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= 030800
(171 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EH1|A Chain A, Ribosome Recycling Factor From Thermus Thermophilus
pdb|2V46|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 1 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 1.
pdb|2V48|Y Chain Y, Structure Of The Ribosome Recycling Factor Bound To The
Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And
Trna-Fmet (Part 3 Of 4). This File Contains The 30s
Subunit, Mrna, P-Site Asl, E-Site Trna And Rrf For
Molecule 2.
pdb|2QBE|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
First 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBG|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Ribosome Recycling
Factor (Rrf). This File Contains The 50s Subunit Of The
Second 70s Ribosome, With Rrf Bound. The Entire Crystal
Structure Contains Two 70s Ribosomes And Is Described In
Remark 400.
pdb|2QBI|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The First 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2QBK|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Gentamicin And Ribosome
Recycling Factor (Rrf). This File Contains The 50s
Subunit Of The Second 70s Ribosome, With Gentamicin And
Rrf Bound. The Entire Crystal Structure Contains Two 70s
Ribosomes And Is Described In Remark 400.
pdb|2Z4L|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The First 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|2Z4N|6 Chain 6, Crystal Structure Of The Bacterial Ribosome From
Escherichia Coli In Complex With Paromomycin And
Ribosome Recycling Factor (Rrf). This File Contains The
50s Subunit Of The Second 70s Ribosome, With Paromomycin
And Rrf Bound. The Entire Crystal Structure Contains Two
70s Ribosomes And Is Described In Remark 400.
pdb|3J0D|J Chain J, Models For The T. Thermophilus Ribosome Recycling Factor
Bound To The E. Coli Post-Termination Complex
pdb|3J0E|G Chain G, Models For The T. Thermophilus Ribosome Recycling Factor
And The E. Coli Elongation Factor G Bound To The E. Coli
Post-Termination Complex
Length = 185
Score = 121 bits (303), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 66/170 (38%), Positives = 102/170 (60%), Gaps = 2/170 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ ++ L L LRTGRA+P +L H+ VE G +PLN +A V+ D +TL + +D
Sbjct: 14 MQKSLEVLEHNLAGLRTGRANPALLLHLKVEYYGAHVPLNQIATVTAPDPRTLVVQSWDQ 73
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
N LK +E AI S LGLNP G L IP LT+E + + + V + +E+ + +IR R
Sbjct: 74 NALKAIEKAIRDSDLGLNPSNKGDALYINIPPLTEERRKDLVRAVRQYAEEGRVAIRNIR 133
Query: 121 QKALDMMKKAGSS--LPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEI 168
++ALD +KK L +D+ KR E E+ ++T +++ AD + + KE+EI
Sbjct: 134 REALDKLKKLAKELHLSEDETKRAEAEIQKITDEFIAKADQLAEKKEQEI 183
>pdb|4GFQ|A Chain A, 2.65 Angstrom Resolution Crystal Structure Of Ribosome
Recycling Factor (Frr) From Bacillus Anthracis
Length = 209
Score = 119 bits (297), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 65/172 (37%), Positives = 103/172 (59%), Gaps = 2/172 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
ME A+ A SREL +R GRAS +LD + V+ G P+ LA ++V +++ L I PYD
Sbjct: 37 MEKAVAAYSRELATVRAGRASASVLDKVQVDYYGAPTPVVQLANITVPEARLLVIQPYDK 96
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
++ ++E AI+ + LGLNP DG + A PALT+E + + KVV K +E+ K ++R R
Sbjct: 97 TSIGDIEKAILKADLGLNPSNDGTVIRIAFPALTEERRRDLVKVVKKYAEEAKVAVRNVR 156
Query: 121 QKALDMMKK--AGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEINE 170
+ D +KK + +D ++ +++ + T KY+ D++ K KEKEI E
Sbjct: 157 RDGNDDLKKLEKAGEITEDDLRGYTEDIQKETDKYIAKVDEIAKNKEKEIME 208
>pdb|1WQF|A Chain A, Crystal Structure Of Ribosome Recycling Factor From
Mycobacterium Tuberculosis
pdb|1WQG|A Chain A, Crystal Structure Of Ribosome Recycling Factor From
Mycobacterium Tuberculosis
