BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 002054
(974 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3CDI|A Chain A, Crystal Structure Of E. Coli Pnpase
Length = 723
Score = 513 bits (1320), Expect = e-145, Method: Compositional matrix adjust.
Identities = 286/705 (40%), Positives = 430/705 (60%), Gaps = 22/705 (3%)
Query: 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGDSVRDFLPLT 113
+L +F+ G +TLETG +AR A AV++ MD+T V TV K +DF PLT
Sbjct: 7 LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S
Sbjct: 67 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
+ + +PDI+A SAAL LS Q+++NPT DEL S L+LV A
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
T LM++ +A+ +SE + + H + ++ L ++AGK + +++ ++E
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
+V+ LAEA + + TD K ER +D I + L +E DE L +
Sbjct: 247 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 302
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
A++ A R+DGR+ D +R + +G LP HGS+LF+RG+TQ L T
Sbjct: 303 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 359
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
TLG +AQ L+ L+G T F+ HY+FPP+ + E G RRE+GHG LA++ +LA
Sbjct: 360 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 419
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
V+P + FPYTVRV SE+ S+GS+SMA+VCG S+ALMDAG+P++ VAG+++GLV E D
Sbjct: 420 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
+Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK GI +I+ L A
Sbjct: 480 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 532
Query: 589 HKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGR 648
RL IL ME+ I+APR +PR+ T+K + D ++ +IG G++ R + EETG
Sbjct: 533 KGARLHILGVMEQAINAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGTT 592
Query: 649 ISV-SDGTLTVVAKNRSVMEKVLEKVDFIIGREIEVGGIYKGVVTSVKEYGAFVEFNGGQ 707
I + DGT+ + A + + + +++ I EIEVG +Y G VT + ++GAFV GG+
Sbjct: 593 IEIEDDGTVKIAATDGEKAKHAIRRIEEITA-EIEVGRVYTGKVTRIVDFGAFVAIGGGK 651
Query: 708 QGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLK 752
+GL+H+S+++ + V +V+D + +GQ++ ++ + D +G I+LS+K
Sbjct: 652 EGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEVDRQGRIRLSIK 696
>pdb|4AID|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
pdb|4AID|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 493 bits (1270), Expect = e-139, Method: Compositional matrix adjust.
Identities = 287/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60 KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
++ E G + + LETG+IAR A+GAV+ M ET VL+T +K +DF PLTV+YQE
Sbjct: 20 RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 79
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
K FA G IP + +REG P E+E LV R+IDRPIRPLF GF +EVQV+ +VL D + D
Sbjct: 80 KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 139
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
PDI+ A SAAL LS +++NPT+DE+ S ++LV A T +
Sbjct: 140 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 199
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
+M++ + +E+SE+ + G+ AH + ++ I LAE A K+ ++ ++ K
Sbjct: 200 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 258
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
+ +L A I A + K +R EA+ + AL DE P D
Sbjct: 259 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 310
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
A+ G+R+DGR + VRPI E G LP HGS+LF+RG+TQ +
Sbjct: 311 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 370
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
TLG + Q +++L G + F+LHY+FPP+ + E G+ RRE+GHG LA +AL +
Sbjct: 371 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 430
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
LP + DFPYT+R+ SE+ S+GS+SMATVCG S+A+MDAG+PL V+G+++GL+ E D
Sbjct: 431 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 489
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
+ +L+DILG EDHLGDMDFK+AGT G+T++Q+DIK AGI I+ + L A
Sbjct: 490 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 543
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
+GR IL M + + APR +P++ T+ D +R +IG G + R+I TG ++
Sbjct: 544 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 603
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
++ DG + V A + + K+ +D+I I E EVG IY G V V ++GAFV F G
Sbjct: 604 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGA 660
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
+ GL+HVS++S+E V++ SDV+ GQ + ++ +G D RG KLS+K V
Sbjct: 661 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 708
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 493 bits (1269), Expect = e-139, Method: Compositional matrix adjust.
Identities = 286/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60 KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
++ E G + + LETG+IAR A+GAV+ M ET VL+T +K +DF PLTV+YQE
Sbjct: 20 RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 79
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
K FA G IP + +REG P E+E LV R+IDRPIRPLF GF +EVQV+ +VL D + D
Sbjct: 80 KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 139
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
PDI+ A SAAL LS +++NPT+DE+ S ++LV A T +
Sbjct: 140 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 199
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
+M++ + +E+SE+ + G+ AH + ++ I LAE A K+ ++ ++ K
Sbjct: 200 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 258
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
+ +L A I A + K +R EA+ + AL DE P D
Sbjct: 259 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 310
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
A+ G+R+DGR + VRPI E G LP HGS+LF+RG+TQ +
Sbjct: 311 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 370
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
TLG + Q +++L G + F+LHY+FPP+ + E G+ RRE+GHG LA +AL +
Sbjct: 371 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 430
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
LP + DFPYT+R+ SE+ S+GS+SMATVCG S+A+MDAG+PL V+G+++GL+ E D
Sbjct: 431 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 489
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
+ +L+DILG EDHLGDMDFK+AGT G+T++Q+DIK AGI I+ + L A
Sbjct: 490 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 543
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
+GR IL M + + APR +P++ T+ D +R +IG G + R+I TG ++
Sbjct: 544 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 603
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
++ DG + V A + + K+ +D+I I E E+G IY G V V ++GAFV F G
Sbjct: 604 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEIGKIYDGKVVKVVDFGAFVNFFGA 660
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
+ GL+HVS++S+E V++ SDV+ GQ + ++ +G D RG KLS+K V
Sbjct: 661 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 708
>pdb|4AM3|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|B Chain B, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
pdb|4AM3|C Chain C, Crystal Structure Of C. Crescentus Pnpase Bound To Rna
Length = 717
Score = 493 bits (1269), Expect = e-139, Method: Compositional matrix adjust.
Identities = 287/708 (40%), Positives = 419/708 (59%), Gaps = 32/708 (4%)
Query: 60 KEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSV-RDFLPLTVDYQE 118
++ E G + + LETG+IAR A+GAV+ M ET VL+T +K +DF PLTV+YQE
Sbjct: 11 RKTIEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQE 70
Query: 119 KQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQD 178
K FA G IP + +REG P E+E LV R+IDRPIRPLF GF +EVQV+ +VL D + D
Sbjct: 71 KTFAAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLEND 130
Query: 179 PDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYACTREK 238
PDI+ A SAAL LS +++NPT+DE+ S ++LV A T +
Sbjct: 131 PDILGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADA 190
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISEQTLEK 298
+M++ + +E+SE+ + G+ AH + ++ I LAE A K+ ++ ++ K
Sbjct: 191 VMMVESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPED-TDAIKAK 249
Query: 299 VSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXX 358
+ +L A I A + K +R EA+ + AL DE P D
Sbjct: 250 MKDLVGADIAAAYK--IQKKQDRYEAVGAAKKKAIAALGL-SDEN-----PTGYDPLKLG 301
Query: 359 XXXXXXXAE---------GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV 409
A+ G+R+DGR + VRPI E G LP HGS+LF+RG+TQ +
Sbjct: 302 AIFKELEADVVRRGILDTGLRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVA 361
Query: 410 TLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAV 469
TLG + Q +++L G + F+LHY+FPP+ + E G+ RRE+GHG LA +AL +
Sbjct: 362 TLGTGDDEQFIDALEGTYKESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPM 421
Query: 470 LPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDP 529
LP + DFPYT+R+ SE+ S+GS+SMATVCG S+A+MDAG+PL V+G+++GL+ E D
Sbjct: 422 LPTKEDFPYTIRLVSEITESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQD- 480
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAH 589
+ +L+DILG EDHLGDMDFK+AGT G+T++Q+DIK AGI I+ + L A
Sbjct: 481 ------GFAVLSDILGDEDHLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAK 534
Query: 590 KGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRI 649
+GR IL M + + APR +P++ T+ D +R +IG G + R+I TG ++
Sbjct: 535 EGRAHILGEMNKAMDAPRADVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAKV 594
Query: 650 SVS-DGTLTVVAKNRSVMEKVLEKVDFI--IGREIEVGGIYKGVVTSVKEYGAFVEFNGG 706
++ DG + V A + + K+ +D+I I E EVG IY G V V ++GAFV F G
Sbjct: 595 DINDDGVVKVSASDGA---KIKAAIDWIKSITDEAEVGKIYDGKVVKVVDFGAFVNFFGA 651
Query: 707 QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVRGNIKLSLKAV 754
+ GL+HVS++S+E V++ SDV+ GQ + ++ +G D RG KLS+K V
Sbjct: 652 KDGLVHVSQISNERVAKPSDVLKEGQMVKVKLLGFDDRGKTKLSMKVV 699
>pdb|3U1K|A Chain A, Crystal Structure Of Human Pnpase
pdb|3U1K|C Chain C, Crystal Structure Of Human Pnpase
pdb|3U1K|B Chain B, Crystal Structure Of Human Pnpase
pdb|3U1K|D Chain D, Crystal Structure Of Human Pnpase
Length = 630
Score = 466 bits (1200), Expect = e-131, Method: Compositional matrix adjust.
