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= psy15811
(581 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1LT7|A Chain A, Oxidized Homo Sapiens Betaine-Homocysteine
S-Methyltransferase In Complex With Four Sm(Iii) Ions
pdb|1LT7|B Chain B, Oxidized Homo Sapiens Betaine-Homocysteine
S-Methyltransferase In Complex With Four Sm(Iii) Ions
pdb|1LT8|A Chain A, Reduced Homo Sapiens Betaine-Homocysteine S-
Methyltransferase In Complex With
S-(Delta-Carboxybutyl)-L- Homocysteine
pdb|1LT8|B Chain B, Reduced Homo Sapiens Betaine-Homocysteine S-
Methyltransferase In Complex With
S-(Delta-Carboxybutyl)-L- Homocysteine
Length = 406
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 11 DGSFTSQVSRHTIKDVDGHPLWSSVYLTTEPEACVETHRDFIRAGADIIQSSCYQANVDN 70
DG F + + V P W+ PEA + HR+F+RAG++++Q+ + A+ D
Sbjct: 26 DGGFVFALEKRGY--VKAGP-WTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFYASEDK 82
Query: 71 LTKLG 75
L G
Sbjct: 83 LENRG 87
>pdb|1UMY|A Chain A, Bhmt From Rat Liver
pdb|1UMY|B Chain B, Bhmt From Rat Liver
pdb|1UMY|C Chain C, Bhmt From Rat Liver
pdb|1UMY|D Chain D, Bhmt From Rat Liver
Length = 407
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 6 KVKLLDGSFTSQVSRHTIKDVDGHPLWSSVYLTTEPEACVETHRDFIRAGADIIQSSCYQ 65
+V + DG F + + V P W+ PEA + HR+F+RAG++++Q+ +
Sbjct: 21 EVVIGDGGFVFALEKRGY--VKAGP-WTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFY 77
Query: 66 ANVDNLTKLG 75
A+ D L G
Sbjct: 78 ASEDKLENRG 87
>pdb|1Q7M|A Chain A, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7M|B Chain B, Cobalamin-Dependent Methionine Synthase (Meth) From
Thermotoga Maritima (Oxidized, Monoclinic)
pdb|1Q7Q|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Q|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From T.
Maritima (Oxidized, Orthorhombic)
pdb|1Q7Z|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q7Z|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex)
pdb|1Q8J|A Chain A, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|1Q8J|B Chain B, Cobalamin-dependent Methionine Synthase (1-566) From
Thermotoga Maritima (cd2+, Hcy, Methyltetrahydrofolate
Complex)
pdb|3BOF|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOF|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+ And Homocysteine
pdb|3BOL|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
pdb|3BOL|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima Complexed With Zn2+
Length = 566
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 55/273 (20%), Positives = 106/273 (38%), Gaps = 46/273 (16%)
Query: 6 KVKLLDGSFTSQVSRHTIKDVDGHPLWSSVYLTTEPEACVETHRDFIRAGADIIQSSCYQ 65
+V LLDG++ ++ ++ D+ P ++ P+ ++ HR +I +G+D+I ++ +
Sbjct: 14 RVLLLDGAYGTEFMKYGYDDL---PEELNI---KAPDVVLKVHRSYIESGSDVILTNTFG 67
Query: 66 ANVDNLTKLGYSEQEALD-LLHKSVQLMNSAKDKENQTPDINLNKTFNLLTGHIETAASI 124
A L K G ++ LD ++ +V++ A G I
Sbjct: 68 ATRMKLRKHGL--EDKLDPIVRNAVRIARRA-------------------AGEKLVFGDI 106
Query: 125 GPYGTVLRDGSEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLALETIPXXXXXXXXX 184
GP G + + + S + R VE +V GVD + ET
