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= 002487
(916 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 = 512 bits (1319), Expect = e-145, Method: Compositional matrix adjust.
Identities = 295/749 (39%), Positives = 415/749 (55%), Gaps = 62/749 (8%)
Query: 85 SFPQPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPL 144
+ P+ K +G + +ETG M RQA+ AV V+ +T ++ +V DFFPL
Sbjct: 6 TLLNPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPL 65
Query: 145 NVNYQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLS 204
VNYQER AAGR G FF+REGR + E L+ RLIDRP+RP +GF +E Q+++ V+S
Sbjct: 66 TVNYQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVS 125
Query: 205 YDGLHFPDXXXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLL 264
+ PD S +P + I RVG + D++++NPT E+++S+LDL++
Sbjct: 126 VNPQVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVV 185
Query: 265 AGSDDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPP 324
AG++ A+LM+E LSE+ ++ AV G + + + + LV+ GKP+ D P
Sbjct: 186 AGTEAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRW-DWQPEPV 244
Query: 325 PE-LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLE-EKVLTILSENGYVSKDETVGIVE 382
E L V +A L +I +K R + ++ E + T+L+E DET
Sbjct: 245 NEALNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAE------DET----- 293
Query: 383 TIPXXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRR 442
E ++ + + +R R
Sbjct: 294 ---------------------------------------LDENELGEILHAIEKNVVRSR 314
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNL 502
++ G R DGR D IR + R G+LPR HGSALFTRGETQ+L TLG + AQ +D L
Sbjct: 315 VLAGEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDEL 374
Query: 503 ESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRV 562
+ F Y+FPP SVGE G +G+P RREIGHG LA+R + V+P + FPYT+RV
Sbjct: 375 MGE-RTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRV 433
Query: 563 ESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDI 622
S ITESNGSSSMASVCG LAL DAGVPIK ++AG+AMG+V + D + ++LSDI
Sbjct: 434 VSEITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNY------VVLSDI 487
Query: 623 TGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCS 682
G ED GDMDFKVAG+ DGI+A QMDIK+ GIT +M+ AL QAK R HIL M +
Sbjct: 488 LGDEDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAI 547
Query: 683 PPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAK 742
P +S+ AP IH +K+ P+KI +IG GG ++++ EETG I+ EDDGTVKI A
Sbjct: 548 NAPRGDISEFAPRIHTIKINPDKIKDVIGKGGSVIRALTEETGT-TIEIEDDGTVKIAAT 606
Query: 743 DLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWL 802
D + + I +T VG +Y ++ I +G FV I G+EGL HIS+++ +
Sbjct: 607 DGEKAKHAIRRIEEITAEIEVGRVY-TGKVTRIVDFGAFVAIGGGKEGLVHISQIADKRV 665
Query: 803 AKAEXXXXXXXXXXXXXIEVNDKGQLRLS 831
K +EV+ +G++RLS
Sbjct: 666 EKVTDYLQMGQEVPVKVLEVDRQGRIRLS 694
>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 = 510 bits (1314), Expect = e-144, Method: Compositional matrix adjust.
Identities = 290/748 (38%), Positives = 420/748 (56%), Gaps = 68/748 (9%)
Query: 94 IPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFS 153
I +G + +++ETG + RQA GAV T GET++ + A DFFPL VNYQE+
Sbjct: 23 IEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTF 82
Query: 154 AAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDX 213
AAG+ GGFFKREGR + E LV RLIDRP+RP +KGF +E Q++ VL +D + PD
Sbjct: 83 AAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDI 142
Query: 214 XXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILM 273
S P I RVG V +++NPT EM++S++DL++AG+ DA++M
Sbjct: 143 LGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMM 202
Query: 274 IEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK------PKMLDTIKLPPPEL 327
+E LSEE+++ V ++ + + + L E K P+ D IK
Sbjct: 203 VESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIK------ 256
Query: 328 YKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPXX 387
++++ G ++ +I+ K R +A+ + ++K + L + DE
Sbjct: 257 -AKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLS-----DEN---------- 300
Query: 388 XXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGG 447
P + + + +FKE+ + +RR I++ G
Sbjct: 301 -------------------------------PTGYDPLKLGAIFKELEADVVRRGILDTG 329
Query: 448 RRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDE 507
R DGR +RPI G+LPR HGSALFTRGETQ++ V TLG Q ID LE +
Sbjct: 330 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 389
Query: 508 VKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTIT 567
+ F L Y+FPP SVGE GR+G+P RREIGHG LA RAL P+LP+ DFPYTIR+ S IT
Sbjct: 390 -ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEIT 448
Query: 568 ESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSED 627
ESNGSSSMA+VCG LA+ DAGVP+ ++G+AMG++L+ D F +LSDI G ED
Sbjct: 449 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFA------VLSDILGDED 502
Query: 628 ASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSN 687
GDMDFKVAG +G+T+ QMDIK+ GIT +M++AL QAK+GR HIL EM K P
Sbjct: 503 HLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRA 562
Query: 688 SLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSL 747
+ AP I + + +KI +IGSGGK ++ I+ TG + +D DDG VK++A D + +
Sbjct: 563 DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAK-VDINDDGVVKVSASDGAKI 621
Query: 748 EKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEX 807
+ + I ++T VG IY +K + +G FV ++GL H+S++S+ +AK
Sbjct: 622 KAAIDWIKSITDEAEVGKIYDGKVVK-VVDFGAFVNFFGAKDGLVHVSQISNERVAKPSD 680
Query: 808 XXXXXXXXXXXXIEVNDKGQLRLSRRAL 835
+ +D+G+ +LS + +
Sbjct: 681 VLKEGQMVKVKLLGFDDRGKTKLSMKVV 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 = 510 bits (1313), Expect = e-144, Method: Compositional matrix adjust.
Identities = 290/748 (38%), Positives = 420/748 (56%), Gaps = 68/748 (9%)
Query: 94 IPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFS 153
I +G + +++ETG + RQA GAV T GET++ + A DFFPL VNYQE+
Sbjct: 14 IEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTF 73
Query: 154 AAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDX 213
AAG+ GGFFKREGR + E LV RLIDRP+RP +KGF +E Q++ VL +D + PD
Sbjct: 74 AAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDI 133
Query: 214 XXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILM 273
S P I RVG V +++NPT EM++S++DL++AG+ DA++M
Sbjct: 134 LGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMM 193
Query: 274 IEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK------PKMLDTIKLPPPEL 327
+E LSEE+++ V ++ + + + L E K P+ D IK
Sbjct: 194 VESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIK------ 247
Query: 328 YKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPXX 387
++++ G ++ +I+ K R +A+ + ++K + L + DE
Sbjct: 248 -AKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLS-----DEN---------- 291
Query: 388 XXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGG 447
P + + + +FKE+ + +RR I++ G
Sbjct: 292 -------------------------------PTGYDPLKLGAIFKELEADVVRRGILDTG 320
Query: 448 RRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDE 507
R DGR +RPI G+LPR HGSALFTRGETQ++ V TLG Q ID LE +
Sbjct: 321 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 380
Query: 508 VKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTIT 567
+ F L Y+FPP SVGE GR+G+P RREIGHG LA RAL P+LP+ DFPYTIR+ S IT
Sbjct: 381 -ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEIT 439
Query: 568 ESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSED 627
ESNGSSSMA+VCG LA+ DAGVP+ ++G+AMG++L+ D F +LSDI G ED
Sbjct: 440 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFA------VLSDILGDED 493
Query: 628 ASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSN 687
GDMDFKVAG +G+T+ QMDIK+ GIT +M++AL QAK+GR HIL EM K P
Sbjct: 494 HLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRA 553
Query: 688 SLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSL 747
+ AP I + + +KI +IGSGGK ++ I+ TG + +D DDG VK++A D + +
Sbjct: 554 DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAK-VDINDDGVVKVSASDGAKI 612
Query: 748 EKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEX 807
+ + I ++T VG IY +K + +G FV ++GL H+S++S+ +AK
Sbjct: 613 KAAIDWIKSITDEAEVGKIYDGKVVK-VVDFGAFVNFFGAKDGLVHVSQISNERVAKPSD 671
Query: 808 XXXXXXXXXXXXIEVNDKGQLRLSRRAL 835
+ +D+G+ +LS + +
Sbjct: 672 VLKEGQMVKVKLLGFDDRGKTKLSMKVV 699
>pdb|4AIM|A Chain A, Crystal Structure Of C. Crescentus Pnpase Bound To Rnase E
Recognition Peptide
Length = 726
Score = 510 bits (1313), Expect = e-144, Method: Compositional matrix adjust.