Identities = 256/620 (41%), Positives = 370/620 (59%), Gaps = 12/620 (1%)
Query: 64 EIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQ 123
++G+R + + +GK+ARFA+G+ V+ +T V+ T S S F+PL VDY++K A
Sbjct: 11 DLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPSPSQFMPLVVDYRQKAAAA 70
Query: 124 GVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIMA 183
G IP Y+RRE ++E+L RIIDR IRPLFPAG++++ QV+ ++L+ DG +PD++A
Sbjct: 71 GRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNEPDVLA 130
Query: 184 ANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA-CTREKTLMI 242
N S AL LSD +++VNPT E+S S LNLV A + + +M+
Sbjct: 131 INGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKSQIVML 190
Query: 243 DVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE-YKLSMISEQTLEKVSN 301
+ A I ++D +++ + ++ +L ++ G K+ KL S + ++
Sbjct: 191 EASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFTPSPEIVKYTHK 250
Query: 302 LAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKALEEECDEESLQVLPKAVDTXXXXXXX 361
LA + AVFTD + K R EA++KI D ++ L+E+ E + ++ +
Sbjct: 251 LAMERLYAVFTDYEHDKVSRDEAVNKIRLDTEEQLKEKFPEADPYEIIESFNVVAKEVFR 310
Query: 362 XXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEA---- 417
E R DGR L +R + CE LHGS+LF RG TQVLCTVT +
Sbjct: 311 SIVLNEYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTFDSLESGIKSD 370
Query: 418 QRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFP 477
Q + ++ G K FMLHY FPP+ NE+GK GLNRRE+GHG LAEKAL V+P DFP
Sbjct: 371 QVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP--RDFP 428
Query: 478 YTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDY 537
+T+RV SEV+ S+GS+SMA+ CGGS+ALMD+G+P+ VAGV++GLV++ DP GEI+DY
Sbjct: 429 FTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGEIEDY 488
Query: 538 RILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILD 597
R+LTDILG+ED+ GDMDFKIAGT G+TA+Q DIK GIP+ I+ E ++ A + +IL
Sbjct: 489 RLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKKEILQ 548
Query: 598 HMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKIEEETGGRIS-VSDGTL 656
M + IS PR N P + T++ + +GP G +K++ ETG IS V + T
Sbjct: 549 IMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGVTISQVDEETF 608
Query: 657 TVVAKNRSVMEKVLEKVDFI 676
+V A S M E DFI
Sbjct: 609 SVFAPTPSAMH---EARDFI 625
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 422 bits (1086), Expect = e-118, Method: Compositional matrix adjust.
Identities = 237/559 (42%), Positives = 338/559 (60%), Gaps = 20/559 (3%)
Query: 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVT-SSKGDSVRDFLPLT 113
+L +F+ G +TLETG +AR A AV++ MD+T V TV K +DF PLT
Sbjct: 7 LLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 66
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S
Sbjct: 67 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 126
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
+ + +PDI+A SAAL LS Q+++NPT DEL S L+LV A
Sbjct: 127 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 186
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
T LM++ +A+ +SE + + H + ++ L ++AGK + +++ ++E
Sbjct: 187 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 246
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
+V+ LAEA + + TD K ER +D I + L +E DE L +
Sbjct: 247 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 302
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
A++ A R+DGR+ D +R + +G LP HGS+LF+RG+TQ L T
Sbjct: 303 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 359
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
TLG +AQ L+ L+G T F+ HY+FPP+ + E G RRE+GHG LA++ +LA
Sbjct: 360 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 419
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
V+P + FPYTVRV SE+ S+GS+SMA+VCG S+ALMDAG+P++ VAG+++GLV E D
Sbjct: 420 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 479
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
+Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK GI +I+ L A
Sbjct: 480 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 532
Query: 589 HKGRLQILDHMEREISAPR 607
RL IL ME+ I+APR
Sbjct: 533 KGARLHILGVMEQAINAPR 551
>pdb|3H1C|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|B Chain B, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|C Chain C, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|G Chain G, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|I Chain I, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|K Chain K, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|M Chain M, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|O Chain O, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|R Chain R, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|T Chain T, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|V Chain V, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
pdb|3H1C|X Chain X, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core Bound To Rnase E And Tungstate
Length = 549
Score = 422 bits (1086), Expect = e-118, Method: Compositional matrix adjust.
Identities = 237/559 (42%), Positives = 338/559 (60%), Gaps = 20/559 (3%)
Query: 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
+L +F+ G +TLETG +AR A AV++ MD+T V TV K +DF PLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
+ + +PDI+A SAAL LS Q+++NPT DEL S L+LV A
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
T LM++ +A+ +SE + + H + ++ L ++AGK + +++ ++E
Sbjct: 181 GTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
+V+ LAEA + + TD K ER +D I + L +E DE L +
Sbjct: 241 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 296
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
A++ A R+DGR+ D +R + +G LP HGS+LF+RG+TQ L T
Sbjct: 297 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 353
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
TLG +AQ L+ L+G T F+ HY+FPP+ + E G RRE+GHG LA++ +LA
Sbjct: 354 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 413
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
V+P + FPYTVRV SE+ S+GS+SMA+VCG S+ALMDAG+P++ VAG+++GLV E D
Sbjct: 414 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 473
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
+Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK GI +I+ L A
Sbjct: 474 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 526
Query: 589 HKGRLQILDHMEREISAPR 607
RL IL ME+ I+APR
Sbjct: 527 KGARLHILGVMEQAINAPR 545
>pdb|3GCM|A Chain A, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|B Chain B, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GCM|C Chain C, Crystal Structure Of E. Coli Polynucleotide Phosphorylase
Bound To Rna And Rnase E
pdb|3GLL|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase (Pnpase)
Core
pdb|3GME|A Chain A, Crystal Structure Of Polynucleotide Phosphorylase In
Complex With Rnase E And Manganese
Length = 549
Score = 422 bits (1084), Expect = e-118, Method: Compositional matrix adjust.
