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= psy13907
(698 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 = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 80/326 (24%), Positives = 141/326 (43%), Gaps = 67/326 (20%)
Query: 272 ILENKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVRAGCDI 331
+L ++ L+DG + ++ K+ G D++ E+ N V+ HR Y+ +G D+
Sbjct: 10 LLSERVLLLDGAYGTEFMKY-GYDDLPEELN--------IKAPDVVLKVHRSYIESGSDV 60
Query: 332 VTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVRVAGSL 391
+ TNT+ A+ +H GL ED+ ++R+AV+ + A EK V G +
Sbjct: 61 ILTNTFGATRMKLRKH-GL-EDKLDPIVRNAVRIARRAAG--EK----------LVFGDI 106
Query: 392 GSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLPAQEE---AM 448
G G + + ST +E + R +E +++ G+D + ET E A+
Sbjct: 107 GPTGELPYP--------LGSTLFEEFYENFRETVEIMVEEGVDGIIFETFSDILELKAAV 158
Query: 449 VLAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLV---------AVG 499
+ A + L A ++F DEK R + +PA A+G
Sbjct: 159 LAAREVSRDVFLIAHMTF---DEK-----------GRSLTGTDPANFAITFDELDIDALG 204
Query: 500 VNC-LAPHYVESLLTSAGR--DVPLLCCPNSGETF-DPGQRIWMNK--DSVPSVDTYVPR 553
+NC L P + + + D L+ PN+G+ + G+ ++ K D +D+Y
Sbjct: 205 INCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSY--- 261
Query: 554 WLDTGVKYVGGCCRTNADDMKNVNQV 579
+ GV GGCC T + +K +V
Sbjct: 262 -YELGVNIFGGCCGTTPEHVKLFRKV 286
>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 = 66.2 bits (160), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 80/325 (24%), Positives = 139/325 (42%), Gaps = 65/325 (20%)
Query: 272 ILENKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHRDYVRAGCDI 331
+L ++ L+DG + ++ K+ G D++ E+ N V+ HR Y+ +G D+
Sbjct: 10 LLSERVLLLDGAYGTEFXKY-GYDDLPEELN--------IKAPDVVLKVHRSYIESGSDV 60
Query: 332 VTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAIASRHVRVAGSL 391
+ TNT+ A+ +H GL ED+ ++R+AV+ + A EK V G +
Sbjct: 61 ILTNTFGATRXKLRKH-GL-EDKLDPIVRNAVRIARRAAG--EK----------LVFGDI 106
Query: 392 GSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETLP--AQEEAMV 449
G G + + ST +E + R +E ++ G+D + ET + +A V
Sbjct: 107 GPTGELPYP--------LGSTLFEEFYENFRETVEIXVEEGVDGIIFETFSDILELKAAV 158
Query: 450 LAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLV---------AVGV 500
LA +E I+ DEK R + +PA A+G+
Sbjct: 159 LAA--REVSRDVFLIAHXTFDEK-----------GRSLTGTDPANFAITFDELDIDALGI 205
Query: 501 NC-LAPHYVESLLTSAGR--DVPLLCCPNSGETF-DPGQRIWMNK--DSVPSVDTYVPRW 554
NC L P + + + D L+ PN+G+ + G+ ++ K D +D+Y
Sbjct: 206 NCSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSY---- 261
Query: 555 LDTGVKYVGGCCRTNADDMKNVNQV 579
+ GV GGCC T + +K +V
Sbjct: 262 YELGVNIFGGCCGTTPEHVKLFRKV 286
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 75/327 (22%), Positives = 126/327 (38%), Gaps = 57/327 (17%)
Query: 263 KDLQKINEFILENKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTHR 322
K + I E + ++ + DGGF L E K P W + +AV HR
Sbjct: 8 KAKRGILERLNAGEVVIGDGGFVFAL-----EKRGYVKAGP-WTPEAAVEHPEAVRQLHR 61
Query: 323 DYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAI-A 381
+++RAG +++ T T+ A SED+ + + YV E I+ ++ + A
Sbjct: 62 EFLRAGSNVMQTFTFYA-----------SEDK----LENRGNYVAEKISGQKVNEAACDI 106
