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= 027597
(221 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 = 228 bits (581), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 112/221 (50%), Positives = 150/221 (67%), Gaps = 1/221 (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 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL-EVLQW 221
+L+LA+ G+VTV E++ L W + RA L+ LL E L W
Sbjct: 183 VLQLAEKNGYVTVSEIKASLKWETERARQVLEHLLKEGLAW 223
>pdb|3CUQ|A Chain A, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 234
Score = 219 bits (559), Expect = 7e-58, Method: Compositional matrix adjust.
Identities = 104/188 (55%), Positives = 135/188 (71%), Gaps = 1/188 (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 LL-EVLQW 221
LL E L W
Sbjct: 192 LLKEGLAW 199
>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 = 125 bits (313), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 67/182 (36%), Positives = 110/182 (60%), Gaps = 13/182 (7%)
Query: 35 MKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA---SNKGFWAELLG 91
+++QL F+ +L +FA+KH ++++ +P FRS+F MC+ +G+DPL+ +K L
Sbjct: 32 LRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFDRDK----HLFT 87
Query: 92 IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK 151
+ DFYYE+ ++++EIC T+ NGG+I+ QEL + RK N V DD ++I LK
Sbjct: 88 VNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKV--HFRKLN---VGLDDLEKSIDMLK 142
Query: 152 VLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDA 211
L +E+ + KK +RSVP EL D +ILE+ G+ ++ ++ L W + R+ A
Sbjct: 143 SL-ECFEIFQIRGKKFLRSVPNELTSDQTKILEICSILGYSSISLLKANLGWEAVRSKSA 201
Query: 212 LD 213
LD
Sbjct: 202 LD 203
>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 = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 94 DFYYELGVQIVEICLATRPHNGGLI-----NLQELCNLLRQRRKSNREAVSEDDCLRAIS 148
D YYELGV I C T P + L N + L QR+K AVS L
Sbjct: 259 DSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPL-----QRKKKRIFAVSSPSKLVTFD 313
Query: 149 KLKVLGNGYEVISVGKKKL 167
V+G + G+KKL
Sbjct: 314 HFVVIGE--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 = 30.0 bits (66), Expect = 0.97, 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|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 = 29.6 bits (65), 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|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 = 28.1 bits (61), Expect = 3.5, 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 = 4.9, 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
>pdb|3OQQ|A Chain A, Crystal Structure Of A Putative Lipoprotein (Bacova_00967)
From Bacteroides Ovatus At 2.08 A Resolution
Length = 435
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 7 IGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFR-SQLEDFARKHKNDIRKNPTF 63
+ GL+S V R L+ + TDL KE+L+T ++E+ ND RK P F
Sbjct: 197 LDGLKSEYVDRITASLILKGGQGTXTDLAKEELSTKNIVKVENKNWNWSNDTRKEPRF 254
>pdb|2L06|A Chain A, Solution Nmr Structure Of The Pbs Linker Polypeptide
Domain (Fragment 254-400) Of Phycobilisome Linker
Protein Apce From Synechocystis Sp. Pcc 6803. Northeast
Structural Genomics Consortium Target Sgr209c
Length = 155
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 4 RPGIGGLQSAAVARDQYRLLGE-NVAKLRT---DLMKEQLATFRSQLEDFARKHKNDIRK 59
+PG+ L+ AV + YR + E ++ K + ++ Q+ +++F R+ + K
Sbjct: 17 KPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRR----LAK 72
Query: 60 NPTFRSQFHE 69
+P +R QF E
Sbjct: 73 SPLYRKQFFE 82
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 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,184,815
Number of Sequences: 62578
Number of extensions: 235044
Number of successful extensions: 690
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: 683
Number of HSP's gapped (non-prelim): 14
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
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: 49 (23.5 bits)