Identities = 289/748 (38%), Positives = 420/748 (56%), Gaps = 68/748 (9%)
Query: 94 IPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFS 153
I +G + +++ETG + RQA GAV T GET++ + A DFFPL VNYQE+
Sbjct: 23 IEWGGKTLVLETGRIARQADGAVLATMGETVVLATAVFAKSQKPGQDFFPLTVNYQEKTF 82
Query: 154 AAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDX 213
AAG+ GGFFKREGR + E LV RLIDRP+RP +KGF +E Q++ VL +D + PD
Sbjct: 83 AAGKIPGGFFKREGRPSEKETLVSRLIDRPIRPLFVKGFKNEVQVVVTVLQHDLENDPDI 142
Query: 214 XXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAILM 273
S P I RVG V +++NPT EM++S++DL++AG+ DA++M
Sbjct: 143 LGMVAASAALCLSGAPFMGPIGAARVGWVDGAYVLNPTLDEMKESKMDLVVAGTADAVMM 202
Query: 274 IEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGK------PKMLDTIKLPPPEL 327
+E LSEE+++ V ++ + + + L E K P+ D IK
Sbjct: 203 VESEIQELSEEIVLGGVNFAHQQMQAVIDAIIDLAEHAAKEPFAFEPEDTDAIK------ 256
Query: 328 YKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIPXX 387
++++ G ++ +I+ K R +A+ + ++K + L + DE
Sbjct: 257 -AKMKDLVGADIAAAYKIQKKQDRYEAVGAAKKKAIAALGLS-----DEN---------- 300
Query: 388 XXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVEGG 447
P + + + +FKE+ + +RR I++ G
Sbjct: 301 -------------------------------PTGYDPLKLGAIFKELEADVVRRGILDTG 329
Query: 448 RRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDE 507
R DGR +RPI G+LPR HGSALFTRGETQ++ V TLG Q ID LE +
Sbjct: 330 LRIDGRDVKTVRPILGEVGILPRTHGSALFTRGETQAIVVATLGTGDDEQFIDALEGTYK 389
Query: 508 VKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTIT 567
+ F L Y+FPP SVGE GR+G+P RREIGHG LA RAL P+LP+ DFPYTIR+ S IT
Sbjct: 390 -ESFLLHYNFPPYSVGETGRMGSPGRREIGHGKLAWRALRPMLPTKEDFPYTIRLVSEIT 448
Query: 568 ESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSED 627
ESNGSSSMA+VCG LA+ DAGVP+ ++G+AMG++L+ D F +LSDI G ED
Sbjct: 449 ESNGSSSMATVCGSSLAMMDAGVPLVRPVSGIAMGLILEQDGFA------VLSDILGDED 502
Query: 628 ASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPPSN 687
GDMDFKVAG +G+T+ QMDIK+ GIT +M++AL QAK+GR HIL EM K P
Sbjct: 503 HLGDMDFKVAGTSEGLTSLQMDIKIAGITPAIMEQALAQAKEGRAHILGEMNKAMDAPRA 562
Query: 688 SLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSSL 747
+ AP I + + +KI +IGSGGK ++ I+ TG + +D DDG VK++A D + +
Sbjct: 563 DVGDFAPKIETINIPTDKIREVIGSGGKVIREIVATTGAK-VDINDDGVVKVSASDGAKI 621
Query: 748 EKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEX 807
+ + I ++T +G IY +K + +G FV ++GL H+S++S+ +AK
Sbjct: 622 KAAIDWIKSITDEAEIGKIYDGKVVK-VVDFGAFVNFFGAKDGLVHVSQISNERVAKPSD 680
Query: 808 XXXXXXXXXXXXIEVNDKGQLRLSRRAL 835
+ +D+G+ +LS + +
Sbjct: 681 VLKEGQMVKVKLLGFDDRGKTKLSMKVV 708
>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 = 427 bits (1098), Expect = e-119, Method: Compositional matrix adjust.
Identities = 244/605 (40%), Positives = 337/605 (55%), Gaps = 60/605 (9%)
Query: 88 QPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVN 147
P+ K +G + +ETG M RQA+ AV V+ +T ++ +V DFFPL VN
Sbjct: 3 NPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVN 62
Query: 148 YQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDG 207
YQER AAGR G FF+REGR + E L+ RLIDRP+RP +GF +E Q+++ V+S +
Sbjct: 63 YQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNP 122
Query: 208 LHFPDXXXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGS 267
PD S +P + I RVG + D++++NPT E+++S+LDL++AG+
Sbjct: 123 QVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGT 182
Query: 268 DDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPE- 326
+ A+LM+E + LSE+ ++ AV G + + + + LV+ GKP+ D P E
Sbjct: 183 EAAVLMVESEAELLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRW-DWQPEPVNEA 241
Query: 327 LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLE-EKVLTILSENGYVSKDETVGIVETIP 385
L V +A L +I +K R + ++ E + T+L+E DET
Sbjct: 242 LNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAE------DET-------- 287
Query: 386 XXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVE 445
E ++ + + +R R++
Sbjct: 288 ------------------------------------LDENELGEILHAIEKNVVRSRVLA 311
Query: 446 GGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESD 505
G R DGR D IR + R G+LPR HGSALFTRGETQ+L TLG + AQ +D L +
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 371
Query: 506 DEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVEST 565
F Y+FPP SVGE G +G+P RREIGHG LA+R + V+P + FPYT+RV S
Sbjct: 372 -RTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSE 430
Query: 566 ITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGS 625
ITESNGSSSMASVCG LAL DAGVPIK ++AG+AMG+V + D + ++LSDI G
Sbjct: 431 ITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNY------VVLSDILGD 484
Query: 626 EDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPP 685
ED GDMDFKVAG+ DGI+A QMDIK+ GIT +M+ AL QAK R HIL M + P
Sbjct: 485 EDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAP 544
Query: 686 SNSLS 690
+S
Sbjct: 545 RGDIS 549
>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 = 427 bits (1097), Expect = e-119, Method: Compositional matrix adjust.
Identities = 244/605 (40%), Positives = 336/605 (55%), Gaps = 60/605 (9%)
Query: 88 QPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVN 147
P+ K +G + +ETG M RQA+ AV V+ +T ++ +V DFFPL VN
Sbjct: 3 NPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVN 62
Query: 148 YQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDG 207
YQER AAGR G FF+REGR + E L+ RLIDRP+RP +GF +E Q+++ V+S +
Sbjct: 63 YQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNP 122
Query: 208 LHFPDXXXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGS 267
PD S +P + I RVG + D++++NPT E+++S+LDL++AG+
Sbjct: 123 QVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGT 182
Query: 268 DDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPE- 326
+ A+LM+E LSE+ ++ AV G + + + + LV+ GKP+ D P E
Sbjct: 183 EAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRW-DWQPEPVNEA 241
Query: 327 LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLE-EKVLTILSENGYVSKDETVGIVETIP 385
L V +A L +I +K R + ++ E + T+L+E DET
Sbjct: 242 LNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAE------DET-------- 287
Query: 386 XXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVE 445
E ++ + + +R R++
Sbjct: 288 ------------------------------------LDENELGEILHAIEKNVVRSRVLA 311
Query: 446 GGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESD 505
G R DGR D IR + R G+LPR HGSALFTRGETQ+L TLG + AQ +D L +
Sbjct: 312 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 371
Query: 506 DEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVEST 565
F Y+FPP SVGE G +G+P RREIGHG LA+R + V+P + FPYT+RV S
Sbjct: 372 -RTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSE 430
Query: 566 ITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGS 625
ITESNGSSSMASVCG LAL DAGVPIK ++AG+AMG+V + D + ++LSDI G
Sbjct: 431 ITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNY------VVLSDILGD 484
Query: 626 EDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPP 685
ED GDMDFKVAG+ DGI+A QMDIK+ GIT +M+ AL QAK R HIL M + P
Sbjct: 485 EDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAP 544
Query: 686 SNSLS 690
+S
Sbjct: 545 RGDIS 549
>pdb|3CDJ|A Chain A, Crystal Structure Of The E. Coli KhS1 DOMAIN TRUNCATED
Pnpase
Length = 559
Score = 425 bits (1092), Expect = e-119, Method: Compositional matrix adjust.