Sbjct: 107 GPTGEL--------PYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAV 158
Query: 185 XXXREFPGQK---AWLSFSCKDDTHTSHGELISSAVTSCLLANPDQIQAIGVNC-VRPSH 240
RE A ++F K + T + + + I A+G+NC + P
Sbjct: 159 LAAREVSRDVFLIAHMTFDEKGRSLTG-----TDPANFAITFDELDIDALGINCSLGPEE 213
Query: 241 VSTLVRCIKQSHPTVQTIVYPNKGVKLLDGSFT 273
+ + + + Q + +V PN G +++ T
Sbjct: 214 ILPIFQELSQ-YTDKFLVVEPNAGKPIVENGKT 245
Score = 37.4 bits (85), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 40/166 (24%), Positives = 67/166 (40%), Gaps = 15/166 (9%)
Query: 410 HRPNVEALVRAGVDYLALETIPXXXXXXXXXXXXREFPGQK---AWLSFSCKDDTHTSHG 466
R VE +V GVD + ET RE A ++F K + T
Sbjct: 128 FRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDVFLIAHMTFDEKGRSLTG-- 185
Query: 467 ELISSAVTSCLLANPDQIQAIGVNC-VRPSHVSTLVRCIKQSHPTVQTIVYPNKGG--VW 523
+ + + I A+G+NC + P + + + + Q + +V PN G V
Sbjct: 186 ---TDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQ-YTDKFLVVEPNAGKPIVE 241
Query: 524 DSVHMKWLDTEDEYSILHYVPQWLEEGVNIIGGCCEVTSYEIQQMR 569
+ + L D +++ ++ + E GVNI GGCC T ++ R
Sbjct: 242 NGKTVYPLKPHD-FAV--HIDSYYELGVNIFGGCCGTTPEHVKLFR 284
>pdb|1Q85|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q85|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+ Complex, Se-Met)
pdb|1Q8A|A Chain A, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
pdb|1Q8A|B Chain B, Cobalamin-Dependent Methionine Synthase (1-566) From
Thermotoga Maritima (Cd2+:l-Hcy Complex, Se-Met)
Length = 566
Score = 38.1 bits (87), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 55/272 (20%), Positives = 103/272 (37%), Gaps = 44/272 (16%)
Query: 6 KVKLLDGSFTSQVSRHTIKDVDGHPLWSSVYLTTEPEACVETHRDFIRAGADIIQSSCYQ 65
+V LLDG++ ++ ++ D+ P ++ P+ ++ HR +I +G+D+I ++ +
Sbjct: 14 RVLLLDGAYGTEFXKYGYDDL---PEELNI---KAPDVVLKVHRSYIESGSDVILTNTFG 67
Query: 66 ANVDNLTKLGYSEQEALD-LLHKSVQLMNSAKDKENQTPDINLNKTFNLLTGHIETAASI 124
A L K G ++ LD ++ +V++ A G I
Sbjct: 68 ATRXKLRKHGL--EDKLDPIVRNAVRIARRA-------------------AGEKLVFGDI 106
Query: 125 GPYGTVLRDGSEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLALETIPXXXXXXXXX 184
GP G + + + S + R VE V GVD + ET
Sbjct: 107 GPTGEL--------PYPLGSTLFEEFYENFRETVEIXVEEGVDGIIFETFSDILELKAAV 158
Query: 185 XXXREFPGQKAWLSFSCKDDTHTSHGELISSAVTSCLLANPDQ--IQAIGVNC-VRPSHV 241
RE F T G ++ + D+ I A+G+NC + P +
Sbjct: 159 LAAREVSRD----VFLIAHXTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEI 214
Query: 242 STLVRCIKQSHPTVQTIVYPNKGVKLLDGSFT 273
+ + + Q + +V PN G +++ T
Sbjct: 215 LPIFQELSQ-YTDKFLVVEPNAGKPIVENGKT 245
Score = 36.2 bits (82), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 40/168 (23%), Positives = 66/168 (39%), Gaps = 13/168 (7%)
Query: 410 HRPNVEALVRAGVDYLALETIPXXXXXXXXXXXXREFPGQKAWLSFSCKDDTHTSHGELI 469
R VE V GVD + ET RE F T G +
Sbjct: 128 FRETVEIXVEEGVDGIIFETFSDILELKAAVLAAREVSRD----VFLIAHXTFDEKGRSL 183
Query: 470 SSAVTSCLLANPDQ--IQAIGVNC-VRPSHVSTLVRCIKQSHPTVQTIVYPNKGG--VWD 524
+ + D+ I A+G+NC + P + + + + Q + +V PN G V +
Sbjct: 184 TGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQ-YTDKFLVVEPNAGKPIVEN 242
Query: 525 SVHMKWLDTEDEYSILHYVPQWLEEGVNIIGGCCEVTSYEIQQMRIMI 572
