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= psy19
(494 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMA|A Chain A, Crystal Structure Of Trmn From Thermus Thermophilus
Length = 354
Score = 98.6 bits (244), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 85/275 (30%), Positives = 126/275 (45%), Gaps = 13/275 (4%)
Query: 198 NSMCSSQNQKTNFTNPE-ENLLKFRVTCNRVGKHTVTSMESERAFGGKLNDTYFWLVDLD 256
+ + + + PE E FRV R G+H TS E ER G L+ Y VDL
Sbjct: 89 DPLGALERAALALPWPELEGAGSFRVEARREGEHPFTSPEVERRVGEALHRAYGVPVDLK 148
Query: 257 DYDIDINLQIRYNEAYVGLPVTQTSLHRRNIVEFNITTLKPTIAYNMVRLASPIPGDVFL 316
+ + + +R EA++G+ +T+ L RR +L P +A ++RLA PG L
Sbjct: 149 RPAVRVRVDVRGEEAFLGVQLTERPLSRRFPKAALRGSLTPVLAQALLRLADARPGMRVL 208
Query: 317 DPMCGGGTIPVECSLSY-PHTFFVCGDINEKLVLKTQANVLHNSGNLNRELKVSPLVCNV 375
DP G GTI +E + + P + GD++EK + + L + + R L+ +
Sbjct: 209 DPFTGSGTIALEAASTLGPTSPVYAGDLDEKRLGLAREAALASGLSWIRFLR-----ADA 263
Query: 376 RQLC-FKPACVDGIVTDLPFGKRVGSKSNNFLLYRLFLIEIGKIVRPQIGRAILLTSDRK 434
R L F P VD I+ + P G R+G K F LY FL ++ P GR LLT
Sbjct: 264 RHLPRFFPE-VDRILANPPHGLRLGRKEGLFHLYWDFLRGALALL-PPGGRVALLTLRPA 321
Query: 435 HLIQALHITSALWKCRKQIKINMSGMKSFVFILNR 469
L +AL AL R + G+ VF+L +
Sbjct: 322 LLKRALPPGFALRHAR---VVEQGGVYPRVFVLEK 353
>pdb|3TLJ|A Chain A, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With S- Adenosyl-L-Homocysteine
pdb|3TLJ|B Chain B, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With S- Adenosyl-L-Homocysteine
pdb|3TM4|A Chain A, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With S- Adenosylmethionine
pdb|3TM4|B Chain B, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With S- Adenosylmethionine
pdb|3TM5|A Chain A, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With Sinefungin
pdb|3TM5|B Chain B, Crystal Structure Of Trm14 From Pyrococcus Furiosus In
Complex With Sinefungin
Length = 373
Score = 73.9 bits (180), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 67/238 (28%), Positives = 117/238 (49%), Gaps = 18/238 (7%)
Query: 213 PEENLLK----FRVTCNRVGKHTVTSMESERAFGG----KLNDTYFWLVDLDDYDIDINL 264
P E +K F V R G H +TS++ R G +L+ LV+LD +
Sbjct: 110 PVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRA 169
Query: 265 QIRYNEAYVGLPVT-QTSLHRRNIVEFNITT-LKPTIAYNMVRLASPIPGDVFLDPMCGG 322
++ + ++G+ T +SLH+R ++ LK +IA M+ LA + G LDPMCG
Sbjct: 170 ELIKDVFFLGIDTTGDSSLHKRPWRVYDHPAHLKASIANAMIELAE-LDGGSVLDPMCGS 228
Query: 323 GTIPVECSLSYPHTFFVCGDINEKLVLKTQANVLHNSGNLNRELKVSPLVCNVRQLCFKP 382
GTI +E +L + + K ++ + N L +G L+ K+ + + QL
Sbjct: 229 GTILIELALRRYSGEIIGIEKYRKHLIGAEMNAL-AAGVLD---KIKFIQGDATQLSQYV 284
Query: 383 ACVDGIVTDLPFGKRVGSKSNNFLLYRLFLIEIGKIVRPQIGRAILLTSDRKHLIQAL 440
VD +++LP+G ++G KS LY F E+ K++ R + +T+++K + +A+
Sbjct: 285 DSVDFAISNLPYGLKIGKKSMIPDLYMKFFNELAKVLEK---RGVFITTEKKAIEEAI 339
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 253 VDLDDYDIDINLQIRYNEAYVGLPVTQTSLHRRNIVE-FNITTLKPTIAYNMVRLASPIP 311
VD D DI +N+ + A + L ++ LH R + I +K T+A +V + P
Sbjct: 131 VDRDAPDIRVNVWLHKETASIALDLSGDGLHLRGYRDRAGIAPIKETLAAAIVMRSGWQP 190
Query: 312 GDVFLDPMCGGGTIPVECSL 331
G LDPMCG GT+ +E ++
Sbjct: 191 GTPLLDPMCGSGTLLIEAAM 210
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 253 VDLDDYDIDINLQIRYNEAYVGLPVTQTSLHRRNIVE-FNITTLKPTIAYNMVRLASPIP 311
VD D DI +N+ + A + L ++ LH R + I +K T+A +V + P
Sbjct: 130 VDRDAPDIRVNVWLHKETASIALDLSGDGLHLRGYRDRAGIAPIKETLAAAIVMRSGWQP 189
Query: 312 GDVFLDPMCGGGTIPVECSL 331
G LDPMCG GT+ +E ++
Sbjct: 190 GTPLLDPMCGSGTLLIEAAM 209
>pdb|3K0B|A Chain A, Crystal Structure Of A Predicted N6-Adenine-Specific Dna
Methylase From Listeria Monocytogenes Str. 4b F2365
Length = 393
Score = 42.4 bits (98), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 36/71 (50%), Gaps = 1/71 (1%)
Query: 262 INLQIRYNEAYVGLPVTQTSLHRRNI-VEFNITTLKPTIAYNMVRLASPIPGDVFLDPMC 320
+ + I +E + + + LH+R + +K T A +V L S P F DP+C
