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= psy4854
(555 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WSR|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSR|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|A Chain A, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
pdb|1WSV|B Chain B, Crystal Structure Of Human T-Protein Of Glycine Cleavage
System
Length = 375
Score = 233 bits (595), Expect = 2e-61, Method: Compositional matrix adjust.
Identities = 129/238 (54%), Positives = 162/238 (68%), Gaps = 11/238 (4%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
+RTPLYD HL+HGGKMV FAG+S+PVQY S T SHLHTR S+FDVSHMLQT + G
Sbjct: 6 RRTPLYDFHLAHGGKMVAFAGWSLPVQYRD-SHTDSHLHTRQHCSLFDVSHMLQTKILGS 64
Query: 257 HREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVD 316
R + +ES+ V D+ EL P +GTLSLFTNE GGI DDLIVT T E L++VSNA + D
Sbjct: 65 DRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWEKD 124
Query: 317 MDLMVAAQDRFKSL---GKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMT 373
+ LM QD+ + L G+D+ L+ L + L+A+QGP ++ +LQ DL L FMT
Sbjct: 125 LALM---QDKVRELQNQGRDVGLEVL---DNALLALQGPTAAQVLQAGVADDLRKLPFMT 178
Query: 374 SRPCTIAGIP-CTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 430
S + G+ C +TR GYTGEDGVEISVP H+ A+L + +VKLAGL ARDSL
Sbjct: 179 SAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSL 236
Score = 109 bits (272), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 51/109 (46%), Positives = 63/109 (57%)
Query: 12 GKRRRETGGFPGASIIQSQIKSGVSRKRTGFTSTGVPIRPGYEIFNANDQRVGAITSGCP 71
GKRRR FPGA +I Q+K V R+R G G P+R I N ++G +TSGCP
Sbjct: 265 GKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCP 324
Query: 72 SPSLKKNIAMGYIEPAYSKVGVELWXXXXXXXXXXXXTKMPFVKSNYYT 120
SPSLKKN+AMGY+ YS+ G L +KMPFV +NYYT
Sbjct: 325 SPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYT 373
Score = 92.4 bits (228), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 53/115 (46%), Positives = 71/115 (61%), Gaps = 7/115 (6%)
Query: 445 LKLSNDRFKSL---GKDIHLQFLSPEERGLIAVQGPLSSTILQRHTDLDLSSLYFMTSRP 501
L L D+ + L G+D+ L+ L + L+A+QGP ++ +LQ DL L FMTS
Sbjct: 125 LALMQDKVRELQNQGRDVGLEVL---DNALLALQGPTAAQVLQAGVADDLRKLPFMTSAV 181
Query: 502 CTIAGIP-CTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 555
+ G+ C +TR GYTGEDGVEISVP H+ A+L + +VKLAGL ARDSL
Sbjct: 182 MEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSL 236
>pdb|1WOO|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOP|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOR|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
pdb|1WOS|A Chain A, Crystal Structure Of T-Protein Of The Glycine Cleavage
System
Length = 364
Score = 138 bits (347), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 99/295 (33%), Positives = 149/295 (50%), Gaps = 27/295 (9%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
+RTPL++ H+ G KMV FAG+ MP+ Y SI + R V +FDVSHM + +V G
Sbjct: 2 KRTPLFEKHVELGAKMVDFAGWEMPLYY--TSIFEEVMAVRKSVGMFDVSHMGEFLVKGP 59
Query: 257 HREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVD 316
+++ + D L GK S+ NE GGI DDL+V K D +V NA+ + D
Sbjct: 60 EAVSFIDFLITNDFSSLPDGKAIYSVMCNENGGIIDDLVVYKVSPDEALMVVNAANIEKD 119
Query: 317 MDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMTSRP 376
