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= psy3650
(435 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Z86|A Chain A, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|B Chain B, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|C Chain C, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
pdb|2Z86|D Chain D, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With
Udp-Glcua And Udp
Length = 625
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 58/109 (53%), Gaps = 8/109 (7%)
Query: 203 TVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKI 262
++++PTYN + L I + + + Y YE+IV DDGS + + ++ +S+ + +
Sbjct: 96 SIVIPTYNRAKILAITLACLCN--QKTIYDYEVIVADDGSKENIEEIVREFESLLNIKYV 153
Query: 263 VLKPRKKKLG--LGTAYMHGLKYATGNFIIIMDADLSHHPKFIPEMIKL 309
R+K G L GL+ A N++ I+D D++ +P ++ ++L
Sbjct: 154 ----RQKDYGYQLCAVRNLGLRAAKYNYVAILDCDMAPNPLWVQSYMEL 198
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 6 YPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLG--LGTAYMHGLKYATGNF 63
Y YE+IV DDGS + + ++ +S+ + + R+K G L GL+ A N+
Sbjct: 122 YDYEVIVADDGSKENIEEIVREFESLLNIKYV----RQKDYGYQLCAVRNLGLRAAKYNY 177
Query: 64 IIIMDADLSHHPKFIPEMIKL 84
+ I+D D++ +P ++ ++L
Sbjct: 178 VAILDCDMAPNPLWVQSYMEL 198
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 203 TVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKI 262
++ +P YN + IV + +++ E+ + DDGS D TL + LQ Y +
Sbjct: 378 SIYIPAYNCSK---YIVRCVESALNQTITDLEVCICDDGSTDDTL---RILQEHYANHPR 431
Query: 263 VLKPRKKKLGLGTAYMHGLKYATGNFIIIMDAD 295
V +K G+G+A ++ G +I +D+D
Sbjct: 432 VRFISQKNKGIGSASNTAVRLCRGFYIGQLDSD 464
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIMD 68
E+ + DDGS D TL + LQ Y + V +K G+G+A ++ G +I +D
Sbjct: 406 EVCICDDGSTDDTL---RILQEHYANHPRVRFISQKNKGIGSASNTAVRLCRGFYIGQLD 462
Query: 69 AD 70
+D
Sbjct: 463 SD 464
>pdb|2Z87|A Chain A, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
Galnac And Udp
pdb|2Z87|B Chain B, Crystal Structure Of Chondroitin Polymerase From
Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
Galnac And Udp
Length = 624
Score = 47.8 bits (112), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/109 (26%), Positives = 58/109 (53%), Gaps = 8/109 (7%)
Query: 203 TVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKI 262
++++PTYN + L I + + + Y YE+IV DDGS + + ++ +S+ + +
Sbjct: 95 SIVIPTYNRAKILAITLACLCN--QKTIYDYEVIVADDGSKENIEEIVREFESLLNIKYV 152
Query: 263 VLKPRKKKLG--LGTAYMHGLKYATGNFIIIMDADLSHHPKFIPEMIKL 309
R+K G L GL+ A N++ I+D D++ +P ++ ++L
Sbjct: 153 ----RQKDYGYQLCAVRNLGLRAAKYNYVAILDCDMAPNPLWVQSYMEL 197
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 6/81 (7%)
Query: 6 YPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLG--LGTAYMHGLKYATGNF 63
Y YE+IV DDGS + + ++ +S+ + + R+K G L GL+ A N+
Sbjct: 121 YDYEVIVADDGSKENIEEIVREFESLLNIKYV----RQKDYGYQLCAVRNLGLRAAKYNY 176
Query: 64 IIIMDADLSHHPKFIPEMIKL 84
+ I+D D++ +P ++ ++L
Sbjct: 177 VAILDCDMAPNPLWVQSYMEL 197
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 6/93 (6%)
Query: 203 TVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKI 262
++ +P YN + IV + +++ E+ + DDGS D TL + LQ Y +
