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= 008060
(579 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 178 bits (452), Expect = 6e-45, Method: Compositional matrix adjust.
Identities = 120/357 (33%), Positives = 179/357 (50%), Gaps = 55/357 (15%)
Query: 23 SWKNPYVLRLAFSAGIGGLLFGYDTGVISGAL-----LYIRDDFKSVDRKTLLQESIVSM 77
+ + Y+ + A +GGLLFGYDT VISG + +++ S L V+
Sbjct: 4 QYNSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVAS 63
Query: 78 AVXXXXXXXXXXXWMNDRFGRRTSILVADFLFFVGAVIMA------AAPNPG-------- 123
A+ + ++RFGRR S+ +A LFF+ V A + NP
Sbjct: 64 ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123
Query: 124 ----ALITGRVFVGLGVGMASMTSPLYISEASPAKIRGALVSTNGFLITSGQFLSYLINL 179
+ R+ G+GVG+ASM SP+YI+E +PA IRG LVS N F I GQ L Y +N
Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183
Query: 180 AFTRAPGT-------WRWMLGVAGIPALLQFILMLLLPESPRWLYRKGREEEAQAILRKV 232
R+ WR+M IPALL +L+ +PESPRWL +G++E+A+ ILRK+
Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243
Query: 233 YPAHEVETEIRDLKESVDXXXXXXXXXXXXNLVKLLKTRTVRRGLIAGVG-------LQV 285
++++K S+D +T R L+ GVG L +
Sbjct: 244 MGNTLATQAVQEIKHSLDH-----------------GRKTGGRLLMFGVGVIVIGVMLSI 286
Query: 286 FQQFVGINTVMYYSPTIVQLSGFASNRTALLLSLVTSGLNAAGSIVSIYFIDRTGRK 342
FQQFVGIN V+YY+P + + G AS ALL +++ +N ++++I +D+ GRK
Sbjct: 287 FQQFVGINVVLYYAPEVFKTLG-ASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRK 342
Score = 63.5 bits (153), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 39/114 (34%), Positives = 61/114 (53%), Gaps = 12/114 (10%)
Query: 454 GWLALVGLALYIIFFSPGMGTAPWIVNSEIYPLRFRGVCGGIAATANWISNLIVAQSFLS 513
G +AL+ + Y+ F+ G W++ SEI+P RG IA A W++N V+ +F
Sbjct: 369 GIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPM 428
Query: 514 LTQAIGTSW---------TFLIFGVISVAALLFVLIFVPETKGLPIEEIEKMLE 558
+ + SW ++ I+G + V A LF+ FVPETKG +EE+E + E
Sbjct: 429 MDK---NSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWE 479
>pdb|3NVN|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
pdb|3NVQ|B Chain B, Molecular Mechanism Of Guidance Cue Recognition
pdb|3NVQ|F Chain F, Molecular Mechanism Of Guidance Cue Recognition
Length = 476
Score = 32.7 bits (73), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 400 CMKCLKASSPDCGFCASHSNKLFPGACLISNS 431
C +CL A+ P CG+C S F G C+ S +
Sbjct: 427 CSECLTATDPHCGWCHSLQRCTFQGDCVHSEN 458
>pdb|1TYE|B Chain B, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|D Chain D, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
pdb|1TYE|F Chain F, Structural Basis For Allostery In Integrins And Binding Of
Ligand- Mimetic Therapeutics To The Platelet Receptor
For Fibrinogen
Length = 440
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 400 CMKCLKASSPDCGFCASHSNKLFPGACLISNSTVKDLCHDESREW 444
C +CL A SP C +C+ + L C + + +KD C ES E+
Sbjct: 13 CQQCL-AVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEF 56
>pdb|2VC2|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist L-739758
pdb|2VDK|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDL|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece
pdb|2VDM|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Tirofiban
pdb|2VDN|B Chain B, Re-Refinement Of Integrin Alphaiibbeta3 Headpiece Bound To
Antagonist Eptifibatide
pdb|2VDO|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide, Hhlggakqagdv
pdb|2VDP|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To Fibrinogen Gamma
Chain Peptide,Lggakqagdv
pdb|2VDQ|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Hhlggakqrgdv
pdb|2VDR|B Chain B, Integrin Alphaiibbeta3 Headpiece Bound To A Chimeric
Fibrinogen Gamma Chain Peptide, Lggakqrgdv
pdb|3FCU|B Chain B, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|D Chain D, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
pdb|3FCU|F Chain F, Structure Of Headpiece Of Integrin Aiibb3 In Open
Conformation
Length = 461
Score = 28.9 bits (63), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 400 CMKCLKASSPDCGFCASHSNKLFPGACLISNSTVKDLCHDESREW 444
C +CL A SP C +C+ + L C + + +KD C ES E+
Sbjct: 13 CQQCL-AVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEF 56
>pdb|3T3M|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3M|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|B Chain B, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
pdb|3T3P|D Chain D, A Novel High Affinity Integrin Alphaiibbeta3 Receptor
Antagonist That Unexpectedly Displaces Mg2+ From The
Beta3 Midas
Length = 472
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 400 CMKCLKASSPDCGFCASHSNKLFPGACLISNSTVKDLCHDESREW 444
C +CL A SP C +C+ + L C + + +KD C ES E+
Sbjct: 13 CQQCL-AVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEF 56
>pdb|2WSC|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSE|4 Chain 4, Improved Model Of Plant Photosystem I
pdb|2WSF|4 Chain 4, Improved Model Of Plant Photosystem I
Length = 251
Score = 28.9 bits (63), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 36/79 (45%), Gaps = 11/79 (13%)
Query: 150 ASPAKIRGALVSTNGF----LITSGQFLSYLINLAFTRAPGTWRW-MLGVAGIPALLQFI 204
ASP + G+L NGF L + L + + RW MLGVAG+ L +
Sbjct: 61 ASPGYLTGSLPGDNGFDPLGLAEDPENLRWFVQAELVNG----RWAMLGVAGM-LLPEVF 115
Query: 205 LMLLLPESPRWLYRKGREE 223
+ + P+W Y G+EE
Sbjct: 116 TSIGIINVPKW-YAAGKEE 133
>pdb|3NID|B Chain B, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NID|D Chain D, The Closed Headpiece Of Integrin Alphaiib Beta3 And Its
Complex With An Alpahiib Beta3 -Specific Antagonist That
Does Not Induce Opening
pdb|3NIF|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIF|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|B Chain B, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
pdb|3NIG|D Chain D, The Closed Headpiece Of Integrin Iib 3 And Its Complex
With An Iib 3 - Specific Antagonist That Does Not Induce
Opening
Length = 471
Score = 28.5 bits (62), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 400 CMKCLKASSPDCGFCASHSNKLFPGACLISNSTVKDLCHDESREW 444
C +CL A SP C +C+ + L C + + +KD C ES E+
Sbjct: 13 CQQCL-AVSPMCAWCSDEALPLGSPRCDLKENLLKDNCAPESIEF 56
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
0.324 0.138 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,857,770
Number of Sequences: 62578
Number of extensions: 539280
Number of successful extensions: 1502
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1489
Number of HSP's gapped (non-prelim): 17
length of query: 579
length of database: 14,973,337
effective HSP length: 104
effective length of query: 475
effective length of database: 8,465,225
effective search space: 4020981875
effective search space used: 4020981875
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)