+ + + F D+ + +S + LIA QGP + LQ + L + + + R
Sbjct: 120 FNWIKSHSKNF-----DVEVSNIS-DTTALIAFQGPKAQETLQELVEDGLEEIAYYSFRK 173
Query: 377 CTIAGIPCTLTRAGYTGEDGVEISVPGEQCTHIVEA---LLSDEDVKLAGLGARDS---- 429
+AG+ ++R GYTGEDG E+ + + + +A LL D + AGLGARD
Sbjct: 174 SIVAGVETLVSRTGYTGEDGFELMLEAKNAPKVWDALMNLLRKIDGRPAGLGARDVCRLE 233
Query: 430 ----LSG-DITLNT-PVPHG---SLKLSNDRFKSLGKDIHLQFLSPEERGLIAVQ 475
L G D+ NT P G +KL+ D +GK+ L+ ER L+A++
Sbjct: 234 ATYLLYGQDMDENTNPFEVGLSWVVKLNKD---FVGKEALLKAKEKVERKLVALE 285
Score = 59.3 bits (142), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 32/87 (36%), Positives = 47/87 (54%), Gaps = 3/87 (3%)
Query: 470 GLIAVQGPLSSTILQRHTDLDLSSLYFMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGE 529
LIA QGP + LQ + L + + + R +AG+ ++R GYTGEDG E+ + +
Sbjct: 142 ALIAFQGPKAQETLQELVEDGLEEIAYYSFRKSIVAGVETLVSRTGYTGEDGFELMLEAK 201
Query: 530 QCTHIVEA---LLSDEDVKLAGLGARD 553
+ +A LL D + AGLGARD
Sbjct: 202 NAPKVWDALMNLLRKIDGRPAGLGARD 228
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 30 QIKSGVSRKRTGFTSTGVPI-RPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAY 88
+ K V RK +G I R GYE+ N +RVG ITSG SP+L K+IA+ + +
Sbjct: 272 KAKEKVERKLVALELSGKRIARKGYEVLK-NGERVGEITSGNFSPTLGKSIALALVSKSV 330
Query: 89 SKVGVEL 95
K+G +L
Sbjct: 331 -KIGDQL 336
>pdb|1YX2|A Chain A, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
pdb|1YX2|B Chain B, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
Length = 365
Score = 130 bits (326), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 85/238 (35%), Positives = 126/238 (52%), Gaps = 13/238 (5%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
+RTPL+DL+ +GGK + F G+ +PVQ+ SI H R+ +FDVSH + V+G
Sbjct: 6 KRTPLFDLYKEYGGKTIDFGGWELPVQFS--SIKKEHEAVRTAAGLFDVSHXGEVEVSGN 63
Query: 257 HREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVD 316
+L+ + DV L PG+ + GG DDL++ + E+ LV NAS +D
Sbjct: 64 DSLSFLQRLXTNDVSALTPGRAQYTAXCYPDGGTVDDLLIYQKGENRYLLVINAS--NID 121
Query: 317 MDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLY-FMTSR 375
DL A + + G D+ + S ++ L+AVQGP + IL+ TD D+S+L F
Sbjct: 122 KDL---AWXKEHAAG-DVQIDNQS-DQIALLAVQGPKAEAILKNLTDADVSALKPFAFID 176
Query: 376 PCTIAGIPCTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKL---AGLGARDSL 430
I+G ++R GYTGEDG EI + HI + ++ D GLGARD+L
Sbjct: 177 EADISGRKALISRTGYTGEDGYEIYCRSDDAXHIWKKIIDAGDAYGLIPCGLGARDTL 234
Score = 59.7 bits (143), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 36/89 (40%), Positives = 49/89 (55%), Gaps = 4/89 (4%)
Query: 471 LIAVQGPLSSTILQRHTDLDLSSLY-FMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGE 529
L+AVQGP + IL+ TD D+S+L F I+G ++R GYTGEDG EI +
Sbjct: 146 LLAVQGPKAEAILKNLTDADVSALKPFAFIDEADISGRKALISRTGYTGEDGYEIYCRSD 205
Query: 530 QCTHIVEALLSDEDVKL---AGLGARDSL 555
HI + ++ D GLGARD+L
Sbjct: 206 DAXHIWKKIIDAGDAYGLIPCGLGARDTL 234
Score = 53.1 bits (126), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 31/85 (36%), Positives = 49/85 (57%), Gaps = 5/85 (5%)
Query: 10 FPGKRRRETGGFPGASIIQSQIKSGVSRKRTGFT--STGVPIRPGYEIFNANDQRVGAIT 67
F K ++E+ F G S++ Q ++G RK G G+P R GYE+F N + VG +T
Sbjct: 260 FAVKHKKESD-FFGKSVLSEQKENGAKRKLVGLEXIEKGIP-RHGYEVFQ-NGKSVGKVT 316
Query: 68 SGCPSPSLKKNIAMGYIEPAYSKVG 92
+G SP+L KN+ + I+ S++G
