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= 003550
(811 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1YDY|A Chain A, Crystal Structure Of Periplasmic Glycerophosphodiester
Phosphodiesterase From Escherichia Coli
pdb|1YDY|B Chain B, Crystal Structure Of Periplasmic Glycerophosphodiester
Phosphodiesterase From Escherichia Coli
Length = 356
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 73/347 (21%), Positives = 136/347 (39%), Gaps = 57/347 (16%)
Query: 402 ASKSANLLVISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDGVPFCLSFINLIN 461
A+ S +VI+ GASG P T A A + G D+++ + M+KD NL+
Sbjct: 25 AADSNEKIVIAHRGASGYLPEHTLPAKAMAYAQGADYLEQDLVMTKDD--------NLVV 76
Query: 462 STNAAQSKFNSITTTIPEIMAGSG-IFSFSLIWDEIQTLI----PQISNPYFKFKLF--R 514
+ + + P+ G ++ DEI++L I N K + + R
Sbjct: 77 LHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGK-KVQTYPGR 135
Query: 515 NPKNKNAGKFMKLSDFLEMAKNANSLSGVLISIE---NAVYLAEKQGMSVTNSVMEALGN 571
P K+ + + +E + N +G I I A + ++G + +E L
Sbjct: 136 FPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLKK 195
Query: 572 AGYNKQTALKVMIQSTDSSVLMKLREK------TSYELVYKVKENIRDALNQ-------- 617
GY + KV +Q D+ L +++ + LV + + Q
Sbjct: 196 YGYTGKDD-KVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTDWNETQQKQPDGSWV 254
Query: 618 -----------TIEDIKKFADSV-----VLSKESVYPLNSAFITSATDIVQRLQSFKLPV 661
++ + ++AD + +L +E+ P N T +VQ Q KL V
Sbjct: 255 NYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGN----IKLTGMVQDAQQNKLVV 310
Query: 662 YVETFSNEFVSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAARY 708
+ T ++ + + + D + Y AG++G+ T+FP A ++
Sbjct: 311 HPYTVRSDKLPE---YTPDVNQLYDALYNKAGVNGLFTDFPDKAVKF 354
Score = 36.6 bits (83), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 47/97 (48%), Gaps = 9/97 (9%)
Query: 94 VVARGGFSGIFPDSSSIAYSLTLITSAPSVILWCDVQLTKDEAGICFPDLKLDNASNIAQ 153
V+A G SG P+ + A ++ A L D+ +TKD+ + D LD +++A
Sbjct: 33 VIAHRGASGYLPEHTLPAKAMAYAQGAD--YLEQDLVMTKDDNLVVLHDHYLDRVTDVAD 90
Query: 154 IFKTQQKNYLVNGVPTPGWFSIDYTLNDLSNIILNQG 190
F + + +++ID+TL+++ ++ +G
Sbjct: 91 RFPDRARK-------DGRYYAIDFTLDEIKSLKFTEG 120
>pdb|1T8Q|A Chain A, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|B Chain B, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|C Chain C, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
pdb|1T8Q|D Chain D, Structural Genomics, Crystal Structure Of
Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Length = 336
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 74/348 (21%), Positives = 133/348 (38%), Gaps = 57/348 (16%)
Query: 401 NASKSANLLVISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDGVPFCLSFINLI 460
NA+ S +VI+ GASG P T A A + G D+++ + +KD NL+
Sbjct: 2 NAADSNEKIVIAHRGASGYLPEHTLPAKAXAYAQGADYLEQDLVXTKDD--------NLV 53
Query: 461 NSTNAAQSKFNSITTTIPEIMAGSG-IFSFSLIWDEIQTLI----PQISNPYFKFKLF-- 513
+ + + P+ G ++ DEI++L I N K + +
Sbjct: 54 VLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEGFDIENGK-KVQTYPG 112
Query: 514 RNPKNKNAGKFMKLSDFLEMAKNANSLSGVLISIE---NAVYLAEKQGMSVTNSVMEALG 570
R P K+ + + +E + N +G I I A + ++G + +E L
Sbjct: 113 RFPXGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQEGKDIAAKTLEVLK 172
Query: 571 NAGYNKQTALKVMIQSTDSSVLMKLREK------TSYELVYKVKENIRDALNQTIED--- 621
GY + KV +Q D+ L +++ + LV + + Q D
Sbjct: 173 KYGYTGKDD-KVYLQCFDADELKRIKNELEPKXGXELNLVQLIAYTDWNETQQKQPDGSW 231
Query: 622 ----------------IKKFADSV-----VLSKESVYPLNSAFITSATDIVQRLQSFKLP 660
+ ++AD + L +E+ P N T VQ Q KL
Sbjct: 232 VNYNYDWXFKPGAXKQVAEYADGIGPDYHXLIEETSQPGN----IKLTGXVQDAQQNKLV 287
Query: 661 VYVETFSNEFVSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAARY 708
V+ T ++ + + + D + Y AG++G+ T+FP A ++
Sbjct: 288 VHPYTVRSDKLPE---YTPDVNQLYDALYNKAGVNGLFTDFPDKAVKF 332
Score = 33.5 bits (75), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 9/97 (9%)
Query: 94 VVARGGFSGIFPDSSSIAYSLTLITSAPSVILWCDVQLTKDEAGICFPDLKLDNASNIAQ 153