pdb|1WQH|A Chain A, Crystal Structure Of Ribosome Recycling Factor From
Mycobacterium Tuberculosis
Length = 185
Score = 114 bits (286), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 62/173 (35%), Positives = 105/173 (60%), Gaps = 4/173 (2%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
ME A+ +L+ +RTGRA+PGM I ++ G P+ LA ++V +++ + I PY+
Sbjct: 13 MEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEA 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
N L+ +E+AI +S LG+NP DG + A+P LT+E + + K E+ K S+R R
Sbjct: 73 NQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAKVSVRNIR 132
Query: 121 QKALDMM---KKAGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEINE 170
+KA++ + +K G + +D++ R EK++D+ T +YV D++ K KE E+ E
Sbjct: 133 RKAMEELHRIRKEGEA-GEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
>pdb|1DD5|A Chain A, Crystal Structure Of Thermotoga Maritima Ribosome
Recycling Factor, Rrf
pdb|1T1M|C Chain C, Binding Position Of Ribosome Recycling Factor (Rrf) On The
E. Coli 70s Ribosome
Length = 185
Score = 107 bits (268), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 62/172 (36%), Positives = 101/172 (58%), Gaps = 2/172 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ + + EL K+RTG+ SP +L+ I V+ GV P+N LA +S+ + +TL I P+D
Sbjct: 13 MKRTLEKIEDELRKMRTGKPSPAILEEIKVDYYGVPTPVNQLATISISEERTLVIKPWDK 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
+ L +E AI +S LGLNP DG + P+ T E + K + E+ K +IR R
Sbjct: 73 SVLSLIEKAINASDLGLNPINDGNVIRLVFPSPTTEQREKWVKKAKEIVEEGKIAIRNIR 132
Query: 121 QKALDMMKKAGSS--LPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEINE 170
++ L +K+ +P+D KRLE E+ +LT ++++ D+V + K++EI E
Sbjct: 133 REILKKIKEDQKEGLIPEDDAKRLENEIQKLTDEFIEKLDEVFEIKKEEIME 184
>pdb|1EK8|A Chain A, Crystal Structure Of The Ribosome Recycling Factor (Rrf)
From Escherichia Coli
pdb|1ZN0|A Chain A, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The
50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf
pdb|1ZN1|A Chain A, Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 70s
Post- Termination Complex
pdb|2RDO|8 Chain 8, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound
pdb|4GAS|Y Chain Y, Allosteric Control Of The Ribosome By Small-Molecule
Antibiotics
Length = 185
Score = 101 bits (251), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 60/170 (35%), Positives = 96/170 (56%), Gaps = 2/170 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ + A +++K+RTGRASP +LD I+VE G PL LA V+V DS+TL IN +D
Sbjct: 13 MDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDR 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
+ +E AI++S LGLNP G + +P LT+E + + K+V +E + ++R R
Sbjct: 73 SMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRNVR 132
Query: 121 QKALDMMKK--AGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEI 168
+ A D +K + +D +R + +V +LT +K + KE E+
Sbjct: 133 RDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAEL 182
>pdb|4GD1|Y Chain Y, Structures Of The Bacterial Ribosome In Classical And
Hybrid States Of Trna Binding
Length = 183
Score = 101 bits (251), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 60/170 (35%), Positives = 96/170 (56%), Gaps = 2/170 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ + A +++K+RTGRASP +LD I+VE G PL LA V+V DS+TL IN +D
Sbjct: 13 MDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDR 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
+ +E AI++S LGLNP G + +P LT+E + + K+V +E + ++R R
Sbjct: 73 SMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRNVR 132
Query: 121 QKALDMMKK--AGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEI 168
+ A D +K + +D +R + +V +LT +K + KE E+
Sbjct: 133 RDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAEL 182
>pdb|1IS1|A Chain A, Crystal Structure Of Ribosome Recycling Factor From Vibrio
Parahaemolyticus