Sbjct: 317 TGTQSPTLGKNVGLALIDSETSEIG 341
>pdb|3GIR|A Chain A, Crystal Structure Of Glycine Cleavage System
Aminomethyltransferase T From Bartonella Henselae
Length = 393
Score = 129 bits (324), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 86/232 (37%), Positives = 118/232 (50%), Gaps = 15/232 (6%)
Query: 200 PLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGKHRE 259
PLY+LH G K FAG+ MP+ Y + + HLHTR+ +FD+SHM V G
Sbjct: 37 PLYELHEKAGAKFGAFAGWRMPLTY-PLGVLKEHLHTRAHAGLFDISHMKLIAVEGPKAV 95
Query: 260 EWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVDMDL 319
E+L D L G+ S NE+ GI DDLI+T+ E LV+NA + D
Sbjct: 96 EFLSYALPVDAALLKIGQSRYSYLLNERAGILDDLILTRLAECRFMLVANAGNAQADF-- 153
Query: 320 MVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMTS-RPCT 378
A+ ++ G + + L ER L+A+QGP ++ +L L + L FM P
Sbjct: 154 ---AELEKRAFGFECQVIAL---ERVLLALQGPQAAAVLA-DAGLPGNELLFMQGFEPQQ 206
Query: 379 IAGIPCTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 430
+TR+GYTGEDG EI++P + E LL D V+ GL ARDSL
Sbjct: 207 ----DWFITRSGYTGEDGFEIALPIGCARALAEKLLGDSRVEWVGLAARDSL 254
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/108 (32%), Positives = 49/108 (45%), Gaps = 1/108 (0%)
Query: 13 KRRRETGGFPGASIIQSQIKSGVSRKRTGFT-STGVPIRPGYEIFNANDQRVGAITSGCP 71
K RE F GA ++ G SR R G T PIR G +F+ R+G +TSG
Sbjct: 284 KNVREKAQFYGAKAFLESLQKGPSRCRVGLKPQTRQPIRAGAVLFDNEGNRIGVVTSGGF 343
Query: 72 SPSLKKNIAMGYIEPAYSKVGVELWXXXXXXXXXXXXTKMPFVKSNYY 119
PS +AMGY+ A+ G E++ +PFV+ Y+
Sbjct: 344 GPSFDGPVAMGYVPVAWKVEGTEVFTELRGKKIALSVHSLPFVEQRYF 391
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 37/89 (41%), Positives = 49/89 (55%), Gaps = 6/89 (6%)
Query: 468 ERGLIAVQGPLSSTILQRHTDLDLSSLYFMTS-RPCTIAGIPCTLTRAGYTGEDGVEISV 526
ER L+A+QGP ++ +L L + L FM P +TR+GYTGEDG EI++
Sbjct: 171 ERVLLALQGPQAAAVLA-DAGLPGNELLFMQGFEPQQ----DWFITRSGYTGEDGFEIAL 225
Query: 527 PGEQCTHIVEALLSDEDVKLAGLGARDSL 555
P + E LL D V+ GL ARDSL
Sbjct: 226 PIGCARALAEKLLGDSRVEWVGLAARDSL 254
>pdb|1V5V|A Chain A, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
pdb|1V5V|B Chain B, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
Length = 401
Score = 117 bits (293), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 71/254 (27%), Positives = 125/254 (49%), Gaps = 25/254 (9%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
+R ++D H H K+ FAG+ MP+ Y SI HL R+ V +FDVSHM + V GK
Sbjct: 6 KRVHIFDWHKEHARKIEEFAGWEMPIWYS--SIKEEHLAVRNAVGIFDVSHMGEIVFRGK 63
Query: 257 HREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNA---SRR 313
++L+ + D+ + GT +L NE+G I+D+ +V + ++ ++ +
Sbjct: 64 DALKFLQYVTTNDISKPPAISGTYTLVLNERGAIKDETLVFNMGNNEYLMICDSDAFEKL 123
Query: 314 KVDMDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMT 373
+ ++F L +I L+ + AVQGP + + + +D++ +++
Sbjct: 124 YAWFTYLKRTIEQFTKLDLEIELKTYDI---AMFAVQGPKARDLAKDLFGIDINEMWWFQ 180
Query: 374 SRPCTIAGIPCTLTRAGYTGEDGVEISVPG--------------EQCTHIVEALLSDED- 418
+R + GI L+R+GYTGE+G E+ + E+ H+ E +L +
Sbjct: 181 ARWVELDGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKK 240
Query: 419 --VKLAGLGARDSL 430
+K GLGARD+L
Sbjct: 241 YGIKPCGLGARDTL 254
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 36/128 (28%), Positives = 65/128 (50%), Gaps = 20/128 (15%)