Identities = 237/559 (42%), Positives = 337/559 (60%), Gaps = 20/559 (3%)
Query: 55 VLETFKEEFEIGSRLITLETGKIARFANGAVVLGMDETKVLSTVTSSK-GDSVRDFLPLT 113
+L +F+ G +TLETG +AR A AV++ MD+T V TV K +DF PLT
Sbjct: 1 MLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLT 60
Query: 114 VDYQEKQFAQGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSS 173
V+YQE+ +A G IP ++ RREG P E E L+ R+IDRPIRPLFP GF +EVQV+A+V+S
Sbjct: 61 VNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSV 120
Query: 174 DGKQDPDIMAANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYA 233
+ + +PDI+A SAAL LS Q+++NPT DEL S L+LV A
Sbjct: 121 NPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVA 180
Query: 234 CTREKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKEYKLSMISE 293
T LM++ +A +SE + + H + ++ L ++AGK + +++ ++E
Sbjct: 181 GTEAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRWDWQPEPVNE 240
Query: 294 QTLEKVSNLAEAHIEAVF--TDPSYSKFERGEALDKIGQDVKKAL---EEECDEESLQVL 348
+V+ LAEA + + TD K ER +D I + L +E DE L +
Sbjct: 241 ALNARVAALAEARLSDAYRITD----KQERYAQVDVIKSETIATLLAEDETLDENELGEI 296
Query: 349 PKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT 408
A++ A R+DGR+ D +R + +G LP HGS+LF+RG+TQ L T
Sbjct: 297 LHAIE---KNVVRSRVLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVT 353
Query: 409 VTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLA 468
TLG +AQ L+ L+G T F+ HY+FPP+ + E G RRE+GHG LA++ +LA
Sbjct: 354 ATLGTARDAQVLDELMGERTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLA 413
Query: 469 VLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVD 528
V+P + FPYTVRV SE+ S+GS+SMA+VCG S+ALMDAG+P++ VAG+++GLV E D
Sbjct: 414 VMPDMDKFPYTVRVVSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGD 473
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDIICECLEHA 588
+Y +L+DILG EDHLGDMDFK+AG+R G++A+Q+DIK GI +I+ L A
Sbjct: 474 -------NYVVLSDILGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQA 526
Query: 589 HKGRLQILDHMEREISAPR 607
RL IL ME+ I+APR
Sbjct: 527 KGARLHILGVMEQAINAPR 545
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 367 bits (941), Expect = e-101, Method: Compositional matrix adjust.
Identities = 254/714 (35%), Positives = 382/714 (53%), Gaps = 39/714 (5%)
Query: 65 IGSRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKGDSVR-DFLPLTVDYQEKQFA 122
G+R I ETG++AR A G+ V +D+ T VLS T+SK + DF PLTVD +E+ +A
Sbjct: 34 FGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYA 93
Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
G IP ++ RREG P E +L R+IDRP+RP F G +E+QV+A++++ + D++
Sbjct: 94 AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVV 153
Query: 183 AANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELSLSDLNLVYAC-------- 234
A NA SA+ L+ Q++ PT EL + ++V A
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDV 213
Query: 235 --------TREKTL-MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
EKT+ ++ A +E+ + AGL A P + Q LA KA K E
Sbjct: 214 AIMMVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGE 273
Query: 286 YKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL--EEECDE 342
+ + + + LE +S + A T K +R LD++ + L E E E
Sbjct: 274 FPVFLDYQDDVLEALSAAVRPELSAALT--IAGKQDREAELDRVKALAAEKLLPEFEGRE 331
Query: 343 ESLQVLPKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD 402
+ + +A+ AE R+DGR + ++R + E +P +HGS+LF RG+
Sbjct: 332 KEISAAYRAL---TKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGE 388
Query: 403 TQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLA 462
TQ+L TL Q+L++L KR+M +Y+FPP+ + E G+ RRE+GHG LA
Sbjct: 389 TQILGVTTLNMLRMEQQLDTLSPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALA 448
Query: 463 EKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522
E+A++ VLP +FPY +R SE + S+GSTSM +VC +M+L++AG+PL+ VAG+++G
Sbjct: 449 ERAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMG 508
Query: 523 LVS-EVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDII 581
L+S E++ T Y LTDILG ED GDMDFK+AGT+ VTA+QLD K GIP ++
Sbjct: 509 LISQEINGET----HYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKI 641
L+ A RL ILD M I P + N+PR+ T+K D + +IGP + +I
Sbjct: 565 AAALKQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQI 623
Query: 642 EEETGGRISV-SDGTLTVVAKNRSVMEKVLEKVDFIIG-REIEVGGIYKGVVTSVKEYGA 699
+E+TG I++ DGT+ + A + E ++ I EVG G V +GA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 700 FVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749
FV G+ GLLH+S++ + V V DV+ VGQ++ + D RG + L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 340 bits (871), Expect = 3e-93, Method: Compositional matrix adjust.
Identities = 251/714 (35%), Positives = 374/714 (52%), Gaps = 39/714 (5%)
Query: 65 IGSRLITLETGKIARFANGAVVLGMDE-TKVLSTVTSSKGDSVR-DFLPLTVDYQEKQFA 122
G+R I ETG++AR A G+ V +D+ T VLS T+SK + DF PLTVD +E+ +A
Sbjct: 34 FGTRTIRFETGRLARQAAGSAVAYLDDDTXVLSATTASKNPKDQLDFFPLTVDVEERXYA 93
Query: 123 QGVIPNTYMRREGAPKERELLVGRIIDRPIRPLFPAGFYHEVQVMASVLSSDGKQDPDIM 182
G IP ++ RREG P E +L R+IDRP+RP F G +E+QV+A++ + + D++
Sbjct: 94 AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIXALNPDHLYDVV 153
Query: 183 AANATSAALMLSDXXXXXXXXXXXXXXXXXQFIVNPTMDELS------------LSD--- 227
A NA SA+ L+ Q++ PT EL L D
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDXVVAGRVLEDGDV 213
Query: 228 -LNLVYACTREKTL-MIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE 285
+ V A EKT+ ++ A +E+ + AGL A P + Q LA KA K E
Sbjct: 214 AIXXVEAEATEKTIQLVKDGAEAPTEEVVAAGLDAAKPFIKVLCKAQADLAAKAAKPTGE 273
Query: 286 YKLSM-ISEQTLEKVSNLAEAHIEAVFTDPSYSKFERGEALDKIGQDVKKAL--EEECDE 342
+ + + + LE +S + A T K +R LD++ + L E E E
Sbjct: 274 FPVFLDYQDDVLEALSAAVRPELSAALT--IAGKQDREAELDRVKALAAEKLLPEFEGRE 331
Query: 343 ESLQVLPKAVDTXXXXXXXXXXXAEGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGD 402
+ + +A+ AE R+DGR + ++R + E +P +HGS+LF RG+
Sbjct: 332 KEISAAYRAL---TKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGE 388
Query: 403 TQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLA 462
TQ+L TL Q+L++L KR+ +Y+FPP+ + E G+ RRE+GHG LA
Sbjct: 389 TQILGVTTLNXLRXEQQLDTLSPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGHGALA 448
Query: 463 EKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVG 522
E+A++ VLP +FPY +R SE + S+GSTS +VC + +L++AG+PL+ VAG++ G
Sbjct: 449 ERAIVPVLPTREEFPYAIRQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAGIAXG 508
Query: 523 LVS-EVDPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIGVTAIQLDIKPAGIPLDII 581
L+S E++ T Y LTDILG ED GD DFK+AGT+ VTA+QLD K GIP ++
Sbjct: 509 LISQEINGET----HYVALTDILGAEDAFGDXDFKVAGTKEFVTALQLDTKLDGIPASVL 564
Query: 582 CECLEHAHKGRLQILDHMEREISAPRTQDDRNSPRLATLKYDNDTLRRLIGPLGALKRKI 641
L+ A RL ILD I P + N+PR+ T+K D + +IGP +I
Sbjct: 565 AAALKQARDARLHILDVXXEAIDTP-DEXSPNAPRIITVKIPVDKIGEVIGPKRQXINQI 623
Query: 642 EEETGGRISV-SDGTLTVVAKNRSVMEKVLEKVDFIIG-REIEVGGIYKGVVTSVKEYGA 699
+E+TG I++ DGT+ + A + E ++ I EVG G V +GA
Sbjct: 624 QEDTGAEITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTTFGA 683
Query: 700 FVEFNGGQQGLLHVSELSH----EPVSRVSDVVSVGQQLSLRCIGQDVRGNIKL 749
FV G+ GLLH+S++ + V V DV+ VGQ++ + D RG + L
Sbjct: 684 FVSLLPGKDGLLHISQIRKLAGGKRVENVEDVLGVGQKVQVEIAEIDSRGKLSL 737
>pdb|3M7N|D Chain D, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|E Chain E, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|F Chain F, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M85|D Chain D, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|E Chain E, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|F Chain F, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