+ L D +++ ++ + E GVNI GGCC T ++ R ++
Sbjct: 243 GKTVYPLKPHD-FAV--HIDSYYELGVNIFGGCCGTTPEHVKLFRKVL 287
>pdb|3RKO|N Chain N, Crystal Structure Of The Membrane Domain Of Respiratory
Complex I From E. Coli At 3.0 Angstrom Resolution
pdb|3RKO|D Chain D, Crystal Structure Of The Membrane Domain Of Respiratory
Complex I From E. Coli At 3.0 Angstrom Resolution
Length = 485
Score = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 35/125 (28%), Positives = 57/125 (45%), Gaps = 13/125 (10%)
Query: 52 IRAGADIIQSSCYQANVDNLTKL-GYSEQEALDLLHKSVQLMNSAKDKENQTPDINLNKT 110
I A A II + + N+ +L GYS L L ++ + QT ++++
Sbjct: 275 IIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIAL--------QTGEMSMEAV 326
Query: 111 FNLLTGHIETAASIGPYGTVLRDGSEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLA 170
L G++ + S+G +G V S Y G DS+ + WHRP + A++ V L+
Sbjct: 327 GVYLAGYLFS--SLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMT--VMMLS 382
Query: 171 LETIP 175
L IP
Sbjct: 383 LAGIP 387
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 300 EACVETHRDFIRGHIETAASIGPYGTVLRDGSEYSGHYVDSMTEADLIAWHRPNVEALV 358
E +E ++ G++ + S+G +G V S Y G DS+ + WHRP + A++
Sbjct: 320 EMSMEAVGVYLAGYLFS--SLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVM 376
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 378 ASIGPYGTVLRDGSEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLALETIP 431
+S+G +G V S Y G DS+ + WHRP + A++ V L+L IP
Sbjct: 336 SSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMT--VMMLSLAGIP 387
>pdb|3V8V|A Chain A, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sam Binding
pdb|3V8V|B Chain B, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sam Binding
Length = 702
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 325 TVLRDG-SEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLALIKPSISSQTAASI--G 381
T R G +EYS H+ S ++A +I R N AG+ L + +Q + G
Sbjct: 245 TRARKGLAEYSSHFYGSDSDARVIQRARTNARL---AGIGELITFEVKDVAQLTNPLPKG 301
Query: 382 PYGTVLRDGSEYSGHYVDSMTEADLIAWH 410
PYGTVL + G +DS E LIA H
Sbjct: 302 PYGTVLSNPP--YGERLDS--EPALIALH 326
>pdb|3V97|A Chain A, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sah Binding
pdb|3V97|B Chain B, Crystal Structure Of Bifunctional Methyltransferase Ycby
(Rlmlk) From Escherichia Coli, Sah Binding
Length = 703
Score = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 31/89 (34%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 325 TVLRDG-SEYSGHYVDSMTEADLIAWHRPNVEALVRAGVDYLALIKPSISSQTAASI--G 381
T R G +EYS H+ S ++A +I R N AG+ L + +Q + G
Sbjct: 246 TRARKGLAEYSSHFYGSDSDARVIQRARTNARL---AGIGELITFEVKDVAQLTNPLPKG 302
Query: 382 PYGTVLRDGSEYSGHYVDSMTEADLIAWH 410
PYGTVL + G +DS E LIA H
Sbjct: 303 PYGTVLSNPP--YGERLDS--EPALIALH 327
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,507,878
Number of Sequences: 62578
Number of extensions: 697895
Number of successful extensions: 1733
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1714
Number of HSP's gapped (non-prelim): 26
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
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)