Query: 445 LKLSNDRFKSLGKDIHLQFLSPEERGLIAVQGPLSSTILQRHTDLDLSSLYFMTSRPCTI 504
LK + ++F L +I L+ + + AVQGP + + + +D++ +++ +R +
Sbjct: 130 LKRTIEQFTKLDLEIELK---TYDIAMFAVQGPKARDLAKDLFGIDINEMWWFQARWVEL 186
Query: 505 AGIPCTLTRAGYTGEDGVEISVPG--------------EQCTHIVEALLSDED---VKLA 547
GI L+R+GYTGE+G E+ + E+ H+ E +L + +K
Sbjct: 187 DGIKMLLSRSGYTGENGFEVYIEDANPYHPDESKRGEPEKALHVWERILEEGKKYGIKPC 246
Query: 548 GLGARDSL 555
GLGARD+L
Sbjct: 247 GLGARDTL 254
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 4/77 (5%)
Query: 21 FPGASIIQSQIKSGVSRKRTGFT--STGVPIRPGYEIFNANDQRVGAITSGCPSPSLKKN 78
F G + Q + GV RK F G+P R GY+++ AN + +G +TSG SP L
Sbjct: 297 FIGKDALLKQKERGVGRKLVHFKMIDKGIP-REGYKVY-ANGEMIGEVTSGTLSPLLNVG 354
Query: 79 IAMGYIEPAYSKVGVEL 95
I + +++ Y+K G+E+
Sbjct: 355 IGIAFVKEEYAKPGIEI 371
>pdb|3A8I|A Chain A, Crystal Structure Of Et-Ehred-5-Ch3-Thf Complex
pdb|3A8I|B Chain B, Crystal Structure Of Et-Ehred-5-Ch3-Thf Complex
pdb|3A8I|C Chain C, Crystal Structure Of Et-Ehred-5-Ch3-Thf Complex
pdb|3A8I|D Chain D, Crystal Structure Of Et-Ehred-5-Ch3-Thf Complex
pdb|3A8J|A Chain A, Crystal Structure Of Et-Ehred Complex
pdb|3A8J|B Chain B, Crystal Structure Of Et-Ehred Complex
pdb|3A8J|C Chain C, Crystal Structure Of Et-Ehred Complex
pdb|3A8J|D Chain D, Crystal Structure Of Et-Ehred Complex
Length = 364
Score = 108 bits (271), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 84/249 (33%), Positives = 123/249 (49%), Gaps = 25/249 (10%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
Q+TPLY+ H G +MV F G+ MP+ YG S H R+ +FDVSHM + G
Sbjct: 3 QQTPLYEQHTLCGARMVDFHGWMMPLHYG--SQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
Query: 257 HREEWLESICVADVHEL-DPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKV 315
E+L + DV +L GK S N GG+ DDLIV ED LV N++ R+
Sbjct: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDDLIVYYFTEDFFRLVVNSATREK 120
Query: 316 DMDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGP----LSSTIL---QRHTDLDLSS 368
D+ + + F G +I ++ ++ +IAVQGP ++T+ QR +
Sbjct: 121 DLSWITQHAEPF---GIEITVR----DDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKP 173
Query: 369 LYFMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARD 428
+ + + IA GYTGE G EI++P E+ AL+ + VK GLGARD
Sbjct: 174 FFGVQAGDLFIA-------TTGYTGEAGYEIALPNEKAADFWRALV-EAGVKPCGLGARD 225
Query: 429 SLSGDITLN 437
+L + +N
Sbjct: 226 TLRLEAGMN 234
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 15/92 (16%)
Query: 471 LIAVQGP----LSSTIL---QRHTDLDLSSLYFMTSRPCTIAGIPCTLTRAGYTGEDGVE 523
+IAVQGP ++T+ QR + + + + IA GYTGE G E
Sbjct: 144 MIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIA-------TTGYTGEAGYE 196
Query: 524 ISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 555
I++P E+ AL+ + VK GLGARD+L
Sbjct: 197 IALPNEKAADFWRALV-EAGVKPCGLGARDTL 227
>pdb|3A8K|A Chain A, Crystal Structure Of Etd97n-Ehred Complex
pdb|3A8K|B Chain B, Crystal Structure Of Etd97n-Ehred Complex
pdb|3A8K|C Chain C, Crystal Structure Of Etd97n-Ehred Complex
pdb|3A8K|D Chain D, Crystal Structure Of Etd97n-Ehred Complex
Length = 364
Score = 107 bits (267), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 83/249 (33%), Positives = 123/249 (49%), Gaps = 25/249 (10%)
Query: 197 QRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGK 256
