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= 046560
(333 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QXZ|A Chain A, Pectate Lyase R236f From Xanthomonas Campestris
pdb|2QXZ|B Chain B, Pectate Lyase R236f From Xanthomonas Campestris
Length = 330
Score = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 222 DDDNKAAELFNSKLLAEMKNLSSFLPQAKIVYVDIYNPLLDLINNPVKSGFSVPDRSCCG 281
D D K + + +N+ S +P + IYN + NN SG +V G
Sbjct: 184 DSDTKNSAARTTYHHNRFENVESRVPLQRFGLSHIYN---NYFNNVTTSGINV---RMGG 237
Query: 282 TGTIETSVLCNQLIPFTCDNVSEFVFWD 309
IE++ N P T + SE +WD
Sbjct: 238 IAKIESNYFENIKNPVTSRDSSEIGYWD 265
>pdb|2QY1|A Chain A, Pectate Lyase A31g/r236f From Xanthomonas Campestris
pdb|2QY1|B Chain B, Pectate Lyase A31g/r236f From Xanthomonas Campestris
Length = 330
Score = 31.2 bits (69), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 36/88 (40%), Gaps = 6/88 (6%)
Query: 222 DDDNKAAELFNSKLLAEMKNLSSFLPQAKIVYVDIYNPLLDLINNPVKSGFSVPDRSCCG 281
D D K + + +N+ S +P + IYN + NN SG +V G
Sbjct: 184 DSDTKNSAARTTYHHNRFENVESRVPLQRFGLSHIYN---NYFNNVTTSGINV---RMGG 237
Query: 282 TGTIETSVLCNQLIPFTCDNVSEFVFWD 309
IE++ N P T + SE +WD
Sbjct: 238 IAKIESNYFENIKNPVTSRDSSEIGYWD 265
>pdb|3HAM|A Chain A, Structure Of The Gentamicin-Aph(2")-Iia Complex
pdb|3HAM|B Chain B, Structure Of The Gentamicin-Aph(2")-Iia Complex
pdb|3HAV|A Chain A, Structure Of The Streptomycin-Atp-Aph(2")-Iia Ternary
Complex
pdb|3HAV|B Chain B, Structure Of The Streptomycin-Atp-Aph(2")-Iia Ternary
Complex
pdb|3HAV|C Chain C, Structure Of The Streptomycin-Atp-Aph(2")-Iia Ternary
Complex
Length = 299
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 6/68 (8%)
Query: 8 CSLERDLASRKLQLQENEKLLGIMAFGDSILDTGN-NNNLISLIKCNFPPYGQDFIGGKP 66
C + D ++ + + N +L G++ FGD + G+ +N+ + L+ C+ +G++F G+
Sbjct: 187 CLVHNDFSANNMIFRNN-RLFGVIDFGD--FNVGDPDNDFLCLLDCSTDDFGKEF--GRK 241
Query: 67 TGRFCNGK 74
++ K
Sbjct: 242 VLKYYQHK 249
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/89 (22%), Positives = 43/89 (48%), Gaps = 1/89 (1%)
Query: 176 LVSWTSTIIKDLYE-VGVRKIAIFSTLPLGCLPILRTLHGGLMRSCGDDDNKAAELFNSK 234
L++ T +K+L++ V + I F +P +L GL+ G D + + K
Sbjct: 209 LLAQNETGLKNLFKLVSLSHIQYFHRVPRIPRSVLVKHRDGLLVGSGCDKGELFDNLIQK 268
Query: 235 LLAEMKNLSSFLPQAKIVYVDIYNPLLDL 263
E+++++ F ++ D+Y PL+++
Sbjct: 269 APEEVEDIARFYDFLEVHPPDVYKPLIEM 297
>pdb|1Q0S|A Chain A, Binary Structure Of T4dam With Adohcy
pdb|1Q0T|A Chain A, Ternary Structure Of T4dam With Adohcy And Dna
pdb|1Q0T|B Chain B, Ternary Structure Of T4dam With Adohcy And Dna
Length = 259
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 27 LLGIMAFGDSILDTGNNNNLISLIKCNFPPYGQD---FIGGKPTGRFCNGKVLTDLIAE 82
+LG +A+ TGN +L+ +K +FP Y + F GG NG VL + I E
Sbjct: 1 MLGAIAY------TGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQE 53
