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= psy9088
(756 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NN6|A Chain A, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 358
Score = 179 bits (454), Expect = 4e-45, Method: Compositional matrix adjust.
Identities = 91/206 (44%), Positives = 133/206 (64%), Gaps = 2/206 (0%)
Query: 427 VDFMSSENWTSISAENGEAVWCPWVK--PSEVLAQVSCNMVIPKATRPNEGLLFINAELS 484
+D + ++ +I G C V+ + VL QVSC +V PK R EG+LF N ELS
Sbjct: 41 LDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVSCELVSPKLNRATEGILFFNLELS 100
Query: 485 PMASPQFETGRQTDTSVMINRFLEKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDG 544
MA+P FE GRQ+D V +NR +E+C + SKCID ESLCVVA EKVW +RVDL++LN+DG
Sbjct: 101 QMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTESLCVVAGEKVWQIRVDLHLLNHDG 160
Query: 545 NLLGCCSIAALAALAHFRHPDVTSTGDQIIIHSAAEKDPIPMTILHYPVTISYAVFNGGS 604
N++ SIAA+ AL HFR PDV+ GD++ +++ E+DP+P++I H P+ +S+A F G+
Sbjct: 161 NIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGT 220
Query: 605 EGSTVPGFTECIQLDTALALSQDRQK 630
P E +D L ++ ++ +
Sbjct: 221 YLLVDPNEREERVMDGLLVIAMNKHR 246
>pdb|2WP8|A Chain A, Yeast Rrp44 Nuclease
Length = 305
Score = 142 bits (359), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 69/213 (32%), Positives = 116/213 (54%), Gaps = 12/213 (5%)
Query: 390 MRDELDDGAYNPLWTMRGFTQTFHFWKESKRAQDWTDVDFMSSENWTSISAENGEAVWCP 449
M +++ A + + Q + + + + DV+ + + +S + G
Sbjct: 1 MAKDIEISASESKFILEALRQNYRL--DGRSFDQFRDVEITFGKEFGDVSVKMGN----- 53
Query: 450 WVKPSEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQT-DTSVMINRFLE 508
++V ++SC + P RP EGL I+ E+SPMA QFE G T + V+ +R +E
Sbjct: 54 ----TKVHCRISCQIAQPYEDRPFEGLFVISTEISPMAGSQFENGNITGEDEVLCSRIIE 109
Query: 509 KCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTS 568
K + S +D+E LC+VA K W VR D++ L+ DG + IA +A L HF+ PD+T
Sbjct: 110 KSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDCDGGFIDASCIAVMAGLMHFKKPDITV 169
Query: 569 TGDQIIIHSAAEKDPIPMTILHYPVTISYAVFN 601
G+QII+H E++P+P+ ILH P+ ++++ FN
Sbjct: 170 HGEQIIVHPVNEREPVPLGILHIPICVTFSFFN 202
>pdb|4IFD|A Chain A, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 304
Score = 141 bits (356), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 66/179 (36%), Positives = 105/179 (58%), Gaps = 10/179 (5%)
Query: 424 WTDVDFMSSENWTSISAENGEAVWCPWVKPSEVLAQVSCNMVIPKATRPNEGLLFINAEL 483
+ DV+ + + +S + G ++V ++SC + P RP EGL I+ E+
Sbjct: 32 FRDVEITFGKEFGDVSVKMGN---------TKVHCRISCQIAQPYEDRPFEGLFVISTEI 82
Query: 484 SPMASPQFETGRQT-DTSVMINRFLEKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNY 542
SPMA QFE G T + V+ +R +EK + S +D+E LC+VA K W VR D++ L+
Sbjct: 83 SPMAGSQFENGNITGEDEVLCSRIIEKSVRRSGALDVEGLCIVAGSKCWAVRADVHFLDC 142
Query: 543 DGNLLGCCSIAALAALAHFRHPDVTSTGDQIIIHSAAEKDPIPMTILHYPVTISYAVFN 601
DG + IA +A L HF+ PD+T G+QII+H E++P+P+ ILH P+ ++++ FN
Sbjct: 143 DGGFIDASCIAVMAGLMHFKKPDITVHGEQIIVHPVNEREPVPLGILHIPICVTFSFFN 201
>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 = 85.5 bits (210), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 46/133 (34%), Positives = 79/133 (59%), Gaps = 1/133 (0%)
Query: 454 SEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
++++ V + P P G++ N+EL PMASP FE G + SV ++R +++C +E
Sbjct: 58 TQIIVGVKPQIGEPFPDTPEMGVILTNSELLPMASPTFEPGPPDERSVELSRVVDRCIRE 117
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQI 573
S+ IDLE LC++ KVW + +DL++++YDGNL +A +AAL R P ++
Sbjct: 118 SRMIDLEKLCIIEGSKVWMLFLDLHIIDYDGNLFDAAVLATVAALLDTRIPAAEVEDGEV 177
Query: 574 IIHSAAEKDPIPM 586
+I+ + P+P+
Sbjct: 178 VINR-EKMQPLPV 189
>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 = 85.5 bits (210), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 68/244 (27%), Positives = 116/244 (47%), Gaps = 22/244 (9%)
Query: 384 EIEAGDMRDELDDGAYNPLWTMRGFTQTFHFWKESKRAQDWTDVDFMSSENWTSISAENG 443