Q+TPLY+ H G +MV F G+ MP+ YG S H R+ +FDVSHM + G
Sbjct: 3 QQTPLYEQHTLCGARMVDFHGWMMPLHYG--SQIDEHHAVRTDAGMFDVSHMTIVDLRGS 60
Query: 257 HREEWLESICVADVHEL-DPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKV 315
E+L + DV +L GK S N GG+ D+LIV ED LV N++ R+
Sbjct: 61 RTREFLRYLLANDVAKLTKSGKALYSGMLNASGGVIDNLIVYYFTEDFFRLVVNSATREK 120
Query: 316 DMDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGP----LSSTIL---QRHTDLDLSS 368
D+ + + F G +I ++ ++ +IAVQGP ++T+ QR +
Sbjct: 121 DLSWITQHAEPF---GIEITVR----DDLSMIAVQGPNAQAKAATLFNDAQRQAVEGMKP 173
Query: 369 LYFMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARD 428
+ + + IA GYTGE G EI++P E+ AL+ + VK GLGARD
Sbjct: 174 FFGVQAGDLFIA-------TTGYTGEAGYEIALPNEKAADFWRALV-EAGVKPCGLGARD 225
Query: 429 SLSGDITLN 437
+L + +N
Sbjct: 226 TLRLEAGMN 234
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 46/92 (50%), Gaps = 15/92 (16%)
Query: 471 LIAVQGP----LSSTIL---QRHTDLDLSSLYFMTSRPCTIAGIPCTLTRAGYTGEDGVE 523
+IAVQGP ++T+ QR + + + + IA GYTGE G E
Sbjct: 144 MIAVQGPNAQAKAATLFNDAQRQAVEGMKPFFGVQAGDLFIA-------TTGYTGEAGYE 196
Query: 524 ISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 555
I++P E+ AL+ + VK GLGARD+L
Sbjct: 197 IALPNEKAADFWRALV-EAGVKPCGLGARDTL 227
>pdb|1VLO|A Chain A, Crystal Structure Of Aminomethyltransferase (T Protein;
Tetrahydrofolate-Dependent) Of Glycine Cleavage System
(Np417381) From Escherichia Coli K12 At 1.70 A
Resolution
Length = 381
Score = 99.4 bits (246), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 80/245 (32%), Positives = 113/245 (46%), Gaps = 27/245 (11%)
Query: 195 AEQRTPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVT 254
A Q+TPLY+ H G + V F G+ P+ YG S H R+ FDVSH +
Sbjct: 13 AAQQTPLYEQHTLCGARXVDFHGWXXPLHYG--SQIDEHHAVRTDAGXFDVSHXTIVDLR 70
Query: 255 GKHREEWLESICVADVHEL-DPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRR 313
G E+L + DV +L GK S N GG+ DDLIV ED LV N++ R
Sbjct: 71 GSRTREFLRYLLANDVAKLTKSGKALYSGXLNASGGVIDDLIVYYFTEDFFRLVVNSATR 130
Query: 314 KVDMDLMVAAQDRFKSLGKDIHLQFLSAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMT 373
+ D+ + + F G +I ++ ++ IAVQGP + ++L+
Sbjct: 131 EKDLSWITQHAEPF---GIEITVR----DDLSXIAVQGP--------NAQAKAATLFNDA 175
Query: 374 SRPCTIAGIPCTLTRA--------GYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLG 425
R P +A GYTGE G EI++P E+ AL+ + VK GLG
Sbjct: 176 QRQAVEGXKPFFGVQAGDLFIATTGYTGEAGYEIALPNEKAADFWRALV-EAGVKPCGLG 234
Query: 426 ARDSL 430
ARD+L
Sbjct: 235 ARDTL 239
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 515 GYTGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARDSL 555
GYTGE G EI++P E+ AL+ + VK GLGARD+L
Sbjct: 200 GYTGEAGYEIALPNEKAADFWRALV-EAGVKPCGLGARDTL 239
>pdb|1PJ5|A Chain A, Crystal Structure Of Dimethylglycine Oxidase Of
Arthrobacter Globiformis In Complex With Acetate
pdb|1PJ6|A Chain A, Crystal Structure Of Dimethylglycine Oxidase Of
Arthrobacter Globiformis In Complex With Folic Acid
pdb|1PJ7|A Chain A, Structure Of Dimethylglycine Oxidase Of Arthrobacter
Globiformis In Complex With Folinic Acid
Length = 830
Score = 62.4 bits (150), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 47/198 (23%), Positives = 92/198 (46%), Gaps = 10/198 (5%)
Query: 218 FSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGKHREEWLESICVADVHELDPGK 277
