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= psy11306
(413 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1GV9|A Chain A, P58ERGIC-53
Length = 260
Score = 290 bits (743), Expect = 9e-79, Method: Compositional matrix adjust.
Identities = 133/231 (57%), Positives = 166/231 (71%), Gaps = 1/231 (0%)
Query: 28 PVERFEYKYSFKPPYLAQKDGSVPFWEYGGNCIASLENVRVAPSLRSQKGAIWTKQTTNF 87
P RFEYKYSFK P+L Q DG+VPFW + GN I S + +R+APSL+SQ+G++WTK F
Sbjct: 26 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSADQIRIAPSLKSQRGSVWTKTKAAF 85
Query: 88 EWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVFGSSDRWKGLGLXXXXXXXXXXX 147
E W V++ FRVTGRGRIGADGLA WYT +G DG VFGS+D W G+G+
Sbjct: 86 ENWEVEVTFRVTGRGRIGADGLAIWYTENQG-LDGPVFGSADMWNGVGIFFDSFDNDGKK 144
Query: 148 XXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKPYPTRARIQYYMNTLTVWFHNGM 207
P I+ V N+G + +DHQNDGA+Q+LA C RDFRNKPYP RA+I YY TLTV +NG
Sbjct: 145 NNPAIVVVGNNGQINYDHQNDGATQALASCQRDFRNKPYPVRAKITYYQKTLTVMINNGF 204
Query: 208 TNNEQDIEVCLRVENIYLPKEGYFGVSAATGGLADDHDILHFLTSSLLPPG 258
T ++ D E C +VEN+ +P +G+FG+SAATGGLADDHD+L FLT L PG
Sbjct: 205 TPDKNDYEFCAKVENMVIPTQGHFGISAATGGLADDHDVLSFLTFQLTEPG 255
Score = 35.8 bits (81), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 16/21 (76%)
Query: 293 PVERFEYKYSFKPPYLAQKDG 313
P RFEYKYSFK P+L Q DG
Sbjct: 26 PHRRFEYKYSFKGPHLVQSDG 46
>pdb|1R1Z|A Chain A, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|B Chain B, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|C Chain C, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
pdb|1R1Z|D Chain D, The Crystal Structure Of The Carbohydrate Recognition
Domain Of The Glycoprotein Sorting Receptor P58ERGIC-53
Reveals A Novel Metal Binding Site And Conformational
Changes Associated With Calcium Ion Binding
Length = 263
Score = 290 bits (742), Expect = 1e-78, Method: Compositional matrix adjust.
Identities = 133/231 (57%), Positives = 166/231 (71%), Gaps = 1/231 (0%)
Query: 28 PVERFEYKYSFKPPYLAQKDGSVPFWEYGGNCIASLENVRVAPSLRSQKGAIWTKQTTNF 87
P RFEYKYSFK P+L Q DG+VPFW + GN I S + +R+APSL+SQ+G++WTK F
Sbjct: 29 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSADQIRIAPSLKSQRGSVWTKTKAAF 88
Query: 88 EWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVFGSSDRWKGLGLXXXXXXXXXXX 147
E W V++ FRVTGRGRIGADGLA WYT +G DG VFGS+D W G+G+
Sbjct: 89 ENWEVEVTFRVTGRGRIGADGLAIWYTENQG-LDGPVFGSADMWNGVGIFFDSFDNDGKK 147
Query: 148 XXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKPYPTRARIQYYMNTLTVWFHNGM 207
P I+ V N+G + +DHQNDGA+Q+LA C RDFRNKPYP RA+I YY TLTV +NG
Sbjct: 148 NNPAIVVVGNNGQINYDHQNDGATQALASCQRDFRNKPYPVRAKITYYQKTLTVMINNGF 207
Query: 208 TNNEQDIEVCLRVENIYLPKEGYFGVSAATGGLADDHDILHFLTSSLLPPG 258
T ++ D E C +VEN+ +P +G+FG+SAATGGLADDHD+L FLT L PG
Sbjct: 208 TPDKNDYEFCAKVENMVIPTQGHFGISAATGGLADDHDVLSFLTFQLTEPG 258
Score = 35.8 bits (81), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 16/21 (76%)
Query: 293 PVERFEYKYSFKPPYLAQKDG 313
P RFEYKYSFK P+L Q DG
Sbjct: 29 PHRRFEYKYSFKGPHLVQSDG 49
>pdb|3A4U|A Chain A, Crystal Structure Of Mcfd2 In Complex With Carbohydrate
Recognition Domain Of Ergic-53
Length = 255
Score = 288 bits (737), Expect = 4e-78, Method: Compositional matrix adjust.