Length = 258
Score = 88.2 bits (217), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 72/242 (29%), Positives = 119/242 (49%), Gaps = 26/242 (10%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G+R+DGR+ DE+RPI E+ L GS G +V+ V P E E L P
Sbjct: 14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-EHLQDP 70
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
Y+ PF + E KR G +RR + ++++A AV+ E FP + + + E
Sbjct: 71 SKAIIRYRYNMAPFSVEE-RKRPGPDRRSIEISKVSKEAFEAVIMKEL-FPRSAIDIFVE 128
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
V+ +D + A + S+AL+DAG+P++ + V+VG D +++ D +
Sbjct: 129 VLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-----------DGQLVLDPMK 177
Query: 546 LEDHLGDMDFKIA-----GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
ED+ G+ D A G + +Q+D + + D + + +E A KG LQI + M+
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE-MQ 233
Query: 601 RE 602
RE
Sbjct: 234 RE 235
>pdb|2BA0|F Chain F, Archaeal Exosome Core
pdb|2BA0|E Chain E, Archaeal Exosome Core
pdb|2BA0|D Chain D, Archaeal Exosome Core
pdb|2BA1|D Chain D, Archaeal Exosome Core
pdb|2BA1|E Chain E, Archaeal Exosome Core
pdb|2BA1|F Chain F, Archaeal Exosome Core
Length = 258
Score = 86.3 bits (212), Expect = 8e-17, Method: Compositional matrix adjust.
Identities = 71/242 (29%), Positives = 118/242 (48%), Gaps = 26/242 (10%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G+R+DGR+ DE+RPI E+ L GS G +V+ V P E L P
Sbjct: 14 DGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAVF--GPREVHP-RHLQDP 70
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
Y+ PF + E KR G +RR + ++++A AV+ E FP + + + E
Sbjct: 71 SKAIIRYRYNMAPFSVEE-RKRPGPDRRSIEISKVSKEAFEAVIMKEL-FPRSAIDIFVE 128
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
V+ +D + A + S+AL+DAG+P++ + V+VG D +++ D +
Sbjct: 129 VLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVGKA-----------DGQLVLDPMK 177
Query: 546 LEDHLGDMDFKIA-----GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHME 600
ED+ G+ D A G + +Q+D + + D + + +E A KG LQI + M+
Sbjct: 178 EEDNFGEADMPFAFLIRNGKIESIALLQMDGR---MTRDEVKQAIELAKKGALQIYE-MQ 233
Query: 601 RE 602
RE
Sbjct: 234 RE 235
>pdb|2WNR|B Chain B, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|D Chain D, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|F Chain F, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
Length = 240
Score = 80.1 bits (196), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 64/191 (33%), Positives = 92/191 (48%), Gaps = 17/191 (8%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
VR DGR DE+RP+ E+G L GSS G ++L V + P EAQ + L P
Sbjct: 16 VREDGRAFDELRPLKIEAGILERADGSSYLEFGGNKIL--VAVYGPREAQ-IRKLQRPDR 72
Query: 429 KRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV-RVNSEVM 487
Y+ PF + E KR G +RR V + +AL L E FP +V V EV+
Sbjct: 73 AVIRCRYNMAPFSVEE-RKRPGPDRRSVEISKITAEALRPALILEK-FPRSVIDVFIEVL 130
Query: 488 ASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGLE 547
++G T A + S+AL DAGIP+++ V + G V + +++ D+ E
Sbjct: 131 EAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGD-----------QVVLDLSEEE 179
Query: 548 DHLGDMDFKIA 558
D G D +A
Sbjct: 180 DKEGQADVPVA 190
>pdb|2BR2|B Chain B, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|D Chain D, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|F Chain F, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|H Chain H, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|J Chain J, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|L Chain L, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|N Chain N, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|P Chain P, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|R Chain R, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|T Chain T, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|V Chain V, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|X Chain X, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|B Chain B, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|D Chain D, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|F Chain F, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|H Chain H, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|J Chain J, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|L Chain L, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|N Chain N, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|P Chain P, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|R Chain R, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|T Chain T, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|V Chain V, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|X Chain X, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
Length = 248
Score = 79.7 bits (195), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G R DGR+ DE+R I E G L GS++F G+T+ + V P E L P
Sbjct: 16 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 72
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
+ Y PF +E K +RRE+ + +AL + + E FP T + V +E
Sbjct: 73 DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 130
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
++ +D + + ++ S+AL DAGIP+++ +AGV+VG V I+ D+
Sbjct: 131 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 179
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
ED G+ D IA + VT QL+ + D + + A KG + I+ ++ERE
Sbjct: 180 TEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 234
>pdb|3L7Z|B Chain B, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|E Chain E, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|H Chain H, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 245
Score = 79.7 bits (195), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G R DGR+ DE+R I E G L GS++F G+T+ + V P E L P
Sbjct: 13 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 69
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
+ Y PF +E K +RRE+ + +AL + + E FP T + V +E
Sbjct: 70 DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 127
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
++ +D + + ++ S+AL DAGIP+++ +AGV+VG V I+ D+
Sbjct: 128 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 176
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
ED G+ D IA + VT QL+ + D + + A KG + I+ ++ERE
Sbjct: 177 TEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 231
>pdb|2JE6|B Chain B, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|B Chain B, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|B Chain B, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 250
Score = 76.3 bits (186), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 72/239 (30%), Positives = 115/239 (48%), Gaps = 23/239 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G R DGR+ DE+R I E G L GS++F G+T+ + V P E L P
Sbjct: 18 DGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAVY--GPKEMHP-RHLSLP 74
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSE 485
+ Y PF +E K +RRE+ + +AL + + E FP T + V +E
Sbjct: 75 DRAVLRVRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAIDVFTE 132
Query: 486 VMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILG 545
++ +D + + ++ S+AL DAGIP+++ +AGV+VG V I+ D+
Sbjct: 133 ILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVGKADGV-----------IILDLNE 181
Query: 546 LEDHLGDMDFKIA--GTRIGVTAIQLDIKPAGIPLDIICECLEHAHKGRLQILDHMERE 602
E G+ D IA + VT QL+ + D + + A KG + I+ ++ERE
Sbjct: 182 TEAMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG-INIIYNLERE 236