FS P+ A TR+ V+++D++ + + V+G + L+ + AD+ + PG
Sbjct: 484 FSSPIA------AAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAK-KPGA 536
Query: 278 GTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVDMDLMVAAQDRFKSLGKDIHLQ 337
T +L + GG++ D+ V + ED+ L +N + + Q + S + ++
Sbjct: 537 VTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVR 596
Query: 338 FLSAEERGLIAVQGPLSSTILQRHTDLDLSS--LYFMTSRPCTIAGIPCTLTRAGYTGED 395
+ I + GPL+ ++ + +D D ++ L + ++ I GIP T R Y GE
Sbjct: 597 DTTGGT-CCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGEL 655
Query: 396 GVEISVPGEQCTHIVEAL 413
G E+ + + +AL
Sbjct: 656 GWELYTSADNGQRLWDAL 673
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 472 IAVQGPLSSTILQRHTDLDLSS--LYFMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGE 529
I + GPL+ ++ + +D D ++ L + ++ I GIP T R Y GE G E+ +
Sbjct: 605 IGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSAD 664
Query: 530 QCTHIVEAL 538
+ +AL
Sbjct: 665 NGQRLWDAL 673
>pdb|3GSI|A Chain A, Crystal Structure Of D552a Dimethylglycine Oxidase Mutant
Of Arthrobacter Globiformis In Complex With
Tetrahydrofolate
Length = 827
Score = 59.3 bits (142), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 46/198 (23%), Positives = 91/198 (45%), Gaps = 10/198 (5%)
Query: 218 FSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGKHREEWLESICVADVHELDPGK 277
FS P+ A TR+ V+++D++ + + V+G + L+ + AD+ + PG
Sbjct: 481 FSSPIA------AAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAK-KPGA 533
Query: 278 GTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVDMDLMVAAQDRFKSLGKDIHLQ 337
T +L + GG++ + V + ED+ L +N + + Q + S + ++
Sbjct: 534 VTYTLLLDHAGGVRSAITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVR 593
Query: 338 FLSAEERGLIAVQGPLSSTILQRHTDLDLSS--LYFMTSRPCTIAGIPCTLTRAGYTGED 395
+ I + GPL+ ++ + +D D ++ L + ++ I GIP T R Y GE
Sbjct: 594 DTTGGT-CCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGEL 652
Query: 396 GVEISVPGEQCTHIVEAL 413
G E+ + + +AL
Sbjct: 653 GWELYTSADNGQRLWDAL 670
Score = 38.1 bits (87), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 472 IAVQGPLSSTILQRHTDLDLSS--LYFMTSRPCTIAGIPCTLTRAGYTGEDGVEISVPGE 529
I + GPL+ ++ + +D D ++ L + ++ I GIP T R Y GE G E+ +
Sbjct: 602 IGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSAD 661
Query: 530 QCTHIVEAL 538
+ +AL
Sbjct: 662 NGQRLWDAL 670
>pdb|2GAG|A Chain A, Heteroteterameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 51/224 (22%), Positives = 86/224 (38%), Gaps = 14/224 (6%)
Query: 199 TPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHLHTRSKVSVFDVSHMLQTV------ 252
T ++ HLSHG + + P Y T R +V D ML
Sbjct: 577 TAMHSWHLSHGAEFEDVGQWKRPWYYPQAGETMDQAVYRESKAVRDSVGMLDATTLGKIE 636
Query: 253 VTGKHREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASR 312
+ GK E+L I +L G G + G I DD + + ED L +
Sbjct: 637 IRGKDAAEFLNRIYTNGYTKLKVGMGRYGVMCKADGMIFDDGVTLRLAEDRFLLHTTTGG 696
Query: 313 RKVDMDLMVAAQDRFKSLGKDIHLQFLSAEER-GLIAVQGPLSSTILQR---HTDLDLSS 368
+D + ++ ++ D+ + S E+ +AV GP S ++ + D+
Sbjct: 697 AADVLDWL---EEWLQTEWPDLDVTCTSVTEQLATVAVVGPRSRDVIAKLASTVDVSNEG 753
Query: 369 LYFMTSRPCTI-AGIPCTLTRAGYTGEDGVEISVPGEQCTHIVE 411
FM + + +GI ++R ++GE EI+VP + E
Sbjct: 754 FKFMAFKDVVLDSGIEARISRISFSGELAFEIAVPAWHGLRVWE 797