Identities = 133/231 (57%), Positives = 166/231 (71%), Gaps = 1/231 (0%)
Query: 28 PVERFEYKYSFKPPYLAQKDGSVPFWEYGGNCIASLENVRVAPSLRSQKGAIWTKQTTNF 87
P RFEYKYSFK P+L Q DG+VPFW + GN I S + +RVAPSL+SQ+G++WTK F
Sbjct: 12 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAF 71
Query: 88 EWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVFGSSDRWKGLGLXXXXXXXXXXX 147
E W V++ FRVTGRGRIGADGLA WY +G +G VFGS+D W G+G+
Sbjct: 72 ENWEVEVTFRVTGRGRIGADGLAIWYAENQG-LEGPVFGSADLWNGVGIFFDSFDNDGKK 130
Query: 148 XXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKPYPTRARIQYYMNTLTVWFHNGM 207
P I+ + N+G + +DHQNDGASQ+LA C RDFRNKPYP RA+I YY NTLTV +NG
Sbjct: 131 NNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGF 190
Query: 208 TNNEQDIEVCLRVENIYLPKEGYFGVSAATGGLADDHDILHFLTSSLLPPG 258
T ++ D E C +VEN+ +P +G+FG+SAATGGLADDHD+L FLT L PG
Sbjct: 191 TPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPG 241
Score = 35.8 bits (81), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 16/21 (76%)
Query: 293 PVERFEYKYSFKPPYLAQKDG 313
P RFEYKYSFK P+L Q DG
Sbjct: 12 PHRRFEYKYSFKGPHLVQSDG 32
>pdb|3LCP|A Chain A, Crystal Structure Of The Carbohydrate Recognition Domain
Of Complex With Mcfd2
pdb|3LCP|B Chain B, Crystal Structure Of The Carbohydrate Recognition Domain
Of Complex With Mcfd2
Length = 247
Score = 288 bits (736), Expect = 5e-78, Method: Compositional matrix adjust.
Identities = 133/231 (57%), Positives = 166/231 (71%), Gaps = 1/231 (0%)
Query: 28 PVERFEYKYSFKPPYLAQKDGSVPFWEYGGNCIASLENVRVAPSLRSQKGAIWTKQTTNF 87
P RFEYKYSFK P+L Q DG+VPFW + GN I S + +RVAPSL+SQ+G++WTK F
Sbjct: 12 PHRRFEYKYSFKGPHLVQSDGTVPFWAHAGNAIPSSDQIRVAPSLKSQRGSVWTKTKAAF 71
Query: 88 EWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVFGSSDRWKGLGLXXXXXXXXXXX 147
E W V++ FRVTGRGRIGADGLA WY +G +G VFGS+D W G+G+
Sbjct: 72 ENWEVEVTFRVTGRGRIGADGLAIWYAENQG-LEGPVFGSADLWNGVGIFFDSFDNDGKK 130
Query: 148 XXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKPYPTRARIQYYMNTLTVWFHNGM 207
P I+ + N+G + +DHQNDGASQ+LA C RDFRNKPYP RA+I YY NTLTV +NG
Sbjct: 131 NNPAIVIIGNNGQIHYDHQNDGASQALASCQRDFRNKPYPVRAKITYYQNTLTVMINNGF 190
Query: 208 TNNEQDIEVCLRVENIYLPKEGYFGVSAATGGLADDHDILHFLTSSLLPPG 258
T ++ D E C +VEN+ +P +G+FG+SAATGGLADDHD+L FLT L PG
Sbjct: 191 TPDKNDYEFCAKVENMIIPAQGHFGISAATGGLADDHDVLSFLTFQLTEPG 241
Score = 35.8 bits (81), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 16/21 (76%)
Query: 293 PVERFEYKYSFKPPYLAQKDG 313
P RFEYKYSFK P+L Q DG
Sbjct: 12 PHRRFEYKYSFKGPHLVQSDG 32
>pdb|2DUO|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN, CA2+-
Bound Form
pdb|2DUO|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN, CA2+-
Bound Form
pdb|2DUP|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
METAL-Free Form
pdb|2DUP|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
METAL-Free Form
pdb|2DUQ|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN-Bound Form
pdb|2DUQ|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN-Bound Form
pdb|2DUR|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
CA2+MAN2-Bound Form
pdb|2DUR|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
CA2+MAN2-Bound Form
pdb|2E6V|A Chain A, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|B Chain B, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|C Chain C, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|D Chain D, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
pdb|2E6V|E Chain E, Crystal Structure Of Vip36 ExoplasmicLUMENAL DOMAIN,
Ca2+MAN3GLCNAC-Bound Form
Length = 253
Score = 143 bits (361), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 82/243 (33%), Positives = 126/243 (51%), Gaps = 12/243 (4%)
Query: 30 ERFEYKYSFKPPYLAQKDGSVPFWEYGGNCIASLENVRVAPSLRSQKGAIWTKQTTNFEW 89
