (14%), Positives = 87/294 (29%), Gaps = 78/294 (26%)
Query: 539 SLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPDQVEPMFRYLKSTFQALQLVVVVLPGK 598
S R T L S + + + P + L+ F +LP
Sbjct: 5 STRPLT--LSHGSLEHVLLV------------PTASFFIASQLQEQFNK------ILPEP 44
Query: 599 TPVYAEVKRVGDTV------LGMATQCVQAKNVNKTSPQTLSNLCLKINVK------LGG 646
T +A LG + V+ V + L + + L G
Sbjct: 45 TEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQ------VLNLCLTEFENCYLEG 98
Query: 647 --INSI---LVPSIRPKVFNEPVI----FMGADVTHPPAGDNKKPSIAAVVGSMDAHPSR 697
I+++ L+ + + + P K S +A+ ++ ++
Sbjct: 99 NDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRP---FDKKSNSALFRAVGEGNAQ 155
Query: 698 -YAATVRV---QQHRQEIIQELSSMV---RLFCADKKEQSGKSGNIPAGTTVDIGITHPT 750
A + Q + + +EL + + D + S ++ + TT+D
Sbjct: 156 LVA----IFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQ 211
Query: 751 EFDFYLCSHQGIQGTS-RPSHYHVLWDDNHFDADELQC----LTYQLCHTYVRC 799
+ + ++ S P D ++ + + C + QL H V
Sbjct: 212 GLNI----LEWLENPSNTP-------DKDYLLSIPISCPLIGVI-QLAHYVVTA 253
Score = 30.0 bits (67), Expect = 4.2
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 25/75 (33%)
Query: 805 IPAPAYYA-H----------------------LVAFRARYHLVEKEHDSGEGSHQSGSSE 841
IPA A +A H +V +R V D S+ +
Sbjct: 1753 IPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAI 1812
Query: 842 DRTPGAMARAITVHA 856
+ PG +A + + A
Sbjct: 1813 N--PGRVAASFSQEA 1825
Score = 29.6 bits (66), Expect = 5.8
Identities = 27/148 (18%), Positives = 41/148 (27%), Gaps = 60/148 (40%)
Query: 73 PPELPMFNCPRRPNLGREGRPIVLRANHFQISMPRGFVHHYEIQIQPDKCPRKVNREIIE 132
P L + G +G+ I R N+ + +E + K+ +EI E
Sbjct: 1669 PVNLTIHFG------GEKGKRI--RENYSAMI--------FETIVDGKLKTEKIFKEINE 1712
Query: 133 TMVHAYSKIFGALKPVFDGRNNLYTRDPLPIGNDRMELEVTLPGEGKDRVFRVAIKWQAQ 192
+ F G L T F Q
Sbjct: 1713 HS----TSY------TFRS----------EKG----LLSAT--------QF-------TQ 1733
Query: 193 VSLFALE----EALEGRTRQIPFDAILA 216
+L +E E L+ + IP DA A
Sbjct: 1734 PALTLMEKAAFEDLKSKGL-IPADATFA 1760
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 41.2 bits (96), Expect = 7e-04
Identities = 17/61 (27%), Positives = 17/61 (27%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRR 84
G T A A A A PPG PP PP P PM
Sbjct: 146 GRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGI 205
Query: 85 P 85
P
Sbjct: 206 P 206
Score = 40.4 bits (94), Expect = 0.001
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGA-MGLIPPNQPPQPVQPP 74
PP G PPG + PP + P G MG+ P P + PP
Sbjct: 174 GPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPP 218
Score = 39.6 bits (92), Expect = 0.002
Identities = 14/66 (21%), Positives = 17/66 (25%), Gaps = 3/66 (4%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQP---VQPPELPMFNCPRRPNL 87
P G G G P V P G + P + P P +
Sbjct: 120 MPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPM 179
Query: 88 GREGRP 93
GR P
Sbjct: 180 GRGAPP 185
Score = 39.6 bits (92), Expect = 0.002
Identities = 13/63 (20%), Positives = 13/63 (20%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGRE 90
A G P P P AP G G G PQ
Sbjct: 107 GRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPT 166
Query: 91 GRP 93
P
Sbjct: 167 QYP 169
Score = 38.1 bits (88), Expect = 0.006
Identities = 20/71 (28%), Positives = 21/71 (29%), Gaps = 1/71 (1%)
Query: 24 CGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPR 83
T P P GP P G PPG MG P +PP P P
Sbjct: 154 AAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPM 213
Query: 84 -RPNLGREGRP 93
P G P
Sbjct: 214 GMPPPGMRPPP 224
Score = 37.7 bits (87), Expect = 0.009
Identities = 17/59 (28%), Positives = 18/59 (30%), Gaps = 3/59 (5%)
Query: 23 TCGGQTKCAGAPPPGAPGAPPGPVAPPGAVP---APPGAMGLIPPNQPPQPVQPPELPM 78
T A A GAP P P APP M PP P P +P
Sbjct: 149 TVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPP 207
Score = 37.7 bits (87), Expect = 0.010
Identities = 14/69 (20%), Positives = 15/69 (21%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRR 84
G G P P A A A P Q P P PM
Sbjct: 126 GLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPP 185
Query: 85 PNLGREGRP 93
P +
Sbjct: 186 PGMMGPPPG 194
Score = 37.3 bits (86), Expect = 0.012
Identities = 10/52 (19%), Positives = 10/52 (19%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP 85
G A A G P P PP M P
Sbjct: 145 QGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMR 196
Score = 36.9 bits (85), Expect = 0.016
Identities = 12/56 (21%), Positives = 14/56 (25%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNL 87
PP G P G P MG P + P P P +
Sbjct: 172 RGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGM 227
Score = 36.2 bits (83), Expect = 0.029
Identities = 12/57 (21%), Positives = 13/57 (22%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLG 88
G A A P P G P P P P P +G
Sbjct: 148 GTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMG 204
Score = 36.2 bits (83), Expect = 0.030
Identities = 10/61 (16%), Positives = 14/61 (22%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREGRP 93
P G A ++ P PP + P P G P
Sbjct: 143 TPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPP 202
Query: 94 I 94
+
Sbjct: 203 M 203
Score = 33.9 bits (77), Expect = 0.15
Identities = 10/62 (16%), Positives = 12/62 (19%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREG 91
G P A A G P + PP + P G
Sbjct: 135 GGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPG 194
Query: 92 RP 93
Sbjct: 195 MR 196
Score = 33.5 bits (76), Expect = 0.24
Identities = 13/62 (20%), Positives = 15/62 (24%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREG 91
A A + GA P G PP P + R P G
Sbjct: 145 QGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPGMRPPMGPPMG 204
Query: 92 RP 93
P
Sbjct: 205 IP 206
Score = 30.0 bits (67), Expect = 2.6
Identities = 15/43 (34%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVA-----PPGAVPAPPGAMGLI 62
G P G PPG PPG P PPG GL+