Identities = 243/600 (40%), Positives = 334/600 (55%), Gaps = 60/600 (10%)
Query: 88 QPVSVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVN 147
P+ K +G + +ETG M RQA+ AV V+ +T ++ +V DFFPL VN
Sbjct: 9 NPIVRKFQYGQHTVTLETGMMARQATAAVMVSMDDTAVFVTVVGQKKAKPGQDFFPLTVN 68
Query: 148 YQERFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDG 207
YQER AAGR G FF+REGR + E L+ RLIDRP+RP +GF +E Q+++ V+S +
Sbjct: 69 YQERTYAAGRIPGSFFRREGRPSEGETLIARLIDRPIRPLFPEGFVNEVQVIATVVSVNP 128
Query: 208 LHFPDXXXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGS 267
PD S +P + I RVG + D++++NPT E+++S+LDL++AG+
Sbjct: 129 QVNPDIVAMIGASAALSLSGIPFNGPIGAARVGYINDQYVLNPTQDELKESKLDLVVAGT 188
Query: 268 DDAILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPE- 326
+ A+LM+E LSE+ ++ AV G + + + + LV+ GKP+ D P E
Sbjct: 189 EAAVLMVESEAQLLSEDQMLGAVVFGHEQQQVVIQNINELVKEAGKPRW-DWQPEPVNEA 247
Query: 327 LYKHVEEIAGEELVKVLQIKNKIPRRKALSSLE-EKVLTILSENGYVSKDETVGIVETIP 385
L V +A L +I +K R + ++ E + T+L+E DET
Sbjct: 248 LNARVAALAEARLSDAYRITDKQERYAQVDVIKSETIATLLAE------DET-------- 293
Query: 386 XXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVE 445
E ++ + + +R R++
Sbjct: 294 ------------------------------------LDENELGEILHAIEKNVVRSRVLA 317
Query: 446 GGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESD 505
G R DGR D IR + R G+LPR HGSALFTRGETQ+L TLG + AQ +D L +
Sbjct: 318 GEPRIDGREKDMIRGLDVRTGVLPRTHGSALFTRGETQALVTATLGTARDAQVLDELMGE 377
Query: 506 DEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVEST 565
F Y+FPP SVGE G +G+P RREIGHG LA+R + V+P + FPYT+RV S
Sbjct: 378 -RTDTFLFHYNFPPYSVGETGMVGSPKRREIGHGRLAKRGVLAVMPDMDKFPYTVRVVSE 436
Query: 566 ITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGS 625
ITESNGSSSMASVCG LAL DAGVPIK ++AG+AMG+V + D + ++LSDI G
Sbjct: 437 ITESNGSSSMASVCGASLALMDAGVPIKAAVAGIAMGLVKEGDNY------VVLSDILGD 490
Query: 626 EDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHILAEMLKCSPPP 685
ED GDMDFKVAG+ DGI+A QMDIK+ GIT +M+ AL QAK R HIL M + P
Sbjct: 491 EDHLGDMDFKVAGSRDGISALQMDIKIEGITKEIMQVALNQAKGARLHILGVMEQAINAP 550
>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 = 360 bits (924), Expect = 2e-99, Method: Compositional matrix adjust.
Identities = 231/685 (33%), Positives = 357/685 (52%), Gaps = 81/685 (11%)
Query: 91 SVKIPFGDRQILVETGHMGRQASGAVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQE 150
+V + G+R++ + +G + R A G+ V G+T + + PS PS F PL V+Y++
Sbjct: 7 AVAVDLGNRKLEISSGKLARFADGSAVVQSGDTAVMVTAVSKTKPS-PSQFMPLVVDYRQ 65
Query: 151 RFSAAGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHF 210
+ +AAGR + +RE T D E+L R+IDR +RP G++++TQ+L +L+ DG++
Sbjct: 66 KAAAAGRIPTNYLRREVGTSDKEILTSRIIDRSIRPLFPAGYFYDTQVLCNLLAVDGVNE 125
Query: 211 PDXXXXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGS-DD 269
PD S++P + + VR+G++ +++VNPT +EM S L+L++AG+
Sbjct: 126 PDVLAINGASVALSLSDIPWNGPVGAVRIGIIDGEYVVNPTRKEMSSSTLNLVVAGAPKS 185
Query: 270 AILMIEGYCDFLSEEMLIQAVQVGQDAVREISNEVKALVEMCG----KPKMLDTIKLPPP 325
I+M+E + + ++ A++VG ++I ++ LV+ G P+ L T P P
Sbjct: 186 QIVMLEASAENILQQDFCHAIKVGVKYTQQIIQGIQQLVKETGVTKRTPQKLFT---PSP 242
Query: 326 ELYKHVEEIAGEELVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVSKDETVGIVETIP 385
E+ K+ ++A E L V E+ VS+DE V +
Sbjct: 243 EIVKYTHKLAMERLYAVFTD---------------------YEHDKVSRDEAVNKIR--- 278
Query: 386 XXXXXXXXXXXXXXXXXXXXXXXHIKPKSRKSTPMLFSEVDVKLVFKEVTSKFLRRRIVE 445
+K K ++ P E F V + R ++
Sbjct: 279 ------------------LDTEEQLKEKFPEADPYEIIES-----FNVVAKEVFRSIVLN 315
Query: 446 GGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLES- 504
+R DGR +R +S + HGSALF RG+TQ L +T D+LES
Sbjct: 316 EYKRCDGRDLTSLRNVSCEVDMFKTLHGSALFQRGQTQVLCTVTF---------DSLESG 366
Query: 505 --DDEV---------KRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSD 553
D+V K F L Y FPP + E+G++ +RRE+GHG LAE+AL PV+P
Sbjct: 367 IKSDQVITAINGIKDKNFMLHYEFPPYATNEIGKVTGLNRRELGHGALAEKALYPVIP-- 424
Query: 554 NDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTD-EFGG 612
DFP+TIRV S + ESNGSSSMAS CGG LAL D+GVPI ++AGVA+G+V TD E G
Sbjct: 425 RDFPFTIRVTSEVLESNGSSSMASACGGSLALMDSGVPISSAVAGVAIGLVTKTDPEKGE 484
Query: 613 DGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRR 672
+L+DI G ED +GDMDFK+AG GITA Q DIK+ GI + ++ +A+QQA ++
Sbjct: 485 IEDYRLLTDILGIEDYNGDMDFKIAGTNKGITALQADIKLPGIPIKIVMEAIQQASVAKK 544
Query: 673 HILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTE 732
IL M K P S ++ P++ ++V K +G GG +K + ETGV I
Sbjct: 545 EILQIMNKTISKPRASRKENGPVVETVQVPLSKRAKFVGPGGYNLKKLQAETGV-TISQV 603
Query: 733 DDGTVKITAKDLSSLEKSKAIISNL 757
D+ T + A S++ +++ I+ +
Sbjct: 604 DEETFSVFAPTPSAMHEARDFITEI 628
>pdb|1E3P|A Chain A, Tungstate Derivative Of Streptomyces Antibioticus Pnpase
Gpsi Enzyme
Length = 757
Score = 296 bits (759), Expect = 3e-80, Method: Compositional matrix adjust.
Identities = 165/376 (43%), Positives = 237/376 (63%), Gaps = 8/376 (2%)
Query: 424 EVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQ 483
E ++ ++ +T +R R++ +R DGR IR +++ +PR HGSALF RGETQ
Sbjct: 331 EKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQ 390
Query: 484 SLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAE 543
L V TL +M Q++D L S KR+ Y+FPP SVGE GR+G+P RREIGHG LAE
Sbjct: 391 ILGVTTLNMLRMEQQLDTL-SPVTRKRYMHNYNFPPYSVGETGRVGSPKRREIGHGALAE 449
Query: 544 RALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGM 603
RA+ PVLP+ +FPY IR S SNGS+SM SVC ++L +AGVP+K +AG+AMG+
Sbjct: 450 RAIVPVLPTREEFPYAIRQVSEALGSNGSTSMGSVCASTMSLLNAGVPLKAPVAGIAMGL 509
Query: 604 VLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKA 663
+ + E G+ + L+DI G+EDA GDMDFKVAG ++ +TA Q+D K+ GI V+ A
Sbjct: 510 I--SQEINGETHYVALTDILGAEDAFGDMDFKVAGTKEFVTALQLDTKLDGIPASVLAAA 567
Query: 664 LQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEE 723
L+QA+D R HIL M++ P + +S +AP I +K+ +KI +IG + + I E+
Sbjct: 568 LKQARDARLHILDVMMEAIDTP-DEMSPNAPRIITVKIPVDKIGEVIGPKRQMINQIQED 626
Query: 724 TGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLT--MVPTVGDIYRNCEIKSIAPYGVF 781
TG E I EDDGT+ I A D + E ++A I+ + P VG+ +K+ +G F
Sbjct: 627 TGAE-ITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTT-FGAF 684
Query: 782 VEIAPGREGLCHISEL 797
V + PG++GL HIS++
Sbjct: 685 VSLLPGKDGLLHISQI 700
Score = 145 bits (365), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 78/207 (37%), Positives = 118/207 (57%), Gaps = 10/207 (4%)
Query: 96 FGDRQILVETGHMGRQASG-AVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSA 154
FG R I ETG + RQA+G AV D +T++ ++ + P + DFFPL V+ +ER A
Sbjct: 34 FGTRTIRFETGRLARQAAGSAVAYLDDDTMVLSATTASKNPKDQLDFFPLTVDVEERMYA 93
Query: 155 AGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDXX 214
AG+ G FF+REGR + +L CRLIDRPLRP+ KG +E Q+++ +++ + H D
Sbjct: 94 AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIMALNPDHLYDVV 153
Query: 215 XXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAG-----SDD 269
+ +P S I GVRV L+ +++ PT E+ED+ D+++AG D
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDMVVAGRVLEDGDV 213
Query: 270 AILMIEGYCDFLSEEMLIQAVQVGQDA 296
AI+M+E + E IQ V+ G +A
Sbjct: 214 AIMMVEAE----ATEKTIQLVKDGAEA 236
>pdb|1E3H|A Chain A, Semet Derivative Of Streptomyces Antibioticus PnpaseGPSI
Enzyme
Length = 757
Score = 267 bits (683), Expect = 2e-71, Method: Compositional matrix adjust.
