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= 025599
(250 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZME|A Chain A, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 258
Score = 239 bits (611), Expect = 9e-64, Method: Compositional matrix adjust.
Identities = 117/237 (49%), Positives = 158/237 (66%), Gaps = 1/237 (0%)
Query: 2 RRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61
RR G G + +A +Y+ G +A+ + M +QL F++ LE+FA KHK +IRKNP
Sbjct: 3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62
Query: 62 TFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ 121
FR QF +MCA +GVDPLAS KGFW+E+LG+GDFYYELGVQI+E+CLA + NGGLI L+
Sbjct: 63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122
Query: 122 ELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQ 181
EL + + R + VS+DD +RAI KLK LG G+ +I VG L++SVP ELN DH
Sbjct: 123 ELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALGTGFGIIPVGGTYLIQSVPAELNMDHTV 182
Query: 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238
+L+LA+ G+VTV E++ L W + RA L+ LL+EGLA +D + YW P
Sbjct: 183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDL-QAPGEAHYWLPA 238
>pdb|3CUQ|A Chain A, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 234
Score = 231 bits (589), Expect = 3e-61, Method: Compositional matrix adjust.
Identities = 109/204 (53%), Positives = 143/204 (70%), Gaps = 1/204 (0%)
Query: 35 MKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGD 94
M +QL F++ LE+FA KHK +IRKNP FR QF +MCA +GVDPLAS KGFW+E+LG+GD
Sbjct: 12 MSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGFWSEMLGVGD 71
Query: 95 FYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG 154
FYYELGVQI+E+CLA + NGGLI L+EL + + R + VS+DD +RAI KLK LG
Sbjct: 72 FYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKFAQDVSQDDLIRAIKKLKALG 131
Query: 155 NGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDI 214
G+ +I VG L++SVP ELN DH +L+LA+ G+VTV E++ L W + RA L+
Sbjct: 132 TGFGIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSEIKASLKWETERARQVLEH 191
Query: 215 LLEEGLAMVDDGHRDRKRRYWFPC 238
LL+EGLA +D + YW P
Sbjct: 192 LLKEGLAWLDL-QAPGEAHYWLPA 214
>pdb|1U5T|A Chain A, Structure Of The Escrt-Ii Endosomal Trafficking Complex
pdb|1W7P|A Chain A, The Crystal Structure Of Endosomal Complex Escrt-Ii
(Vps22VPS25VPS36)
Length = 233
Score = 130 bits (327), Expect = 7e-31, Method: Compositional matrix adjust.
Identities = 74/222 (33%), Positives = 128/222 (57%), Gaps = 14/222 (6%)
Query: 19 QYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDP 78
+Y + + + + ++ +++QL F+ +L +FA+KH ++++ +P FRS+F MC+ +G+DP
Sbjct: 16 KYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDP 75
Query: 79 LA---SNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNR 135
L+ +K L + DFYYE+ ++++EIC T+ NGG+I+ QEL + RK N
Sbjct: 76 LSLFDRDK----HLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKV--HFRKLN- 128
Query: 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVD 195
V DD ++I LK L +E+ + KK +RSVP EL D +ILE+ G+ ++
Sbjct: 129 --VGLDDLEKSIDMLKSL-ECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILGYSSIS 185
Query: 196 EVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237
++ L W + R+ ALD ++ GL + D + YW P
Sbjct: 186 LLKANLGWEAVRSKSALDEMVANGLLWI-DYQGGAEALYWDP 226
>pdb|3K11|A Chain A, Crystal Structure Of Putative Glycosyl Hydrolase
(Np_813087.1) From Bacteroides Thetaiotaomicron Vpi-5482
At 1.80 A Resolution
Length = 445
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 75 GVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLIN 119
GV L S +GFW +LL D Y E + + N G I+
Sbjct: 302 GVTALQSGEGFWHQLLDCNDSYLETSATAIYVYCLAHAINKGWID 346
>pdb|1Q7M|A Chain A, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7M|B Chain B, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7Q|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Q|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Z|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q7Z|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q8J|A Chain A, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|1Q8J|B Chain B, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|3BOF|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOF|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOL|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
pdb|3BOL|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
Length = 566
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 94 DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVL 153
D YYELGV I C T P + L QR+K AVS L V+
Sbjct: 259 DSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVI 318
Query: 154 GNGYEVISVGKKKL 167
G + G+KKL
Sbjct: 319 GE--RINPAGRKKL 330
>pdb|1Q85|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q85|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q8A|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
pdb|1Q8A|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
Length = 566
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 30/74 (40%), Gaps = 2/74 (2%)
Query: 94 DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVL 153
D YYELGV I C T P + L QR+K AVS L V+
Sbjct: 259 DSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRIFAVSSPSKLVTFDHFVVI 318
Query: 154 GNGYEVISVGKKKL 167
G + G+KKL
Sbjct: 319 GE--RINPAGRKKL 330
>pdb|2HIV|A Chain A, Atp-Dependent Dna Ligase From S. Solfataricus
pdb|2HIX|A Chain A, Atp Dependent Dna Ligase From S. Solfataricus Bound To Atp
Length = 621
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 156 GYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRL 201
GY + +G+K L++++ N D N + L + G + EV RRL
Sbjct: 75 GYPELGIGEKFLIKAISIATNTDENSVENLYKTIG--DLGEVARRL 118
>pdb|4GL2|A Chain A, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
pdb|4GL2|B Chain B, Structural Basis For Dsrna Duplex Backbone Recognition By
Mda5
Length = 699
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 5 PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKH--KNDIRKNPT 62
PG+GG A A + L N+ +KE L ++Q+++ +K + R++P
Sbjct: 191 PGVGGATKQAKAEEHILKLCANLDAFTIKTVKENLDQLKNQIQEPCKKFAIADATREDP- 249
Query: 63 FRSQFHEMCAKV 74
F+ + E+ ++
Sbjct: 250 FKEKLLEIMTRI 261
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
0.321 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,970,840
Number of Sequences: 62578
Number of extensions: 268737
Number of successful extensions: 788
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 781
Number of HSP's gapped (non-prelim): 14
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)