V+A G SG P+ + A + A L D+ TKD+ + D LD +++A
Sbjct: 11 VIAHRGASGYLPEHTLPAKAXAYAQGAD--YLEQDLVXTKDDNLVVLHDHYLDRVTDVAD 68
Query: 154 IFKTQQKNYLVNGVPTPGWFSIDYTLNDLSNIILNQG 190
F + + +++ID+TL+++ ++ +G
Sbjct: 69 RFPDRARK-------DGRYYAIDFTLDEIKSLKFTEG 98
>pdb|3BWV|A Chain A, Crystal Structure Of Deoxyribonucleotidase-like Protein
(np_764060.1) From Staphylococcus Epidermidis Atcc 12228
At 1.55 A Resolution
pdb|3BWV|B Chain B, Crystal Structure Of Deoxyribonucleotidase-like Protein
(np_764060.1) From Staphylococcus Epidermidis Atcc 12228
At 1.55 A Resolution
Length = 180
Score = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 323 SLYLLPHTTIVLDAHKERLEVFASNFANDIPISFNYSYDPLTEYLSFIDNGDFSVDG--- 379
+L + PH V+ E +++ + A D+P SF+ Y+ L EY F+D F G
Sbjct: 67 NLDVXPHAQEVVKQLNEHYDIYIATAAXDVPTSFHDKYEWLLEYFPFLDPQHFVFCGRKN 126
Query: 380 -VLSDF 384
+L+D+
Sbjct: 127 IILADY 132
>pdb|1W5N|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations D131c And D139c)
pdb|1W5N|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations D131c And D139c)
Length = 337
Score = 35.8 bits (81), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1W5O|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c And D139c)
pdb|1W5O|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c And D139c)
Length = 337
Score = 35.8 bits (81), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1W5P|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c, D139c, P132e)
pdb|1W5P|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c, D139c, P132e)
Length = 337
Score = 35.8 bits (81), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1W5Q|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c, D139c, P132e, K229r)
pdb|1W5Q|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c, D131c, D139c, P132e, K229r)
Length = 337
Score = 35.8 bits (81), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|2PZ0|A Chain A, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) From T. Tengcongensis
pdb|2PZ0|B Chain B, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) From T. Tengcongensis
Length = 252
Score = 35.8 bits (81), Expect = 0.091, Method: Composition-based stats.
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 405 SANLLVISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDG 449
S LVI+ G S + P T A+++A+ G D I+ VQ++KDG
Sbjct: 9 SMKTLVIAHRGDSKNVPENTIAAFKRAMELGADGIELDVQLTKDG 53
>pdb|1W56|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c And D131c)
pdb|1W56|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c And D131c)
Length = 337
Score = 35.8 bits (81), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1W5M|A Chain A, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c And D139c)
pdb|1W5M|B Chain B, Stepwise Introduction Of Zinc Binding Site Into
Porphobilinogen Synthase Of Pseudomonas Aeruginosa
(Mutations A129c And D139c)
Length = 337
Score = 35.8 bits (81), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1W54|A Chain A, Stepwise Introduction Of A Zinc Binding Site Into
Porphobilinogen Synthase From Pseudomonas Aeruginosa
(mutation D139c)
pdb|1W54|B Chain B, Stepwise Introduction Of A Zinc Binding Site Into
Porphobilinogen Synthase From Pseudomonas Aeruginosa
(mutation D139c)
Length = 337
Score = 35.8 bits (81), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|2C14|A Chain A, 5-(4-Carboxy-2-Oxo-Butylamino)-4-Oxo-Pentanoic Acid Acid
Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C14|B Chain B, 5-(4-Carboxy-2-Oxo-Butylamino)-4-Oxo-Pentanoic Acid Acid
Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C16|A Chain A, 5-(4-Carboxy-2-Oxo-Butane-1-Sulfinyl)-4-Oxo-Pentanoic Acid
Acid Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C16|B Chain B, 5-(4-Carboxy-2-Oxo-Butane-1-Sulfinyl)-4-Oxo-Pentanoic Acid