>pdb|1YFJ|A Chain A, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|B Chain B, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|C Chain C, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|D Chain D, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|E Chain E, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFJ|F Chain F, T4dam In Complex With Adohcy And 15-Mer Oligonucleotide
Showing Semi-Specific And Specific Contact
pdb|1YFL|A Chain A, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|B Chain B, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|D Chain D, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
pdb|1YFL|E Chain E, T4dam In Complex With Sinefungin And 16-Mer
Oligonucleotide Showing Semi-Specific And Specific
Contact And Flipped Base
Length = 259
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 27 LLGIMAFGDSILDTGNNNNLISLIKCNFPPYGQD---FIGGKPTGRFCNGKVLTDLIAE 82
+LG +A+ TGN +L+ +K +FP Y + F GG NG VL + I E
Sbjct: 1 MLGAIAY------TGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQE 53
>pdb|1YF3|A Chain A, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
Making Non- And Semi-Specific (~14) CONTACT
pdb|1YF3|B Chain B, T4dam In Complex With Adohcy And 13-Mer Oligonucleotide
Making Non- And Semi-Specific (~14) CONTACT
Length = 259
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 27 LLGIMAFGDSILDTGNNNNLISLIKCNFPPYGQD---FIGGKPTGRFCNGKVLTDLIAE 82
+LG +A+ TGN +L+ +K +FP Y + F GG NG VL + I E
Sbjct: 1 MLGAIAY------TGNKQSLLPELKSHFPKYNRFVDLFCGGLSVSLNVNGPVLANDIQE 53
>pdb|3UZR|A Chain A, Crystal Structure Of Aminoglycoside Phosphotransferase
Aph(2'')-Ib, Apo Form
pdb|4DCA|A Chain A, Crystal Structure Of Aminoglycoside Phosphotransferase
Aph(2'')-Ib, Adp-Bound
Length = 320
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 24 NEKLLGIMAFGDSILDTGN-NNNLISLIKCNFPPYGQDFIGGKPTGRFCNGKV 75
N +L G++ FGD + G+ +N+ + L+ C+ +G++F G+ ++ K
Sbjct: 223 NNRLFGVIDFGD--FNVGDPDNDFLCLLDCSTDDFGKEF--GRKVLKYYQHKA 271
>pdb|3RF7|A Chain A, Crystal Structure Of An Iron-Containing Alcohol
Dehydrogenase (Sden_2133) From Shewanella Denitrificans
Os-217 At 2.12 A Resolution
Length = 375
Score = 27.7 bits (60), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 9/79 (11%)
Query: 222 DDDNKAAELFNSKLLAEMKNLS--SFLPQAKIVYVDIYNPL-------LDLINNPVKSGF 272
D+ + FN+KL + L S AK V + + NP DLI NP
Sbjct: 96 DELTAQVKAFNTKLPVSVVGLGGGSTXDLAKAVSLXLTNPGSSSEYQGWDLIKNPAVHHI 155
Query: 273 SVPDRSCCGTGTIETSVLC 291
+P S G T+VLC
Sbjct: 156 GIPTVSGTGAEASRTAVLC 174
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 0.139 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,183,313
Number of Sequences: 62578
Number of extensions: 445446
Number of successful extensions: 1076
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 1074
Number of HSP's gapped (non-prelim): 17
length of query: 333
length of database: 14,973,337
effective HSP length: 99
effective length of query: 234
effective length of database: 8,778,115
effective search space: 2054078910
effective search space used: 2054078910
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: 52 (24.6 bits)