Sbjct: 189 MGPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMRGLL 231
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae}
SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 41.0 bits (95), Expect = 0.002
Identities = 13/52 (25%), Positives = 15/52 (28%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
Q + P A P P A G MG+ P P Q L
Sbjct: 12 AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLT 63
Score = 39.0 bits (90), Expect = 0.007
Identities = 8/44 (18%), Positives = 10/44 (22%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
P A + PP G + P Q Q
Sbjct: 31 PPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQID 74
Score = 38.7 bits (89), Expect = 0.009
Identities = 15/129 (11%), Positives = 28/129 (21%), Gaps = 4/129 (3%)
Query: 4 PFPTTPDISNDLNFGNSIFTCGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIP 63
P P + + Q A V P + P
Sbjct: 49 PQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTP 108
Query: 64 PNQPPQPVQPPELPMFNCPRRPNLGREGRPIVLRANHFQISMPRGFVHHYEIQIQPDKCP 123
Q QP+ P + N+ + + ++ + + P P
Sbjct: 109 LQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPID----LLTELPPPITDLTLPPPPLVIP 164
Query: 124 RKVNREIIE 132
+ E
Sbjct: 165 PERMLVPSE 173
Score = 38.3 bits (88), Expect = 0.012
Identities = 17/93 (18%), Positives = 24/93 (25%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGRE 90
A PP P A G P P Q + ++
Sbjct: 27 AQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLH 86
Query: 91 GRPIVLRANHFQISMPRGFVHHYEIQIQPDKCP 123
P+V + Q +P + Q QP P
Sbjct: 87 NVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAP 119
Score = 36.7 bits (84), Expect = 0.034
Identities = 7/50 (14%), Positives = 10/50 (20%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFN 80
P P P A + P+ Q P +
Sbjct: 21 TPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLH 70
Score = 34.8 bits (79), Expect = 0.13
Identities = 8/55 (14%), Positives = 14/55 (25%), Gaps = 2/55 (3%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNL 87
G P+ P P Q PP+ + + ++ L
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPAA--AGMSYGQMGMPPQGAVPSMGQQQFL 62
Score = 31.3 bits (70), Expect = 1.5
Identities = 15/133 (11%), Positives = 37/133 (27%), Gaps = 2/133 (1%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGRE 90
P P A + + +P + P +L P +L
Sbjct: 98 QPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLP 157
Query: 91 GRPIVLRANHFQISMPRGFVHHYEIQIQPDKCPRKVNREIIETMVHAYSKIFGALKPVFD 150
P+V+ + I+ + P+ N +++ + + + ++D
Sbjct: 158 PPPLVIPPERMLVPSELSNASPDYIRSTLNAVPK--NSSLLKKSKLPFGLVIRPYQHLYD 215
Query: 151 GRNNLYTRDPLPI 163
+ + I
Sbjct: 216 DIDPPPLNEDGLI 228
Score = 29.0 bits (64), Expect = 8.3
Identities = 7/40 (17%), Positives = 7/40 (17%)
Query: 39 PGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPM 78
P G P P Q P M
Sbjct: 6 KRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQM 45
>2g5d_A GNA33; hydrolase, beta barrel; 1.95A {Neisseria gonorrhoeae fa
1090} SCOP: b.52.1.4 PDB: 2g6g_A
Length = 422
Score = 36.5 bits (83), Expect = 0.038
Identities = 10/56 (17%), Positives = 15/56 (26%), Gaps = 2/56 (3%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFN 80
G Q++ P GP P G P + V +P +
Sbjct: 1 GSQSRSIQTFPQPDTSVINGPDRPAGI--PDPAGTTVAGGGAVYTVVPHLSMPHWA 54
>3oun_A Putative uncharacterized protein TB39.8; peptidoglycan, Ser/Thr
kinase, pseudokinase, FHA domain, REG phosphorylation;
HET: TPO; 2.71A {Mycobacterium tuberculosis}
Length = 157
Score = 34.5 bits (79), Expect = 0.053
Identities = 19/104 (18%), Positives = 26/104 (25%), Gaps = 8/104 (7%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPP-GAMGLIPPNQPPQPVQPPELPMFNCPR 83
G + + P G P G G AP G + Q
Sbjct: 13 GLVPRGSHMPQGGGYAEPAGRDYDYGQSGAPDYGQPAPGGYSGYGQGGYGSAGTSVTLQL 72
Query: 84 RPNLGRE----GRPIVL-RANHFQISMPRGFV--HHYEIQIQPD 120
GR ++ R Q +P V H EI+
Sbjct: 73 DDGSGRTYQLREGSNIIGRGQDAQFRLPDTGVSRRHLEIRWDGQ 116
Score = 34.5 bits (79), Expect = 0.059
Identities = 10/68 (14%), Positives = 17/68 (25%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREGR 92
+ P G P G A P P ++ + G G
Sbjct: 7 HHHHSSGLVPRGSHMPQGGGYAEPAGRDYDYGQSGAPDYGQPAPGGYSGYGQGGYGSAGT 66
Query: 93 PIVLRANH 100
+ L+ +
Sbjct: 67 SVTLQLDD 74
>2kpy_A Major pollen allergen ART V 1; defensin-like, poly-proline; NMR
{Artemisia vulgaris}
Length = 108
Score = 32.9 bits (74), Expect = 0.10
Identities = 21/51 (41%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 33 APPPGAPGAPPGPVAPP--GAVPAPPGAMGLIPPNQ----PPQPVQPPELP 77
PPGA APPG PP G P+PP G PP PP P P
Sbjct: 55 KSPPGATPAPPGAAPPPAAGGSPSPPADGGSPPPPADGGSPPVDGGSPPPP 105
Score = 30.9 bits (69), Expect = 0.49
Identities = 18/51 (35%), Positives = 18/51 (35%), Gaps = 2/51 (3%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPE 75
G GA PP A G P P P PP A G PP P P
Sbjct: 59 GATPAPPGAAPPPAAGGSPSP--PADGGSPPPPADGGSPPVDGGSPPPPST 107
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 34.3 bits (78), Expect = 0.10
Identities = 14/46 (30%), Positives = 15/46 (32%), Gaps = 4/46 (8%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
A P G G P A PG P A P PP P +
Sbjct: 183 AAFPQGGRGRGRFPGAVPGGDRFPGPAG----PGGPPPPFPAGQTH 224
Score = 33.9 bits (77), Expect = 0.17
Identities = 13/50 (26%), Positives = 14/50 (28%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
G + A PPG P G P G P P PP
Sbjct: 166 GQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPP 215
Score = 33.2 bits (75), Expect = 0.25
Identities = 15/56 (26%), Positives = 17/56 (30%), Gaps = 1/56 (1%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFN 80
G G+ P G PGAVP G P PP P P +
Sbjct: 172 GKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPP-PPFPAGQTHHH 226
Score = 33.2 bits (75), Expect = 0.26
Identities = 10/47 (21%), Positives = 13/47 (27%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPM 78
G G PG P G + ++ P P P P
