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= psy13560
(629 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1REQ|A Chain A, Methylmalonyl-Coa Mutase
pdb|1REQ|C Chain C, Methylmalonyl-Coa Mutase
pdb|2REQ|A Chain A, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|2REQ|C Chain C, Methylmalonyl-Coa Mutase, Non-Productive Coa Complex, In
Open Conformation Representing Substrate-Free State
pdb|3REQ|A Chain A, Methylmalonyl-Coa Mutase, Substrate-Free State (Poor
Quality Structure)
pdb|6REQ|A Chain A, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|6REQ|C Chain C, Methylmalonyl-Coa Mutase, 3-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|A Chain A, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|7REQ|C Chain C, Methylmalonyl-Coa Mutase, 2-Carboxypropyl-Coa Inhibitor
Complex
pdb|4REQ|A Chain A, Methylmalonyl-Coa Mutase Substrate Complex
pdb|4REQ|C Chain C, Methylmalonyl-Coa Mutase Substrate Complex
Length = 727
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 37/171 (21%), Positives = 68/171 (39%), Gaps = 23/171 (13%)
Query: 193 NGTVFSFCSL------ETLITPEQFAEVLCDD-----LDLNPLLFVPAIAQSIRQQTDAF 241
NG V +L E + PEQ A + +D + N ++ P + I + A+
Sbjct: 167 NGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAY 226
Query: 242 PAENL-------LDEVHDQRVVIKLNIHVGNTSLVDQIEWDMSEKENS--AEKFAVRLCT 292
+ N+ + H Q +I + T L D +++ + + ++FA RL
Sbjct: 227 TSANMPKWNSISISGYHMQEAGATADIEMAYT-LADGVDYIRAGESVGLNVDQFAPRLSF 285
Query: 293 ELGLGGEFVTAIAYSIRGQLSWHQRTYAFSEAPLPVVEAPFRSHSESDQWS 343
G+G F +A ++ W + + F P R+HS++ WS
Sbjct: 286 FWGIGMNFFMEVAKLRAARMLWAKLVHQF--GPKNPKSMSLRTHSQTSGWS 334
Score = 32.0 bits (71), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 33/155 (21%), Positives = 63/155 (40%), Gaps = 17/155 (10%)
Query: 454 ETLITPEQFAEVLCDD-----LDLNPLLFVPAIAQSIRQQTDAFPAENL-------LDEV 501
E + PEQ A + +D + N ++ P + I + A+ + N+ +
Sbjct: 183 EQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGY 242
Query: 502 HDQRVVIKLNIHVGNTSLVDQIEWDMSEKENS--AEKFAVRLCTELGLGGEFVTAIAYSI 559
H Q +I + T L D +++ + + ++FA RL G+G F +A
Sbjct: 243 HMQEAGATADIEMAYT-LADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLR 301
Query: 560 RGQLSWHQRTYAFSEAPLPVVEAPFRSHSESDQWS 594
++ W + + F P R+HS++ WS
Sbjct: 302 AARMLWAKLVHQF--GPKNPKSMSLRTHSQTSGWS 334
>pdb|5REQ|A Chain A, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
pdb|5REQ|C Chain C, Methylmalonyl-Coa Mutase, Y89f Mutant, Substrate Complex
Length = 727
Score = 34.3 bits (77), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 37/171 (21%), Positives = 68/171 (39%), Gaps = 23/171 (13%)
Query: 193 NGTVFSFCSL------ETLITPEQFAEVLCDD-----LDLNPLLFVPAIAQSIRQQTDAF 241
NG V +L E + PEQ A + +D + N ++ P + I + A+
Sbjct: 167 NGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAY 226
Query: 242 PAENL-------LDEVHDQRVVIKLNIHVGNTSLVDQIEWDMSEKENS--AEKFAVRLCT 292
+ N+ + H Q +I + T L D +++ + + ++FA RL
Sbjct: 227 TSANMPKWNSISISGYHMQEAGATADIEMAYT-LADGVDYIRAGESVGLNVDQFAPRLSF 285
Query: 293 ELGLGGEFVTAIAYSIRGQLSWHQRTYAFSEAPLPVVEAPFRSHSESDQWS 343
G+G F +A ++ W + + F P R+HS++ WS
Sbjct: 286 FWGIGMNFFMEVAKLRAARMLWAKLVHQF--GPKNPKSMSLRTHSQTSGWS 334
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 33/155 (21%), Positives = 63/155 (40%), Gaps = 17/155 (10%)
Query: 454 ETLITPEQFAEVLCDD-----LDLNPLLFVPAIAQSIRQQTDAFPAENL-------LDEV 501
E + PEQ A + +D + N ++ P + I + A+ + N+ +
Sbjct: 183 EQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGY 242
Query: 502 HDQRVVIKLNIHVGNTSLVDQIEWDMSEKENS--AEKFAVRLCTELGLGGEFVTAIAYSI 559
H Q +I + T L D +++ + + ++FA RL G+G F +A
Sbjct: 243 HMQEAGATADIEMAYT-LADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLR 301
Query: 560 RGQLSWHQRTYAFSEAPLPVVEAPFRSHSESDQWS 594
++ W + + F P R+HS++ WS
Sbjct: 302 AARMLWAKLVHQF--GPKNPKSMSLRTHSQTSGWS 334
>pdb|3V96|B Chain B, Complex Of Matrix Metalloproteinase-10 Catalytic Domain
(Mmp-10cd) With Tissue Inhibitor Of Metalloproteinases-1
(Timp-1)
Length = 165
Score = 28.9 bits (63), Expect = 8.1, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 10/85 (11%)
Query: 7 GDKPISFQIEENGDFYCIGSEVGNYLRMFRGSLYKKYPGLFRRTISNEERKRLLDTAGIN 66
D ISF ++E+GDFY G+ L Y PGL+ +++ K D +G N
Sbjct: 58 ADIMISFAVKEHGDFYSFDGP-GHSL----AHAYPPGPGLYGDIHFDDDEKWTEDASGTN 112
Query: 67 -----SHCLASSVTLLKVSEVEDIL 86
+H L S+ L + E ++
Sbjct: 113 LFLVAAHELGHSLGLFHSANTEALM 137
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 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,526,753
Number of Sequences: 62578
Number of extensions: 784346
Number of successful extensions: 1672
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1670
Number of HSP's gapped (non-prelim): 5
length of query: 629
length of database: 14,973,337
effective HSP length: 105
effective length of query: 524
effective length of database: 8,402,647
effective search space: 4402987028
effective search space used: 4402987028
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: 54 (25.4 bits)