Length = 185
Score = 98.2 bits (243), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 61/172 (35%), Positives = 100/172 (58%), Gaps = 2/172 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ ++ AL L+K+RTGRA P +L I VE G PLN +A V D++TL+I +D
Sbjct: 13 MDKSVEALKNNLSKVRTGRAHPSLLSGISVEYYGAATPLNQVANVVAEDARTLAITVFDK 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
+++E AI+ S LGLNP G + +P LT+E + + K+V +E + ++R R
Sbjct: 73 ELTQKVEKAIMMSDLGLNPMSAGTIIRVPLPPLTEERRKDLVKIVRGEAEGGRVAVRNIR 132
Query: 121 QKALDMMKK--AGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEINE 170
+ A + +K + +D+ ++ ++E+ +LT VK D+V AKEKE+ E
Sbjct: 133 RDANNDLKALLKDKEISEDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELME 184
>pdb|1ISE|A Chain A, Crystal Structure Of A Mutant Of Ribosome Recycling Factor
From Escherichia Coli, Arg132gly
Length = 185
Score = 97.8 bits (242), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 59/170 (34%), Positives = 95/170 (55%), Gaps = 2/170 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ + A +++K+RTGRASP +LD I+VE G PL LA V+V DS+TL IN +D
Sbjct: 13 MDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTLKINVFDR 72
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
+ +E AI++S LGLNP G + +P LT+E + + K+V +E + ++R
Sbjct: 73 SMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQARVAVRNVG 132
Query: 121 QKALDMMKK--AGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEI 168
+ A D +K + +D +R + +V +LT +K + KE E+
Sbjct: 133 RDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAEL 182
>pdb|1GE9|A Chain A, Solution Structure Of The Ribosome Recycling Factor
Length = 184
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 53/168 (31%), Positives = 95/168 (56%), Gaps = 2/168 (1%)
Query: 1 MEAAIVALSRELTKLRTGRASPGMLDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYDP 60
M+ A+ E+ LRT RAS +++ I VE G K+P+ L +SV + + I +D
Sbjct: 16 MKKAVEYYKNEIAGLRTSRASTALVEEIKVEYYGSKVPIKQLGTISVPEHNQIVIQVWDQ 75
Query: 61 NTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSR 120
N + +E AI L LNP V G + +P LT+E + + +++ K +E+ + +R R
Sbjct: 76 NAVPAIEKAI-REELNLNPTVQGNVIRVTLPPLTEERRRELVRLLHKITEEARVRVRNVR 134
Query: 121 QKALDMMKKAGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEI 168
++A +M+++ + +D+ KR + + +LT KY+ + + +AKEKEI
Sbjct: 135 REAKEMIEEL-EGISEDEKKRALERLQKLTDKYIDEINKLMEAKEKEI 181
>pdb|3A9U|A Chain A, Crystal Structures And Enzymatic Mechanisms Of A Populus
Tomentosa 4- Coumarate--Coa Ligase
pdb|3A9V|A Chain A, Crystal Structures And Enzymatic Mechanisms Of A Populus
Tomentosa 4- Coumarate--Coa Ligase
pdb|3NI2|A Chain A, Crystal Structures And Enzymatic Mechanisms Of A Populus
Tomentosa 4- Coumarate:coa Ligase
Length = 536
Score = 32.0 bits (71), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 98 IQAMCKVVAKTSEDVKQS-----IRRSRQKALDMMKKAGSSLPKDQMKRLEKEVDELTKK 152
+ AMC AK D+K +R + K +D + G+SLP++Q + D++ K
Sbjct: 338 VLAMCLAFAKEPFDIKPGACGTVVRNAEMKIVD--PETGASLPRNQPGEICIRGDQIMKG 395
Query: 153 YVKSADDVCKAKEKE 167
Y+ + + +KE
Sbjct: 396 YLNDPEATSRTIDKE 410
>pdb|2H00|A Chain A, Human Methyltransferase 10 Domain Containing Protein
pdb|2H00|B Chain B, Human Methyltransferase 10 Domain Containing Protein
pdb|2H00|C Chain C, Human Methyltransferase 10 Domain Containing Protein
Length = 254
Score = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 27/111 (24%), Positives = 48/111 (43%), Gaps = 11/111 (9%)
Query: 50 SKTLSINPYDPNTLKELESAIVSSPLGLNPRVDGQRLIAAIPALTKEHIQAMCKVVAKTS 109
S +S+N DP ++ L ++ GL+ + +RLI +P L +I + ++
Sbjct: 2 SGRVSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVP-LRLNYIHWVEDLIGHQD 60
Query: 110 EDVKQSIRRSRQKALDMMKKAGSSLP-----KDQMKRLEKEVDELTKKYVK 155
D K ++RR +D+ A P + L EVD++ Y K
Sbjct: 61 SD-KSTLRR----GIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAK 106
>pdb|1WIH|A Chain A, Solution Structure Of Rsgi Ruh-021, A Domain Ii Of