Sbjct: 170 GEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPP 216
Score = 32.8 bits (74), Expect = 0.38
Identities = 11/50 (22%), Positives = 14/50 (28%)
Query: 18 GNSIFTCGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQP 67
G+S + G P PG P P PP G +
Sbjct: 179 GSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTHHHHH 228
Score = 30.1 bits (67), Expect = 2.4
Identities = 13/53 (24%), Positives = 14/53 (26%), Gaps = 2/53 (3%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
G+ K P G A PG P P P PP P
Sbjct: 169 SGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGP--PPPFP 219
Score = 28.1 bits (62), Expect = 10.0
Identities = 9/56 (16%), Positives = 11/56 (19%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPN 86
+G PPG + G P P P P
Sbjct: 165 SGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPA 220
>1dx0_A Prion protein; brain, repeat; NMR {Bos taurus} SCOP: d.6.1.1 PDB:
1dx1_A 1qlx_A 1qlz_A
Length = 219
Score = 34.4 bits (78), Expect = 0.11
Identities = 9/57 (15%), Positives = 11/57 (19%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREG 91
P G P G P Q P + P G+
Sbjct: 2 SKKRPKPGGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPH 58
Score = 32.5 bits (73), Expect = 0.36
Identities = 15/59 (25%), Positives = 18/59 (30%), Gaps = 2/59 (3%)
Query: 32 GAPPPGAPGAPPGP--VAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLG 88
G P G G P G P G P G P+ Q +N P +P
Sbjct: 39 GQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGTHGQWNKPSKPKTN 97
Score = 32.1 bits (72), Expect = 0.51
Identities = 11/50 (22%), Positives = 14/50 (28%), Gaps = 1/50 (2%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
G T + P G+PG P G P G P+
Sbjct: 11 GWNTGGSRYPGQGSPGGNRYP-PQGGGGWGQPHGGGWGQPHGGGWGQPHG 59
Score = 31.7 bits (71), Expect = 0.79
Identities = 11/49 (22%), Positives = 12/49 (24%), Gaps = 2/49 (4%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
+ K G G P PG PP G QP
Sbjct: 4 KRPKPGGGWNTGGSRYPGQG--SPGGNRYPPQGGGGWGQPHGGGWGQPH 50
Score = 31.0 bits (69), Expect = 1.2
Identities = 13/69 (18%), Positives = 15/69 (21%), Gaps = 1/69 (1%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRR 84
GG G P G P G G Q +P + P N
Sbjct: 43 GGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGTHGQWNKPSK-PKTNMKHV 101
Query: 85 PNLGREGRP 93
G
Sbjct: 102 AGAAAAGAV 110
Score = 30.2 bits (67), Expect = 2.4
Identities = 10/65 (15%), Positives = 13/65 (20%), Gaps = 3/65 (4%)
Query: 32 GAPPPGAPGAPP---GPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLG 88
P G P G P G P G P+
Sbjct: 30 YPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGGWGQGGTHGQWN 89
Query: 89 REGRP 93
+ +P
Sbjct: 90 KPSKP 94
Score = 30.2 bits (67), Expect = 2.6
Identities = 11/49 (22%), Positives = 11/49 (22%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
GQ G P G G G G G QP
Sbjct: 21 GQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGG 69
Score = 29.4 bits (65), Expect = 3.6
Identities = 10/50 (20%), Positives = 11/50 (22%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
GG G+ PG P G G QP
Sbjct: 9 GGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPH 58
>2wd6_A Agglutinin receptor; cell adhesion, secreted, V-region, cell WALL,
AG I/II protei surface adhesin, peptidoglycan-anchor;
2.30A {Streptococcus gordonii}
Length = 349
Score = 34.8 bits (79), Expect = 0.11
Identities = 18/60 (30%), Positives = 22/60 (36%), Gaps = 2/60 (3%)
Query: 16 NFGNSIFTCGGQTKCAGAP-PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
GN F G P P AP AP P+ P P + N+P PV+ P
Sbjct: 291 KSGNIWFAFNSNINAIGVPTKPVAPTAPTQPMYET-EKPLEPAPVAPSYENEPTPPVKTP 349
>2gqb_A Conserved hypothetical protein; hypothetical protein conserved
unknown protein, structural genomics, PSI; NMR
{Rhodopseudomonas palustris} SCOP: a.282.1.1
Length = 130
Score = 32.8 bits (74), Expect = 0.14
Identities = 8/42 (19%), Positives = 10/42 (23%)
Query: 17 FGNSIFTCGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGA 58
FG + G + A AP P A
Sbjct: 4 FGKIMSAIFGDSAAASPGGAQAPATTGAAGTAPTAPQPTAAP 45
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 34.5 bits (78), Expect = 0.15
Identities = 14/58 (24%), Positives = 15/58 (25%), Gaps = 4/58 (6%)
Query: 32 GAPPPGAPGAP-PGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLG 88
G P PG+ G PG P A PG P P G
Sbjct: 323 GRPEPGSAGTWNPGRPEPGSAGTWNPGR---PEPGSAGTWNTGSSGSSSFRPDSSGHG 377
Score = 33.7 bits (76), Expect = 0.23
Identities = 19/67 (28%), Positives = 20/67 (29%), Gaps = 9/67 (13%)
Query: 32 GAPPPGAPG-APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQP----PELPMFNCPRRPN 86
G P PG+ G PG P A PG P P P P RP
Sbjct: 297 GRPEPGSAGTWNPGRPEPGSAGTWNPGR----PEPGSAGTWNPGRPEPGSAGTWNPGRPE 352
Query: 87 LGREGRP 93
G G
Sbjct: 353 PGSAGTW 359
Score = 33.3 bits (75), Expect = 0.30
Identities = 16/69 (23%), Positives = 17/69 (24%), Gaps = 1/69 (1%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAP-PGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRR 84
QTK G A V+ G P P G P P R
Sbjct: 239 QQTKMVLETFGGDGHARGDSVSQGTGLAPGSPRKPGTSSIGNVNPGSYGPGSSGTWNPGR 298
Query: 85 PNLGREGRP 93
P G G
Sbjct: 299 PEPGSAGTW 307
Score = 33.3 bits (75), Expect = 0.31
Identities = 10/40 (25%), Positives = 12/40 (30%), Gaps = 5/40 (12%)
Query: 32 GAPPPGAPGAP-PGPVAPPGAVPAPPGAMGLIPPNQPPQP 70
G P PG+ G G P G +P P
Sbjct: 349 GRPEPGSAGTWNTGSSGSSSFRPDSSGH----GNIRPSSP 384
Score = 32.5 bits (73), Expect = 0.62
Identities = 12/49 (24%), Positives = 14/49 (28%), Gaps = 3/49 (6%)
Query: 32 GAPPPGAPGAP-PGPVAP--PGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
G P PG+ G PG P G P+ P P
Sbjct: 336 GRPEPGSAGTWNPGRPEPGSAGTWNTGSSGSSSFRPDSSGHGNIRPSSP 384
Score = 31.4 bits (70), Expect = 1.3
Identities = 10/43 (23%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQP 73
AG PG P P P P A + +P
Sbjct: 330 AGTWNPGRPE-PGSAGTWNPGRPEPGSAGTWNTGSSGSSSFRP 371