Acid Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C19|A Chain A, 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid
Acid Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C19|B Chain B, 5-(4-Carboxy-2-Oxo-Butylsulfanyl)-4-Oxo-Pentanoic Acid
Acid Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
Length = 337
Score = 35.8 bits (81), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1GZG|A Chain A, Complex Of A Mg2-Dependent Porphobilinogen Synthase From
Pseudomonas Aeruginosa (Mutant D139n) With
5-Fluorolevulinic Acid
pdb|1GZG|B Chain B, Complex Of A Mg2-Dependent Porphobilinogen Synthase From
Pseudomonas Aeruginosa (Mutant D139n) With
5-Fluorolevulinic Acid
Length = 337
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|1B4K|A Chain A, High Resolution Crystal Structure Of A Mg2-Dependent
5-Aminolevulinic Acid Dehydratase
pdb|1B4K|B Chain B, High Resolution Crystal Structure Of A Mg2-Dependent
5-Aminolevulinic Acid Dehydratase
pdb|2WOQ|A Chain A, Porphobilinogen Synthase (Hemb) In Complex With
5-Acetamido- 4-Oxohexanoic Acid (Alaremycin 2)
Length = 337
Score = 35.8 bits (81), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVKPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|2C13|A Chain A, 5-Hydroxy-Levulinic Acid Bound To Porphobilinogen Synthase
From Pseudomonas Aeruginosa
pdb|2C13|B Chain B, 5-Hydroxy-Levulinic Acid Bound To Porphobilinogen Synthase
From Pseudomonas Aeruginosa
Length = 337
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVXPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|2C15|A Chain A, 5-(4-Carboxy-2-Oxo-Butoxy)-4-Oxo-Pentanoic Acid Acid Bound
To Porphobilinogen Synthase From Pseudomonas Aeruginosa
pdb|2C15|B Chain B, 5-(4-Carboxy-2-Oxo-Butoxy)-4-Oxo-Pentanoic Acid Acid Bound
To Porphobilinogen Synthase From Pseudomonas Aeruginosa
pdb|2C18|A Chain A, 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid
Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
pdb|2C18|B Chain B, 5-(4-Carboxy-2-Oxo-Butane-1-Sulfonyl)-4-Oxo-Pentanoic Acid
Bound To Porphobilinogen Synthase From Pseudomonas
Aeruginosa
Length = 337
Score = 35.4 bits (80), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 610 NIRDALNQTIEDIKKFADSVVLSKESVYPLNSAFITSATDIVQRLQ-SFKLPVYVETFSN 668
N +AL++ D+ + AD V++ Y DIV+R++ F+ P +V S
Sbjct: 238 NSDEALHEVAADLAEGADMVMVXPGMPY----------LDIVRRVKDEFRAPTFVYQVSG 287
Query: 669 EF------VSQAWDFFSDPTVEINTYYEGAGIDGVITEFPMTAA-RYRRNR 712
E+ + W +E T ++ AG DG++T F AA + RR R
Sbjct: 288 EYAMHMGAIQNGW-LAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR 337
>pdb|3I10|A Chain A, Crystal Structure Of Putative Glycerophosphoryl Diester
Phosphodiesterase (Np_812074.1) From Bacteroides
Thetaiotaomicron Vpi-5482 At 1.35 A Resolution
Length = 278
Score = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 404 KSANLLVISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDGVPFCLSFINLINST 463
KS +LV++ G P + A AI+ VD ++ +Q +KDG L N ++ T
Sbjct: 14 KSNKVLVVAHRGNWRSAPENSTAAIDSAIAXKVDIVEIDIQKTKDG-QLILXHDNTLDRT 72
Query: 464 NAAQSKFNSIT 474
+ + + T
Sbjct: 73 TTGKGEIKNWT 83
>pdb|1U8V|A Chain A, Crystal Structure Of 4-Hydroxybutyryl-Coa Dehydratase From
Clostridium Aminobutyricum: Radical Catalysis Involving
A [4fe-4s] Cluster And Flavin
pdb|1U8V|B Chain B, Crystal Structure Of 4-Hydroxybutyryl-Coa Dehydratase From
Clostridium Aminobutyricum: Radical Catalysis Involving
A [4fe-4s] Cluster And Flavin
pdb|1U8V|C Chain C, Crystal Structure Of 4-Hydroxybutyryl-Coa Dehydratase From
Clostridium Aminobutyricum: Radical Catalysis Involving
A [4fe-4s] Cluster And Flavin
pdb|1U8V|D Chain D, Crystal Structure Of 4-Hydroxybutyryl-Coa Dehydratase From
Clostridium Aminobutyricum: Radical Catalysis Involving
A [4fe-4s] Cluster And Flavin
Length = 490
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 343 VFASNFANDIPISFNYSYDPLTEYLSFIDNGDFSVDGVLS----DFPLTPSAAVD 393
VF++ + D NY + TEYL +I D VDG ++ D L PSA D