Ribosome Recycling Factor From Mouse Cdna
Length = 84
Score = 31.2 bits (69), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 25 LDHIIVETGGVKMPLNHLAVVSVLDSKTLSINPYD-PNTLKELESAIVSSPLGLNPRVDG 83
LDHI V T K+ LN + +S+ + + +N P AI S + LNP V+G
Sbjct: 8 LDHITVVTADGKVALNQIGQISMKSPQVILVNMASFPECTAAAIKAIRESGMNLNPEVEG 67
Query: 84 QRLIAAIPALT 94
+ IP +T
Sbjct: 68 TLIRVPIPKVT 78
>pdb|4DKJ|A Chain A, Cpg Specific Methyltransferase In Complex With Target Dna
Length = 403
Score = 29.6 bits (65), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 49 DSKTLSINPYDPNTLKELESAIVSSPLGLNPRVDGQRLIAAI----PALT 94
+ K L++N Y+ T +E +S I+S PL + + + I P LT
Sbjct: 270 NYKYLNLNKYETTTFRETKSNIISRPLKNYTTFNSENYVYNINGIGPTLT 319
>pdb|3Q5D|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 1
Length = 447
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 407 KXGGEEFSRRYLQQLESEIDELYIQYIKHND 437
>pdb|4IDP|A Chain A, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|B Chain B, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|C Chain C, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|D Chain D, Human Atlastin-1 1-446, N440t, Gppnhp
Length = 447
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 408 KXGGEEFSRRYLQQLESEIDELYIQYIKHND 438
>pdb|3Q5E|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|C Chain C, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|E Chain E, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|G Chain G, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
Length = 447
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 407 KMGGEEFSRRYLQQLESEIDELYIQYIKHND 437
>pdb|3QNU|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Hexagonal Form
pdb|3QOF|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|B Chain B, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|C Chain C, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|D Chain D, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
Length = 459
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 419 KMGGEEFSRRYLQQLESEIDELYIQYIKHND 449
>pdb|4IDQ|A Chain A, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|B Chain B, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|C Chain C, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|D Chain D, Human Atlastin-1 1-446, N440t, Gdpalf4-
Length = 447
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 408 KMGGEEFSRRYLQQLESEIDELYIQYIKHND 438
>pdb|4IDN|A Chain A, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDN|B Chain B, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDO|A Chain A, Human Atlastin-1 1-446, C-his6, Gdpalf4-
pdb|4IDO|B Chain B, Human Atlastin-1 1-446, C-his6, Gdpalf4-
Length = 457
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 128 KKAGSSLPKDQMKRLEKEVDELTKKYVKSAD 158
K G + +++LE E+DEL +Y+K D
Sbjct: 407 KMGGEEFSRRYLQQLESEIDELYIQYIKHND 437
>pdb|1NY9|A Chain A, Antibiotic Binding Domain Of A Tipa-Class Multidrug
Resistance Transcriptional Regulator
Length = 143
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 107 KTSEDVKQSIRRSRQKALDMMKKAGSSLPKDQMKRLEKEVDELTKKYV 154
+ E+V++ R A K+ +S K+ +R++ E DELT+++V
Sbjct: 20 QYEEEVRE--RWGNTDAYRQSKEKTASYTKEDWQRIQDEADELTRRFV 65
>pdb|4FGV|A Chain A, Crystal Structure Of Free Crm1 (crystal Form 1)
pdb|4HZK|A Chain A, Crystal Structure Of Free Crm1 (crystal Form 2)
pdb|4HZK|B Chain B, Crystal Structure Of Free Crm1 (crystal Form 2)
Length = 1086
Score = 27.7 bits (60), Expect = 3.0, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 7/68 (10%)
Query: 101 MCKVVAKTSEDVKQSIRRSRQKALDMMKKAGSSLPKDQMKRLEKEVDELTKKYVKSADDV 160
M ++ A TS+ + +++ R + A M K G ++ ++KE+ +L + +V+ A+D+
Sbjct: 723 MLQMYAATSQLISEAVARDGEIATKMPKVRG-------LRTIKKEILKLVETFVEKAEDL 775
Query: 161 CKAKEKEI 168
+ + I
Sbjct: 776 QAVRSQMI 783
