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= psy13508
(621 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1EIZ|A Chain A, Ftsj Rna Methyltransferase Complexed With S-
Adenosylmethionine
pdb|1EJ0|A Chain A, Ftsj Rna Methyltransferase Complexed With S-
Adenosylmethionine, Mercury Derivative
Length = 180
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 49/199 (24%), Positives = 84/199 (42%), Gaps = 41/199 (20%)
Query: 306 ENGSPLLGPGELLYFADVCAGPGGFSEYVLYRKKWRAKGIGFTLTGSHDFKLDDFFAGPS 365
+ L PG + D+ A PGG+S+YV+ + + + I L
Sbjct: 14 QQSDKLFKPG--MTVVDLGAAPGGWSQYVVTQIGGKGRIIACDLL--------------- 56
Query: 366 ETFEPYYGVKG-NGDVYDPENILSLHEFVMKSTKGR----GVHFMMADGGFSVEGQENIQ 420
+P GV GD D E VMK+ R V +M+D ++ G +
Sbjct: 57 -PMDPIVGVDFLQGDFRD--------ELVMKALLERVGDSKVQVVMSDMAPNMSGTPAVD 107
Query: 421 EILSKRLYLCQFLVSLF--IVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKP 476
+ + +YL + + + ++ P G FV KVF + F + L + + +V + KP
Sbjct: 108 --IPRAMYLVELALEMCRDVLAPGGSFVVKVFQGEGFDEY----LREIRSLFTKVKVRKP 161
Query: 477 NTSRPANSERYIVCKWKRP 495
++SR + E YIV ++P
Sbjct: 162 DSSRARSREVYIVATGRKP 180
Score = 33.9 bits (76), Expect = 0.26, Method: Composition-based stats.
Identities = 30/113 (26%), Positives = 55/113 (48%), Gaps = 14/113 (12%)
Query: 66 EFVMKSSKGR----GVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLF--IVRPEGH 119
E VMK+ R V +M+D ++ G + + + +YL + + + ++ P G
Sbjct: 74 ELVMKALLERVGDSKVQVVMSDMAPNMSGTPAVD--IPRAMYLVELALEMCRDVLAPGGS 131
Query: 120 FVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIVCKWKRP 170
FV KVF + F + L + + +V + KP++SR + E YIV ++P
Sbjct: 132 FVVKVFQGEGFDEY----LREIRSLFTKVKVRKPDSSRARSREVYIVATGRKP 180
>pdb|2NYU|A Chain A, Crystal Structure Of Human Ftsj Homolog 2 (E.Coli) Protein
In Complex With S-Adenosylmethionine
pdb|2NYU|B Chain B, Crystal Structure Of Human Ftsj Homolog 2 (E.Coli) Protein
In Complex With S-Adenosylmethionine
Length = 196
Score = 36.2 bits (82), Expect = 0.061, Method: Composition-based stats.
Identities = 54/220 (24%), Positives = 91/220 (41%), Gaps = 49/220 (22%)
Query: 281 FLNRAAMKMANMDKRLNSMFTQPVRENGSPLLGPGELLYFADVCAGPGGFSEYVLYRKKW 340
+ +R+A K+ +++R +L PG L D A PG +S+ + +K
Sbjct: 2 YRSRSAFKLLEVNER-------------HQILRPG--LRVLDCGAAPGAWSQVAV--QKV 44
Query: 341 RAKG------IGFTLTGS--HDFKLDD-FFAGPSETFEPYYGVKGNGDVYDPENILSLHE 391
A G +GF L H F L+ F P+ DV DP +
Sbjct: 45 NAAGTDPSSPVGFVLGVDLLHIFPLEGATFLCPA-------------DVTDPRT----SQ 87
Query: 392 FVMKSTKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLF--IVRPEGHFVCKV 449
+++ GR +++D + G ++ + + LC L+S+ I++P G F+CK
Sbjct: 88 RILEVLPGRRADVILSDMAPNATGFRDLDH--DRLISLCLTLLSVTPDILQPGGTFLCKT 145
Query: 450 FDMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIV 489
+ S L L ++ V I KP SR +SE Y +
Sbjct: 146 WA--GSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFL 183
Score = 33.9 bits (76), Expect = 0.27, Method: Composition-based stats.