E + ++S PY S+P W++ G+ I + + VR+ P RS++G+IW Q +
Sbjct: 4 EHLKREHSLIKPYQGVGSSSMPLWDFQGSTILTSQYVRLTPDERSKEGSIWNHQPCFLKD 63
Query: 90 WNVDIVFRVTGRGR--IGADGLAFWYTSEKGSYDGEVFGSSDRWKGLG--LXXXXXXXXX 145
W + + F+V G G+ + DG+A WYT ++ G VFGS D + GL L
Sbjct: 64 WEMHVHFKVHGTGKKNLHGDGIALWYTRDR-LVPGPVFGSKDNFHGLAIFLDTYPNDETT 122
Query: 146 XXXXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKPYPTRARIQYYMNTLTVWFHN 205
PYI +VN+G++++DH DG LAGC DFRN+ + T ++Y LTV
Sbjct: 123 ERVFPYISVMVNNGSLSYDHSKDGRWTELAGCTADFRNRDHDTFLAVRYSRGRLTV---- 178
Query: 206 GMTNNEQDIE--VCLRVENIYLPKEGYFGVSAATGGLADDHDILHFLTSSLLPPGAKQQE 263
MT+ E E C+ + + LP YFG SA TG L+D+HDI+ L+ +E
Sbjct: 179 -MTDLEDKNEWKNCIDITGVRLPTGYYFGASAGTGDLSDNHDIISMKLFQLMVEHTPDEE 237
Query: 264 QVN 266
++
Sbjct: 238 NID 240
>pdb|2A6X|A Chain A, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Y131f Mutant
pdb|2A6X|B Chain B, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Y131f Mutant
Length = 226
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 45/186 (24%), Positives = 70/186 (37%), Gaps = 27/186 (14%)
Query: 73 RSQKGAIW------TKQTTNFEWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVF- 125
++ KG++W K EW FR + +G GLAFW E+F
Sbjct: 48 KNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKG-----GLAFWLKQGNEGDSTELFG 102
Query: 126 GSSDRWKGLGLXXXXXXXXXXXXXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKP 185
GSS ++ GL + + A +NDG D + +S A CL +++
Sbjct: 103 GSSKKFNGLMILLRLDDKLGES----VTAFLNDGTKDLDIE---SSPYFASCLFQYQDSM 155
Query: 186 YPTRARIQYYMNTLTVWFHNGMTNNEQDIEVCLRVENIYLPKEGYF--GVSAATGGLADD 243
P+ R+ Y N L N + + D VC + + F G SA +
Sbjct: 156 VPSTLRLTY--NPL----DNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKES 209
Query: 244 HDILHF 249
+IL
Sbjct: 210 FEILKM 215
>pdb|2A6V|A Chain A, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Potassium-Bound Form
pdb|2A6V|B Chain B, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Potassium-Bound Form
pdb|2A6W|A Chain A, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Metal-Free Form
pdb|2A6W|B Chain B, Crystal Structure Of Emp46p Carbohydrate Recognition
Domain (Crd), Metal-Free Form
Length = 226
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 45/186 (24%), Positives = 69/186 (37%), Gaps = 27/186 (14%)
Query: 73 RSQKGAIW------TKQTTNFEWWNVDIVFRVTGRGRIGADGLAFWYTSEKGSYDGEVF- 125
++ KG++W K EW FR + +G GLAFW E+F
Sbjct: 48 KNTKGSLWLKPEYSIKDAMTIEWTFRSFGFRGSTKG-----GLAFWLKQGNEGDSTELFG 102
Query: 126 GSSDRWKGLGLXXXXXXXXXXXXXPYIMAVVNDGNMAFDHQNDGASQSLAGCLRDFRNKP 185
GSS ++ GL + Y+ NDG D + +S A CL +++
Sbjct: 103 GSSKKFNGLMILLRLDDKLGESVTAYL----NDGTKDLDIE---SSPYFASCLFQYQDSM 155
Query: 186 YPTRARIQYYMNTLTVWFHNGMTNNEQDIEVCLRVENIYLPKEGYF--GVSAATGGLADD 243
P+ R+ Y N L N + + D VC + + F G SA +
Sbjct: 156 VPSTLRLTY--NPL----DNHLLKLQMDNRVCFQTRKVKFMGSSPFRIGTSAINDASKES 209
Query: 244 HDILHF 249
+IL
Sbjct: 210 FEILKM 215
>pdb|2CN2|A Chain A, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|B Chain B, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|C Chain C, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
pdb|2CN2|D Chain D, Crystal Structures Of Clostridium Thermocellum
Xyloglucanase
Length = 737
Score = 28.1 bits (61), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 373 SQGGGIPHQVVPGQPMPMINNDALLASQNSLLST 406
S GG+ + VPGQP ++ + +LAS L T
Sbjct: 227 STDGGVTWKAVPGQPKGLLPHHGVLASNGXLYIT 260
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
0.316 0.133 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,505,427
Number of Sequences: 62578
Number of extensions: 517142
Number of successful extensions: 1262
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1243
Number of HSP's gapped (non-prelim): 16
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)