Identities = 160/376 (42%), Positives = 229/376 (60%), Gaps = 8/376 (2%)
Query: 424 EVDVKLVFKEVTSKFLRRRIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQ 483
E ++ ++ +T +R R++ +R DGR IR +++ +PR HGSALF RGETQ
Sbjct: 331 EKEISAAYRALTKSLVRERVIAEKKRIDGRGVTDIRTLAAEVEAIPRVHGSALFERGETQ 390
Query: 484 SLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAE 543
L V TL + Q++D L S KR+ Y+FPP SVGE GR+G+P RREIGHG LAE
Sbjct: 391 ILGVTTLNXLRXEQQLDTL-SPVTRKRYXHNYNFPPYSVGETGRVGSPKRREIGHGALAE 449
Query: 544 RALEPVLPSDNDFPYTIRVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGM 603
RA+ PVLP+ +FPY IR S SNGS+S SVC +L +AGVP+K +AG+A G+
Sbjct: 450 RAIVPVLPTREEFPYAIRQVSEALGSNGSTSXGSVCASTXSLLNAGVPLKAPVAGIAXGL 509
Query: 604 VLDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDGITAFQMDIKVGGITLPVMKKA 663
+ + E G+ + L+DI G+EDA GD DFKVAG ++ +TA Q+D K+ GI V+ A
Sbjct: 510 I--SQEINGETHYVALTDILGAEDAFGDXDFKVAGTKEFVTALQLDTKLDGIPASVLAAA 567
Query: 664 LQQAKDGRRHILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEE 723
L+QA+D R HIL + P + S +AP I +K+ +KI +IG + + I E+
Sbjct: 568 LKQARDARLHILDVXXEAIDTP-DEXSPNAPRIITVKIPVDKIGEVIGPKRQXINQIQED 626
Query: 724 TGVEAIDTEDDGTVKITAKDLSSLEKSKAIISNLT--MVPTVGDIYRNCEIKSIAPYGVF 781
TG E I EDDGT+ I A D + E ++A I+ + P VG+ +K+ +G F
Sbjct: 627 TGAE-ITIEDDGTIYIGAADGPAAEAARATINGIANPTSPEVGERILGSVVKTTT-FGAF 684
Query: 782 VEIAPGREGLCHISEL 797
V + PG++GL HIS++
Sbjct: 685 VSLLPGKDGLLHISQI 700
Score = 136 bits (343), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 77/207 (37%), Positives = 113/207 (54%), Gaps = 10/207 (4%)
Query: 96 FGDRQILVETGHMGRQASG-AVTVTDGETIIYTSVCLADVPSEPSDFFPLNVNYQERFSA 154
FG R I ETG + RQA+G AV D +T + ++ + P + DFFPL V+ +ER A
Sbjct: 34 FGTRTIRFETGRLARQAAGSAVAYLDDDTXVLSATTASKNPKDQLDFFPLTVDVEERXYA 93
Query: 155 AGRTSGGFFKREGRTKDHEVLVCRLIDRPLRPTLIKGFYHETQILSWVLSYDGLHFPDXX 214
AG+ G FF+REGR + +L CRLIDRPLRP+ KG +E Q+++ + + + H D
Sbjct: 94 AGKIPGSFFRREGRPSEDAILTCRLIDRPLRPSFKKGLRNEIQVVATIXALNPDHLYDVV 153
Query: 215 XXXXXXXXXXXSEVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAG-----SDD 269
+ +P S I GVRV L+ +++ PT E+ED+ D ++AG D
Sbjct: 154 AINAASASTQLAGLPFSGPIGGVRVALIRGQWVAFPTHTELEDAVFDXVVAGRVLEDGDV 213
Query: 270 AILMIEGYCDFLSEEMLIQAVQVGQDA 296
AI +E + E IQ V+ G +A
Sbjct: 214 AIXXVEAE----ATEKTIQLVKDGAEA 236
>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 = 92.8 bits (229), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 79/231 (34%), Positives = 122/231 (52%), Gaps = 22/231 (9%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNL 502
I++ G+R+DGR D +R I G+L A GSA+F G T+++A + G K+M R +L
Sbjct: 13 ILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAV-YGPKEMHPRHLSL 71
Query: 503 ESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
D V R ++Y P S E + APSRREI + ALE + + FP T I
Sbjct: 72 -PDRAVLR--VRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAID 126
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
V + I +++ S + S+ LAL DAG+P++ IAGVA+G DG +I+ D
Sbjct: 127 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVG--------KADG--VIILD 176
Query: 622 ITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPVMKKALQQAKDG 670
+ +ED G+ D +A + + +T FQ++ G +T ++A A G
Sbjct: 177 LNETEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG 224
>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 = 92.4 bits (228), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 79/231 (34%), Positives = 122/231 (52%), Gaps = 22/231 (9%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNL 502
I++ G+R+DGR D +R I G+L A GSA+F G T+++A + G K+M R +L
Sbjct: 10 ILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAV-YGPKEMHPRHLSL 68
Query: 503 ESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
D V R ++Y P S E + APSRREI + ALE + + FP T I
Sbjct: 69 -PDRAVLR--VRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAID 123
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
V + I +++ S + S+ LAL DAG+P++ IAGVA+G DG +I+ D
Sbjct: 124 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVG--------KADG--VIILD 173
Query: 622 ITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPVMKKALQQAKDG 670
+ +ED G+ D +A + + +T FQ++ G +T ++A A G
Sbjct: 174 LNETEDMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG 221
>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 = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 78/231 (33%), Positives = 121/231 (52%), Gaps = 22/231 (9%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNL 502
I++ G+R+DGR D +R I G+L A GSA+F G T+++A + G K+M R +L
Sbjct: 15 ILDDGKRTDGRKPDELRSIKIELGVLKNADGSAIFEMGNTKAIAAV-YGPKEMHPRHLSL 73
Query: 503 ESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
D V R ++Y P S E + APSRREI + ALE + + FP T I
Sbjct: 74 -PDRAVLR--VRYHMTPFSTDE-RKNPAPSRREIELSKVIREALESAVLVEL-FPRTAID 128
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
V + I +++ S + S+ LAL DAG+P++ IAGVA+G DG +I+ D
Sbjct: 129 VFTEILQADAGSRLVSLMAASLALADAGIPMRDLIAGVAVG--------KADG--VIILD 178
Query: 622 ITGSEDASGDMDFKVAG--NEDGITAFQMDIKVGGITLPVMKKALQQAKDG 670
+ +E G+ D +A + + +T FQ++ G +T ++A A G
Sbjct: 179 LNETEAMWGEADMPIAMMPSLNQVTLFQLN---GSMTPDEFRQAFDLAVKG 226
>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 = 71.6 bits (174), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 74/239 (30%), Positives = 114/239 (47%), Gaps = 25/239 (10%)
Query: 442 RIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDN 501
+++ G R DGR D +RPI +L RA GS G+ + +A + G +++ R +
Sbjct: 10 KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAV-FGPREVHPR--H 66
Query: 502 LESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-I 560
L+ + Y +Y+ P SV E R G P RR I +++ A E V+ + FP + I
Sbjct: 67 LQDPSKAIIRY-RYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKEL-FPRSAI 123
Query: 561 RVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILS 620
+ + +++ S A + +AL DAGVP+K I VA+G DG L+L
Sbjct: 124 DIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVG--------KADGQ-LVL- 173
Query: 621 DITGSEDASGDMDFKVA-----GNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHI 674
D ED G+ D A G + I QMD G +T +K+A++ AK G I
Sbjct: 174 DPMKEEDNFGEADMPFAFLIRNGKIESIALLQMD---GRMTRDEVKQAIELAKKGALQI 229
>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 = 71.6 bits (174), Expect = 2e-12, Method: Composition-based stats.