Score = 30.6 bits (68), Expect = 2.2
Identities = 11/62 (17%), Positives = 13/62 (20%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREG 91
+ G P PG+ G P P RP G G
Sbjct: 259 VSQGTGLAPGSPRKPGTSSIGNVNPGSYGPGSSGTWNPGRPEPGSAGTWNPGRPEPGSAG 318
Query: 92 RP 93
Sbjct: 319 TW 320
Score = 30.6 bits (68), Expect = 2.4
Identities = 18/64 (28%), Positives = 21/64 (32%), Gaps = 3/64 (4%)
Query: 32 GAPPPGAPGAP-PGPVAPPGAVPAPPGAMGLIPPNQPPQPVQP-PELPMFNCPRRPNLGR 89
G+ PG+ G PG P A PG P +P P P RP G
Sbjct: 284 GSYGPGSSGTWNPGRPEPGSAGTWNPGRPEPGSA-GTWNPGRPEPGSAGTWNPGRPEPGS 342
Query: 90 EGRP 93
G
Sbjct: 343 AGTW 346
Score = 29.4 bits (65), Expect = 5.7
Identities = 8/44 (18%), Positives = 10/44 (22%), Gaps = 1/44 (2%)
Query: 31 AGAPPPGAPG-APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQP 73
AG PG P G + + N P
Sbjct: 343 AGTWNPGRPEPGSAGTWNTGSSGSSSFRPDSSGHGNIRPSSPDW 386
Score = 29.1 bits (64), Expect = 6.2
Identities = 14/65 (21%), Positives = 16/65 (24%), Gaps = 3/65 (4%)
Query: 32 GAPPPGAPG---APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLG 88
G G PG PG+ G P +P P P
Sbjct: 274 GTSSIGNVNPGSYGPGSSGTWNPGRPEPGSAGTWNPGRPEPGSAGTWNPGRPEPGSAGTW 333
Query: 89 REGRP 93
GRP
Sbjct: 334 NPGRP 338
>1pcx_A Protein transport protein SEC24; 2.50A {Saccharomyces cerevisiae}
SCOP: a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
PDB: 1pd0_A 1pd1_A
Length = 810
Score = 34.2 bits (77), Expect = 0.24
Identities = 13/47 (27%), Positives = 17/47 (36%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPM 78
AP G P A G P P + +PP + PP L +
Sbjct: 1 AAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPPPITDLTLPPPPLVI 47
>1o91_A Collagen alpha 1(VIII) chain; C1Q_LIKE_domain, extracellular
matrix, adhesion, connective tissue, repeat; HET: CPS;
1.9A {Mus musculus} SCOP: b.22.1.1
Length = 178
Score = 32.7 bits (74), Expect = 0.27
Identities = 10/50 (20%), Positives = 12/50 (24%), Gaps = 3/50 (6%)
Query: 26 GQTKCAGAP-PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
P P G P + G V P G + P P
Sbjct: 4 HHHAVMPTPSPQGEYL-PDMGLGIDG-VKTPHAYAGKKGKHGGPAYEMPA 51
>2grx_C Protein TONB; beta barrel, outer membrane, heterocomplex,
inter-protein beta sheet, protein-protein, metal
transport; HET: GCN KDO GMH FTT DAO MYR FCI; 3.30A
{Escherichia coli} SCOP: d.212.1.2 PDB: 1xx3_A
Length = 229
Score = 33.1 bits (75), Expect = 0.28
Identities = 10/64 (15%), Positives = 18/64 (28%), Gaps = 4/64 (6%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP-NLGREG 91
P +P P + + + P+ + + P R L EG
Sbjct: 108 ESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQ---YPARAQALRIEG 164
Query: 92 RPIV 95
+ V
Sbjct: 165 QVKV 168
Score = 31.6 bits (71), Expect = 0.79
Identities = 17/55 (30%), Positives = 21/55 (38%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP 85
A A P P + PP AV PP + P P P P E P+ +P
Sbjct: 30 APAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKP 84
Score = 30.5 bits (68), Expect = 1.8
Identities = 13/45 (28%), Positives = 15/45 (33%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
PP A PP PV P P P P +P P+
Sbjct: 45 LEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPK 89
Score = 28.9 bits (64), Expect = 5.4
Identities = 10/53 (18%), Positives = 12/53 (22%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP 85
P A V P P P +P +P P P
Sbjct: 27 ELPAPAQPISVTMVTPADLEPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVI 79
Score = 28.9 bits (64), Expect = 5.5
Identities = 16/61 (26%), Positives = 21/61 (34%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGREGR 92
PP P P P P P + + P P+P P + P+R E R
Sbjct: 51 VQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVKPVESR 110
Query: 93 P 93
P
Sbjct: 111 P 111
>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
fusion, viral P glycoprotein B, HSV-1, membrane; HET:
NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
3nwd_A*
Length = 703
Score = 33.8 bits (77), Expect = 0.30
Identities = 11/45 (24%), Positives = 14/45 (31%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPE 75
A PG PG A G P P P+P + +
Sbjct: 3 AAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKK 47
Score = 31.5 bits (71), Expect = 1.4
Identities = 13/50 (26%), Positives = 16/50 (32%)
Query: 36 PGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP 85
P AP +P P A G PP P P+ P+ P
Sbjct: 2 PAAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNP 51
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 33.2 bits (75), Expect = 0.34
Identities = 9/48 (18%), Positives = 12/48 (25%), Gaps = 6/48 (12%)
Query: 31 AGAPPPGAPGAP-PGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
+ P P P PP PA PP+ +
Sbjct: 33 SDFLAALHPPVTVPDPAPPPPPAPAAGN-----PPDTVTGDSVLQRIL 75
Score = 33.2 bits (75), Expect = 0.42
Identities = 16/72 (22%), Positives = 21/72 (29%), Gaps = 1/72 (1%)
Query: 4 PFPTTPDISNDLNFGNSIFTCGGQTKCAGAPPPGAPG-APPGPVAPPGAVPAPPGAMGLI 62
P S+ + S+ + A PP P APP P AP P +
Sbjct: 11 SSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSV 70
Query: 63 PPNQPPQPVQPP 74
P P
Sbjct: 71 LQRILRGPTGPG 82
Score = 32.8 bits (74), Expect = 0.48
Identities = 8/56 (14%), Positives = 11/56 (19%), Gaps = 1/56 (1%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPP-QPVQPPELPMFNCPRRP 85
+ P A + L + P P P P P
Sbjct: 6 HHHHHSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNP 61
Score = 32.8 bits (74), Expect = 0.56
Identities = 13/45 (28%), Positives = 13/45 (28%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
A A PP V P P P A G P V L
Sbjct: 32 ASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDSVLQRILR 76
Score = 32.8 bits (74), Expect = 0.56
Identities = 13/51 (25%), Positives = 15/51 (29%), Gaps = 5/51 (9%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPE 75
G A A + PP VP P PP P PP+
Sbjct: 18 GSHMVIPSASVTSAASDFLAALHPPVTVPDPAP-----PPPPAPAAGNPPD 63
