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= 020905
(320 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3K2T|A Chain A, Crystal Structure Of Lmo2511 Protein From Listeria
Monocytogenes, Northeast Structural Genomics Consortium
Target Lkr84a
Length = 57
Score = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/53 (45%), Positives = 32/53 (60%)
Query: 242 IVRMKFFEMPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVI 294
IVR K F + P+ EA+ Q+ + H FY + + ET NIVY RK G YG+I
Sbjct: 2 IVRTKQFSLKPMDSEEAVLQMNLLGHSFYVYTDAETNGTNIVYSRKDGKYGLI 54
>pdb|3KA5|A Chain A, Crystal Structure Of Ribosome-Associated Protein Y
(Psrp-1) From Clostridium Acetobutylicum. Northeast
Structural Genomics Consortium Target Id Car123a
pdb|3KA5|B Chain B, Crystal Structure Of Ribosome-Associated Protein Y
(Psrp-1) From Clostridium Acetobutylicum. Northeast
Structural Genomics Consortium Target Id Car123a
Length = 65
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 39/56 (69%)
Query: 242 IVRMKFFEMPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK 297
IV+ K F + P + EA+ + E + H+F+ F+N ++ E+N+VYKRK G YG+I P+
Sbjct: 2 IVKTKRFAIKPXSEEEAVLEXELLGHNFFVFQNGDSNEVNVVYKRKDGNYGLIEPE 57
>pdb|3LYV|A Chain A, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
pdb|3LYV|B Chain B, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
pdb|3LYV|C Chain C, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
pdb|3LYV|D Chain D, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
pdb|3LYV|E Chain E, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
pdb|3LYV|F Chain F, Crystal Structure Of A Domain Of Ribosome-Associated
Factor Streptococcus Pyogenes Serotype M6. Northeast
Structural Ge Consortium Target Id Dr64a
Length = 66
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 32/56 (57%)
Query: 242 IVRMKFFEMPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK 297
+VR K + P V EA Q E + HDF+ + + E G NI+Y+R+ G G+I K
Sbjct: 3 VVRTKNVTLKPXDVEEARLQXELLGHDFFIYTDSEDGATNILYRREDGNLGLIEAK 58
>pdb|4HEI|A Chain A, 2a X-Ray Structure Of Hpf From Vibrio Cholerae
pdb|4HEI|B Chain B, 2a X-Ray Structure Of Hpf From Vibrio Cholerae
Length = 95
Score = 40.8 bits (94), Expect = 0.001, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 51/104 (49%), Gaps = 9/104 (8%)
Query: 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEV 158
+++ IQG +++LTD+++++V K K H + V V L V ++R+
Sbjct: 1 MQINIQGHHIDLTDSMQDYVHSKFDKLERFFDH-INHVQVILRVE--------KLRQIAE 51
Query: 159 TLFTKKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEKESDH 202
+ A D E +YA+ID + + R+L K KEK S H
Sbjct: 52 ATLHVNQAEIHAHADDENMYAAIDSLVDKLVRQLNKHKEKLSSH 95
>pdb|4FYL|A Chain A, High-Resolution X-Ray Structure Of Hpf From Vibrio
Cholerae
pdb|4FYL|B Chain B, High-Resolution X-Ray Structure Of Hpf From Vibrio
Cholerae
Length = 95
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 30/100 (30%), Positives = 48/100 (48%), Gaps = 9/100 (9%)
Query: 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFT 162
IQG +++LTD+++++V K K H + V V L V ++R+
Sbjct: 5 IQGHHIDLTDSMQDYVHSKFDKLERFFDH-INHVQVILRVE--------KLRQIAEATLH 55
Query: 163 KKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEKESDH 202
+ A D E +YA+ID + + R+L K KEK S H
Sbjct: 56 VNQAEIHAHADDENMYAAIDSLVDKLVRQLNKHKEKLSSH 95
>pdb|2YWQ|A Chain A, Crystal Structure Of Thermus Thermophilus Protein Y
N-Terminal Domain
pdb|2YWQ|B Chain B, Crystal Structure Of Thermus Thermophilus Protein Y
N-Terminal Domain
pdb|2YWQ|C Chain C, Crystal Structure Of Thermus Thermophilus Protein Y
N-Terminal Domain
pdb|2YWQ|D Chain D, Crystal Structure Of Thermus Thermophilus Protein Y
N-Terminal Domain
Length = 105
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 27/101 (26%), Positives = 54/101 (53%), Gaps = 4/101 (3%)
Query: 105 GKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKK 164
G+NLE+TD ++++VE+K+ + + ++ V LS+ G + +V L
Sbjct: 8 GRNLEITDAIRDYVEKKLAR-LDRYQDGELXAKVVLSLAGSPHVEKKARAEIQVDL---P 63
Query: 165 HGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEKESDHGRH 205
G+VR EE+ +YA+ID ++ ++++ +E+ RH
Sbjct: 64 GGLVRVEEEDADLYAAIDRAVDRLETQVKRFRERRYVGKRH 104
>pdb|2RQL|A Chain A, Solution Structure Of The E. Coli Ribosome Hibernation
Promoting Factor Hpf
Length = 95
Score = 32.3 bits (72), Expect = 0.34, Method: Composition-based stats.