EI AG MRD + + KE KR D D+ E + E
Sbjct: 8 EIVAGIMRDHI-----------------INLLKEGKRIDDRGFEDYRPIEIEVGV-IEKA 49
Query: 444 EAVWCPWVKPSEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMI 503
E + ++VL + ++ P PN G++ N EL P+ASP FE G + ++ +
Sbjct: 50 EGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIEL 109
Query: 504 NRFLEKCFKESKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRH 563
R +++ +ESK ++LE + +V + V V +D++VL++DGNL+ IAA+AAL + R
Sbjct: 110 ARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARV 169
Query: 564 PDVTSTGDQIIIHSAAEKDPIPMTILHYPVTISYAVFNGGSEGSTVPGFTECIQLDTALA 623
P V + + + E +P+P+ + PVT + G+ P E + +D +
Sbjct: 170 PKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKI----GNILVVDPSLDEELVMDGKIT 225
Query: 624 LSQD 627
++ D
Sbjct: 226 ITTD 229
>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 = 84.7 bits (208), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 55/190 (28%), Positives = 95/190 (50%), Gaps = 4/190 (2%)
Query: 413 HFWKESKRAQDWTDVDFMSSE-NWTSISAENGEAVWCPWVKPSEVLAQVSCNMVIPKATR 471
F KE+ R +F ++ N SIS +G A+ + + V+ V P
Sbjct: 18 RFLKENCRPDGRELGEFRTTTVNIGSISTADGSALV--KLGNTTVICGVKAEFAAPSTDA 75
Query: 472 PNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESKCIDLESLCVVAEEKVW 531
P++G + N +L P+ S +F +G + + + ++F+ + S+ I E LC+ + VW
Sbjct: 76 PDKGYVVPNVDLPPLCSSRFRSGPPGEEAQVASQFIADVIENSQIIQKEDLCISPGKLVW 135
Query: 532 NVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQIIIHSAAEKDPIPMTILHY 591
+ DL L+YDGN+L C+ A LAAL + + P+VT + + +K + I +
Sbjct: 136 VLYCDLICLDYDGNILDACTFALLAALKNVQLPEVTINEETALAEVNLKKKSY-LNIRTH 194
Query: 592 PVTISYAVFN 601
PV S+AVF+
Sbjct: 195 PVATSFAVFD 204
>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 = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 48/144 (33%), Positives = 79/144 (54%), Gaps = 4/144 (2%)
Query: 456 VLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESK 515
VLA + P PN+G L +N EL P+A FE G + ++ + R +++ ++SK
Sbjct: 63 VLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSK 122
Query: 516 CIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQIII 575
+DL L + + VW V +D+ VL+Y GN+L C++A++AAL + + V + I +
Sbjct: 123 ALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISV 182
Query: 576 HSAAEKDPIPMTILHYP-VTISYA 598
+ +P L+YP VTIS A
Sbjct: 183 NKNEVVGKLP---LNYPVVTISVA 203
>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 = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 48/144 (33%), Positives = 79/144 (54%), Gaps = 4/144 (2%)
Query: 456 VLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESK 515
VLA + P PN+G L +N EL P+A FE G + ++ + R +++ ++SK
Sbjct: 65 VLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYETFEPGPPDENAIELARVVDRSLRDSK 124
Query: 516 CIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQIII 575
+DL L + + VW V +D+ VL+Y GN+L C++A++AAL + + V + I +
Sbjct: 125 ALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKVEQHSNGISV 184
Query: 576 HSAAEKDPIPMTILHYP-VTISYA 598
+ +P L+YP VTIS A
Sbjct: 185 NKNEVVGKLP---LNYPVVTISVA 205
>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 = 80.9 bits (198), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 49/144 (34%), Positives = 80/144 (55%), Gaps = 8/144 (5%)
Query: 456 VLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKESK 515
VLA + P PN+G L +N EL P+A FE G + ++ + R +++ ++SK
Sbjct: 63 VLAGTKLEIDKPYEDTPNQGNLIVNVELLPLAYTTFEPGPPDENAIELARVVDRSLRDSK 122
Query: 516 CIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQIII 575
+DL L + + VW V +D+ VL+Y GN+L C++A++AAL + + V +QI +
Sbjct: 123 ALDLTKLVIEPGKSVWTVWLDVYVLDYGGNVLDACTLASVAALYNTKVYKV----EQISV 178
Query: 576 HSAAEKDPIPMTILHYP-VTISYA 598
+ +P L+YP VTIS A
Sbjct: 179 NKNEVVGKLP---LNYPVVTISVA 199
>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 = 72.4 bits (176), Expect = 9e-13, Method: Compositional matrix adjust.