Score = 32.0 bits (72), Expect = 0.86
Identities = 11/49 (22%), Positives = 13/49 (26%), Gaps = 3/49 (6%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
+G P G+ P A PP P P PP
Sbjct: 7 HHHHSSGLVPRGSHMVIPSASVTSAASDFLAALH---PPVTVPDPAPPP 52
Score = 31.3 bits (70), Expect = 1.5
Identities = 8/66 (12%), Positives = 12/66 (18%), Gaps = 14/66 (21%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPG--------------AMGLIPPNQPPQPVQPPEL 76
P G + P G G P P
Sbjct: 54 PAPAAGNPPDTVTGDSVLQRILRGPTGPGTTSLAPAVRYGRQPGPEAPASAPPAAGRAVP 113
Query: 77 PMFNCP 82
+++ P
Sbjct: 114 GLYHHP 119
>2uv8_A Fatty acid synthase subunit alpha (FAS2); fatty acid biosynthesis,
malonyl/palmitoyl transferase, phosphopantetheine,
transferase; HET: GVL FMN; 3.10A {Saccharomyces
cerevisiae} PDB: 2vkz_A* 3hmj_A*
Length = 1887
Score = 33.8 bits (77), Expect = 0.35
Identities = 12/41 (29%), Positives = 15/41 (36%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPV 71
A AP P A P AP A P A ++P +
Sbjct: 108 APAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKAS 148
Score = 31.1 bits (70), Expect = 2.1
Identities = 8/45 (17%), Positives = 10/45 (22%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPE 75
P P A A P A +PV+
Sbjct: 105 KEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVKASL 149
Score = 30.3 bits (68), Expect = 3.2
Identities = 8/45 (17%), Positives = 9/45 (20%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
P P P A P A P E+
Sbjct: 97 LAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIA 141
>2vg3_A Undecaprenyl pyrophosphate synthetase; transferase, cell WALL
biogenesis/degradation, cell cycle, P transferase; HET:
GPP; 1.8A {Mycobacterium tuberculosis} PDB: 2vg2_A*
2vg4_A
Length = 284
Score = 32.9 bits (76), Expect = 0.41
Identities = 12/52 (23%), Positives = 13/52 (25%), Gaps = 2/52 (3%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQP--VQPPELPMFNCPR 83
P P P P P P A P P P +P P
Sbjct: 6 PAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPN 57
>1pk8_A RAT synapsin I; ATP binding, ATP grAsp, calcium (II) ION,
membrane protein; HET: ATP; 2.10A {Rattus norvegicus}
SCOP: c.30.1.5 d.142.1.3 PDB: 1px2_A*
Length = 422
Score = 32.5 bits (73), Expect = 0.57
Identities = 9/45 (20%), Positives = 11/45 (24%), Gaps = 3/45 (6%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
PPP A P + + A P P P
Sbjct: 33 PPPPSAASPGATPGSAAASAERASTA---APVASPAAPSPGSSGG 74
Score = 32.5 bits (73), Expect = 0.61
Identities = 7/44 (15%), Positives = 9/44 (20%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
G PP P + A PG+
Sbjct: 20 NGYMTDLQRPQPPPPPPSAASPGATPGSAAASAERASTAAPVAS 63
Score = 31.7 bits (71), Expect = 1.1
Identities = 11/41 (26%), Positives = 13/41 (31%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PP P + P A PG+ A P P P
Sbjct: 30 QPPPPPPSAASPGATPGSAAASAERASTAAPVASPAAPSPG 70
>1nay_A CCP4, collagen-like peptide; collagen assembly, structural
protein; 2.60A {Synthetic} SCOP: k.3.1.1
Length = 56
Score = 29.3 bits (65), Expect = 0.60
Identities = 18/36 (50%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 42 PPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
PPGP PPG P PPG G P PP PE P
Sbjct: 2 PPGPPGPPGP-PGPPGPPGPPGPPGPPGSGYIPEAP 36
Score = 27.4 bits (60), Expect = 3.4
Identities = 18/42 (42%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 35 PPGAPGAP--PGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PPG PG P PGP PPG PPG G + P+ Q
Sbjct: 5 PPGPPGPPGPPGPPGPPG----PPGPPGSGYIPEAPRDGQAY 42
>2uv9_A Fatty acid synthase alpha subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; 3.1A
{Thermomyces lanuginosus} PDB: 2uvb_A*
Length = 1878
Score = 32.6 bits (74), Expect = 0.65
Identities = 14/45 (31%), Positives = 16/45 (35%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPE 75
A + AP A P A P A PAP A PV +
Sbjct: 105 AASSADAAPAAAPAAPAAPAAAPAPAPASAGPAAPVQDAPVTATD 149
Score = 29.9 bits (67), Expect = 4.2
Identities = 11/45 (24%), Positives = 12/45 (26%), Gaps = 4/45 (8%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
A A AP A P A A P P + P
Sbjct: 104 AAASSADAAPAAAPAAPAAPAAAPAP----APASAGPAAPVQDAP 144
Score = 29.9 bits (67), Expect = 4.4
Identities = 12/43 (27%), Positives = 13/43 (30%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
P P A A P A PA P A P P +
Sbjct: 99 PEPTPAAASSADAAPAAAPAAPAAPAAAPAPAPASAGPAAPVQ 141
>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface
adhesin WALL, peptidoglycan-anchor, cell adhesion; HET:
PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A
Length = 497
Score = 32.6 bits (72), Expect = 0.71
Identities = 11/51 (21%), Positives = 11/51 (21%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRP 85
P PP AP P PV P P R
Sbjct: 440 AVNVPKVTKEKPTPPVKPTAPTKPTYETEKPLKPAPVAPNYEKEPTPPTRL 490
Score = 30.2 bits (66), Expect = 3.1
Identities = 7/44 (15%), Positives = 11/44 (25%), Gaps = 2/44 (4%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
PG ++ A+ P + PP P
Sbjct: 416 VVPGKDNTDGKKPNIWYSLNGKIRAVN--VPKVTKEKPTPPVKP 457
>4af8_A Metacaspase MCA2; hydrolase, cysteine peptidase,
caspase/hemoglobin fold; 1.40A {Trypanosoma brucei}
PDB: 4afp_A 4afv_A 4afr_A
Length = 367
Score = 32.3 bits (72), Expect = 0.74
Identities = 10/70 (14%), Positives = 15/70 (21%), Gaps = 4/70 (5%)
Query: 1 MAIPFPTTPDISNDLNFGNSIFTCGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMG 60
+ +++ + G PP V A G G
Sbjct: 24 LITQLCDAGQLADYVGLGWLNAVSSQPY----LVQALGLQPPPRRVDVDAAFRDAKGLHG 79
Query: 61 LIPPNQPPQP 70
P P P
Sbjct: 80 HQPWVATPLP 89
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.1 bits (69), Expect = 0.77
Identities = 8/39 (20%), Positives = 18/39 (46%), Gaps = 13/39 (33%)
Query: 708 RQEIIQELSSMVRLFCADKKEQSGKSGNIPA---GTTVD 743
+Q + ++L + ++L+ D S PA T++
Sbjct: 19 KQAL-KKLQASLKLYADD----SA-----PALAIKATME 47
Score = 29.1 bits (64), Expect = 3.2