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 467 EERGLIAVQGPLSSTILQR---HTDLDLSSLYFMTSRPCTI-AGIPCTLTRAGYTGEDGV 522
E+ +AV GP S ++ + D+ FM + + +GI ++R ++GE
Sbjct: 724 EQLATVAVVGPRSRDVIAKLASTVDVSNEGFKFMAFKDVVLDSGIEARISRISFSGELAF 783
Query: 523 EISVPGEQCTHIVE 536
EI+VP + E
Sbjct: 784 EIAVPAWHGLRVWE 797
>pdb|1VRQ|A Chain A, Crystal Structure Of Heterotetrameric Sarcosine Oxidase
From Corynebacterium Sp. U-96 In Complex With Folinic
Acid
pdb|1X31|A Chain A, Crystal Structure Of Heterotetrameric Sarcosine Oxidase
From Corynebacterium Sp. U-96
pdb|3AD7|A Chain A, Heterotetrameric Sarcosine Oxidase From Corynebacterium
Sp. U-96 In Complex With Methylthio Acetate
pdb|3AD8|A Chain A, Heterotetrameric Sarcosine Oxidase From Corynebacterium
Sp. U-96 In Complex With Pyrrole 2-Carboxylate
pdb|3AD9|A Chain A, Heterotetrameric Sarcosine Oxidase From Corynebacterium
Sp. U-96 Sarcosine-Reduced Form
pdb|3ADA|A Chain A, Heterotetrameric Sarcosine Oxidase From Corynebacterium
Sp. U-96 In Complex With Sulfite
Length = 964
Score = 50.1 bits (118), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 50/224 (22%), Positives = 94/224 (41%), Gaps = 14/224 (6%)
Query: 199 TPLYDLHLSHGGKMVPFAGFSMPVQY---GAVSITASHLH---TRSKVSVFDVSHMLQTV 252
T ++ HL+HG K + P Y G A + R V + D S + +
Sbjct: 576 TAMHPWHLAHGAKFEDVGQWKRPWYYPQDGESMDEAVYRECKAVRDSVGMLDASTLGKIE 635
Query: 253 VTGKHREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASR 312
+ GK E+L + +L G G + G I DD + + ED + +
Sbjct: 636 IRGKDAAEFLNRMYTNGYTKLKVGMGRYGVMCKADGMIFDDGVTLRLAEDRFLMHTTTGG 695
Query: 313 RKVDMDLMVAAQDRFKSLGKDIHLQFLSAEER-GLIAVQGPLSSTILQR-HTDLDLS--S 368
+D + ++ ++ ++ + S E+ +AV GP S ++ + + LD+S +
Sbjct: 696 AADVLDWL---EEWLQTEWPELDVTCTSVTEQLATVAVVGPRSRDVIAKLASSLDVSNDA 752
Query: 369 LYFMTSRPCTI-AGIPCTLTRAGYTGEDGVEISVPGEQCTHIVE 411
FM + T+ +GI ++R ++GE EI++P + E
Sbjct: 753 FKFMAFQDVTLDSGIEARISRISFSGELAFEIAIPAWHGLQVWE 796
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 39/74 (52%), Gaps = 4/74 (5%)
Query: 467 EERGLIAVQGPLSSTILQR-HTDLDLS--SLYFMTSRPCTI-AGIPCTLTRAGYTGEDGV 522
E+ +AV GP S ++ + + LD+S + FM + T+ +GI ++R ++GE
Sbjct: 723 EQLATVAVVGPRSRDVIAKLASSLDVSNDAFKFMAFQDVTLDSGIEARISRISFSGELAF 782
Query: 523 EISVPGEQCTHIVE 536
EI++P + E
Sbjct: 783 EIAIPAWHGLQVWE 796
>pdb|3TFH|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFH|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFI|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFI|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFJ|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
pdb|3TFJ|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
Length = 369
Score = 49.7 bits (117), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 41/186 (22%), Positives = 86/186 (46%), Gaps = 11/186 (5%)
Query: 220 MPVQYGAVSITASHLHTRSKVSVFDVSHMLQTVVTGKHREEWLESICVADVHELDPGKGT 279
+P +G SI S+ H + V ++DV+ Q ++GK E ++ + D+ + G+
Sbjct: 37 LPAAFG--SIEDSYKHLKEHVQIWDVAAERQVEISGKDSAELVQLMTCRDLSKSKIGRCY 94
Query: 280 LSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASRRKVDMDLMVAAQDRFKSLGKDIHLQFL 339
+E G + +D +V K L+++ + +S A D D++ A+ D+ +
Sbjct: 95 YCPIIDENGNLVNDPVVLK-LDENKWWISIA-----DSDVIFFAKGLASGHKFDVKIVEP 148