>pdb|2HSI|A Chain A, Crystal Structure Of Putative Peptidase M23 From
Pseudomonas Aeruginosa, New York Structural Genomics
Consortium
pdb|2HSI|B Chain B, Crystal Structure Of Putative Peptidase M23 From
Pseudomonas Aeruginosa, New York Structural Genomics
Consortium
Length = 282
Score = 27.7 bits (60), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 80 RVDGQRLIA--AIPALTKEHIQAMCKVVAKTSEDVKQSI--RRSRQKALDMM-KKAGSSL 134
R +G+R IA IP TK Q + A + + + S+ + R++ + + K+ + L
Sbjct: 64 REEGRRWIAVVGIPLSTKPGPQKLEVRAATGNHEERFSVGSKHYREQRITLKNKRQVNPL 123
Query: 135 PKDQMKRLEKEVDELTKKY 153
P+D +KR+E+E+ E T Y
Sbjct: 124 PED-LKRIERELAEQTAAY 141
>pdb|2H5N|A Chain A, Crystal Structure Of Protein Of Unknown Function Pg1108
From Porphyromonas Gingivalis W83
pdb|2H5N|B Chain B, Crystal Structure Of Protein Of Unknown Function Pg1108
From Porphyromonas Gingivalis W83
pdb|2H5N|C Chain C, Crystal Structure Of Protein Of Unknown Function Pg1108
From Porphyromonas Gingivalis W83
pdb|2H5N|D Chain D, Crystal Structure Of Protein Of Unknown Function Pg1108
From Porphyromonas Gingivalis W83
Length = 133
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 121 QKALDMMKKAGSSLPKDQMKRLEKEVDELTKKYVKSADDVCKAKEKEINE 170
Q +D++ KA S+ Q L +DE KKYV S V A + +I++
Sbjct: 54 QDQVDLLLKASDSIEASQAVALIARMDEERKKYVASYLGVIMASDGDIDD 103
>pdb|2GQD|A Chain A, The Crystal Structure Of B-Ketoacyl-Acp Synthase Ii (Fabf)
From Staphylococcus Aureus
pdb|2GQD|B Chain B, The Crystal Structure Of B-Ketoacyl-Acp Synthase Ii (Fabf)
From Staphylococcus Aureus
Length = 437
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 32 TGGVKMPLNHLAVVSVLDSKTLSIN 56
TGG + P+ H+A+ S+ LS N
Sbjct: 212 TGGTEAPITHMAIAGFSASRALSTN 236
>pdb|3JVO|A Chain A, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|B Chain B, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|C Chain C, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|D Chain D, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|E Chain E, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|F Chain F, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|G Chain G, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|H Chain H, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|I Chain I, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|J Chain J, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|K Chain K, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|L Chain L, Crystal Structure Of Bacteriophage Hk97 Gp6
pdb|3JVO|M Chain M, Crystal Structure Of Bacteriophage Hk97 Gp6
Length = 108
Score = 27.3 bits (59), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 123 ALDMMKKAGSSLPKDQMKRLEKEVDELTKKYVKSADDVC 161
A+D++ SL K Q++ E + DEL Y ++A D C
Sbjct: 2 AIDVLDVISLSLFKQQIEFEEDDRDELITLYAQAAFDYC 40
>pdb|3O04|A Chain A, Crystal Structure Of The Beta-Keto-Acyl Carrier Protein
Synthase Ii (Lmo2201) From Listeria Monocytogenes
Length = 413
Score = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 32 TGGVKMPLNHLAVVSVLDSKTLSINPYDPNT 62
TGG + P+ ++ +K LS+NP DP T
Sbjct: 188 TGGAEAPITKXSLAGFTANKALSLNP-DPET 217
>pdb|3L9T|A Chain A, The Crystal Structure Of Smu.31 From Streptococcus Mutans
Ua159
Length = 240
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 82 DGQRLIAAIPALTKEHIQAMCKVVAKTSEDVKQSIRRSRQKALDMMKKAGSSLPKDQMKR 141
+G R+ P KE+ + +A EDV + +R+S AL + K L K ++K
Sbjct: 161 EGLRIWTNRPYF-KENPNEAIRRIADLKEDVSEYVRKSVGNALRDISKKFPDLVKIELKN 219
Query: 142 LEKEVDELTKKY 153
+ E E+ + Y
Sbjct: 220 WKLESKEINQVY 231
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
0.312 0.128 0.341
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,538,221
Number of Sequences: 62578
Number of extensions: 164734
Number of successful extensions: 659
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 630
Number of HSP's gapped (non-prelim): 40
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)