Identities = 9/42 (21%), Positives = 15/42 (35%), Gaps = 14/42 (33%)
Query: 545 QQLQKISNDAGMPIIGQPCFCKYATGPDQVEPMFRYLKSTFQ 586
Q L+K+ + YA D P +K+T +
Sbjct: 20 QALKKLQASLKL----------YA--DDSA-PALA-IKATME 47
Score = 28.8 bits (63), Expect = 4.7
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 6/25 (24%)
Query: 405 QRCIKKLTDMQTSTMIKATA-RSAP 428
++ +KKL Q S +K A SAP
Sbjct: 19 KQALKKL---QAS--LKLYADDSAP 38
>3a0m_A Collagen-like peptide; triple-helix, model peptide, twinned
crystal, STRU protein; 1.02A {Synthetic}
Length = 27
Score = 28.3 bits (63), Expect = 0.77
Identities = 18/26 (69%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMG 60
PPG PG PPGPV PPG P PPG G
Sbjct: 4 PPGPPG-PPGPVGPPGP-PGPPGPPG 27
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 30.6 bits (68), Expect = 1.1
Identities = 11/51 (21%), Positives = 12/51 (23%), Gaps = 8/51 (15%)
Query: 33 APPPGAPGAPPGPVAPPGA--------VPAPPGAMGLIPPNQPPQPVQPPE 75
P A A P P A + QP VQ E
Sbjct: 1 GPLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQE 51
>2f6a_E Collagen; CNA, mscramm, adhesion, ECM, cell adhesion/structural
protein complex; 3.29A {Staphylococcus aureus}
Length = 30
Score = 27.9 bits (62), Expect = 1.1
Identities = 17/34 (50%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 41 APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PPGP PPG PPG G P PP P PP
Sbjct: 1 GPPGPPGPPG----PPGPRGRTGPPGPPGPPGPP 30
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics;
5.00A {Barmah forest virus}
Length = 253
Score = 31.1 bits (70), Expect = 1.3
Identities = 11/53 (20%), Positives = 18/53 (33%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPN 86
P P APP P + A+G + + + + P P +P
Sbjct: 23 IPQPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQKKPKKTPPPKPK 75
Score = 29.6 bits (66), Expect = 4.2
Identities = 7/55 (12%), Positives = 10/55 (18%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPN 86
G AP P P A P + + +
Sbjct: 11 GRRWRPAPVQRYIPQPQPPAPPRRRRGPSQLQQLVAALGALALQPKQKQKRAQKK 65
>1jer_A Cucumber stellacyanin; electron transport, copper, glycoprotein,
hydroxylation; 1.60A {Cucumis sativus} SCOP: b.6.1.1
Length = 138
Score = 30.4 bits (68), Expect = 1.3
Identities = 16/66 (24%), Positives = 21/66 (31%), Gaps = 14/66 (21%)
Query: 7 TTPDISNDLNFGNSIFTCGGQTKCAG--------------APPPGAPGAPPGPVAPPGAV 52
T+P I G F C T C+ P +PP V PP +
Sbjct: 73 TSPVIERLDELGMHYFVCTVGTHCSNGQKLSINVVAANATVSMPPPSSSPPSSVMPPPVM 132
Query: 53 PAPPGA 58
P P +
Sbjct: 133 PPPSPS 138
>1cag_A Collagen-like peptide; 1.85A {} SCOP: k.3.1.1 PDB: 1cgd_A
Length = 30
Score = 27.6 bits (61), Expect = 1.5
Identities = 16/26 (61%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPG 57
G P P P APPGP PPG P PPG
Sbjct: 6 GPPGPPGPPAPPGPPGPPGP-PGPPG 30
Score = 26.8 bits (59), Expect = 2.5
Identities = 18/26 (69%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMG 60
PPG PG PPGP APPG P PPG G
Sbjct: 4 PPGPPG-PPGPPAPPGP-PGPPGPPG 27
Score = 25.6 bits (56), Expect = 6.5
Identities = 20/33 (60%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQP 67
PPG PG PPGP PP A P PPG G PP P
Sbjct: 1 PPGPPG-PPGPPGPP-APPGPPGPPG--PPGPP 29
Score = 25.3 bits (55), Expect = 7.8
Identities = 15/29 (51%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPGAMG 60
G P P P PP P PPG P PPG G
Sbjct: 3 GPPGPPGPPGPPAPPGPPGP-PGPPGPPG 30
>1bkv_A T3-785; collagen, hydroxyproline, hydrogen bonding; 2.00A {}
SCOP: k.3.1.1
Length = 30
Score = 27.6 bits (61), Expect = 1.5
Identities = 17/33 (51%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 42 PPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PPGP PPG GA GL P PP P PP
Sbjct: 1 PPGPPGPPGIT----GARGLAGPPGPPGPPGPP 29
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 31.6 bits (71), Expect = 1.6
Identities = 12/50 (24%), Positives = 13/50 (26%)
Query: 30 CAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMF 79
A G P G P PG P P P P P +
Sbjct: 1507 GFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAY 1556
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 31.0 bits (70), Expect = 1.6
Identities = 13/51 (25%), Positives = 13/51 (25%), Gaps = 2/51 (3%)
Query: 26 GQTKCAGAPPPGAPGAPPGPVAPPGAVPAP--PGAMGLIPPNQPPQPVQPP 74
PP APP P G P PPQ PP
Sbjct: 373 EMMAMMQKMQQQQAAYPPQGYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPP 423
Score = 30.7 bits (69), Expect = 2.1
Identities = 17/52 (32%), Positives = 19/52 (36%), Gaps = 2/52 (3%)
Query: 25 GGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQP-VQPPE 75
Q + A PP G P G P G P G P PP P PP+
Sbjct: 380 KMQQQQAAYPPQGYAPPPQGY-PPQGYPPQGYPPQGYPPQGYPPPPQGAPPQ 430
Score = 29.1 bits (65), Expect = 7.5
Identities = 18/50 (36%), Positives = 18/50 (36%), Gaps = 4/50 (8%)
Query: 26 GQTKCAGAPPPGAP---GAPPGPVAPPGAVPAPPGAMGL-IPPNQPPQPV 71
G PP G PP P G P P GA PP PPQ V
Sbjct: 392 GYAPPPQGYPPQGYPPQGYPPQGYPPQGYPPPPQGAPPQGAPPAAPPQGV 441
>2y5t_F C1; immune system, antibody, rheumatoid arthritis; 2.20A {Mus
musculus}
Length = 38
Score = 27.3 bits (60), Expect = 1.8
Identities = 17/34 (50%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 41 APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PPGP PPG P PPGA GL P PP
Sbjct: 1 GPPGPPGPPGP-PGPPGARGLTGRPGDAGPPGPP 33
Score = 25.8 bits (56), Expect = 8.3
Identities = 19/35 (54%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 35 PPGAPGAPPGPVAPPGA--VPAPPGAMGLIPPNQP 67
PPG PG PPGP PPGA + PG G PP P
Sbjct: 2 PPGPPG-PPGPPGPPGARGLTGRPGDAG--PPGPP 33
>1m0u_A GST2 gene product; flight muscle protein, sigma, transferase;
HET: GSH; 1.75A {Drosophila melanogaster} SCOP:
a.45.1.1 c.47.1.5
Length = 249
Score = 30.5 bits (69), Expect = 1.8
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 33 APPPGAPGAPPG-PVAPPGAVPAPPGAMG--LIPPNQPPQPVQPP 74
A P A GAPP APP A A G PP +P +P++
Sbjct: 5 AQAPPAEGAPPAEGEAPPPAEGAEGAVEGGEAAPPAEPAEPIKHS 49
