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= 027892
(217 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J9A|A Chain A, Oligoribonuclease
Length = 184
Score = 159 bits (403), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 85/179 (47%), Positives = 109/179 (60%), Gaps = 1/179 (0%)
Query: 36 KMPLVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQN 95
K L+WIDLE TGL E +RI+EIA I+TD L EGP L +HQ+ E L+ +WCQ
Sbjct: 7 KQNLIWIDLEXTGLDPEKERIIEIATIVTDKNLNILAEGPVLAVHQSDELLNKXNDWCQK 66
Query: 96 HHEASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLA 155
H +GL +++ S LTER AE Q ++F+KK V + GNS+ D FL KY PDLA
Sbjct: 67 THSENGLIERIKASKLTERAAELQTLDFLKKWVPKGASPICGNSIAQDKRFLVKYXPDLA 126
Query: 156 SLFSHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKENIFKTN 214
F + +DVS++K L RW P KE H ALDDIRESI EL YY+E+ K +
Sbjct: 127 DYFHYRHLDVSTLKELAARWKPEILEGF-KKENTHLALDDIRESIKELAYYREHFXKLD 184
>pdb|2IGI|A Chain A, Crystal Structure Of E. Coli Oligoribonuclease
pdb|2IGI|B Chain B, Crystal Structure Of E. Coli Oligoribonuclease
Length = 180
Score = 154 bits (388), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 79/174 (45%), Positives = 109/174 (62%), Gaps = 1/174 (0%)
Query: 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHE 98
L+WIDLEMTGL E DRI+EIA ++TD L EGP + +HQ+ E L M +W H
Sbjct: 7 LIWIDLEMTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALMDDWNVRTHT 66
Query: 99 ASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF 158
ASGL ++V S + +REAE +EF+K+ V + GNS+ D FL KYMP+L + F
Sbjct: 67 ASGLVERVKASTMGDREAELATLEFLKQWVPAGKSPICGNSIGQDRRFLFKYMPELEAYF 126
Query: 159 SHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKENIFK 212
+ +DVS++K L RW P +K+ H+A+DDIRES+ EL YY+E+ K
Sbjct: 127 HYRYLDVSTLKELARRWKPEILDGF-TKQGTHQAMDDIRESVAELAYYREHFIK 179
>pdb|1YTA|A Chain A, Crystal Structure Of Oligoribonuclease, The Lone Essential
Exoribonuclease In Escherichia Coli
pdb|1YTA|B Chain B, Crystal Structure Of Oligoribonuclease, The Lone Essential
Exoribonuclease In Escherichia Coli
pdb|1YTA|C Chain C, Crystal Structure Of Oligoribonuclease, The Lone Essential
Exoribonuclease In Escherichia Coli
pdb|1YTA|D Chain D, Crystal Structure Of Oligoribonuclease, The Lone Essential
Exoribonuclease In Escherichia Coli
Length = 180
Score = 144 bits (363), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 76/174 (43%), Positives = 104/174 (59%), Gaps = 1/174 (0%)
Query: 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHE 98
L+WIDLE TGL E DRI+EIA ++TD L EGP + +HQ+ E L +W H
Sbjct: 7 LIWIDLEXTGLDPERDRIIEIATLVTDANLNILAEGPTIAVHQSDEQLALXDDWNVRTHT 66
Query: 99 ASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF 158
ASGL ++V S +REAE +EF+K+ V + GNS+ D FL KY P+L + F
Sbjct: 67 ASGLVERVKASTXGDREAELATLEFLKQWVPAGKSPICGNSIGQDRRFLFKYXPELEAYF 126
Query: 159 SHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKENIFK 212
+ +DVS++K L RW P +K+ H+A DDIRES+ EL YY+E+ K
Sbjct: 127 HYRYLDVSTLKELARRWKPEILDGF-TKQGTHQAXDDIRESVAELAYYREHFIK 179
>pdb|3TR8|A Chain A, Structure Of An Oligoribonuclease (Orn) From Coxiella
Burnetii
pdb|3TR8|B Chain B, Structure Of An Oligoribonuclease (Orn) From Coxiella
Burnetii
Length = 186
Score = 141 bits (355), Expect = 3e-34, Method: Compositional matrix adjust.