Query: 382 SRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIETL 441
+R V G A + G Y+ + E+ ++E ++ +D L E
Sbjct: 107 ARQVADEGD-----ALVAGGVSQTPSYLSCKSETEVKKIFHQQLEVFMKKNVDFLIAEYF 161
Query: 442 PAQEEAMVLAELIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVGVN 501
EEA+ E +K K + C + HG G A + A VGVN
Sbjct: 162 EHVEEAVWAVEALKT--SGKPIAATMCIGPEGDLHGVSPGECAVRLVKAGAA---IVGVN 216
Query: 502 CLAPHY-----------VESLLTSAGRDVPLLCCPNSGETFDPGQRIWMNKDSVP----- 545
C H+ ++ L +A L+ P + T D G++ +++ P
Sbjct: 217 C---HFDPSTSLQTIKLMKEGLEAARLKAYLMSQPLAYHTPDCGKQGFIDLPEFPFGLEP 273
Query: 546 ------SVDTYVPRWLDTGVKYVGGCC 566
+ Y + GV+Y+GGCC
Sbjct: 274 RVATRWDIQKYAREAYNLGVRYIGGCC 300
>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 = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 75/329 (22%), Positives = 129/329 (39%), Gaps = 63/329 (19%)
Query: 266 QKINEFILE----NKLYLIDGGFSSQLSKHVGEDNVTEKDNPLWCSAFLHSNRQAVIDTH 321
+K + ILE ++ + DGGF L K K P W + +AV H
Sbjct: 7 KKAKKGILERLNAGEIVIGDGGFVFALEK-----RGYVKAGP-WTPEAAVEHPEAVRQLH 60
Query: 322 RDYVRAGCDIVTTNTYQASVEGFVQHLGLSEDQSVQLIRDAVKYVKEAIALEEKRDPAI- 380
R+++RAG +++ T T+ AS ED+ + + YV E I+ +E + A
Sbjct: 61 REFLRAGSNVMQTFTFYAS-----------EDK----LENRGNYVLEKISGQEVNEAAAD 105
Query: 381 ASRHVRVAGSLGSYGAFLHDGSEYRGDYIDSTTPQELIDYHRPRIEALIQGGIDLLAIET 440
+R V G A + G Y+ + + E+ ++E ++ +D L E
Sbjct: 106 IARQVADEGD-----ALVAGGVSQTPSYLSAKSETEVKKVFLQQLEVFMKKNVDFLIAEY 160
Query: 441 LPAQEEAMVLAE-LIKEYPGLKAWISFSCKDEKHTCHGDKFGLIARDVYAKNPAQLVAVG 499
EEA+ E LI + A ++ + + HG G A + A +G
Sbjct: 161 FEHVEEAVWAVETLIASGKPVAATMAIGPEGD---LHGVPPGEAAVRLVK---AGASIIG 214
Query: 500 VNCLAPHY-----------VESLLTSAGRDVPLLCCPNSGETFDPGQRIWMNKDSVP--- 545
VNC H+ ++ L +A L+ P + T D ++ +++ P
Sbjct: 215 VNC---HFDPTISLKTVKLMKEGLEAAQLKAHLMSQPLAYHTPDANKQGFIDLPEFPFGL 271
Query: 546 --------SVDTYVPRWLDTGVKYVGGCC 566
+ Y + GV+Y+GGCC
Sbjct: 272 EPRVATRWDIQKYAREAYNLGVRYIGGCC 300
>pdb|3ENN|A Chain A, 2.1a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
FROM BRUCELLA Melitensis (P43212)
pdb|3ENN|B Chain B, 2.1a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
FROM BRUCELLA Melitensis (P43212)
pdb|3ENN|C Chain C, 2.1a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
FROM BRUCELLA Melitensis (P43212)
pdb|3ENN|D Chain D, 2.1a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
FROM BRUCELLA Melitensis (P43212)
Length = 249
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 141 KFGLIARDVYAKNPAQLVA---VGVNCLAPHYVESLLTSAEVEGQSLELPVNNTLISRKP 197
K GLI ++K+ AQ +A V VNC+AP ++ES +T E Q + ++ P
Sbjct: 160 KAGLIG---FSKSLAQEIASRNVTVNCIAPGFIESAMTGKLNEKQK------DAIMGNIP 210
Query: 198 IQLLSIELELAAA 210
++ + + ++AAA
Sbjct: 211 MKRMGVGADIAAA 223
>pdb|3EMK|A Chain A, 2.5a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
From Brucella Melitensis
pdb|3EMK|B Chain B, 2.5a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
From Brucella Melitensis
pdb|3EMK|C Chain C, 2.5a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
From Brucella Melitensis
pdb|3EMK|D Chain D, 2.5a Crystal Structure Of GlucoseRIBITOL DEHYDROGENASE
From Brucella Melitensis
Length = 246
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 12/73 (16%)