>3aja_A Putative uncharacterized protein; alpha-beta hydrolase, serine
esterase, cutinase, lipase, HYD; 2.90A {Mycobacterium
smegmatis}
Length = 302
Score = 30.7 bits (68), Expect = 2.1
Identities = 13/34 (38%), Positives = 13/34 (38%)
Query: 36 PGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQ 69
P P PP PPG V PPG P Q
Sbjct: 4 PDTPATPPPSAEPPGGVVVPPGTRKPRPEFQSAD 37
>3a1h_A Collagen-like peptide; collagen helix, HOST-guest peptide,
twinned crystal, structu protein; 1.08A {Synthetic}
Length = 27
Score = 26.8 bits (59), Expect = 2.2
Identities = 17/26 (65%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMG 60
PPG PG PPGP PPG P PPG G
Sbjct: 4 PPGPPG-PPGPTGPPGP-PGPPGPPG 27
>3pon_A MBL collagen-like peptide; collagen peptide, MBL collagen-like
region, complement prote lectin pathway of complement;
1.50A {Synthetic} PDB: 3pob_B
Length = 29
Score = 26.7 bits (59), Expect = 3.0
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 32 GAPPPGAPGAPPGPVAPPGAVPAPPG 57
G P P P PPG + PPG P PPG
Sbjct: 2 GPPGPPGPPGPPGKLGPPGP-PGPPG 26
Score = 25.9 bits (57), Expect = 5.0
Identities = 17/34 (50%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 41 APPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
PPGP PPG PPG +G P PP P PP
Sbjct: 2 GPPGPPGPPG----PPGKLG---PPGPPGPPGPP 28
>3adm_A Collagen-like peptide; triple helix, model peptide, structural
protein; HET: HYP; 1.18A {Synthetic}
Length = 27
Score = 26.4 bits (58), Expect = 3.1
Identities = 17/26 (65%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMG 60
PPG PG PPGP PPG P PPG G
Sbjct: 4 PPGPPG-PPGPSGPPGP-PGPPGPPG 27
>1y0f_B Collagen I alpha 2; native, in SITU, triple-helix, supermolecular,
packing structure; 5.16A {Rattus norvegicus} SCOP:
i.25.1.1 PDB: 1ygv_B 3hqv_B 3hr2_B
Length = 1026
Score = 30.5 bits (69), Expect = 3.1
Identities = 14/47 (29%), Positives = 15/47 (31%), Gaps = 4/47 (8%)
Query: 32 GAPPPGAPGAP--PGPVAPPGA--VPAPPGAMGLIPPNQPPQPVQPP 74
A P G G P G PPG + PPG G P
Sbjct: 698 DAGPTGMTGFPGAAGRTGPPGPSGLTGPPGPPGAAGKEGIRGPRGDQ 744
Score = 28.9 bits (65), Expect = 8.1
Identities = 14/40 (35%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
GAPG P G G+ P G G I PP P
Sbjct: 143 RVGAPG-PAGARGSDGS-VGPVGPAGPIGSAGPPGFPGAP 180
>2wuh_B Collagen peptide; receptor-peptide complex, transferase,
nucleotide-binding, tyrosine-protein kinase; 1.60A
{Homo sapiens}
Length = 29
Score = 26.4 bits (58), Expect = 3.1
Identities = 16/28 (57%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 35 PPGAPGAPPGPVAPPGAV--PAPPGAMG 60
PPG PG PPGP PG + P PPG G
Sbjct: 3 PPGPPG-PPGPRGQPGVLGFPGPPGPPG 29
>4dmt_A Collagen III derived peptide; collagen triple helix, VON
willebrand factor, structural Pro; 1.39A {Synthetic}
Length = 32
Score = 26.5 bits (58), Expect = 3.3
Identities = 15/30 (50%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 41 APPGPVAPPGAVPAPPGAMGLIPPNQPPQP 70
PPGP PPG PG MG P PP P
Sbjct: 2 GPPGPPGPPGP-RGQPGVMGFPGPPGPPGP 30
>3abn_A Collagen-like peptide; collagen-helix, structural protein; HET:
HYP; 1.02A {Synthetic}
Length = 27
Score = 26.4 bits (58), Expect = 3.5
Identities = 17/26 (65%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMG 60
PPG PG PPGP PPG P PPG G
Sbjct: 4 PPGPPG-PPGPDGPPGP-PGPPGPPG 27
>1jvr_A HTLV-II MA, MA, human T-cell leukemia virus type II matrix protein;
HTLV-II matrix protein, retroviral matrix protein; NMR
{Human t-lymphotropic virus 2} SCOP: a.61.1.2
Length = 137
Score = 28.7 bits (63), Expect = 4.0
Identities = 10/46 (21%), Positives = 15/46 (32%)
Query: 27 QTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQ 72
+ + + + P P P P P P + PP P Q
Sbjct: 90 KNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQ 135
Score = 27.9 bits (61), Expect = 8.8
Identities = 12/37 (32%), Positives = 14/37 (37%), Gaps = 4/37 (10%)
Query: 38 APGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
+P AP PV P P PP P+ PP
Sbjct: 94 SPSAPAAPVPTPICPTTTPPP----PPPPSPEAHVPP 126
>1y0f_A Collagen I alpha 1; native, in SITU, triple-helix, supermolecular,
packing structure; 5.16A {Rattus norvegicus} SCOP:
i.25.1.1 PDB: 1ygv_A 3hqv_A 3hr2_A
Length = 1054
Score = 30.1 bits (68), Expect = 4.0
Identities = 23/63 (36%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 32 GAP-PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELPMFNCPRRPNLGRE 90
G P P GA G PG G VP PPGA+G Q P P R G
Sbjct: 419 GFPGPKGAAG-EPGKAGERG-VPGPPGAVGP-AGKDGEAGAQGPPGPAGPAGERGEQGPA 475
Query: 91 GRP 93
G P
Sbjct: 476 GSP 478
Score = 29.7 bits (67), Expect = 5.4
Identities = 13/46 (28%), Positives = 14/46 (30%), Gaps = 3/46 (6%)
Query: 25 GGQTKCAGAPPPGAPGAP--PGPVAPPGAVPAPPGAMGLIPPNQPP 68
G + PPGA G G G P P G G P
Sbjct: 431 GKAGERGVPGPPGAVGPAGKDGEAGAQGP-PGPAGPAGERGEQGPA 475
Score = 29.7 bits (67), Expect = 6.0
Identities = 16/45 (35%), Positives = 16/45 (35%), Gaps = 3/45 (6%)
Query: 35 PPGAPGAP--PGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
PPGA G G P GA PG G PP V P
Sbjct: 408 PPGARGQAGVMGFPGPKGA-AGEPGKAGERGVPGPPGAVGPAGKD 451
>3h1t_A Type I site-specific restriction-modification system, R
(restriction) subunit; hydrolase, restriction enzyme
HSDR, ATP-binding; 2.30A {Vibrio vulnificus}
Length = 590
Score = 29.7 bits (67), Expect = 4.3
Identities = 18/111 (16%), Positives = 28/111 (25%), Gaps = 22/111 (19%)
Query: 721 LFCADKKE---QSGKSGN--IPAGTTVDIGITHPTEFDFYLCSHQGIQGTSRPSHYHVLW 775
LF AD+ G + Y +Q I R + +
Sbjct: 239 LFLADRNVLVDDPKDKTFTPFGDARHKIEGGKVVKSREIYFAIYQSIASDERRPGLYKEF 298
Query: 776 DDNHFD---ADELQCLTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHL 823
+ FD DE CH R + + L F + +
Sbjct: 299 PQDFFDLIIIDE--------CH------RGSARDNSNWREILEYFEPAFQI 335
>3icg_A Endoglucanase D; cellulase, xylanase, carbohydrate binding DOM
glucanase, carbohydrate metabolism, cellulose
degradation, glycosidase; HET: BTB; 2.10A {Clostridium
cellulovorans}
Length = 515