>pdb|2PNZ|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Udp And Gmp
pdb|2PO0|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Adp In Double Conformation
pdb|2PO1|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With A Single Stranded 10-Mer Poly(A) Rna
pdb|2PO2|A Chain A, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Cdp
Length = 249
Score = 75.9 bits (185), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 64/206 (31%), Positives = 101/206 (49%), Gaps = 19/206 (9%)
Query: 368 GVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPP 427
G R+DGR+ E+RPI E G L +GS+ G +++ V P E + L P
Sbjct: 15 GRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVY--GPRELHP-KHLQRPD 71
Query: 428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYT-VRVNSEV 486
+ Y+ PF + E K+ G +RR + + + AL L E FP T + V EV
Sbjct: 72 RAILRVRYNMAPFSVEE-RKKPGPDRRSIEISKVIKGALEPALILEM-FPRTAIDVFIEV 129
Query: 487 MASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSEVDPSTGEIKDYRILTDILGL 546
+ +D T +A + S+AL DAGIP+++ VA + G + GE I+ D+
Sbjct: 130 LQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIE------GE-----IVLDLNKE 178
Query: 547 EDHLGDMDFKIA--GTRIGVTAIQLD 570
ED+ G+ D +A + +T +Q+D
Sbjct: 179 EDNYGEADVPVAIMPLKNDITLLQMD 204
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 54/73 (73%)
Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
EIEVG +Y G VT + ++GAFV GG++GL+H+S+++ + V +V+D + +GQ++ ++ +
Sbjct: 2 EIEVGRVYTGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVL 61
Query: 740 GQDVRGNIKLSLK 752
D +G I+LS+K
Sbjct: 62 EVDRQGRIRLSIK 74
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 57/211 (27%), Positives = 92/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
+R DGR+ D++RP+ + L GS L S G T+V+CT ++ P L G
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
YS P + V R+G E+ + +A+ + T+
Sbjct: 55 GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
V+ +V+ +DG T+ A + G +A+ DA I P+++ VA VSVG+V++
Sbjct: 113 WVDCDVIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
RIL D+ ED +D + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 64.7 bits (156), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/84 (36%), Positives = 53/84 (63%), Gaps = 1/84 (1%)
Query: 677 IGREIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSL 736
+ + EVG +Y G VT ++ YGAFV + QGL+H+SE++H V +++ +SVG ++ +
Sbjct: 1 MAAKFEVGSVYTGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQV 60
Query: 737 RCIGQD-VRGNIKLSLKAVSPRPE 759
+ + D +G I LS++A PE
Sbjct: 61 KVLAVDEEKGKISLSIRATQAAPE 84
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 63.9 bits (154), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 57/211 (27%), Positives = 91/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
+R DGR+ D++RP+ + L GS L S G T+V+CT ++ P L G
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
YS P + V R+G E+ + +A+ + T+
Sbjct: 55 GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
V+ +V+ +DG T A + G +A+ DA I P+++ VA VSVG+V++
Sbjct: 113 WVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
RIL D+ ED +D + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 63.5 bits (153), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 57/211 (27%), Positives = 91/211 (43%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
+R DGR+ D++RP+ + L GS L S G T+V+CT ++ P L G
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
YS P + V R+G E+ + +A+ + T+
Sbjct: 55 GQGWITAEYSMLPRATQQRTIRESVQGRIGGATHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
V+ +V+ +DG T A + G +A+ DA I P+++ VA VSVG+V++
Sbjct: 113 WVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
RIL D+ ED +D + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192
>pdb|2NN6|B Chain B, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 249
Score = 62.8 bits (151), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 48/162 (29%), Positives = 72/162 (44%), Gaps = 10/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
+G RVDGR+ E+R I G GS+ +G+T+ L V P E + + P
Sbjct: 14 QGYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVY--GPHEIRGSRARALP 71
Query: 427 PTKRFMLHYSFPPFCINEVGKRVGLNRREVGHG----TLAEKALLAVLPPENDFPYTVRV 482
YS F E +R +R+ G E A+L L P + V
Sbjct: 72 DRALVNCQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYV-- 129
Query: 483 NSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLV 524
+V+ +DG T A V ++A++DAGIP+++ V S G V
Sbjct: 130 --QVLQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV 169
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 56/211 (26%), Positives = 90/211 (42%), Gaps = 38/211 (18%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPAEAQRLESLVGP 426
+R DGR+ D++RP+ + L GS L S G T+V+CT ++ P L G
Sbjct: 1 MRSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASVIENVP------NWLKGK 54
Query: 427 PTKRFMLHYSFPPFCINE------VGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV 480
YS P + V R+G E+ + +A+ + T+
Sbjct: 55 GQGWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQR--MIGRAMRTAVELTKIGERTI 112
Query: 481 RVNSEVMASDGSTSMATVCGGSMALMDAGI-----------PLQEHVAGVSVGLVSEVDP 529
V+ +V+ +DG A + G +A+ DA I P+++ VA VSVG+V++
Sbjct: 113 WVDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVND--- 169
Query: 530 STGEIKDYRILTDILGLEDHLGDMDFKIAGT 560
RIL D+ ED +D + GT
Sbjct: 170 --------RILLDLNFEEDSAAQVDMNVVGT 192
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 60.8 bits (146), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 65/251 (25%), Positives = 109/251 (43%), Gaps = 42/251 (16%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
+RVDGR+ E+R I+ + L GS L GDT+V+C+ T+ +R+ PP
Sbjct: 11 MRVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI-----EERV-----PPF 60
Query: 429 KR------FMLHYSFPPFCINEVGKRVGLNRREVGHGT----LAEKALLAVLPPENDFPY 478
R Y+ P + R + G L +AL AV+ E
Sbjct: 61 MRGEGKGWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIGRALRAVVDLEALGER 120
Query: 479 TVRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEV 527
TV ++ +V+ +DG T A++ G +A++ A IP+++++A SVG+V E
Sbjct: 121 TVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIVEE- 179
Query: 528 DPSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG-VTAIQLDIKPAGIPLDIICECLE 586
++ D+ ED D+D + T G +Q + A + E L+
Sbjct: 180 ---------QGVVLDLNYAEDSKADVDMNVIMTGKGQFVEVQGTGEEATFSRAQLNELLD 230
Query: 587 HAHKGRLQILD 597
A +G Q++D
Sbjct: 231 AAEQGIFQLID 241
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 59.7 bits (143), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 58/209 (27%), Positives = 87/209 (41%), Gaps = 30/209 (14%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
R GR D++RPI GS L GDT+V+CTV+ AE+ L G
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS----AESGVPRFLKGQGQG 58
Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHG----TLAEKALLAVLPPENDFPYTVRVNSE 485
Y P E +R ++ G L ++L A L T+ ++ +
Sbjct: 59 WLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENTLYIDCD 118
Query: 486 VMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVDPSTGEI 534
V+ +DG T A++ G ++AL+DA G PL++ VA VSVG+ V
Sbjct: 119 VIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIYQGVP------ 172
Query: 535 KDYRILTDILGLEDHLGDMDFKIAGTRIG 563
+ D+ LED + D + T G
Sbjct: 173 -----VLDLDYLEDSAAETDLNVVXTDAG 196
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 61/215 (28%), Positives = 89/215 (41%), Gaps = 42/215 (19%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
R GR D++RPI GS L GDT+V+CTV+ AE+ L G