Identities = 34/92 (36%), Positives = 55/92 (59%)
Query: 454 SEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
++V+ V P P+ G++ +NAEL P+ASP FE G + S+ + R +++ +E
Sbjct: 56 TQVVVGVKMQPGEPAPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRE 115
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGN 545
S+ +DL L + EKVW V VD++ L+ DGN
Sbjct: 116 SEAVDLSKLVIEEGEKVWIVFVDIHALDDDGN 147
>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 = 72.0 bits (175), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 34/92 (36%), Positives = 55/92 (59%)
Query: 454 SEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
++V+ V P P+ G++ +NAEL P+ASP FE G + S+ + R +++ +E
Sbjct: 56 TQVVVGVKMQPGEPYPDTPDRGVIIVNAELVPLASPTFEPGPPDENSIELARVVDRGIRE 115
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGN 545
S+ +DL L + EKVW V VD++ L+ DGN
Sbjct: 116 SEAVDLSKLVIEEGEKVWIVFVDIHALDDDGN 147
>pdb|2NN6|E Chain E, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 305
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 41/119 (34%), Positives = 58/119 (48%)
Query: 454 SEVLAQVSCNMVIPKATRPNEGLLFINAELSPMASPQFETGRQTDTSVMINRFLEKCFKE 513
+++L V M PK +PNEG L + S A+P+FE D I L + F
Sbjct: 70 TDILVGVKAEMGTPKLEKPNEGYLEFFVDCSASATPEFEGRGGDDLGTEIANTLYRIFNN 129
Query: 514 SKCIDLESLCVVAEEKVWNVRVDLNVLNYDGNLLGCCSIAALAALAHFRHPDVTSTGDQ 572
+DL++LC+ E W + VD+ +L GNL SIA AAL + R P V D+
Sbjct: 130 KSSVDLKTLCISPREHCWVLYVDVLLLECGGNLFDAISIAVKAALFNTRIPRVRVLEDE 188
>pdb|4DSD|A Chain A, Crystal Structure Of A Putative Periplasmic Protein
(Bacova_05534) From Bacteroides Ovatus Atcc 8483 At 1.75
A Resolution
pdb|4DSD|B Chain B, Crystal Structure Of A Putative Periplasmic Protein
(Bacova_05534) From Bacteroides Ovatus Atcc 8483 At 1.75
A Resolution
Length = 129
Score = 29.3 bits (64), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 423 DWTDVDFMSSENWTSISAENGEAV---WCPWVKPSEVLAQVSCNMVIPKATRPNEGLLFI 479
D T++DF S NW +SA+ G+ V P + + A N + K R +G
Sbjct: 50 DGTEIDFDSKGNWEEVSAKKGQTVPVSIVPGFAVNYLKAHNFVNEGVTKVERDRKGY--- 106
Query: 480 NAELSPMASPQFE 492
ELS S +F+
Sbjct: 107 EIELSTGLSFKFD 119
>pdb|2RML|A Chain A, Solution Structure Of The N-Terminal Soluble Domains Of
Bacillus Subtilis Copa
Length = 147
Score = 29.3 bits (64), Expect = 8.1, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 632 GVDSAYANLVNKTDRILLDEGEKDSGETKVKVEKVGPGIADLISKSDIE 680
GV A NL +T ++ D E + + K+EK+G + ++ DIE
Sbjct: 33 GVTDANVNLATETSNVIYDPAETGTAAIQEKIEKLGYHVVTEKAEFDIE 81
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
0.317 0.133 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,670,120
Number of Sequences: 62578
Number of extensions: 871261
Number of successful extensions: 2011
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1993
Number of HSP's gapped (non-prelim): 16
length of query: 756
length of database: 14,973,337
effective HSP length: 106
effective length of query: 650
effective length of database: 8,340,069
effective search space: 5421044850
effective search space used: 5421044850
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)