Score = 29.8 bits (66), Expect = 4.5
Identities = 6/26 (23%), Positives = 7/26 (26%), Gaps = 1/26 (3%)
Query: 22 FTCGGQTKCAGAPPPGAPGAPPGPVA 47
FT G C P P+
Sbjct: 477 FTVNGTE-CTVKKGELEGKPIPNPLL 501
>4auo_C Triple-helical collagen peptide; hydrolase-peptide complex; 3.00A
{Synthetic construct}
Length = 40
Score = 26.3 bits (58), Expect = 5.4
Identities = 15/36 (41%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQP 70
PPG PG P G G + PG G P PP P
Sbjct: 5 PPGPPG-PQGLAGQRG-IVGLPGQRGERGPPGPPGP 38
>3pod_A MBL collagen-like peptide; collagen peptide, complement proteins,
lectin pathway of COM MAsp-1 CUB1 and CUB2 domains,
bloodstream, unknown function; 1.50A {Synthetic}
Length = 26
Score = 25.6 bits (56), Expect = 5.6
Identities = 15/23 (65%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 35 PPGAPGAPPGPVAPPGAVPAPPG 57
PPG PG PPG + PPG P PPG
Sbjct: 3 PPGPPG-PPGKLGPPGP-PGPPG 23
>2pne_A 6.5 kDa glycine-rich antifreeze protein; chemical protein
synthesis, native chemical ligation; 0.98A {Synthetic}
PDB: 3boi_A 3bog_A* 3bog_C*
Length = 81
Score = 27.3 bits (61), Expect = 5.9
Identities = 11/50 (22%), Positives = 12/50 (24%), Gaps = 2/50 (4%)
Query: 26 GQTKCAGAP-PPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPP 74
G C G G G PG G G G+ P
Sbjct: 24 GGPGCDGGHGGNGGNG-NPGCAGGVGGAGGASGGTGVGGRGGKGGSGTPK 72
>2wsc_E PSAE, PSI-E A, photosystem I reaction center subunit IV A,
chloroplastic; photosynthesis, electron transfer,
membrane proteins, large complexes; HET: CL1 PQN BCR
LMU LMG SUC UNL; 3.30A {Arabidopsis thaliana} PDB:
2wse_E* 2wsf_E* 2o01_E* 3lw5_E*
Length = 143
Score = 28.4 bits (62), Expect = 6.3
Identities = 9/39 (23%), Positives = 12/39 (30%), Gaps = 5/39 (12%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQ 69
+ +P AP GA P PP P+
Sbjct: 49 PAPASSSSKDSPAAAAAPDGATATKP-----KPPPIGPK 82
Score = 27.7 bits (60), Expect = 9.0
Identities = 10/34 (29%), Positives = 10/34 (29%)
Query: 37 GAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQP 70
A P A AP GA P P P
Sbjct: 48 DPAPASSSSKDSPAAAAAPDGATATKPKPPPIGP 81
>1mv3_A MYC box dependent interacting protein 1; tumor suppressor,
endocytosis/exocytosis complex; NMR {Homo sapiens}
SCOP: b.34.2.1
Length = 213
Score = 28.9 bits (63), Expect = 6.4
Identities = 10/44 (22%), Positives = 13/44 (29%)
Query: 34 PPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPPQPVQPPELP 77
P G P +P P + PP PP P +
Sbjct: 10 IRVNHEPEPAGGATPGATLPKSPSQLRKGPPVPPPPKHTPSKEV 53
>2g0w_A LMO2234 protein; putative sugar isomerase, structural genomics,
joint center structural genomics, JCSG, protein
structure initiative; HET: MSE PG4; 1.70A {Listeria
monocytogenes} SCOP: c.1.15.4
Length = 296
Score = 29.1 bits (65), Expect = 6.8
Identities = 11/89 (12%), Positives = 28/89 (31%), Gaps = 12/89 (13%)
Query: 516 YTGVEIRVWAIACFAPQRTVREDSLRSFTQQLQKISNDAGMPIIGQPCFCKYATGPDQVE 575
+ G+ +R ED + +I ++ M + ++ T D+
Sbjct: 50 FDGIGLRAENYVDALAAGLTDED--------MLRILDEHNMKVTEVEYITQWGTAEDRTA 101
Query: 576 PMFRYLKSTFQALQLV----VVVLPGKTP 600
+ ++TF +L + +
Sbjct: 102 EQQKKEQTTFHMARLFGVKHINCGLLEKI 130
>1ei8_A Collagen-like peptide (Pro-HYP-Gly)4-PG-(Pro-HYP- Gly)5; triple
helix, contractIle protein; 2.00A {Synthetic} SCOP:
k.3.1.1
Length = 29
Score = 25.6 bits (56), Expect = 7.0
Identities = 16/24 (66%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 35 PPGAPG-APPGPVAPPGAVPAPPG 57
PPG PG PPGP PPG P PPG
Sbjct: 7 PPGPPGPGPPGPPGPPGP-PGPPG 29
>3m1c_B GL, envelope glycoprotein L; glycoprotein H, GH/GL, envelope
protein, HER simplex virus, disulfide bond, HOST cell
MEMB HOST endosome; HET: NAG XYL; 3.00A {Human
herpesvirus 2}
Length = 204
Score = 28.5 bits (62), Expect = 8.3
Identities = 8/47 (17%), Positives = 13/47 (27%)
Query: 22 FTCGGQTKCAGAPPPGAPGAPPGPVAPPGAVPAPPGAMGLIPPNQPP 68
+ PP + + P A P A+ PP +
Sbjct: 144 RDLRPANTTSTWEPPVSSDDEASSQSKPLATQPPVLALSNAPPRRVS 190
>3ah9_A Collagen-like peptide; triple helix, model peptide, structural
protein; 1.08A {Synthetic} PDB: 2cuo_A 2d3f_A 2d3h_A
3a19_A 1x1k_A 3ai6_A*
Length = 27
Score = 25.3 bits (55), Expect = 8.5
Identities = 15/27 (55%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 42 PPGPVAPPGAVPAPPGAMGLIPPNQPP 68
PPGP PPG P PPG G P PP
Sbjct: 1 PPGPPGPPG-PPGPPGPPGPPGPPGPP 26
>2ff4_A Probable regulatory protein EMBR; winged-helix, tetratricopeptide
repeat, beta-sandwich, trans; HET: DNA TPO; 1.90A
{Mycobacterium tuberculosis} SCOP: a.4.6.1 a.118.8.3
b.26.1.2 PDB: 2fez_A*
Length = 388
Score = 28.5 bits (64), Expect = 8.9
Identities = 3/28 (10%), Positives = 4/28 (14%)
Query: 31 AGAPPPGAPGAPPGPVAPPGAVPAPPGA 58
P A + A
Sbjct: 256 RQQPLDAKKSAKTTAAGTVTVLDQRTMA 283
>1jni_A NAPB;, diheme cytochrome C NAPB; dihaem cytochrome C, proteolytic
fragment, nitrate reductase subunit, oxidoreductase;
HET: HEM; 1.25A {Haemophilus influenzae} SCOP: a.138.1.3
Length = 123
Score = 27.3 bits (60), Expect = 9.9
Identities = 19/81 (23%), Positives = 20/81 (24%), Gaps = 13/81 (16%)
Query: 33 APPPGAPGAPPGPVAPPGAVPAPPGAMGLIP---PNQPPQ--------PVQPPELPMFNC 81
AP G PP A P L NQPP V NC
Sbjct: 2 APAVGKDLTQAAENIPP-AFHNAPRQGELPALNYVNQPPMVPHSVANYQVTKNVNQCLNC 60
Query: 82 PRRPNLGREGRPIVLRANHFQ 102
N G + HF
Sbjct: 61 HSPENSRLSGATRI-SPTHFM 80
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
0.321 0.136 0.418
Gapped
Lambda K H
0.267 0.0519 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 13,508,971
Number of extensions: 840598
Number of successful extensions: 3106
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2518
Number of HSP's successfully gapped: 309
Length of query: 865
Length of database: 6,701,793
Length adjustment: 102
Effective length of query: 763
Effective length of database: 3,853,851
Effective search space: 2940488313
Effective search space used: 2940488313
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (28.2 bits)