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS----AESGVPRFLKGQGQG 58
Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGT----------LAEKALLAVLPPENDFPYT 479
Y P G+R N+RE G L ++L A L T
Sbjct: 59 WLTAEYGMLP---RSTGER---NQREASRGKQGGRTLEIQRLIGRSLRAALDLSKLGENT 112
Query: 480 VRVNSEVMASDGSTSMATVCGGSMALMDA-----------GIPLQEHVAGVSVGLVSEVD 528
+ ++ +V+ +DG T A++ G ++AL+DA G PL++ VA VSVG+ V
Sbjct: 113 LYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIYQGVP 172
Query: 529 PSTGEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563
+ D+ LED + D + T G
Sbjct: 173 -----------VLDLDYLEDSAAETDLNVVMTDAG 196
>pdb|1OYP|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYP|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|B Chain B, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|C Chain C, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|D Chain D, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|E Chain E, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
pdb|1OYR|F Chain F, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 55.1 bits (131), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 50/173 (28%), Positives = 80/173 (46%), Gaps = 19/173 (10%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
+R DGRQ DE+RPI + + GS L + G+T+V+C A E + L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICN----ASVEDRVPPFLRGGGK 56
Query: 429 KRFMLHYSFPPFCINEVGKRVG----LNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
YS P N+ R ++ R + L +AL AV+ E T+ ++
Sbjct: 57 GWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 485 EVMASDGSTSMATVCGGSMA-------LMDAGI----PLQEHVAGVSVGLVSE 526
+V+ +DG T A++ G +A L+ AG P+ + +A +SVG+ E
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKE 169
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 49/173 (28%), Positives = 80/173 (46%), Gaps = 19/173 (10%)
Query: 369 VRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPT 428
+R DGRQ DE+RPI + + GS L + G+T+V+C A E + L G
Sbjct: 1 MRHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICN----ASVEDRVPPFLRGGGK 56
Query: 429 KRFMLHYSFPPFCINEV----GKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNS 484
YS P N+ + ++ R + L +AL AV+ E T+ ++
Sbjct: 57 GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 485 EVMASDGSTSMATVCGGSMA-------LMDAGI----PLQEHVAGVSVGLVSE 526
+V+ +DG T A++ G +A L+ AG P+ + +A +SVG+ E
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGIDKE 169
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 11/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVG 425
EG+R+DGR+ +E+R P GSS +G+ +++ V P E RL+S +
Sbjct: 12 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKEP-RLKSQMD 68
Query: 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE---NDFPYTV-R 481
+ + F E K N R V + +L+ + N +P TV
Sbjct: 69 TSKALLNVSVNITKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 125
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGL 523
+ V+ DG + + G ++AL+DAGI + ++++G+SVGL
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 167
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 45/162 (27%), Positives = 77/162 (47%), Gaps = 11/162 (6%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLP-ILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVG 425
EG+R+DGR+ +E+R P GSS +G+ +++ V P E RL+S +
Sbjct: 10 EGLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK--GPKEP-RLKSQMD 66
Query: 426 PPTKRFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPE---NDFPYTV-R 481
+ + F E K N R V + +L+ + N +P TV
Sbjct: 67 TSKALLNVSVNINKFSKFERSKSSHKNERRVLE---IQTSLVRMFEKNVMLNIYPRTVID 123
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGL 523
+ V+ DG + + G ++AL+DAGI + ++++G+SVGL
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGL 165
>pdb|2EQS|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Atp-Dependent Rna Helicase Dhx8
Length = 103
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 43/66 (65%), Gaps = 4/66 (6%)
Query: 678 GREIEVGGIYKGVVTSVKEYGAFVEFNG---GQQGLLHVSELSHEP-VSRVSDVVSVGQQ 733
G E +G IY G VTS+ ++G FV+ G +GL+H+SEL E V+ V+DVVS GQ+
Sbjct: 7 GEEPTIGDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQR 66
Query: 734 LSLRCI 739
+ ++ +
Sbjct: 67 VKVKVL 72
>pdb|3BZC|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form I
pdb|3BZK|A Chain A, Crystal Structure Of The Tex Protein From Pseudomonas
Aeruginosa, Crystal Form 2
Length = 785
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 46/147 (31%), Positives = 76/147 (51%), Gaps = 11/147 (7%)
Query: 627 LRRLIGPLGALKR----KIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIG---- 678
+R LIG LKR K +ET G +V+D L + K + +F G
Sbjct: 591 IRSLIGDSAFLKRLDPKKFTDETFGLPTVTD-ILKELDKPGRDPRPEFKTAEFQEGVESL 649
Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
++++ G + +GVVT+V +GAFV+ Q GL+H+S LS + V +VV G + ++
Sbjct: 650 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 709
Query: 739 IGQDV-RGNIKLSLKAVSPRPEADVKG 764
+ D+ R + LS++ +S P V+G
Sbjct: 710 MEVDIPRNRVGLSMR-MSDTPGEKVEG 735
>pdb|2OCE|A Chain A, Crystal Structure Of Tex Family Protein Pa5201 From
Pseudomonas Aeruginosa
Length = 780
Score = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 46/147 (31%), Positives = 76/147 (51%), Gaps = 11/147 (7%)
Query: 627 LRRLIGPLGALKR----KIEEETGGRISVSDGTLTVVAKNRSVMEKVLEKVDFIIG---- 678
+R LIG LKR K +ET G +V+D L + K + +F G
Sbjct: 592 IRSLIGDSAFLKRLDPKKFTDETFGLPTVTD-ILKELDKPGRDPRPEFKTAEFQEGVESL 650
Query: 679 REIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
++++ G + +GVVT+V +GAFV+ Q GL+H+S LS + V +VV G + ++
Sbjct: 651 KDLKPGMVLEGVVTNVTNFGAFVDIGVHQDGLVHISALSEKFVKDPYEVVKAGDIVKVKV 710
Query: 739 IGQDV-RGNIKLSLKAVSPRPEADVKG 764
+ D+ R + LS++ +S P V+G
Sbjct: 711 MEVDIPRNRVGLSMR-MSDTPGEKVEG 736
>pdb|3B4T|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|E Chain E, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
pdb|3B4T|F Chain F, Crystal Structure Of Mycobacterium Tuberculosis Rnase Ph,
The Mycobacterium Tuberculosis Structural Genomics
Consortium Target Rv1340
Length = 262
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 59/212 (27%), Positives = 82/212 (38%), Gaps = 35/212 (16%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCT--VTLGAPAEAQRLESLVGPP 427
R DGR E+RP+ G GS L G T+VLCT VT G P R G
Sbjct: 7 REDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTASVTEGVP----RWRKATG-- 60
Query: 428 TKRFMLHYSFPPFCINEVGKRVGLNRREVGH----GTLAEKALLAVLPPENDFPYTVRVN 483
Y+ P + R + R G L ++L A + T+ ++
Sbjct: 61 LGWLTAEYAMLPSATHSRSDRESVRGRLSGRTQEISRLIGRSLRACIDLAALGENTIAID 120
Query: 484 SEVMASDGSTSMATVCGGSMALMDAGI------------PLQEHVAGVSVGLVSEVDPST 531
+V+ +DG T A + G +AL DA PL +A VSVG+V
Sbjct: 121 CDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV------- 173
Query: 532 GEIKDYRILTDILGLEDHLGDMDFKIAGTRIG 563
D RI D+ ED ++D + T G
Sbjct: 174 ----DGRIRVDLPYEEDSRAEVDMNVVATDTG 201
>pdb|3HKM|A Chain A, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|B Chain B, Crystal Structure Of Rice(Oryza Sativa) Rrp46
pdb|3HKM|C Chain C, Crystal Structure Of Rice(Oryza Sativa) Rrp46
Length = 246
Score = 48.1 bits (113), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 71/165 (43%), Gaps = 23/165 (13%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
E R DGR +++RP C L HGS+ +++GDT VL V P + G
Sbjct: 2 EESRADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAVYGPKPGTRK------GE 55
Query: 427 PTKRFMLHYSFPPFCINEVGKR-----VGLNRREVGHGTLAEKALLAVLPPENDFPYTVR 481
++ + + P ++GK+ + L R TL LL V P T
Sbjct: 56 NPEKASIEVVWKPM-TGQIGKQEKEYEMTLKR------TLQSICLLTVHP-----NTTTS 103