Identities = 67/210 (31%), Positives = 105/210 (50%), Gaps = 19/210 (9%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNL 502
I E GRR DGR +RPI G+L A+GSA G+ + +A + G +++ + +L
Sbjct: 11 IDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAV-YGPRELHPK--HL 67
Query: 503 ESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
+ D ++Y+ P SV E + G P RR I + + ALEP L + FP T I
Sbjct: 68 QRPDRAI-LRVRYNMAPFSVEERKKPG-PDRRSIEISKVIKGALEPALILEM-FPRTAID 124
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
V + +++ + +A + LAL DAG+P++ +A A G + +G I+ D
Sbjct: 125 VFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKI--------EGE--IVLD 174
Query: 622 ITGSEDASGDMDFKVA--GNEDGITAFQMD 649
+ ED G+ D VA ++ IT QMD
Sbjct: 175 LNKEEDNYGEADVPVAIMPLKNDITLLQMD 204
>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 = 70.1 bits (170), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 73/239 (30%), Positives = 114/239 (47%), Gaps = 25/239 (10%)
Query: 442 RIVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDN 501
+++ G R DGR D +RPI +L RA GS G+ + +A + G +++ ++
Sbjct: 10 KLIVDGLRLDGRKFDELRPIKIEASVLKRADGSCYLEMGKNKVIAAV-FGPREVHP--EH 66
Query: 502 LESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-I 560
L+ + Y +Y+ P SV E R G P RR I +++ A E V+ + FP + I
Sbjct: 67 LQDPSKAIIRY-RYNMAPFSVEERKRPG-PDRRSIEISKVSKEAFEAVIMKEL-FPRSAI 123
Query: 561 RVESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILS 620
+ + +++ S A + +AL DAGVP+K I VA+G DG L+L
Sbjct: 124 DIFVEVLQADAGSRTACLNAASVALVDAGVPMKGMITSVAVG--------KADGQ-LVL- 173
Query: 621 DITGSEDASGDMDFKVA-----GNEDGITAFQMDIKVGGITLPVMKKALQQAKDGRRHI 674
D ED G+ D A G + I QMD G +T +K+A++ AK G I
Sbjct: 174 DPMKEEDNFGEADMPFAFLIRNGKIESIALLQMD---GRMTRDEVKQAIELAKKGALQI 229
>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 = 68.9 bits (167), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 68/225 (30%), Positives = 100/225 (44%), Gaps = 22/225 (9%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R DGR D +RP+ G+L RA GS+ G + L V G ++ +I L+ D
Sbjct: 17 REDGRAFDELRPLKIEAGILERADGSSYLEFGGNKIL-VAVYGPREA--QIRKLQRPDRA 73
Query: 509 KRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IRVESTIT 567
+Y+ P SV E R G P RR + + AL P L + FP + I V +
Sbjct: 74 V-IRCRYNMAPFSVEERKRPG-PDRRSVEISKITAEALRPALILEK-FPRSVIDVFIEVL 130
Query: 568 ESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSED 627
E+ G + A + +AL DAG+P++ + A G V D ++ D++ ED
Sbjct: 131 EAEGGTRCAGITAASVALADAGIPMRDMVVACAAGKVGDQ----------VVLDLSEEED 180
Query: 628 ASGDMDFKVA--GNEDGITAFQMDIKVGGITLPVMKKALQQAKDG 670
G D VA IT Q D G +T ++AL A +G
Sbjct: 181 KEGQADVPVAILPRTREITLLQSD---GNLTPEEFERALDLAVEG 222
>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 = 63.2 bits (152), Expect = 7e-10, Method: Composition-based stats.
Identities = 62/226 (27%), Positives = 99/226 (43%), Gaps = 16/226 (7%)
Query: 447 GRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDD 506
G R DGR A +R I +R G+ +A GSA +G T++LAV+ + R L
Sbjct: 15 GYRVDGRRAGELRKIQARMGVFAQADGSAYIEQGNTKALAVVYGPHEIRGSRARALPDRA 74
Query: 507 EVKRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTI 566
V QYS S GE R R+ G + E + + I + +
Sbjct: 75 LVN---CQYSSATFSTGERKRRPHGDRKSCEMGLQLRQTFEAAILTQLHPRSQIDIYVQV 131
Query: 567 TESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSE 626
+++G + A V LA+ DAG+P++ + + G V DGT L+D++ E
Sbjct: 132 LQADGGTYAACVNAATLAVLDAGIPMRDFVCACSAGFV--------DGTA--LADLSHVE 181
Query: 627 DASGDMDFKVA--GNEDGITAFQMDIKVGGITLP-VMKKALQQAKD 669
+A+G +A I +MD ++ L V++ A Q A+D
Sbjct: 182 EAAGGPQLALALLPASGQIALLEMDARLHEDHLERVLEAAAQAARD 227
>pdb|1UDS|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R126a Mutant From Aquifex Aeolicus
Length = 255
Score = 54.7 bits (130), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 92/215 (42%), Gaps = 42/215 (19%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
RSDGR D +RP+S + L GS L + G+T+ + ++ + + N
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV-----IENVPNWLKGKGQ 56
Query: 509 KRFYLQYSFPPSSVGE-------VGRIGAPS---RREIGHGTLAERALEPVLPSDNDFPY 558
+YS P + + GRIG + +R IG RA+ +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIG------RAMRTAVELTKIGER 110
Query: 559 TIRVESTITESNGSSSMASVCGGCLALQDAGV-----------PIKCSIAGVAMGMVLDT 607
TI V+ + +++G ++ A++ G +A+ DA + PIK +A V++G+V D
Sbjct: 111 TIWVDCDVIQADGGTATAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDR 170
Query: 608 DEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
IL D+ ED++ +D V G G
Sbjct: 171 ----------ILLDLNFEEDSAAQVDMNVVGTGSG 195
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 14/106 (13%)
Query: 227 EVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAIL-----MIEGYCDFL 281
E P +A V VG+V D+ +++ +E +Q+D+ + G+ L M E Y
Sbjct: 152 ETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYS--F 209
Query: 282 SEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPEL 327
+++ LI+ + + Q + E L+E+ K ++ K EL
Sbjct: 210 TKDELIKMLDLAQKGINE-------LIELQKKLYVIQDGKWERSEL 248
>pdb|1UDO|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
R86a Mutant From Aquifex Aeolicus
Length = 255
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 91/215 (42%), Gaps = 42/215 (19%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
RSDGR D +RP+S + L GS L + G+T+ + ++ + + N
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV-----IENVPNWLKGKGQ 56
Query: 509 KRFYLQYSFPPSSVGE-------VGRIGAPS---RREIGHGTLAERALEPVLPSDNDFPY 558
+YS P + + GRIG + +R IG RA+ +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGATHEIQRMIG------RAMRTAVELTKIGER 110
Query: 559 TIRVESTITESNGSSSMASVCGGCLALQDAGV-----------PIKCSIAGVAMGMVLDT 607
TI V+ + +++G + A++ G +A+ DA + PIK +A V++G+V D
Sbjct: 111 TIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDR 170
Query: 608 DEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
IL D+ ED++ +D V G G
Sbjct: 171 ----------ILLDLNFEEDSAAQVDMNVVGTGSG 195
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 14/106 (13%)
Query: 227 EVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAIL-----MIEGYCDFL 281
E P +A V VG+V D+ +++ +E +Q+D+ + G+ L M E Y
Sbjct: 152 ETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYS--F 209
Query: 282 SEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPEL 327
+++ LI+ + + Q + E L+E+ K ++ K EL
Sbjct: 210 TKDELIKMLDLAQKGINE-------LIELQKKLYVIQDGKWERSEL 248
>pdb|1UDN|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Aquifex Aeolicus
Length = 255
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 91/215 (42%), Gaps = 42/215 (19%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
RSDGR D +RP+S + L GS L + G+T+ + ++ + + N
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV-----IENVPNWLKGKGQ 56
Query: 509 KRFYLQYSFPPSSVGE-------VGRIGAPS---RREIGHGTLAERALEPVLPSDNDFPY 558
+YS P + + GRIG + +R IG RA+ +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIG------RAMRTAVELTKIGER 110
Query: 559 TIRVESTITESNGSSSMASVCGGCLALQDAGV-----------PIKCSIAGVAMGMVLDT 607
TI V+ + +++G + A++ G +A+ DA + PIK +A V++G+V D
Sbjct: 111 TIWVDCDVIQADGGTRTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDR 170
Query: 608 DEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
IL D+ ED++ +D V G G
Sbjct: 171 ----------ILLDLNFEEDSAAQVDMNVVGTGSG 195
