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= 020275
(328 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 71.2 bits (173), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 81/317 (25%), Positives = 138/317 (43%), Gaps = 55/317 (17%)
Query: 23 VIDGGFATQLETHGASINDPLWSALYLIKQPHLVKRVHLEYLEAGADILVTSSYQATIPG 82
++DG + T+ +G D L L IK P +V +VH Y+E+G+D+++T+++ AT
Sbjct: 17 LLDGAYGTEFMKYGY---DDLPEELN-IKAPDVVLKVHRSYIESGSDVILTNTFGATRMK 72
Query: 83 FLSRGLSIEEAESLLEKSVTLAVEARDKFWDAVKKVPGHNYNRALVAASIGSYGAYLADG 142
GL ++ + ++ +V +A ++ G LV IG G
Sbjct: 73 LRKHGLE-DKLDPIVRNAVRIA-----------RRAAGEK----LVFGDIGPTGEL---- 112
Query: 143 SEYSGNYGPGVDL-EKLKDFHRRRLQVLVESGPDLLAFETIPN--KXXXXXXXXXXXXXN 199
Y G L E+ + R ++++VE G D + FET + + +
Sbjct: 113 -----PYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRD 167
Query: 200 IQIPSWICFS----SVDGENAPSGESFKECLDIINKSGKVNAVGINCA--PPQFVENLIC 253
+ + + + F S+ G + + + LDI +A+GINC+ P E ++
Sbjct: 168 VFLIAHMTFDEKGRSLTGTDPANFAITFDELDI-------DALGINCSLGP----EEILP 216
Query: 254 YFKEL---TKKAIVVYPNSGEVWDGRAKKWLPSKCLGDGKFESFATRWRDSGAKLIGGCC 310
F+EL T K +VV PN+G+ K P L F + + G + GGCC
Sbjct: 217 IFQELSQYTDKFLVVEPNAGKPIVENGKTVYP---LKPHDFAVHIDSYYELGVNIFGGCC 273
Query: 311 RTTPSTIQAVSKVLKER 327
TTP ++ KVL R
Sbjct: 274 GTTPEHVKLFRKVLGNR 290
>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 = 68.9 bits (167), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 78/311 (25%), Positives = 128/311 (41%), Gaps = 43/311 (13%)
Query: 23 VIDGGFATQLETHGASINDPLWSALYLIKQPHLVKRVHLEYLEAGADILVTSSYQATIPG 82
++DG + T+ +G D L L IK P +V +VH Y+E+G+D+++T+++ AT
Sbjct: 17 LLDGAYGTEFXKYGY---DDLPEELN-IKAPDVVLKVHRSYIESGSDVILTNTFGATRXK 72
Query: 83 FLSRGLSIEEAESLLEKSVTLAVEARDKFWDAVKKVPGHNYNRALVAASIGSYGAYLADG 142
GL ++ + ++ +V +A A LV IG G
Sbjct: 73 LRKHGLE-DKLDPIVRNAVRIARRAA---------------GEKLVFGDIGPTGEL---- 112
Query: 143 SEYSGNYGPGVDL-EKLKDFHRRRLQVLVESGPDLLAFETIPNKXXXXXXXXXXXXXNIQ 201
Y G L E+ + R +++ VE G D + FET + +
Sbjct: 113 -----PYPLGSTLFEEFYENFRETVEIXVEEGVDGIIFETFSDILELKAAVLAAREVSRD 167
Query: 202 IPSWICFSSVDGENAPSGESFKECLDIINKSGKVNAVGINCA--PPQFVENLICYFKEL- 258
+ I + D + + I ++A+GINC+ P E ++ F+EL
Sbjct: 168 V-FLIAHXTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGP----EEILPIFQELS 222
Query: 259 --TKKAIVVYPNSGEVWDGRAKKWLPSKCLGDGKFESFATRWRDSGAKLIGGCCRTTPST 316
T K +VV PN+G+ K P L F + + G + GGCC TTP
Sbjct: 223 QYTDKFLVVEPNAGKPIVENGKTVYP---LKPHDFAVHIDSYYELGVNIFGGCCGTTPEH 279
Query: 317 IQAVSKVLKER 327
++ KVL R
Sbjct: 280 VKLFRKVLGNR 290
>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 = 58.9 bits (141), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 79/325 (24%), Positives = 130/325 (40%), Gaps = 47/325 (14%)
Query: 18 AGGCAVIDGGFATQLETHGASINDPLWSALYLIKQPHLVKRVHLEYLEAGADILVTSSYQ 77
AG + DGGF LE G P W+ ++ P V+++H E+L AG++++ T ++
Sbjct: 19 AGEVVIGDGGFVFALEKRGYVKAGP-WTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFY 77
Query: 78 ATIPGFLSRGLSIEE---AESLLEKSVTLAVEARDKFWDAVKKVPGHNYNRALVAASIGS 134