Sbjct: 151 LEVSILKDEVTLTIDTSGAGLHKRGYRLAQGSAPIKETXAAALVLLTSWHPDRPFYDPVC 210
Query: 321 GGGTIPVECSL 331
G GTIP+E +L
Sbjct: 211 GSGTIPIEAAL 221
>pdb|3LDU|A Chain A, The Crystal Structure Of A Possible Methylase From
Clostridium Difficile 630
Length = 385
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 273 VGLPVTQTSLHRRNIVE-FNITTLKPTIAYNMVRLASPIPGDVFLDPMCGGGTIPVECS 330
+ + T +LH+R E N ++ T+A ++ L G V +DP CG GTI +E +
Sbjct: 156 ISIDTTGDALHKRGYREKANKAPIRETLAAGLIYLTPWKAGRVLVDPXCGSGTILIEAA 214
>pdb|3LDG|A Chain A, Crystal Structure Of Smu.472, A Putative Methyltransferase
Complexed With Sah
Length = 384
Score = 35.4 bits (80), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 259 DIDINLQIRYNEAYVGLPVTQTSLHRRNI-VEFNITTLKPTIAYNMVRLASPIPGDVFLD 317
+ I + + ++A V + T SL +R E +K A ++ L++ P F+D
Sbjct: 141 EFKIEISLLKDQARVXIDTTGPSLFKRGYRTEKGGAPIKENXAAAIILLSNWFPDKPFVD 200
Query: 318 PMCGGGTIPVECS 330
P CG GT +E +
Sbjct: 201 PTCGSGTFCIEAA 213
>pdb|1VBK|A Chain A, Crystal Structure Of Ph1313 From Pyrococcus Horikoshii Ot3
pdb|1VBK|B Chain B, Crystal Structure Of Ph1313 From Pyrococcus Horikoshii Ot3
Length = 307
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 36/69 (52%), Gaps = 10/69 (14%)
Query: 219 KFRVTCNRVGKH-TVTSMESERAFGGKLNDTYFWLVDLDDYDIDINLQIRYNEAYV---- 273
KFRVT R+ K + S+E + G + + VDL +YDI+I ++I +AY+
Sbjct: 108 KFRVTARRITKEFPLDSLEIQAKVGEYILNNENCEVDLKNYDIEIGIEIMQGKAYIYTEK 167
Query: 274 -----GLPV 277
GLP+
Sbjct: 168 IKGWGGLPI 176
>pdb|3UFB|A Chain A, Crystal Structure Of A Modification Subunit Of A Putative
Type I Restriction Enzyme From Vibrio Vulnificus Yj016
Length = 530
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 32/118 (27%), Positives = 51/118 (43%), Gaps = 21/118 (17%)
Query: 294 TLKPTIAYNMVRLASPIPGDVFLDPMCGGGTIPVECSLSYPHTFFVCGDINEKLVLK--- 350
T +P + + MV + P G+ LDP CG G VE ++ H C + ++ VL+
Sbjct: 201 TPRPVVRF-MVEVMDPQLGESVLDPACGTGGFLVE---AFEHLERQCKTVEDREVLQESS 256
Query: 351 -------------TQANVLHNSGNLNRELKVSPLVCNVRQLCFKPACVDGIVTDLPFG 395
Q N+L + R + L +R++ K VD I+T+ PFG
Sbjct: 257 IFGGEAKSLPYLLVQMNLLLHGLEYPRIDPENSLRFPLREMGDKDR-VDVILTNPPFG 313
>pdb|2JHJ|A Chain A, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
pdb|2JHJ|B Chain B, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
Length = 295
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 7/53 (13%)
Query: 42 DLLLMKSIGRVFFNIDLKDIEKVKEL------RGIDNILFIIATFENFGFSNK 88
DL + +++ R++FN +++ EKV+E+ R +ILF + ++ F FS K
Sbjct: 240 DLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRF-FSKK 291
>pdb|2JHN|A Chain A, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
pdb|2JHN|B Chain B, 3-Methyladenine Dna-Glycosylase From Archaeoglobus
Fulgidus
Length = 295
Score = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 7/53 (13%)
Query: 42 DLLLMKSIGRVFFNIDLKDIEKVKEL------RGIDNILFIIATFENFGFSNK 88
DL + +++ R++FN +++ EKV+E+ R +ILF + ++ F FS K
Sbjct: 240 DLGVRRAVSRLYFNGEIQSAEKVREIARERFGRFARDILFYLFLYDRF-FSKK 291
>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 768
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 235 MESERAFGGKLNDTYFWLVDLDDYDIDINLQIRYNEAYVG 274
+ SER++ K N+ Y L+ Y D L++ NE Y+G
Sbjct: 242 LSSERSYWRKANEAYMALIMDARYSKDRILELYMNEVYLG 281
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
0.320 0.137 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,339,257
Number of Sequences: 62578
Number of extensions: 590084
Number of successful extensions: 1300
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1284
Number of HSP's gapped (non-prelim): 19
length of query: 494
length of database: 14,973,337
effective HSP length: 103
effective length of query: 391
effective length of database: 8,527,803
effective search space: 3334370973
effective search space used: 3334370973
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)