Score = 30.0 bits (66), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 14/106 (13%)
Query: 227 EVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAIL-----MIEGYCDFL 281
E P +A V VG+V D+ +++ +E +Q+D+ + G+ L M E Y
Sbjct: 152 ETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYS--F 209
Query: 282 SEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPEL 327
+++ LI+ + + Q + E L+E+ K ++ K EL
Sbjct: 210 TKDELIKMLDLAQKGINE-------LIELQKKLYVIQDGKWERSEL 248
>pdb|1UDQ|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
T125a Mutant From Aquifex Aeolicus
Length = 255
Score = 53.5 bits (127), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 54/215 (25%), Positives = 91/215 (42%), Gaps = 42/215 (19%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
RSDGR D +RP+S + L GS L + G+T+ + ++ + + N
Sbjct: 2 RSDGRKEDQLRPVSIQRDFLEYPEGSCLISFGKTKVICTASV-----IENVPNWLKGKGQ 56
Query: 509 KRFYLQYSFPPSSVGE-------VGRIGAPS---RREIGHGTLAERALEPVLPSDNDFPY 558
+YS P + + GRIG + +R IG RA+ +
Sbjct: 57 GWITAEYSMLPRATQQRTIRESVQGRIGGRTHEIQRMIG------RAMRTAVELTKIGER 110
Query: 559 TIRVESTITESNGSSSMASVCGGCLALQDAGV-----------PIKCSIAGVAMGMVLDT 607
TI V+ + +++G + A++ G +A+ DA + PIK +A V++G+V D
Sbjct: 111 TIWVDCDVIQADGGARTAAITGAFVAVADAIIKLHKEGIIEETPIKDFVAAVSVGIVNDR 170
Query: 608 DEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
IL D+ ED++ +D V G G
Sbjct: 171 ----------ILLDLNFEEDSAAQVDMNVVGTGSG 195
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 26/106 (24%), Positives = 49/106 (46%), Gaps = 14/106 (13%)
Query: 227 EVPNSKVIAGVRVGLVGDKFIVNPTTQEMEDSQLDLLLAGSDDAIL-----MIEGYCDFL 281
E P +A V VG+V D+ +++ +E +Q+D+ + G+ L M E Y
Sbjct: 152 ETPIKDFVAAVSVGIVNDRILLDLNFEEDSAAQVDMNVVGTGSGRLSEVHTMGEEYS--F 209
Query: 282 SEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPEL 327
+++ LI+ + + Q + E L+E+ K ++ K EL
Sbjct: 210 TKDELIKMLDLAQKGINE-------LIELQKKLYVIQDGKWERSEL 248
>pdb|1R6L|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa
Length = 239
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 51/218 (23%), Positives = 86/218 (39%), Gaps = 48/218 (22%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R GR AD +RPI A GS L G+T+ + ++ ++ V
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS--------------AESGV 48
Query: 509 KRFY---------LQYSFPPSSVGEVGRIGAPSRREIGHG----TLAERALEPVLPSDND 555
RF +Y P S GE + A ++ G L R+L L
Sbjct: 49 PRFLKGQGQGWLTAEYGXLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKL 108
Query: 556 FPYTIRVESTITESNGSSSMASVCGGCLALQDA-----------GVPIKCSIAGVAMGMV 604
T+ ++ + +++G + AS+ G +AL DA G P+K +A V++G+
Sbjct: 109 GENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQXVAAVSVGIY 168
Query: 605 LDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
G P++ D+ ED++ + D V + G
Sbjct: 169 --------QGVPVL--DLDYLEDSAAETDLNVVXTDAG 196
>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 = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 42/158 (26%), Positives = 74/158 (46%), Gaps = 14/158 (8%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R+DGR + +RP S L RAHGSA + +G+T LA + G K ++ +N E
Sbjct: 5 RADGRNPNQLRPFSCTRNPLDRAHGSARWAQGDTIVLAAV-YGPKPGTRKGENPE----- 58
Query: 509 KRFYLQYSFPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITE 568
+ ++ + P + G+IG ++E + +R L+ + T V +
Sbjct: 59 -KASIEVVWKPMT----GQIG---KQEKEYEMTLKRTLQSICLLTVHPNTTTSVILQVVG 110
Query: 569 SNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLD 606
++GS ++ C AL AG+P+K + G++ D
Sbjct: 111 NDGSLLPCAINACCAALVFAGIPLKHLAVAIGCGVLED 148
>pdb|1OYS|A Chain A, Crystal Structure Of The Phosphorolytic Exoribonuclease
Rnase Ph From Bacillus Subtilis
Length = 245
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 82/203 (40%), Gaps = 29/203 (14%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R DGR D +RPI+ + GS L T G T+ + ++ D R+
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVED-----RVPPFLRGGGK 56
Query: 509 KRFYLQYSFPPSSVGEV----GRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVES 564
+YS P + + G S R + L RAL V+ + TI ++
Sbjct: 57 GWITAEYSMLPQATNQQTIQESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 565 TITESNGSSSMASVCGGCLA-------LQDAGV----PIKCSIAGVAMGMVLDTDEFGGD 613
+ +++G + AS+ G LA L AG PI +A +++G+ D
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI---------D 167
Query: 614 GTPLILSDITGSEDASGDMDFKV 636
IL D+ ED+S ++D V
Sbjct: 168 KEQGILLDLNYEEDSSAEVDMNV 190
>pdb|1R6M|A Chain A, Crystal Structure Of The Trna Processing Enzyme Rnase Ph
From Pseudomonas Aeruginosa In Complex With Phosphate
Length = 239
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 52/218 (23%), Positives = 88/218 (40%), Gaps = 48/218 (22%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R GR AD +RPI A GS L G+T+ + ++ ++ V
Sbjct: 3 RPSGRAADQLRPIRITRHYTKHAEGSVLVEFGDTKVICTVS--------------AESGV 48
Query: 509 KRF-------YL--QYSFPPSSVGEVGRIGAPSRREIGHGT----LAERALEPVLPSDND 555
RF +L +Y P S GE + A ++ G L R+L L
Sbjct: 49 PRFLKGQGQGWLTAEYGMLPRSTGERNQREASRGKQGGRTLEIQRLIGRSLRAALDLSKL 108
Query: 556 FPYTIRVESTITESNGSSSMASVCGGCLALQDA-----------GVPIKCSIAGVAMGMV 604
T+ ++ + +++G + AS+ G +AL DA G P+K +A V++G+
Sbjct: 109 GENTLYIDCDVIQADGGTRTASITGATVALIDALAVLKKRGALKGNPLKQMVAAVSVGIY 168
Query: 605 LDTDEFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
G P++ D+ ED++ + D V + G
Sbjct: 169 --------QGVPVL--DLDYLEDSAAETDLNVVMTDAG 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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 51/203 (25%), Positives = 82/203 (40%), Gaps = 29/203 (14%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R DGR D +RPI+ + GS L T G T+ + ++ D R+
Sbjct: 2 RHDGRQHDELRPITFDLDFISHPEGSVLITAGNTKVICNASVED-----RVPPFLRGGGK 56
Query: 509 KRFYLQYSFPPSSVGEV----GRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVES 564
+YS P + + G S R + L RAL V+ + TI ++
Sbjct: 57 GWITAEYSMLPRATNQRTIRESSKGKISGRTMEIQRLIGRALRAVVDLEKLGERTIWIDC 116
Query: 565 TITESNGSSSMASVCGGCLA-------LQDAGV----PIKCSIAGVAMGMVLDTDEFGGD 613
+ +++G + AS+ G LA L AG PI +A +++G+ D
Sbjct: 117 DVIQADGGTRTASITGAFLAMAIAIGKLIKAGTIKTNPITDFLAAISVGI---------D 167
Query: 614 GTPLILSDITGSEDASGDMDFKV 636
IL D+ ED+S ++D V
Sbjct: 168 KEQGILLDLNYEEDSSAEVDMNV 190
>pdb|1SRO|A Chain A, S1 Rna Binding Domain, Nmr, 20 Structures
Length = 76
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 763 VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEXXXXXXXXXXXXXIEV 822
VG +Y ++ I +G FV I G+EGL HIS+++ + K +EV
Sbjct: 5 VGRVYTG-KVTRIVDFGAFVAIGGGKEGLVHISQIADKRVEKVTDYLQMGQEVPVKVLEV 63
Query: 823 NDKGQLRLS 831
+ +G++RLS
Sbjct: 64 DRQGRIRLS 72
>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 = 37.7 bits (86), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 48/214 (22%), Positives = 85/214 (39%), Gaps = 37/214 (17%)
Query: 448 RRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDE 507
+R DGR +RP+ G GS L G T+ L + + + +
Sbjct: 6 KREDGRLDHELRPVIITRGFTENPAGSVLIEFGHTKVLCTAS-----VTEGVPRWRKATG 60
Query: 508 VKRFYLQYSFPPSSVGE-------VGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTI 560
+ +Y+ PS+ GR+ + +EI L R+L + TI
Sbjct: 61 LGWLTAEYAMLPSATHSRSDRESVRGRLSGRT-QEISR--LIGRSLRACIDLAALGENTI 117
Query: 561 RVESTITESNGSSSMASVCGGCLALQDAGV------------PIKCSIAGVAMGMVLDTD 608
++ + +++G + A++ G +AL DA P+ C+IA V++G+V