Query: 340 SAEERGLIAVQGPLSSTILQRHTDLDLSSLYFMTSRPCTIAGIPCTLTRAGYTGEDGVEI 399
+ ++A+QGP S ++++ ++ L F G + R+G++ + G E+
Sbjct: 149 VVD---IMAIQGPKSFALMEKVFGKKITELKFFGFDYFDFEGTKHLIARSGWSKQGGYEV 205
Query: 400 SVPGEQ 405
V Q
Sbjct: 206 YVENTQ 211
>pdb|2GAH|A Chain A, Heterotetrameric Sarcosine: Structure Of A Diflavin
Metaloenzyme At 1.85 A Resolution
Length = 965
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 48/224 (21%), Positives = 84/224 (37%), Gaps = 14/224 (6%)
Query: 199 TPLYDLHLSHGGKMVPFAGFSMPVQYGAVSITASHL------HTRSKVSVFDVSHMLQTV 252
T + HLSHG + + P Y T R V D + + +
Sbjct: 577 TAXHSWHLSHGAEFEDVGQWKRPWYYPQAGETXDQAVYRESKAVRDSVGXLDATTLGKIE 636
Query: 253 VTGKHREEWLESICVADVHELDPGKGTLSLFTNEQGGIQDDLIVTKTLEDSLFLVSNASR 312
+ GK E+L I +L G G + G I DD + + ED L +
Sbjct: 637 IRGKDAAEFLNRIYTNGYTKLKVGXGRYGVXCKADGXIFDDGVTLRLAEDRFLLHTTTGG 696
Query: 313 RKVDMDLMVAAQDRFKSLGKDIHLQFLSAEER-GLIAVQGPLSSTILQR---HTDLDLSS 368
+D + ++ ++ D+ + S E+ +AV GP S ++ + D+
Sbjct: 697 AADVLDWL---EEWLQTEWPDLDVTCTSVTEQLATVAVVGPRSRDVIAKLASTVDVSNEG 753
Query: 369 LYFMTSRPCTI-AGIPCTLTRAGYTGEDGVEISVPGEQCTHIVE 411
F + + +GI ++R ++GE EI+VP + E
Sbjct: 754 FKFXAFKDVVLDSGIEARISRISFSGELAFEIAVPAWHGLRVWE 797
>pdb|3UGF|A Chain A, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis
pdb|3UGF|B Chain B, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis
pdb|3UGG|A Chain A, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis In Complex With 1-Kestose
pdb|3UGG|B Chain B, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis In Complex With 1-Kestose
pdb|3UGH|A Chain A, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis In Complex With 6-Kestose
pdb|3UGH|B Chain B, Crystal Structure Of A 6-Sst6-Sft From Pachysandra
Terminalis In Complex With 6-Kestose
Length = 546
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/97 (24%), Positives = 39/97 (40%), Gaps = 5/97 (5%)
Query: 392 TGEDGVEISVPGEQCTHIVEALLSDEDVKLAGLGARDSLSGDITLNTPVPHGSLKLSNDR 451
TGE G+E SV G + H+++A + ++ +G D + T + P + L D
Sbjct: 221 TGEKGLETSVNGPKVKHVLKASIDEQQRDYYAIGTYDLGTNKWTPDNPEEDVGIGLRYDW 280
Query: 452 FKSLGKDIHLQFLSP--EERGLIAVQGPLSSTILQRH 486
K F P + R + A L S + R
Sbjct: 281 GKYYASKT---FYDPKKQRRVVWAWTKELDSEVADRE 314
>pdb|3TTG|A Chain A, Crystal Structure Of Putative Aminomethyltransferase From
Leptospirillum Rubarum
Length = 355
Score = 29.3 bits (64), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 26 IIQSQIKSGVSRKRTGFTSTGVPIRPGYE----IFNAND-QRVGAITSGCPSPSLKKNIA 80
+ + + + ++R GF G P P E +FN D G +T S L I
Sbjct: 266 VTRLKFQGHLNRSLAGFRLEGGPF-PKXEFPVTLFNPKDGNEAGILTRTSSSDILGSGIG 324
Query: 81 MGYIEPAYSKVGVEL 95
+GYI+ +S+ G EL
Sbjct: 325 LGYIKRNFSENGTEL 339
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 0.136 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,045,856
Number of Sequences: 62578
Number of extensions: 649233
Number of successful extensions: 1342
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1267
Number of HSP's gapped (non-prelim): 42
length of query: 555
length of database: 14,973,337
effective HSP length: 104
effective length of query: 451
effective length of database: 8,465,225
effective search space: 3817816475
effective search space used: 3817816475
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)