Query: 482 VNSEVMASDGSTSMATVCGGSMALMDAGIPLQEHVAGVSVGLVSE 526
V +V+ +DGS + AL+ AGIPL+ + G++ +
Sbjct: 104 VILQVVGNDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLED 148
>pdb|2CQO|A Chain A, Solution Structure Of The S1 Rna Binding Domain Of Human
Hypothetical Protein Flj11067
Length = 119
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 49/74 (66%), Gaps = 4/74 (5%)
Query: 686 IYKGVVTSVKEYGAFVEFNGG-QQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCIGQDVR 744
I++G V V +YGAF++ G +QGL+H + +S V + S++V VG ++ ++ IG++++
Sbjct: 25 IFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMK 84
Query: 745 GN---IKLSLKAVS 755
+ + LS+K V+
Sbjct: 85 NDRIKVSLSMKVVN 98
>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 237
Score = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 17/164 (10%)
Query: 379 VRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFP 438
+R CE L GS+ F +GDT VL V PAE + + + T +L P
Sbjct: 30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVY--GPAEVKVSKEIFNKATLEVILR---P 84
Query: 439 PFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATV 498
+ V ++ +R + T E +L L P ++ V +V++ GS +
Sbjct: 85 KIGLPGVAEK---SRERLIRNT-CEAVVLGTLHPRT----SITVVLQVVSDAGSLLACCL 136
Query: 499 CGGSMALMDAGIPLQEHVAGVSVGLVSE----VDPSTGEIKDYR 538
MAL+DAG+P++ GV+ L S+ +DP++ + K+ R
Sbjct: 137 NAACMALVDAGVPMRALFCGVACALDSDGTLVLDPTSKQEKEAR 180
>pdb|1Q8K|A Chain A, Solution Structure Of Alpha Subunit Of Human Eif2
Length = 308
Score = 41.2 bits (95), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 46/79 (58%), Gaps = 5/79 (6%)
Query: 682 EVGGIYKGVVTSVKEYGAFV---EFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRC 738
EV + V S++E GA+V E+N + G++H+SELS + ++ ++ +G+ ++
Sbjct: 12 EVEDVVMVNVRSIQEMGAYVSLLEYNNIE-GMIHLSELSRRRIRSINKLIRIGRNECVKV 70
Query: 739 IGQDV-RGNIKLSLKAVSP 756
I D +G I LS + VSP
Sbjct: 71 IRVDKEKGYIDLSKRRVSP 89
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 682 EVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
E G V + YGAF+E + G++ +H+SE++ V + D + GQ++ + I
Sbjct: 9 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVI 68
Query: 740 GQDVR-GNIKLSLKAVS 755
D R G+I LSL+ V+
Sbjct: 69 RVDPRKGHIDLSLRRVT 85
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 42/77 (54%), Gaps = 3/77 (3%)
Query: 682 EVGGIYKGVVTSVKEYGAFVEFNG--GQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
E G V + YGAF+E + G++ +H+SE++ V + D + GQ++ + I
Sbjct: 10 EEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVI 69
Query: 740 GQDVR-GNIKLSLKAVS 755
D R G+I LSL+ V+
Sbjct: 70 RVDPRKGHIDLSLRRVT 86
>pdb|4IFD|D Chain D, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 245
Score = 38.9 bits (89), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 46/179 (25%), Positives = 80/179 (44%), Gaps = 27/179 (15%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTK 429
R+D + + + E G L + GSS F DT+V+C+VT P E + + L PT+
Sbjct: 13 RLDSAEKKKKMSVQAEIGILDHVDGSSEFVSQDTKVICSVT--GPIEPKARQEL---PTQ 67
Query: 430 RFMLHYSFPPFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTV-RVNSEVMA 488
L P K V R +V L +A+L L + +P + ++ +++
Sbjct: 68 -LALEIIVRP------AKGVATTREKVLEDKL--RAVLTPLITRHCYPRQLCQITCQILE 118
Query: 489 S-----DGSTSMATVC--GGSMALMDAGIPLQEHVAGVSVGLVSE-----VDPSTGEIK 535
S + S + C +AL+DAGI L A + + ++ + VDP+ ++K
Sbjct: 119 SGEDEAEFSLRELSCCINAAFLALVDAGIALNSMCASIPIAIIKDTSDIIVDPTAEQLK 177
>pdb|2K52|A Chain A, Structure Of Uncharacterized Protein Mj1198 From
Methanocaldococcus Jannaschii. Northeast Structural
Genomics Target Mjr117b
Length = 80
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 6/65 (9%)
Query: 680 EIEVGGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELSHEPVSRVSDVVSVGQQLSLRCI 739
++E G YKGVVT +++YGAF+ N +GLL ++ +S + ++VG ++ ++ I
Sbjct: 2 DVEPGKFYKGVVTRIEKYGAFINLNEQVRGLLRPRDM----ISLRLENLNVGDEIIVQAI 57
Query: 740 GQDVR 744
DVR
Sbjct: 58 --DVR 60
>pdb|2PNZ|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Udp And Gmp
pdb|2PO0|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Adp In Double Conformation
pdb|2PO1|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With A Single Stranded 10-Mer Poly(A) Rna
pdb|2PO2|B Chain B, Crystal Structure Of The P. Abyssi Exosome Rnase Ph Ring
Complexed With Cdp
Length = 277
Score = 38.1 bits (87), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV--TLGAP 414
EG R+D R ++ RPI E G + GS+L G TQVL + +LG P
Sbjct: 24 EGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEP 73
Score = 30.4 bits (67), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 50/118 (42%), Gaps = 14/118 (11%)
Query: 68 RLITLETGKIARFANGAVVLGMDETKVLSTVTSSKGDSVRDFLPLTVDYQEKQFAQGVIP 127
R I +E G I + A G+ ++ + T+VL + +S G+ D + V + P
Sbjct: 37 RPIEIEVGVIEK-AEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASP 95
Query: 128 NTYMRREGAPKERELLVGRIIDRPIRP----------LFPAGFYHEVQVMASVLSSDG 175
T+ G P ER + + R+IDR IR + P V + VL DG
Sbjct: 96 -TF--EPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDG 150
>pdb|2NN6|C Chain C, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 278
Score = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 35/76 (46%), Gaps = 7/76 (9%)
Query: 367 EGVRVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGP 426
E R DGR+L E R G++ GS+L G+T V+C V +A+
Sbjct: 22 ENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGV------KAEFAAPSTDA 75
Query: 427 PTKRFML-HYSFPPFC 441
P K +++ + PP C
Sbjct: 76 PDKGYVVPNVDLPPLC 91
>pdb|3KRN|A Chain A, Crystal Structure Of C. Elegans Cell-Death-Related
Nuclease 5(Crn-5)
pdb|3KRN|B Chain B, Crystal Structure Of C. Elegans Cell-Death-Related
Nuclease 5(Crn-5)
Length = 222
Score = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 38/155 (24%), Positives = 62/155 (40%), Gaps = 18/155 (11%)
Query: 379 VRPIYCESGNLPILHGSSLFSRGDTQVLCTVTLGAPAEAQRLESLVGPPTKRFMLHYSFP 438
+R + CE L GS+ FS+G T + + + A + + L S+
Sbjct: 5 LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASK------ASDEAMTLDISYR 58
Query: 439 PFCINEVGKRVGLNRREVGHGTLAEKALLAVLPPENDFPYTVRVNSEVMASDGSTSMATV 498
C + K LN + H TL+ L + P T+ V + DGS +
Sbjct: 59 ANCGDN--KFNVLNN--IIHSTLSNAINLELFPHT-----TISVTVHGIQDDGSMGAVAI 109
Query: 499 CGGSMALMDAGIPLQEHVAGVSVGLVSE---VDPS 530
G AL+D G+P + GV + V + +DP+
Sbjct: 110 NGACFALLDNGMPFETVFCGVLIVRVKDELIIDPT 144
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 35.4 bits (80), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 689 GVVTSVKEYGAFVEFNGGQQGLLHVSEL 716
G VT++ +YG FVE G +GL+HVSE+
Sbjct: 36 GRVTNLTDYGCFVEIEEGVEGLVHVSEM 63
>pdb|2WNR|A Chain A, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|C Chain C, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
pdb|2WNR|E Chain E, The Structure Of Methanothermobacter Thermautotrophicus
Exosome Core Assembly
Length = 271
Score = 33.5 bits (75), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTV--TLGAP 414
R+DGR L E R I E+G + GSS G+TQ++ V +G P
Sbjct: 25 RIDGRSLHEFRDISIETGVISKAEGSSRVKLGNTQIIVGVKPQIGEP 71
>pdb|3M85|G Chain G, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|H Chain H, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
pdb|3M85|I Chain I, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
Active Site
Length = 259
Score = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL--GAPA 415
R+DGR DE R + + GS+L GDTQV+ V + G PA
Sbjct: 23 RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKMQPGEPA 70
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 32.0 bits (71), Expect = 1.7, Method: Composition-based stats.