Sbjct: 112 VFSTTYEIDQKYGTNY-HKNFTEYLKYIQENDLIVDGAMTDPKGDRGLAPSAQKD 165
>pdb|2Q7N|A Chain A, Crystal Structure Of Leukemia Inhibitory Factor In Complex
With Lif Receptor (Domains 1-5)
pdb|2Q7N|C Chain C, Crystal Structure Of Leukemia Inhibitory Factor In Complex
With Lif Receptor (Domains 1-5)
Length = 488
Score = 32.7 bits (73), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 460 INSTNAAQSKFN------SITTTIPEIMAGSGIF---SFSLIWDEIQTLIPQISNPYFKF 510
IN N QSKF S+ PEI+ S F S L W++ + +P SN ++
Sbjct: 69 INYLNGFQSKFTLNEKDVSLIPETPEILDLSADFFTSSLLLKWNDRGSALPHPSNATWEI 128
Query: 511 KLFRNPKNK 519
K+ +NP+ +
Sbjct: 129 KVLQNPRTE 137
>pdb|1ZCC|A Chain A, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
pdb|1ZCC|B Chain B, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
pdb|1ZCC|C Chain C, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
pdb|1ZCC|D Chain D, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
pdb|1ZCC|E Chain E, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
pdb|1ZCC|F Chain F, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase From Agrobacterium Tumefaciens Str.C58
Length = 248
Score = 32.7 bits (73), Expect = 0.91, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 36/74 (48%)
Query: 410 VISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDGVPFCLSFINLINSTNAAQSK 469
++S GA+ P T A A+ G D+I+ V+ S DGV + + L +TN
Sbjct: 4 IVSHRGANRFAPENTFAAADLALQQGADYIELDVRESADGVLYVIHDETLDRTTNGTGPV 63
Query: 470 FNSITTTIPEIMAG 483
+ +++ I + AG
Sbjct: 64 GHMLSSEIDTLDAG 77
>pdb|3QVQ|A Chain A, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|B Chain B, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|C Chain C, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
pdb|3QVQ|D Chain D, The Structure Of An Oleispira Antarctica Phosphodiesterase
Olei02445 In Complex With The Product
Sn-Glycerol-3-Phosphate
Length = 252
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 410 VISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDGVPFCLSFINLINSTNAAQSK 469
VI+ G+SG P T + A G+ +++ V +S DG+P L +T+
Sbjct: 12 VIAHRGSSGQAPENTLASLHLAGQQGIKWVEIDVXLSGDGIPVIFHDDYLSRTTDGDGLI 71
Query: 470 FNSITTTIPEIMAGS 484
+ + + ++ AGS
Sbjct: 72 YKTPLAELKQLDAGS 86
>pdb|1O1Z|A Chain A, Crystal Structure Of Glycerophosphodiester
Phosphodiesterase (Gdpd) (Tm1621) From Thermotoga
Maritima At 1.60 A Resolution
Length = 234
Score = 30.0 bits (66), Expect = 4.8, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 408 LLVISKNGASGDYPSCTNLAYQKAISDGVDFIDCPVQMSKDG 449
++V+ G S Y T A+ KAI G + ++ V++SKDG
Sbjct: 13 VIVLGHRGYSAKYLENTLEAFMKAIEAGANGVELDVRLSKDG 54
>pdb|1UTY|A Chain A, Crystal Structure Of The Rna Binding Domain Of Bluetongue
Virus Non-Structural Protein 2(Ns2)
pdb|1UTY|B Chain B, Crystal Structure Of The Rna Binding Domain Of Bluetongue
Virus Non-Structural Protein 2(Ns2)
Length = 187
Score = 29.6 bits (65), Expect = 7.1, Method: Composition-based stats.
Identities = 17/68 (25%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 158 QQKNYLVNGVPTPGWFSIDYTLNDLSNIILNQGVYSRTDKFDGNGFQILTVQDMARQIKP 217
+ K Y++N VP PG + I + +S ++ GV + T++++ F+ ++V MA +++
Sbjct: 52 EPKGYVLN-VPGPGAYRIQDGQDIISLMLTPHGVEATTERWEEWKFEGVSVTPMATRVQY 110
Query: 218 PGLWLNIQ 225
G+ ++ +
Sbjct: 111 NGVMVDAE 118
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
0.318 0.134 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,266,523
Number of Sequences: 62578
Number of extensions: 848010
Number of successful extensions: 2002
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1984
Number of HSP's gapped (non-prelim): 35
length of query: 811
length of database: 14,973,337
effective HSP length: 107
effective length of query: 704
effective length of database: 8,277,491
effective search space: 5827353664
effective search space used: 5827353664
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)