Sbjct: 118 AIDCDVLQADGGTRTAAITGAYVALADAVTYLSAAGKLSDPRPLSCAIAAVSVGVV---- 173
Query: 609 EFGGDGTPLILSDITGSEDASGDMDFKVAGNEDG 642
DG I D+ ED+ ++D V + G
Sbjct: 174 ----DGR--IRVDLPYEEDSRAEVDMNVVATDTG 201
>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 = 37.4 bits (85), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 433 EVTSKFLRRRIV---EGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVI 488
E+ + +R I+ + G+R D R + RPI G++ +A GSAL G TQ L I
Sbjct: 8 EIVAGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGI 66
>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 = 37.4 bits (85), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 42/152 (27%), Positives = 62/152 (40%), Gaps = 18/152 (11%)
Query: 458 IRPISSRCGLLPRAHGSALFTRGETQSLA-VITLGDKQMAQRIDNLESDDEVKRFYLQYS 516
+R + LL R GSA F +G+T LA V + ++++ I N + L+
Sbjct: 30 LRHFACEQNLLSRPDGSASFLQGDTSVLAGVYGPAEVKVSKEIFN--------KATLEVI 81
Query: 517 FPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYTIRVESTITESNGSSSMA 576
P +IG P E L E V+ +I V + GS
Sbjct: 82 LRP-------KIGLPGVAEKSRERLIRNTCEAVVLGTLHPRTSITVVLQVVSDAGSLLAC 134
Query: 577 SVCGGCLALQDAGVPIKCSIAGVAMGMVLDTD 608
+ C+AL DAGVP++ GVA LD+D
Sbjct: 135 CLNAACMALVDAGVPMRALFCGVACA--LDSD 164
>pdb|1YZ6|A Chain A, Crystal Structure Of Intact Alpha Subunit Of Aif2 From
Pyrococcus Abyssi
Length = 274
Score = 35.8 bits (81), Expect = 0.11, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 772 IKSIAPYGVFVEIA--PGREGLCHISELSSNWLAKAEXXXXXXXXXXXXXIEVND-KGQL 828
+K I YG F+E+ PG+E HISE++S W+ I V+ KG +
Sbjct: 18 VKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHI 77
Query: 829 RLSRR 833
LS R
Sbjct: 78 DLSLR 82
>pdb|3AEV|A Chain A, Crystal Structure Of AEIF2ALPHA-Adim2p-Rrna Complex From
Pyrococcus Horikoshii Ot3
Length = 275
Score = 35.8 bits (81), Expect = 0.11, Method: Composition-based stats.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 772 IKSIAPYGVFVEIA--PGREGLCHISELSSNWLAKAEXXXXXXXXXXXXXIEVND-KGQL 828
+K I YG F+E+ PG+E HISE++S W+ I V+ KG +
Sbjct: 19 VKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHI 78
Query: 829 RLSRR 833
LS R
Sbjct: 79 DLSLR 83
>pdb|3DD6|A Chain A, Crystal Structure Of Rph, An Exoribonuclease From Bacillus
Anthracis At 1.7 A Resolution
Length = 255
Score = 35.0 bits (79), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 46/209 (22%), Positives = 86/209 (41%), Gaps = 41/209 (19%)
Query: 449 RSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLAVITLGDKQMAQRIDNLESDDEV 508
R DGR +R I L GS L G+T+ + T+ +R+ +
Sbjct: 12 RVDGREKTELRHIHIHTNYLKHPEGSVLIEVGDTKVICSATI-----EERVPPFMRGEGK 66
Query: 509 KRFYLQYSFPP----------SSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPY 558
+Y+ P SS G+V +R IG RAL V+ +
Sbjct: 67 GWVTAEYAMIPRATEQRTIRESSKGKVTGRTMEIQRLIG------RALRAVVDLEALGER 120
Query: 559 TIRVESTITESNGSSSMASVCGGCLAL-----------QDAGVPIKCSIAGVAMGMVLDT 607
T+ ++ + +++G + AS+ G +A+ + + +P+K +A ++G+V
Sbjct: 121 TVWIDCDVIQADGGTRTASITGAYVAMVLAFEKLLQAEKVSKIPVKDYLAATSVGIV--- 177
Query: 608 DEFGGDGTPLILSDITGSEDASGDMDFKV 636
+E G ++ D+ +ED+ D+D V
Sbjct: 178 EEQG------VVLDLNYAEDSKADVDMNV 200
>pdb|2WP8|B Chain B, Yeast Rrp44 Nuclease
Length = 246
Score = 34.7 bits (78), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 50/211 (23%), Positives = 92/211 (43%), Gaps = 21/211 (9%)
Query: 447 GRRSDGRFADGIRPISSRCGLLPRA-HGSALFTRGETQSLAVITLGDKQMAQRIDNLESD 505
G R DGR + +R S P A GS+ +G + + ++ G K+ L+S
Sbjct: 11 GLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK-GPKE-----PRLKSQ 64
Query: 506 DEVKRFYLQYSFPPSSVGEVGRIGAP---SRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
+ + L S + + R + RR + T R E + N +P T I
Sbjct: 65 MDTSKALLNVSVNINKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVML-NIYPRTVID 123
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
+E + E +G + + G LAL DAG+ + I+G+++G+ D TPL+ ++
Sbjct: 124 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLY--------DTTPLLDTN 175
Query: 622 ITGSEDASGDMDFKVAGNEDGITAFQMDIKV 652
+ E+A + V G + ++ ++ K+
Sbjct: 176 -SLEENAMSTVTLGVVGKSEKLSLLLVEDKI 205
>pdb|4IFD|B Chain B, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 248
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 50/211 (23%), Positives = 92/211 (43%), Gaps = 21/211 (9%)
Query: 447 GRRSDGRFADGIRPISSRCGLLPRA-HGSALFTRGETQSLAVITLGDKQMAQRIDNLESD 505
G R DGR + +R S P A GS+ +G + + ++ G K+ L+S
Sbjct: 13 GLRLDGRRWNELRRFESSINTHPHAADGSSYMEQGNNKIITLVK-GPKE-----PRLKSQ 66
Query: 506 DEVKRFYLQYSFPPSSVGEVGRIGAP---SRREIGHGTLAERALEPVLPSDNDFPYT-IR 561
+ + L S + + R + RR + T R E + N +P T I
Sbjct: 67 MDTSKALLNVSVNITKFSKFERSKSSHKNERRVLEIQTSLVRMFEKNVML-NIYPRTVID 125
Query: 562 VESTITESNGSSSMASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSD 621
+E + E +G + + G LAL DAG+ + I+G+++G+ D TPL+ ++
Sbjct: 126 IEIHVLEQDGGIMGSLINGITLALIDAGISMFDYISGISVGLY--------DTTPLLDTN 177
Query: 622 ITGSEDASGDMDFKVAGNEDGITAFQMDIKV 652
+ E+A + V G + ++ ++ K+
Sbjct: 178 -SLEENAMSTVTLGVVGKSEKLSLLLVEDKI 207
>pdb|2KHI|A Chain A, Nmr Structure Of The Domain 4 Of The E. Coli Ribosomal
Protein S1
Length = 115
Score = 33.9 bits (76), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 772 IKSIAPYGVFVEIAPGREGLCHISELSSNWLAK 804
+ ++ YG FVEI G EGL H+SE+ +W K
Sbjct: 38 VTNLTDYGCFVEIEEGVEGLVHVSEM--DWTNK 68
>pdb|1MJF|A Chain A, Putative Spermidine Synthetase From Pyrococcus Furiosus
Pfu- 132382
pdb|1MJF|B Chain B, Putative Spermidine Synthetase From Pyrococcus Furiosus
Pfu- 132382
Length = 281
Score = 33.5 bits (75), Expect = 0.62, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 690 SKHAPLIH---IMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTEDDGTVKITAKDLSS 746
S H PL+H + KP+++ +I G G V+ +++ E I E D V + +KDL
Sbjct: 60 SYHEPLVHPAMLAHPKPKRVLVIGGGDGGTVREVLQHDVDEVIMVEIDEDVIMVSKDLIK 119
Query: 747 LE 748
++
Sbjct: 120 ID 121
>pdb|3L7Z|A Chain A, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|D Chain D, Crystal Structure Of The S. Solfataricus Archaeal Exosome
pdb|3L7Z|G Chain G, Crystal Structure Of The S. Solfataricus Archaeal Exosome
Length = 271
Score = 33.1 bits (74), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLA 486
+ E G R DGR RP+S +A GSAL G T LA
Sbjct: 22 LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA 65
>pdb|2BR2|A Chain A, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|C Chain C, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|E Chain E, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|G Chain G, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|I Chain I, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|K Chain K, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|M Chain M, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|O Chain O, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|S Chain S, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|U Chain U, Rnase Ph Core Of The Archaeal Exosome
pdb|2BR2|W Chain W, Rnase Ph Core Of The Archaeal Exosome
pdb|2C37|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C37|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With U8
Rna