Sbjct: 377 SIYIPAYNCSK---YIVRCVESALNQTITDLEVCICDDGSTDDTL---RILQEHYANHPR 430
Query: 263 VLKPRKKKLGLGTAYMHGLKYATGNFIIIMDAD 295
V +K G+G+A ++ G +I +D+D
Sbjct: 431 VRFISQKNKGIGSASNTAVRLCRGFYIGQLDSD 463
Score = 33.9 bits (76), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 32/62 (51%), Gaps = 3/62 (4%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIMD 68
E+ + DDGS D TL + LQ Y + V +K G+G+A ++ G +I +D
Sbjct: 405 EVCICDDGSTDDTL---RILQEHYANHPRVRFISQKNKGIGSASNTAVRLCRGFYIGQLD 461
Query: 69 AD 70
+D
Sbjct: 462 SD 463
>pdb|3E25|A Chain A, Crystal Structure Of M. Tuberculosis Glucosyl-3-
Phosphoglycerate Synthase
pdb|3E26|A Chain A, Crystal Structure Of M. Tuberculosis Glucosyl-3-
Phosphoglycerate Synthase
Length = 337
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 69/143 (48%), Gaps = 29/143 (20%)
Query: 171 NYTIGEVPISFVDRVVFTTQAIMSGDSVKNKYTVLLPTYNEKENLPIIVYLITKYMDEGN 230
+TIGE+ +A +G ++ +V+LP NE+ + ++ I+ +D
Sbjct: 30 GWTIGEL------------EAAKAGRTI----SVVLPALNEEATIESVIDSISPLVD--G 71
Query: 231 YPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKIV-----LKPRKKKLGLGTAYMHGLKYAT 285
E+IV+D GS D T ++++I ++V L + G G A L +
Sbjct: 72 LVDELIVLDSGSTDDT-----EIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATS 126
Query: 286 GNFIIIMDADL-SHHPKFIPEMI 307
G+ ++ +D+DL + HP F+P ++
Sbjct: 127 GDIVVFIDSDLINPHPLFVPWLV 149
Score = 38.1 bits (87), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 11/80 (13%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIV-----LKPRKKKLGLGTAYMHGLKYATGNF 63
E+IV+D GS D T ++++I ++V L + G G A L +G+
Sbjct: 75 ELIVLDSGSTDDT-----EIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDI 129
Query: 64 IIIMDADL-SHHPKFIPEMI 82
++ +D+DL + HP F+P ++
Sbjct: 130 VVFIDSDLINPHPLFVPWLV 149
>pdb|4DDZ|A Chain A, Crystal Structure Of Glucosyl-3-Phosphoglycerate Synthase
From Mycobacterium Tuberculosis
pdb|4DE7|A Chain A, Crystal Structure Of Glucosyl-3-Phosphoglycerate Synthase
From Mycobacterium Tuberculosis In Complex With Mg2+ And
Uridine- Diphosphate (Udp)
pdb|4DEC|A Chain A, Crystal Structure Of Glucosyl-3-Phosphoglycerate Synthase
From Mycobacterium Tuberculosis In Complex With Mn2+,
Uridine-Diphosphate (Udp) And Phosphoglyceric Acid (Pga)
Length = 344
Score = 45.4 bits (106), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 36/143 (25%), Positives = 69/143 (48%), Gaps = 29/143 (20%)
Query: 171 NYTIGEVPISFVDRVVFTTQAIMSGDSVKNKYTVLLPTYNEKENLPIIVYLITKYMDEGN 230
+TIGE+ +A +G ++ +V+LP NE+ + ++ I+ +D
Sbjct: 50 GWTIGEL------------EAAKAGRTI----SVVLPALNEEATIESVIDSISPLVD--G 91
Query: 231 YPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKIV-----LKPRKKKLGLGTAYMHGLKYAT 285
E+IV+D GS D T ++++I ++V L + G G A L +
Sbjct: 92 LVDELIVLDSGSTDDT-----EIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATS 146
Query: 286 GNFIIIMDADL-SHHPKFIPEMI 307
G+ ++ +D+DL + HP F+P ++
Sbjct: 147 GDIVVFIDSDLINPHPLFVPWLV 169
Score = 37.7 bits (86), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 11/80 (13%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIV-----LKPRKKKLGLGTAYMHGLKYATGNF 63
