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= 020693
(322 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4ATI|A Chain A, Mitf:m-Box Complex
pdb|4ATI|B Chain B, Mitf:m-Box Complex
pdb|4ATK|A Chain A, Mitf:e-Box Complex
pdb|4ATK|B Chain B, Mitf:e-Box Complex
Length = 118
Score = 34.7 bits (78), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 3/61 (4%)
Query: 261 AKRGQATNSHSLAERVRREKISERMRLLQELVPGCNK---ITGKAVMLDEIINYVQSLQQ 317
AK Q ++H+L ER RR I++R++ L L+P N K +L ++Y++ LQ+
Sbjct: 22 AKERQKKDNHNLIERRRRFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQR 81
Query: 318 Q 318
+
Sbjct: 82 E 82
>pdb|4F3L|B Chain B, Crystal Structure Of The Heterodimeric Clock:bmal1
Transcriptional Activator Complex
Length = 387
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 255 EYIHMRAKRGQATNSHSLAERVRREKISERMRLLQELVPGCNKITGKAVMLDEIINYVQS 314
EY + + A +HS E+ RR+K++ + L LVP CN ++ K L + VQ
Sbjct: 2 EYAEHQGRIKNAREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQH 61
Query: 315 LQ 316
++
Sbjct: 62 MK 63
>pdb|2DT8|A Chain A, Fatty Acid Binding Of A Degv Family Protein From Thermus
Thermophilus
Length = 280
Score = 31.2 bits (69), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 10/79 (12%)
Query: 17 SAMNCSSGMMPQKLPG-MQMNSVPMYKSVSGPDHFYGSGWEPIV------SLNQGESFGV 69
+ + S+ +PQ L G + + VP+Y ++SG + WE I + +G +F
Sbjct: 4 TLVTDSTSDLPQDLRGRLGVRVVPLYVNLSGAIY---RDWEEITPTEIFQKVREGAAFPT 60
Query: 70 SSMVSHNEFAPSYPVALEN 88
+S S +FA Y ALE
Sbjct: 61 TSQPSPEDFARVYREALEE 79
>pdb|1R05|A Chain A, Solution Structure Of Max B-Hlh-Lz
pdb|1R05|B Chain B, Solution Structure Of Max B-Hlh-Lz
Length = 87
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 270 HSLAERVRREKISERMRLLQELVPGCN-KITGKAVMLDEIINYVQSLQQQVEVL 322
H+ ER RR+ I + L++ VP + +A +LD+ Y+Q ++++V L
Sbjct: 8 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKVHTL 61
>pdb|4H10|A Chain A, Intermolecular Recognition Revealed By The Complex
Structure Of Human Clock-bmal1 Basic Helix-loop-helix
Domains With E-box Dna
Length = 73
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 266 ATNSHSLAERVRREKISERMRLLQELVPGCNKITGKAVMLDEIINYVQSLQ 316
A +HS E+ RR+K++ + L LVP CN ++ K L + VQ ++
Sbjct: 9 AREAHSQIEKRRRDKMNSFIDELASLVPTCNAMSRKLDKLTVLRMAVQHMK 59
>pdb|2HXT|A Chain A, Crystal Structure Of L-Fuconate Dehydratase From
Xanthomonas Campestris Liganded With Mg++ And
D-Erythronohydroxamate
Length = 441
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 68 GVSSMVSHNEFAPSYPVA--LENQGMSSTSNLDQYSSDPSFVE----LVPKIPGFGSGNF 121
G+ +V H A + +E++ + +L Q+ DP ++ L P++PGF +
Sbjct: 356 GLCELVQHLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEMH 415
Query: 122 SEMVSSFGLPE 132
++ F P+
Sbjct: 416 PASIAEFSYPD 426
>pdb|2HXU|A Chain A, Crystal Structure Of K220a Mutant Of L-Fuconate
Dehydratase From Xanthomonas Campestris Liganded With
Mg++ And L-Fuconate
Length = 441
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 68 GVSSMVSHNEFAPSYPVA--LENQGMSSTSNLDQYSSDPSFVE----LVPKIPGFGSGNF 121
G+ +V H A + +E++ + +L Q+ DP ++ L P++PGF +
Sbjct: 356 GLCELVQHLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEMH 415
Query: 122 SEMVSSFGLPE 132
++ F P+
Sbjct: 416 PASIAEFSYPD 426
>pdb|2HNE|A Chain A, Crystal Structure Of L-fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|2HNE|B Chain B, Crystal Structure Of L-fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|2HNE|C Chain C, Crystal Structure Of L-fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|2HNE|D Chain D, Crystal Structure Of L-fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
Length = 436
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 68 GVSSMVSHNEFAPSYPVA--LENQGMSSTSNLDQYSSDPSFVE----LVPKIPGFGSGNF 121
G+ +V H A + +E++ + +L Q+ DP ++ L P++PGF +
Sbjct: 356 GLCELVQHLAMADFVAITGKMEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEMH 415
Query: 122 SEMVSSFGLPE 132
++ F P+
Sbjct: 416 PASIAEFSYPD 426
>pdb|1YEY|A Chain A, Crystal Structure Of L-Fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|1YEY|B Chain B, Crystal Structure Of L-Fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|1YEY|C Chain C, Crystal Structure Of L-Fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
pdb|1YEY|D Chain D, Crystal Structure Of L-Fuconate Dehydratase From
Xanthomonas Campestris Pv. Campestris Str. Atcc 33913
Length = 444
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 68 GVSSMVSHNEFAPSYPVA--LENQGMSSTSNLDQYSSDPSFVE----LVPKIPGFGSGNF 121
G+ +V H A + E++ + +L Q+ DP ++ L P++PGF +
Sbjct: 359 GLCELVQHLAXADFVAITGKXEDRAIEFVDHLHQHFLDPVRIQHGRYLAPEVPGFSAEXH 418
Query: 122 SEMVSSFGLPE 132
++ F P+
Sbjct: 419 PASIAEFSYPD 429
>pdb|1NKP|B Chain B, Crystal Structure Of Myc-Max Recognizing Dna
pdb|1NKP|E Chain E, Crystal Structure Of Myc-Max Recognizing Dna
Length = 83
Score = 27.7 bits (60), Expect = 9.2, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 270 HSLAERVRREKISERMRLLQELVPGCN-KITGKAVMLDEIINYVQSLQQQ 318
H+ ER RR+ I + L++ VP + +A +LD+ Y+Q ++++
Sbjct: 6 HNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRK 55
>pdb|1BO1|A Chain A, Phosphatidylinositol Phosphate Kinase Type Ii Beta
pdb|1BO1|B Chain B, Phosphatidylinositol Phosphate Kinase Type Ii Beta
Length = 416
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 47 PDHFYGSGWEPIVSLNQGESFGVSSMVSHNEFAPSYPVALENQGMSSTSNLDQYSSDPSF 106
P F + P+V N E FG+ N S P+ ++QG T L Y D F
Sbjct: 90 PSRFKFKEYCPMVFRNLRERFGIDDQDYQNSVTRSAPINSDSQGRCGTRFLTTY--DRRF 147
Query: 107 V 107
V
Sbjct: 148 V 148
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
0.309 0.127 0.361
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,339,310
Number of Sequences: 62578
Number of extensions: 368484
Number of successful extensions: 568
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 564
Number of HSP's gapped (non-prelim): 18
length of query: 322
length of database: 14,973,337
effective HSP length: 99
effective length of query: 223
effective length of database: 8,778,115
effective search space: 1957519645
effective search space used: 1957519645
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (24.3 bits)