pdb|2C38|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C39|A Chain A, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|E Chain E, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|G Chain G, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|I Chain I, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|K Chain K, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|M Chain M, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|O Chain O, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|Q Chain Q, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|S Chain S, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|U Chain U, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C39|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With Adp
pdb|2C38|C Chain C, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
pdb|2C38|W Chain W, Rnase Ph Core Of The Archaeal Exosome In Complex With A5
Rna
Length = 275
Score = 33.1 bits (74), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLA 486
+ E G R DGR RP+S +A GSAL G T LA
Sbjct: 22 LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA 65
>pdb|2JE6|A Chain A, Structure Of A 9-Subunit Archaeal Exosome
pdb|2JEA|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Rna
pdb|2JEB|A Chain A, Structure Of A 9-Subunit Archaeal Exosome Bound To Mn Ions
pdb|4BA1|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
pdb|4BA2|A Chain A, Archaeal Exosome (rrp4-rrp41(d182a)-rrp42) Bound To
Inorganic Phosphate
Length = 277
Score = 33.1 bits (74), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%)
Query: 443 IVEGGRRSDGRFADGIRPISSRCGLLPRAHGSALFTRGETQSLA 486
+ E G R DGR RP+S +A GSAL G T LA
Sbjct: 24 LFEKGIRQDGRKLTDYRPLSITLDYAKKADGSALVKLGTTMVLA 67
>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 = 32.7 bits (73), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 50/188 (26%), Positives = 71/188 (37%), Gaps = 30/188 (15%)
Query: 458 IRPISSRCGLLPRAHGSALFTRGETQSLAVITL-GDKQMAQRIDNLESDDEVKRFYLQYS 516
+R + L A GSA F++G T A + GD ++ + DE + Y
Sbjct: 5 LREMRCELSFLKNADGSACFSQGATCIWASCSGPGDVHASK------ASDEAMTLDISYR 58
Query: 517 FPPSSVGEVGRIGAPSRREIGHGTLAERALEPVLPSDNDFPYT-IRVESTITESNGSSSM 575
G I H TL+ A+ L FP+T I V + +GS
Sbjct: 59 ------ANCGDNKFNVLNNIIHSTLS-NAINLEL-----FPHTTISVTVHGIQDDGSMGA 106
Query: 576 ASVCGGCLALQDAGVPIKCSIAGVAMGMVLDTDEFGGDGTPLILSDITGSEDAS-GDMDF 634
++ G C AL D G+P + GV + V D LI+ E AS G + F
Sbjct: 107 VAINGACFALLDNGMPFETVFCGVLIVRVKD---------ELIIDPTAKQEAASTGRVLF 157
Query: 635 KVAGNEDG 642
V DG
Sbjct: 158 SVCKGSDG 165
>pdb|2BH8|A Chain A, Combinatorial Protein 1b11
pdb|2BH8|B Chain B, Combinatorial Protein 1b11
Length = 101
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 9/76 (11%)
Query: 731 TEDDGTVKITAKDLSSLEKSKAIISNLTMVPTVGDIYRNCEIKSIAPYGVFVEIAPGREG 790
T DDG+ + S+ A+ N P GD +IKSI +G+F+ + G +G
Sbjct: 34 TPDDGSKDVFVH-FSAGSSGAAVRGN----PQQGDRVEG-KIKSITDFGIFIGLDGGIDG 87
Query: 791 LCHISELSSNWLAKAE 806
L H+S++S W A+AE
Sbjct: 88 LVHLSDIS--W-AQAE 100
>pdb|2K4K|A Chain A, Solution Structure Of Gsp13 From Bacillus Subtilis
Length = 130
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 2/73 (2%)
Query: 763 VGDIYRNCEIKSIAPYGVFVEIAPGREGLCHISELSSNWLAKAEXXXXXXXXXXXXXIEV 822
VG +Y ++ + YG FV + +GL HISE++ ++ + V
Sbjct: 7 VGSVY-TGKVTGLQAYGAFVALDEETQGLVHISEVTHGFVKDINEHLSVGDEVQVKVLAV 65
Query: 823 N-DKGQLRLSRRA 834
+ +KG++ LS RA
Sbjct: 66 DEEKGKISLSIRA 78
>pdb|3TYW|A Chain A, Crystal Structure Of Cyp105n1 From Streptomyces Coelicolor
A3(2)
pdb|3TYW|B Chain B, Crystal Structure Of Cyp105n1 From Streptomyces Coelicolor
A3(2)
pdb|3TYW|C Chain C, Crystal Structure Of Cyp105n1 From Streptomyces Coelicolor
A3(2)
pdb|3TYW|D Chain D, Crystal Structure Of Cyp105n1 From Streptomyces Coelicolor
A3(2)
pdb|4FXB|A Chain A, Crystal Structure Of Cyp105n1 From Streptomyces
Coelicolor: A Cytochrome P450 Oxidase In The Coelibactin
Siderophore Biosynthetic Pathway
pdb|4FXB|B Chain B, Crystal Structure Of Cyp105n1 From Streptomyces
Coelicolor: A Cytochrome P450 Oxidase In The Coelibactin
Siderophore Biosynthetic Pathway
Length = 417
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 51/95 (53%), Gaps = 7/95 (7%)
Query: 281 LSEEMLIQAVQVGQDAVREISNEVKALVEMCGKPKMLDTIKLPPPELYKHVEEI--AGEE 338
++ E L+ + + +A RE + + AL + +LD +LP EL K + + A +E
Sbjct: 234 VTTEQLLSTLGITINAGRETTTSMIALSTLL----LLDRPELPA-ELRKDPDLMPAAVDE 288
Query: 339 LVKVLQIKNKIPRRKALSSLEEKVLTILSENGYVS 373
L++VL + + IP R A +E T+ +++G ++
Sbjct: 289 LLRVLSVADSIPLRVAAEDIELSGRTVPADDGVIA 323
>pdb|1WE8|A Chain A, Solution Structure Of Kh Domain In Protein Bab28342
Length = 104
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 682 SPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVE-AIDTEDDGTV 737
S S L+++ P+ + V + IIG GG+ ++SI + +G + D E +GT+
Sbjct: 2 SSGSSGILTENTPVFEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTL 58
>pdb|1PEM|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEO|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEQ|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|1PEU|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
Typhimurium
pdb|2BQ1|E Chain E, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
Salmonella Typhimurium
pdb|2BQ1|F Chain F, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
Salmonella Typhimurium
Length = 714
Score = 30.0 bits (66), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 35/152 (23%), Positives = 62/152 (40%), Gaps = 41/152 (26%)
Query: 475 ALFTRGETQSLAVITLGDKQMAQRIDNLESDDEVKRFYLQYSFPPSSVGEVGRIGAPSRR 534
ALF+ + Q GD +++R D L +D V++ Y+ + R
Sbjct: 307 ALFSPYDIQRRYGKPFGDIAISERYDELIADPHVRKTYI------------------NAR 348
Query: 535 EIGHGTLAERALEPVLPSDNDFPYTIRVESTITESN---GSSSMASVCGGCLALQDA--- 588
+ TLAE E + +PY I E T+ +N G +M+++C L + A
Sbjct: 349 DFFQ-TLAEIQFE------SGYPY-IMFEDTVNRANPIAGRINMSNLCSEILQVNSASRY 400
Query: 589 ---------GVPIKCSIAGVAMGMVLDTDEFG 611
G I C++ + + V+D+ + G
Sbjct: 401 DDNLDYTHIGHDISCNLGSLNIAHVMDSPDIG 432
>pdb|2OPU|A Chain A, Solution Nmr Structure Of The First Domain Of Ksrp
Length = 89
Score = 30.0 bits (66), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 46/88 (52%), Gaps = 10/88 (11%)
Query: 674 ILAEMLKCSPPPSNSLSKHAPLIHIMKVKPEKINLIIGSGGKKVKSIIEETGVEAIDTED 733
I +++ PPP S+++ +V + LIIG GG+++ I +++G + + D
Sbjct: 1 ISSQLGPIHPPPRTSMTEE------YRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPD 54
Query: 734 DGTVKITAKDLS----SLEKSKAIISNL 757
G + + L+ S++K+K ++ ++
Sbjct: 55 SGGLPERSVSLTGAPESVQKAKMMLDDI 82
>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 = 29.3 bits (64), Expect = 9.6, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 458 IRPISSRCGLLPRAHGSALFTRGETQSLAVIT 489
+RP+ +R GLL +A GSA G T+ L ++
Sbjct: 36 LRPVYARAGLLSQAKGSAYLEAGGTKVLCAVS 67
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 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,929,744
Number of Sequences: 62578
Number of extensions: 1005220
Number of successful extensions: 1938
Number of sequences better than 100.0: 56
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1832
Number of HSP's gapped (non-prelim): 77
length of query: 916
length of database: 14,973,337
effective HSP length: 108
effective length of query: 808
effective length of database: 8,214,913
effective search space: 6637649704
effective search space used: 6637649704
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (26.2 bits)