E+IV+D GS D T ++++I ++V L + G G A L +G+
Sbjct: 95 ELIVLDSGSTDDT-----EIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDI 149
Query: 64 IIIMDADL-SHHPKFIPEMI 82
++ +D+DL + HP F+P ++
Sbjct: 150 VVFIDSDLINPHPLFVPWLV 169
>pdb|3CKJ|A Chain A, Crystal Structure Of A Mycobacterial Protein
pdb|3CKN|A Chain A, Crystal Structure Of A Mycobacterial Protein
pdb|3CKO|A Chain A, Crystal Structure Of A Mycobacterial Protein
pdb|3CKQ|A Chain A, Crystal Structure Of A Mycobacterial Protein
pdb|3CKV|A Chain A, Crystal Structure Of A Mycobacterial Protein
Length = 329
Score = 44.3 bits (103), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/120 (25%), Positives = 57/120 (47%), Gaps = 3/120 (2%)
Query: 189 TQAIMSGDSVKNKYTVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLD 248
T A + +V+LP +E++ + ++ I+ +D E+IV+D GS D T
Sbjct: 37 TVAELEAAKAGRTISVVLPALDEEDTIGSVIDSISPLVD--GLVDELIVLDSGSTDDTEI 94
Query: 249 AAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIMDADL-SHHPKFIPEMI 307
A + S + L + G G A L + G+ ++ +D+DL + HP F+P ++
Sbjct: 95 RAVAAGARVVSREQALPEVPIRPGKGEALWRSLAASRGDIVVFVDSDLINPHPMFVPWLV 154
Score = 37.7 bits (86), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 1/75 (1%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIMD 68
E+IV+D GS D T A + S + L + G G A L + G+ ++ +D
Sbjct: 80 ELIVLDSGSTDDTEIRAVAAGARVVSREQALPEVPIRPGKGEALWRSLAASRGDIVVFVD 139
Query: 69 ADL-SHHPKFIPEMI 82
+DL + HP F+P ++
Sbjct: 140 SDLINPHPMFVPWLV 154
>pdb|3BCV|A Chain A, Crystal Structure Of A Putative Glycosyltransferase From
Bacteroides Fragilis
pdb|3BCV|B Chain B, Crystal Structure Of A Putative Glycosyltransferase From
Bacteroides Fragilis
Length = 240
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 8/90 (8%)
Query: 201 KYTVLLPTYNEKENLPIIV-YLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGS 259
K +V++P YN ++ L V L+ + + + EII+IDD SPD + Y +
Sbjct: 6 KVSVIVPIYNVEKYLDQCVQALLAQTLSD----IEIILIDDESPDNCPKICDDYAAQYPN 61
Query: 260 EKIVLKPRKKKLGLGTAYMHGLKYATGNFI 289
K++ KK GLG A GL ATG ++
Sbjct: 62 IKVI---HKKNAGLGXACNSGLDVATGEYV 88
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFI 64
EII+IDD SPD + Y + K++ KK GLG A GL ATG ++
Sbjct: 36 EIILIDDESPDNCPKICDDYAAQYPNIKVI---HKKNAGLGXACNSGLDVATGEYV 88
>pdb|3F1Y|A Chain A, Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter
Xylanophilus
pdb|3F1Y|C Chain C, Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter
Xylanophilus
pdb|3KIA|A Chain A, Crystal Structure Of Mannosyl-3-Phosphoglycerate Synthase
From Rubrobacter Xylanophilus
pdb|3KIA|C Chain C, Crystal Structure Of Mannosyl-3-Phosphoglycerate Synthase
From Rubrobacter Xylanophilus
pdb|3O3P|A Chain A, Crystal Structure Of R. Xylanophilus Mpgs In Complex With
Gdp-Mannose
pdb|3O3P|B Chain B, Crystal Structure Of R. Xylanophilus Mpgs In Complex With
Gdp-Mannose
Length = 387
Score = 32.3 bits (72), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 23/93 (24%), Positives = 40/93 (43%)
Query: 203 TVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSEKI 262
+ +LP+ N + + I+ I + +I+V+D S DGT A + SE