Identities = 77/179 (43%), Positives = 105/179 (58%), Gaps = 3/179 (1%)
Query: 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHE 98
L+W+DLE TGL E DRI+EIA I+T+ L EGP IHQ + L + W +HH
Sbjct: 11 LIWLDLEXTGLDPERDRIIEIATIVTNSHLDILAEGPAFAIHQPDKLLTAXDNWNTSHHT 70
Query: 99 ASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF 158
ASGL ++V +S + E EAE + F++K V L GNSV D FL +Y P L F
Sbjct: 71 ASGLLERVKNSSVDEVEAETLTLAFLEKYVSAGKSPLCGNSVCQDRRFLSRYXPRLNQFF 130
Query: 159 SHVLVDVSSIKALCMRWYPRDYRKVPSKEQKHRALDDIRESIMELKYYKENIFKTNLKK 217
+ +DV+++K L RW P+ KE +H AL DIR+SI EL+YY+ ++ NL K
Sbjct: 131 HYRHLDVTTLKILAQRWAPQ-IAAAHIKESQHLALQDIRDSIEELRYYRAHLL--NLSK 186
>pdb|2GBZ|A Chain A, The Crystal Structure Of Xc847 From Xanthomonas
Campestris: A 3-5 Oligoribonuclease Of Dnaq Fold Family
With A Novel Opposingly-Shifted Helix
Length = 194
Score = 139 bits (349), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 74/173 (42%), Positives = 103/173 (59%), Gaps = 7/173 (4%)
Query: 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHE 98
L+WIDLEMTGL + D I+EIA I+TD +L EGP+L I + E L++M EW +N H
Sbjct: 11 LIWIDLEMTGLDTDRDSIIEIATIVTDAQLNVLAEGPELAIAHSLETLEAMDEWNRNQHR 70
Query: 99 ASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLF 158
SGL ++VL S +T +AE Q V F+ + + + GNS+ D FL + M L F
Sbjct: 71 RSGLWQRVLDSQVTHAQAEAQTVAFLGEWIRAGASPMCGNSICQDRRFLHRQMSRLERYF 130
Query: 159 SHVLVDVSSIKALCMRWYPRDYRKVPS---KEQKHRALDDIRESIMELKYYKE 208
+ +DVS+IK L RW P V S K H AL D+R+SI EL++Y++
Sbjct: 131 HYRNLDVSTIKELARRWAP----AVASGFAKSSAHTALSDVRDSIDELRHYRQ 179
>pdb|2P1J|A Chain A, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
pdb|2P1J|B Chain B, Crystal Structure Of A Polc-Type Dna Polymerase Iii
Exonuclease Domain From Thermotoga Maritima
Length = 186
Score = 31.2 bits (69), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 25/119 (21%), Positives = 56/119 (47%), Gaps = 15/119 (12%)
Query: 39 LVWIDLEMTGLKIEVDRILEIACIITDGKLTKSVEGPDLVIHQTKECLDSMGEWCQNHHE 98
V +D E TGL +VD I+EI + G ++ + + E + E
Sbjct: 14 FVVLDFETTGLDPQVDEIIEIGAVKIQGG---------QIVDEYHTLIKPSREISRKSSE 64
Query: 99 ASGLTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASL 157
+G+T+++L + + E + + F++ ++ ++A N+ + D+ FL+ ++ + L
Sbjct: 65 ITGITQEMLENKRSIEEVLPEFLGFLEDSI-----IVAHNANF-DYRFLRLWIKKVMGL 117
>pdb|1EI3|A Chain A, Crystal Structure Of Native Chicken Fibrinogen
pdb|1EI3|D Chain D, Crystal Structure Of Native Chicken Fibrinogen
Length = 491
Score = 30.0 bits (66), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 102 LTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGN--------SVYVDFMFLKKYMPD 153
+TKKV+ RE ++VE + + G+ L G S DF L + +PD
Sbjct: 296 VTKKVISGPDGPRE---EIVEKMVSSDGSDCSHLQGGREGSTYHFSGTGDFHKLDRLLPD 352
Query: 154 LASLFSHVLVDVSSIKAL 171
L S F+H V SS ++
Sbjct: 353 LESFFTHDSVSTSSRHSI 370
>pdb|1M1J|A Chain A, Crystal Structure Of Native Chicken Fibrinogen With Two
Different Bound Ligands
pdb|1M1J|D Chain D, Crystal Structure Of Native Chicken Fibrinogen With Two
Different Bound Ligands
Length = 491
Score = 30.0 bits (66), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 11/78 (14%)
Query: 102 LTKKVLHSGLTEREAEKQVVEFVKKNVGTYTPLLAGN--------SVYVDFMFLKKYMPD 153
+TKKV+ RE ++VE + + G+ L G S DF L + +PD
Sbjct: 296 VTKKVISGPDGPRE---EIVEKMVSSDGSDCSHLQGGREGSTYHFSGTGDFHKLDRLLPD 352
Query: 154 LASLFSHVLVDVSSIKAL 171
L S F+H V SS ++
Sbjct: 353 LESFFTHDSVSTSSRHSI 370
>pdb|2L9S|B Chain B, Solution Structure Of Pf1 Sid1-Msin3a Pah2 Complex
Length = 94
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 19/44 (43%)
Query: 124 VKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDVSS 167
K+ G YTP L VY L K DL S F L D +S
Sbjct: 51 AKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDANS 94
>pdb|1G1E|B Chain B, Nmr Structure Of The Human Mad1 Transrepression Domain Sid
In Complex With Mammalian Sin3a Pah2 Domain
pdb|1S5Q|B Chain B, Solution Structure Of Mad1 Sid-Msin3a Pah2 Complex
pdb|1S5R|B Chain B, Solution Structure Of Hbp1 Sid-Msin3a Pah2 Complex
Length = 89
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 17/42 (40%)
Query: 124 VKKNVGTYTPLLAGNSVYVDFMFLKKYMPDLASLFSHVLVDV 165
K+ G YTP L VY L K DL S F L D
Sbjct: 48 AKEAGGNYTPALTEQEVYAQVARLFKNQEDLLSEFGQFLPDA 89
>pdb|3HK4|A Chain A, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|B Chain B, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|C Chain C, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
pdb|3HK4|D Chain D, Crystal Structure Of A Putative Snoal-Like Polyketide
Cyclase [carbohydrate Phosphatase] (Mlr7391) From
Mesorhizobium Loti At 1.96 A Resolution
Length = 136
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 70 KSVEGPDLVIHQTKECLDSMGEWCQNHHEASG 101
++ EGP V H KE L +W Q +HE G
Sbjct: 54 EAXEGPXAVSH-GKEALRQKSQWWQENHEVHG 84
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
0.317 0.132 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,197,172
Number of Sequences: 62578
Number of extensions: 240891
Number of successful extensions: 1676
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1660
Number of HSP's gapped (non-prelim): 21
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)