Query: 141 KFGLIARDVYAKNPAQLVA---VGVNCLAPHYVESLLTSAEVEGQSLELPVNNTLISRKP 197
K GLI ++K+ AQ +A V VNC+AP ++ES +T E Q + ++ P
Sbjct: 157 KAGLIG---FSKSLAQEIASRNVTVNCIAPGFIESAMTGKLNEKQK------DAIMGNIP 207
Query: 198 IQLLSIELELAAA 210
++ + + ++AAA
Sbjct: 208 MKRMGVGADIAAA 220
>pdb|3LHA|A Chain A, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
SPACEGROUP P41 21 2
pdb|3LHA|B Chain B, Crystal Structure Of Mouse Vps26b(R240sG241AE242S) IN
SPACEGROUP P41 21 2
Length = 340
Score = 32.7 bits (73), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 32/76 (42%)
Query: 621 GEIVIEQTELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVF 680
G+I E+ IK +E+ +++ ET G + I +I +G G IPI +
Sbjct: 195 GKIYFLSVEIKIKHMEIDIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGSSIPIRLFL 254
Query: 681 PRLFTCPTLITSNFKI 696
PT+ N K
Sbjct: 255 AGYELTPTMRDINKKF 270
>pdb|3LH8|A Chain A, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
pdb|3LH8|B Chain B, Crystal Structure Of Mouse Vps26b In Spacegroup P41 21 2
pdb|3LH9|A Chain A, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
SPACEGROUP P41 21 2
pdb|3LH9|B Chain B, Crystal Structure Of Mouse Vps26b(L197sR199E) IN
SPACEGROUP P41 21 2
Length = 340
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 32/76 (42%)
Query: 621 GEIVIEQTELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVF 680
G+I E+ IK +E+ +++ ET G + I +I +G G IPI +
Sbjct: 195 GKIYFLSVEIKIKHMEIDIIKRETTGTGPNVYHENDTIAKYEIMDGAPVRGESIPIRLFL 254
Query: 681 PRLFTCPTLITSNFKI 696
PT+ N K
Sbjct: 255 AGYELTPTMRDINKKF 270
>pdb|2FAU|A Chain A, Crystal Structure Of Human Vps26
Length = 341
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 32/76 (42%)
Query: 621 GEIVIEQTELPIKSVELQLVRVETCGCAEGYSRDATEIQNIQIGEGNVFTGIPIPIYMVF 680
G+I + I+ +ELQL++ E G + + I +I +G G IPI +
Sbjct: 195 GKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFL 254
Query: 681 PRLFTCPTLITSNFKI 696
PT+ N K
Sbjct: 255 AGYDPTPTMRDVNKKF 270
>pdb|2YYB|A Chain A, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
pdb|2YYB|B Chain B, Crystal Structure Of Ttha1606 From Thermus Thermophilus
Hb8
Length = 242
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 76 PQELIDYHRPRIEALIQGGIDLLAIET-LPAQEE 108
P ++ +H+ R+E L QGGI+L A L A EE
Sbjct: 72 PFPIVGHHKRRLETLFQGGINLYAAHLPLDAHEE 105
Score = 29.3 bits (64), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 414 PQELIDYHRPRIEALIQGGIDLLAIET-LPAQEE 446
P ++ +H+ R+E L QGGI+L A L A EE
Sbjct: 72 PFPIVGHHKRRLETLFQGGINLYAAHLPLDAHEE 105
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
0.319 0.136 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,208,758
Number of Sequences: 62578
Number of extensions: 924321
Number of successful extensions: 2258
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2245
Number of HSP's gapped (non-prelim): 16
length of query: 698
length of database: 14,973,337
effective HSP length: 106
effective length of query: 592
effective length of database: 8,340,069
effective search space: 4937320848
effective search space used: 4937320848
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: 55 (25.8 bits)