Identities = 30/114 (26%), Positives = 52/114 (45%), Gaps = 10/114 (8%)
Query: 53 GDVYDPENILSLHEFVMKSSKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLF 112
DV DP + +++ GR +++D + G ++ + + LC L+S+
Sbjct: 78 ADVTDPRT----SQRILEVLPGRRADVILSDMAPNATGFRDLDH--DRLISLCLTLLSVT 131
Query: 113 --IVRPEGHFVCKVFDMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIV 164
I++P G F+CK + S L L ++ V I KP SR +SE Y +
Sbjct: 132 PDILQPGGTFLCKTWA--GSQSRRLQRRLTEEFQNVRIIKPEASRKESSEVYFL 183
>pdb|3LKV|A Chain A, Crystal Structure Of Conserved Domain Protein From Vibrio
Cholerae O1 Biovar Eltor Str. N16961
Length = 302
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 41 LLKNVLQCVKGNGDVYDP--ENILSLHEFVMKSSKGRGVHFMMADGGFSVEGQENIQEIL 98
L+K +L VK G VY+P N +SL E + S+ G+ + A S + Q Q I
Sbjct: 132 LIKEILPNVKSIGVVYNPGEANAVSLXELLKLSAAKHGIKLVEATALKSADVQSATQAIA 191
Query: 99 SKRLYLCQFLVSLFIVRPEGHFVC 122
K + + + EG V
Sbjct: 192 EKSDVIYALIDNTVASAIEGXIVA 215
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 22 VEGDKKLSIDNETKFCSPNLLKNVLQCVKGNGDVYDPEN 60
VEG L +DN T SP+ L+ V + GDVY P +
Sbjct: 44 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 82
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 22 VEGDKKLSIDNETKFCSPNLLKNVLQCVKGNGDVYDPEN 60
VEG L +DN T SP+ L+ V + GDVY P +
Sbjct: 67 VEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRD 105
>pdb|3NDY|A Chain A, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
pdb|3NDY|B Chain B, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
pdb|3NDY|C Chain C, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
pdb|3NDY|D Chain D, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
pdb|3NDZ|A Chain A, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
Bound To Cellotriose
pdb|3NDZ|B Chain B, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
Bound To Cellotriose
pdb|3NDZ|C Chain C, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
Bound To Cellotriose
pdb|3NDZ|D Chain D, The Structure Of The Catalytic And Carbohydrate Binding
Domain Of Endoglucanase D From Clostridium Cellulovorans
Bound To Cellotriose
Length = 345
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 11 ALSEDDMDSWIVEGDKKLSIDNETKFCSPNLLKNVLQCVKGNGDVYDPENI---LSLHEF 67
A+ + SW + DK S+D+E +KN V G + N ++ E+
Sbjct: 232 AMDINGTSSWGSDYDKS-SLDSEFDAVYNKFVKNGRAVVIGEMGSINKNNTAARVTHAEY 290
Query: 68 VMKSSKGRGVHFMMADGGFSVEGQ 91
KS+K RG+ + D G+SV G+
Sbjct: 291 YAKSAKARGLTPIWWDNGYSVAGK 314
>pdb|4I17|A Chain A, Crystal Structure Of A Hypothetical Protein (Bf2334) From
Bacteroides Fragilis Nctc 9343 At 1.50 A Resolution
Length = 228
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 532 KSDANFFDYLVTSN-NVINRIAGLGKHAIYRYREDSNRWVSETSLGIQLSPG 582
K A++FD + N N+ N A +GK A YR +++ +++ + GI+ PG
Sbjct: 59 KEAADYFDIAIKKNYNLAN--AYIGKSAAYRDXKNNQEYIATLTEGIKAVPG 108
>pdb|2D0T|A Chain A, Crystal Structure Of 4-Phenylimidazole Bound Form Of Human
Indoleamine 2,3-Dioxygenase
pdb|2D0T|B Chain B, Crystal Structure Of 4-Phenylimidazole Bound Form Of Human
Indoleamine 2,3-Dioxygenase
pdb|2D0U|A Chain A, Crystal Structure Of Cyanide Bound Form Of Human
Indoleamine 2,3-Dioxygenase
pdb|2D0U|B Chain B, Crystal Structure Of Cyanide Bound Form Of Human
Indoleamine 2,3-Dioxygenase
Length = 406
Score = 29.6 bits (65), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 29/63 (46%), Gaps = 9/63 (14%)
Query: 8 HLPALSEDDMDSWIVEGDKKLSIDNETKFCSPNLLKNVLQCV-------KGNGDVYD--P 58
HLP L E VE LSID+ T S L + VL C+ KG+GDV P
Sbjct: 48 HLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLP 107
Query: 59 ENI 61
NI
Sbjct: 108 RNI 110
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
0.323 0.139 0.425
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,539,122
Number of Sequences: 62578
Number of extensions: 871129
Number of successful extensions: 1463
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1455
Number of HSP's gapped (non-prelim): 15
length of query: 621
length of database: 14,973,337
effective HSP length: 105
effective length of query: 516
effective length of database: 8,402,647
effective search space: 4335765852
effective search space used: 4335765852
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)