Sbjct: 97 SAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENE 156
Query: 263 VLKPRKKKLGLGTAYMHGLKYATGNFIIIMDAD 295
++ G G A L G+ ++ +DAD
Sbjct: 157 LMSGYGDAHGKGDAMWRALSVTRGDLVLYIDAD 189
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 28/62 (45%)
Query: 9 EIIVIDDGSPDGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIMD 68
+I+V+D S DGT A + SE ++ G G A L G+ ++ +D
Sbjct: 128 QILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYID 187
Query: 69 AD 70
AD
Sbjct: 188 AD 189
>pdb|4AQ5|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 522
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 43/92 (46%), Gaps = 17/92 (18%)
Query: 201 KYTVLLPTYNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSPDGTLDAAKQLQSIYGSE 260
K+T L YN E I + L+T +D +YP E I+ID P+ + G
Sbjct: 168 KFTAL--NYNANE---ISMDLMTDTIDGKDYPIEWIIID---PEAFTEN--------GEW 211
Query: 261 KIVLKPRKKKLGLGTAYMHGLKYATGNFIIIM 292
+I+ KP KK + G + +G Y F +I+
Sbjct: 212 EIIHKPAKKNI-YGDKFPNGTNYQDVTFYLII 242
>pdb|3CS3|A Chain A, Crystal Structure Of Sugar-Binding Transcriptional
Regulator (Laci Family) From Enterococcus Faecalis
Length = 277
Score = 29.3 bits (64), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 54/121 (44%), Gaps = 10/121 (8%)
Query: 188 TTQAIMSGDSVKNKYTVLLPT----YNEKENLPIIVYLITKYMDEGNYPYEIIVIDDGSP 243
TQAI +V +K +LL Y+ +E L + +T++ PYEII D P
Sbjct: 106 ATQAIEQFVNVGSKKVLLLSGPEKGYDSQERLAVSTRELTRF----GIPYEIIQGDFTEP 161
Query: 244 DGTLDAAKQLQSIYGSEKIVLKPRKKKLGLGT-AYMHGLKYATGNFIIIMDADLSHHPKF 302
G AAK++ S +E + + ++ +G Y+ Y G I I+ D S F
Sbjct: 162 SG-YAAAKKILSQPQTEPVDVFAFNDEMAIGVYKYVAETNYQMGKDIRIIGFDNSELGAF 220
Query: 303 I 303
+
Sbjct: 221 V 221
>pdb|2D7I|A Chain A, Crsytal Structure Of Pp-Galnac-T10 With Udp, Galnac And
Mn2+
pdb|2D7R|A Chain A, Crystal Structure Of Pp-galnac-t10 Complexed With
Galnac-ser On Lectin Domain
Length = 570
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 9 EIIVIDDGSPDGTLDAA-KQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIM 67
EI+++DD S L + +++ S +I+ KK+ GL M G ATG+ I +
Sbjct: 146 EIVLVDDFSDREHLKKPLEDYMALFPSVRILRT--KKREGLIRTRMLGASVATGDVITFL 203
Query: 68 DADLSHHPKFIPEMI 82
D+ + ++P ++
Sbjct: 204 DSHCEANVNWLPPLL 218
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 234 EIIVIDDGSPDGTLDAA-KQLQSIYGSEKIVLKPRKKKLGLGTAYMHGLKYATGNFIIIM 292
EI+++DD S L + +++ S +I+ KK+ GL M G ATG+ I +
Sbjct: 146 EIVLVDDFSDREHLKKPLEDYMALFPSVRILRT--KKREGLIRTRMLGASVATGDVITFL 203
Query: 293 DADLSHHPKFIPEMI 307
D+ + ++P ++
Sbjct: 204 DSHCEANVNWLPPLL 218
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
0.320 0.139 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,129,291
Number of Sequences: 62578
Number of extensions: 470005
Number of successful extensions: 1265
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1244
Number of HSP's gapped (non-prelim): 24
length of query: 435
length of database: 14,973,337
effective HSP length: 102
effective length of query: 333
effective length of database: 8,590,381
effective search space: 2860596873
effective search space used: 2860596873
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: 53 (25.0 bits)