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 684 GGIYKGVVTSVKEYGAFVEFNGGQQGLLHVSELS 717
G +G + S+ ++G F+ +GG GL+H+S++S
Sbjct: 62 GDRVEGKIKSITDFGIFIGLDGGIDGLVHLSDIS 95
>pdb|2BA0|I Chain I, Archaeal Exosome Core
pdb|2BA0|H Chain H, Archaeal Exosome Core
pdb|2BA0|G Chain G, Archaeal Exosome Core
pdb|2BA1|G Chain G, Archaeal Exosome Core
pdb|2BA1|H Chain H, Archaeal Exosome Core
pdb|2BA1|I Chain I, Archaeal Exosome Core
pdb|3M7N|G Chain G, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|H Chain H, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
pdb|3M7N|I Chain I, Archaeoglobus Fulgidus Exosome With Rna Bound To The
Active Site
Length = 259
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 370 RVDGRQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVTL 411
R+DGR DE R + + GS+L GDTQV+ V +
Sbjct: 23 RIDGRGFDEFRKVEIIPNVIEKAEGSALVKLGDTQVVVGVKM 64
>pdb|2KAU|A Chain A, The Crystal Structure Of Urease From Klebsiella Aerogenes
At 2.2 Angstroms Resolution
pdb|1KRC|A Chain A, Crystal Structure Of Klebsiella Aerogenes Urease, Its
Apoenzyme And Two Active Site Mutants
pdb|1KRB|A Chain A, Crystal Structure Of Klebsiella Aerogenes Urease, Its
Apoenzyme And Two Active Site Mutants
pdb|1KRA|A Chain A, Crystal Structure Of Klebsiella Aerogenes Urease, Its
Apoenzyme And Two Active Site Mutants
pdb|1FWA|A Chain A, Klebsiella Aerogenes Urease, C319a Variant At Ph 7.5
pdb|1FWB|A Chain A, Klebsiella Aerogenes Urease, C319a Variant At Ph 6.5
pdb|1FWC|A Chain A, Klebsiella Aerogenes Urease, C319a Variant At Ph 8.5
pdb|1FWD|A Chain A, Klebsiella Aerogenes Urease, C319a Variant At Ph 9.4
pdb|1FWE|A Chain A, Klebsiella Aerogenes Urease, C319a Variant With
Acetohydroxamic Acid (Aha) Bound
pdb|1FWF|A Chain A, Klebsiella Aerogenes Urease, C319d Variant
pdb|1FWG|A Chain A, Klebsiella Aerogenes Urease, C319s Variant
pdb|1FWH|A Chain A, Klebsiella Aerogenes Urease, C319y Variant
pdb|1FWI|A Chain A, Klebsiella Aerogenes Urease, H134a Variant
pdb|1FWJ|A Chain A, Klebsiella Aerogenes Urease, Native
pdb|1A5K|A Chain A, K217e Variant Of Klebsiella Aerogenes Urease
pdb|1A5L|A Chain A, K217c Variant Of Klebsiella Aerogenes Urease
pdb|1A5M|A Chain A, K217a Variant Of Klebsiella Aerogenes Urease
pdb|1A5N|A Chain A, K217a Variant Of Klebsiella Aerogenes Urease, Chemically
Rescued By Formate And Nickel
pdb|1A5O|A Chain A, K217c Variant Of Klebsiella Aerogenes Urease, Chemically
Rescued By Formate And Nickel
pdb|1EF2|C Chain C, Crystal Structure Of Manganese-Substituted Klebsiella
Aerogenes Urease
pdb|1EJR|A Chain A, Crystal Structure Of The D221a Variant Of Klebsiella
Aerogenes Urease
pdb|1EJS|A Chain A, Crystal Structure Of The H219n Variant Of Klebsiella
Aerogenes Urease
pdb|1EJT|A Chain A, Crystal Structure Of The H219q Variant Of Klebsiella
Aerogenes Urease
pdb|1EJU|A Chain A, Crystal Structure Of The H320n Variant Of Klebsiella
Aerogenes Urease
pdb|1EJV|A Chain A, Crystal Structure Of The H320q Variant Of Klebsiella
Aerogenes Urease
pdb|1EJX|A Chain A, Crystal Structure Of Wild-Type Klebsiella Aerogenes Urease
At 100k
pdb|1EJW|A Chain A, Crystal Structure Of Wild-type Klebsiella Aerogenes Urease
At 298k
pdb|4EP8|A Chain A, Initial Urease Structure For Radiation Damage Experiment
At 100 K
pdb|4EPB|A Chain A, Final Urease Structure For Radiation Damage Experiment At
100 K
pdb|4EPD|A Chain A, Initial Urease Structure For Radiation Damage Experiment
At 300 K
pdb|4EPE|A Chain A, Final Urease Structure For Radiation Damage Experiment At
300 K
Length = 100
Score = 31.6 bits (70), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 5/85 (5%)
Query: 236 REKTLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQ----KKEYKLSMI 291
REK ++ A ++E+ L GL+L +PE+V + I + GK +E + +
Sbjct: 6 REKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLT 65
Query: 292 SEQTLEKVSNL-AEAHIEAVFTDPS 315
EQ +E V + + +EA F D S
Sbjct: 66 REQVMEGVPEMIPDIQVEATFPDGS 90
>pdb|2NN6|F Chain F, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 272
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 374 RQLDEVRPIYCESGNLPILHGSSLFSRGDTQVLCTVT 410
R +RP+Y +G L GS+ G T+VLC V+
Sbjct: 31 RDPTRLRPVYARAGLLSQAKGSAYLEAGGTKVLCAVS 67
>pdb|3ZHE|A Chain A, Structure Of The C. Elegans Smg5-smg7 Complex
pdb|3ZHE|C Chain C, Structure Of The C. Elegans Smg5-smg7 Complex
Length = 420
Score = 30.8 bits (68), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 10/80 (12%)
Query: 239 TLMIDVQAREISEKDLEAGLRLAHPEAVKYLEPQIRLAEKAGKQKKE---YKLSMISEQT 295
TL I + +R IS K L A EA+ ++ + +QK E KLS+ ++
Sbjct: 270 TLYITIYSRTISSKCLLA-------EAISWISDSAEILGHLDEQKNEPHFQKLSVFAKTK 322
Query: 296 LEKVSNLAEAHIEAVFTDPS 315
++++L HI +VFT S
Sbjct: 323 WNELNDLVMNHINSVFTSMS 342
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.315 0.134 0.376
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,197,984
Number of Sequences: 62578
Number of extensions: 1049833
Number of successful extensions: 2633
Number of sequences better than 100.0: 59
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 2481
Number of HSP's gapped (non-prelim): 76
length of query: 974
length of database: 14,973,337
effective HSP length: 108
effective length of query: 866
effective length of database: 8,214,913
effective search space: 7114114658
effective search space used: 7114114658
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)