Identities = 29/116 (25%), Positives = 46/116 (39%), Gaps = 33/116 (28%)
Query: 99 VKLIIQGKNLELTDTVKNHVEEKVGK------------AVLKHSHLVREVDVRLSVRGGE 146
++L I G N+E+T+ ++ V K K VLK + D L V GGE
Sbjct: 1 MQLNITGNNVEITEALREFVTAKFAKLEQYFDRINQVYVVLKVEKVTHTSDATLHVNGGE 60
Query: 147 FGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEKESDH 202
+ A + + +YA+ID + + R+L K K+K H
Sbjct: 61 ---------------------IHASAEGQDMYAAIDGLIDKLARQLTKHKDKLKQH 95
>pdb|3V2C|Y Chain Y, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Yfia Of The 1st Ribosome In The Asu
pdb|3V2E|Y Chain Y, Crystal Structure Of Yfia Bound To The 70s Ribosome. This
Pdb Entry Contains Coordinates For The 30s Subunit With
Bound Yfia Of The 2nd Ribosome In The Asu
Length = 119
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 9/96 (9%)
Query: 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFT 162
I K +E+T ++ HV +++ K +HL+ + K P+ + T+ T
Sbjct: 5 ITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHII--------LSKEPQGFVADATINT 56
Query: 163 KKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEK 198
+GV+ A E +Y +I+ + + ++R+L K++ K
Sbjct: 57 -PNGVLVASGKHEDMYTAINELINKLERQLNKLQHK 91
>pdb|1VOQ|AA Chain a, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOS|AA Chain a, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOV|AA Chain a, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOX|AA Chain a, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400.
pdb|1VOZ|AA Chain a, Crystal Structure Of Five 70s Ribosomes From Escherichia
Coli In Complex With Protein Y. This File Contains The
30s Subunit Of One 70s Ribosome. The Entire Crystal
Structure Contains Five 70s Ribosomes And Is Described
In Remark 400
Length = 90
Score = 31.2 bits (69), Expect = 0.75, Method: Composition-based stats.
Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 9/96 (9%)
Query: 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFT 162
I K +E+T ++ HV +++ K +HL+ + K P+ + T+ T
Sbjct: 4 ITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHII--------LSKEPQGFVADATINT 55
Query: 163 KKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEK 198
+GV+ A E +Y +I+ + + ++R+L K++ K
Sbjct: 56 -PNGVLVASGKHEDMYTAINELINKLERQLNKLQHK 90
>pdb|1U4C|A Chain A, Structure Of Spindle Checkpoint Protein Bub3
pdb|1U4C|B Chain B, Structure Of Spindle Checkpoint Protein Bub3
Length = 349
Score = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 81 VHTKPLPVRMSWDGPLSSVKLIIQGKNLELTDTVK 115
+ +K L + SWDG L+ K IQ KN++L +++
Sbjct: 20 IPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSLR 54
>pdb|2I3T|A Chain A, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
pdb|2I3T|C Chain C, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
pdb|2I3T|E Chain E, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
pdb|2I3T|G Chain G, Bub3 Complex With Mad3 (Bubr1) Glebs Motif
Length = 341
Score = 31.2 bits (69), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 81 VHTKPLPVRMSWDGPLSSVKLIIQGKNLELTDTVK 115
+ +K L + SWDG L+ K IQ KN++L +++
Sbjct: 20 IPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSLR 54
>pdb|2I3S|A Chain A, Bub3 Complex With Bub1 Glebs Motif
pdb|2I3S|C Chain C, Bub3 Complex With Bub1 Glebs Motif
pdb|2I3S|E Chain E, Bub3 Complex With Bub1 Glebs Motif
Length = 349
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 81 VHTKPLPVRMSWDGPLSSVKLIIQGKNLELTDTVK 115
+ +K L + SWDG L+ K IQ KN++L +++
Sbjct: 20 IPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSLR 54
>pdb|1YFQ|A Chain A, High Resolution S. Cerevisiae Bub3 Mitotic Checkpoint
Protein
Length = 342
Score = 31.2 bits (69), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 81 VHTKPLPVRMSWDGPLSSVKLIIQGKNLELTDTVK 115
+ +K L + SWDG L+ K IQ KN++L +++
Sbjct: 20 IPSKSLLLITSWDGSLTVYKFDIQAKNVDLLQSLR 54
>pdb|1N3G|A Chain A, Solution Structure Of The Ribosome-Associated Cold Shock
Response Protein Yfia Of Escherichia Coli
Length = 113
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 9/96 (9%)
Query: 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFT 162
I K +E+T ++ HV +++ K +HL+ + K P+ + T+ T
Sbjct: 5 ITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHII--------LSKEPQGFVADATINT 56
Query: 163 KKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEK 198
+GV+ A E +Y +I+ + + ++R+L K++ K
Sbjct: 57 -PNGVLVASGKHEDMYTAINELINKLERQLNKLQHK 91
>pdb|1L4S|A Chain A, Solution Structure Of Ribosome Associated Factor Y
Length = 112
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 23/96 (23%), Positives = 48/96 (50%), Gaps = 9/96 (9%)
Query: 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFT 162
I K +E+T ++ HV +++ K +HL+ + K P+ + T+ T
Sbjct: 4 ITSKQMEITPAIRQHVADRLAKLEKWQTHLINPHII--------LSKEPQGFVADATINT 55
Query: 163 KKHGVVRAEEDAETVYASIDLVSSIIQRKLRKIKEK 198
+GV+ A E +Y +I+ + + ++R+L K++ K
Sbjct: 56 -PNGVLVASGKHEDMYTAINELINKLERQLNKLQHK 90
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 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,654,836
Number of Sequences: 62578
Number of extensions: 351337
Number of successful extensions: 642
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 625
Number of HSP's gapped (non-prelim): 26
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
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: 51 (24.3 bits)