A+ +RG + E + + E + +A + D+ ALVA +
Sbjct: 78 ASEDKLENRGNYVAEKISGQKVNEAACDIARQVADE-------------GDALVAGGVSQ 124
Query: 135 YGAYLADGSEYSGNYGPGVDLEKLKDFHRRRLQVLVESGPDLLAFETIPNKXXXXXXXXX 194
+YL+ SE E K FH ++L+V ++ D L E +
Sbjct: 125 TPSYLSCKSE----------TEVKKIFH-QQLEVFMKKNVDFLIAEYFEHVEEAVWAVEA 173
Query: 195 XXXXNIQIPSWICFSSVDGENAPSGESFKECLDIINKSGKVNAVGINCA-PPQFVENLIC 253
I + +C + E G S EC + K+G VG+NC P I
Sbjct: 174 LKTSGKPIAATMC---IGPEGDLHGVSPGECAVRLVKAGAA-IVGVNCHFDPSTSLQTIK 229
Query: 254 YFKE-----LTKKAIVVYPNSGEVWDGRAKKWLPSKCLGDGKFESFATRW------RDS- 301
KE K ++ P + D + ++ G ATRW R++
Sbjct: 230 LMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEPRVATRWDIQKYAREAY 289
Query: 302 --GAKLIGGCCRTTPSTIQAVSKVL 324
G + IGGCC P I+A+++ L
Sbjct: 290 NLGVRYIGGCCGFEPYHIRAIAEEL 314
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 69/326 (21%), Positives = 127/326 (38%), Gaps = 49/326 (15%)
Query: 18 AGGCAVIDGGFATQLETHGASINDPLWSALYLIKQPHLVKRVHLEYLEAGADILVTSSYQ 77
AG + DGGF LE G P W+ ++ P V+++H E+L AG++++ T ++
Sbjct: 19 AGEIVIGDGGFVFALEKRGYVKAGP-WTPEAAVEHPEAVRQLHREFLRAGSNVMQTFTFY 77
Query: 78 ATIPGFLSRGLSIEE---AESLLEKSVTLAVEARDKFWDAVKKVPGHNYNRALVAASIGS 134
A+ +RG + E + + E + +A + D+ ALVA +
Sbjct: 78 ASEDKLENRGNYVLEKISGQEVNEAAADIARQVADE-------------GDALVAGGVSQ 124
Query: 135 YGAYLADGSEYSGNYGPGVDLEKLKDFHRRRLQVLVESGPDLLAFETIPNKXXXXXXXXX 194
+YL+ SE ++K ++L+V ++ D L E +
Sbjct: 125 TPSYLSAKSE-----------TEVKKVFLQQLEVFMKKNVDFLIAEYFEHVEEAVWAVET 173
Query: 195 XXXXNIQIPSWICFSSV-DGENAPSGESFKECLDIINKSGKVNAVGINCA-PPQFVENLI 252
+ + + D P GE+ + ++ + +G+NC P +
Sbjct: 174 LIASGKPVAATMAIGPEGDLHGVPPGEA---AVRLVKAGASI--IGVNCHFDPTISLKTV 228
Query: 253 CYFKE-----LTKKAIVVYPNSGEVWDGRAKKWLPSKCLGDGKFESFATRW------RDS 301
KE K ++ P + D + ++ G ATRW R++
Sbjct: 229 KLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGLEPRVATRWDIQKYAREA 288
Query: 302 ---GAKLIGGCCRTTPSTIQAVSKVL 324
G + IGGCC P I+A+++ L
Sbjct: 289 YNLGVRYIGGCCGFEPYHIRAIAEEL 314
>pdb|4FXG|C Chain C, Complement C4 In Complex With Masp-2
pdb|4FXG|F Chain F, Complement C4 In Complex With Masp-2
pdb|4FXK|C Chain C, Human Complement C4
Length = 291
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 132 IGSYGAYLADGSEYSGNYGPGVDLEKLKDFHRRRLQVLVESGPD-LLAFETIPN 184
+G G +AD + SG + DLEKL R + GP LL F+++P
Sbjct: 25 VGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVSHFETEGPHVLLYFDSVPT 78
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
0.316 0.134 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,038,555
Number of Sequences: 62578
Number of extensions: 414518
Number of successful extensions: 917
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 903
Number of HSP's gapped (non-prelim): 14
length of query: 328
length of database: 14,973,337
effective HSP length: 99
effective length of query: 229
effective length of database: 8,778,115
effective search space: 2010188335
effective search space used: 2010188335
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)