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= 040782
(435 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ZBK|A Chain A, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|C Chain C, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|E Chain E, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
pdb|2ZBK|G Chain G, Crystal Structure Of An Intact Type Ii Dna Topoisomerase:
Insights Into Dna Transfer Mechanisms
Length = 389
Score = 197 bits (500), Expect = 1e-50, Method: Compositional matrix adjust.
Identities = 118/365 (32%), Positives = 195/365 (53%), Gaps = 27/365 (7%)
Query: 97 ILQIARSILAGNGFSFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRKSTITVK 156
L + + G ++P R SN +Y + ++L +K R F L+ ++ TV
Sbjct: 25 FLNLVEQLKKGEPLVMEIPMRTLSNAIYDEKRKLLLLGEKKLRRNFLDLNEAKRFMQTVL 84
Query: 157 ILSLIHQLCLRNIHVTKRDLFY-----------------TDVKLFQDQTQSDAVLDDVAC 199
+ S+I+ + + + T RDL+Y ++ + +Q +SD+V+ D+
Sbjct: 85 MASIIYDALVSDEYPTIRDLYYRGKHSLLLKSIEGNKIVSEENTWDEQKESDSVIVDIEV 144
Query: 200 ILGCTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGKAIPPNIDRVGDMQSDAMF 259
R + +++ EKG VVG L D+ID +K G G AI P D + + DA F
Sbjct: 145 FTSLLREEMLILSKEKGKVVGNLRIRSGNDVIDLSKTGHGAYAIEPTPDLIDFIDVDAEF 204
Query: 260 ILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDP 319
+L+VEKDA + +L F+ ++ I++T+ GQPD ATR F+R++ ELKLPV L D+DP
Sbjct: 205 VLVVEKDAVFQQLHRAGFWKQYKSILITSAGQPDRATRRFVRRLNEELKLPVYILTDADP 264
Query: 320 YGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL-----DKYKIPEQCR----LPM 370
YG I SV+ GS ++SY+S L TPD K+LG+ D+ K + E R +
Sbjct: 265 YGWYIFSVFRIGSISLSYESERLATPDAKFLGVSMGDIFGNSRKKPYLSEAERKNYIIKA 324
Query: 371 TEQDIKTGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQ 430
+ DIK +++ ++ K W EE+N ++ K K EI+A++S G ++L+ Y+P K+
Sbjct: 325 KDADIKRAEEIKNYEWF-KTKAWQEEINTFLQRKAKLEIEAMASKGLKFLAFQYIPEKIT 383
Query: 431 QKDWL 435
KD++
Sbjct: 384 NKDYI 388
>pdb|1D3Y|A Chain A, Structure Of The Dna Topoisomerase Vi A Subunit
pdb|1D3Y|B Chain B, Structure Of The Dna Topoisomerase Vi A Subunit
Length = 301
Score = 166 bits (421), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 106/304 (34%), Positives = 164/304 (53%), Gaps = 19/304 (6%)
Query: 147 TVRKSTI---TVKILSLIHQLCLRNIHVTKRDLFYTDVKL----FQDQTQSDAVLDDVAC 199
TV ++ I T K+L QL + T R+ +Y F DQ S+ V++D+
Sbjct: 1 TVNQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASNNVIEDLEA 60
Query: 200 ILGCTRSSLNVIAAEKGV-VVGRLIF---SDNGDMI-DCTKMGMGGKAIPPNIDRVGDMQ 254
LG R L I E G VVG L + G+++ DCTK+G G IP ++ ++ +++
Sbjct: 61 ALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKLGTGAYNIPNDVTKL-NLE 119
Query: 255 SDAMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLAL 314
+DA FIL +E + RL +RF+++ CI+V+ KG P ATR F++++ E LPVL
Sbjct: 120 TDADFILAIETSGMFARLNAERFWDKHNCILVSLKGVPARATRRFIKRLHEEHDLPVLVF 179
Query: 315 VDSDPYG-LKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQ 373
D DPYG L I GS + + L+ P + +G+ P D+ Y +P P+ EQ
Sbjct: 180 TDGDPYGYLNIYRTLKVGSGKAIHLADKLSIPAARLIGVTPQDIIDYDLPTH---PLKEQ 236
Query: 374 DIKTGKDLLE-EDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQ-Q 431
DIK KD L+ +DFV+ P W + L M+ +AE Q+L+ +G +Y+ YLP K++ +
Sbjct: 237 DIKRIKDGLKNDDFVRSFPEWQKALKQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDE 296
Query: 432 KDWL 435
WL
Sbjct: 297 STWL 300
>pdb|2Q2E|A Chain A, Crystal Structure Of The Topoisomerase Vi Holoenzyme From
Methanosarcina Mazei
Length = 369
Score = 147 bits (370), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 106/355 (29%), Positives = 180/355 (50%), Gaps = 29/355 (8%)
Query: 97 ILQIARSILAGNGF------SFQVPSRASSNQLYVPELDRIVLKDKTTLRPFASLSTVRK 150
+L+IA I N F S +PSR +N Y E D V D+ + R S TV+
Sbjct: 20 LLEIAEKIY--NQFEEEVVPSVSLPSRTKANLEYSDESDVWVYGDRESER---SAKTVKG 74
Query: 151 STITVKILS----LIHQLCLRNIHVTKRDLFYT----DVKLFQDQTQSDAVLDDVACILG 202
+ +K LI++ RN T R+L+Y D F++Q +SD +++D+ +
Sbjct: 75 AFQLLKTTYATDFLINEHLARNRGSTLRELYYISEGWDYAKFKEQGESDRLIEDLEILTS 134
Query: 203 CTRSSLNVIAAEKGVVV-GRLIFSDN---GDM-IDCTK-MGMGGKAIPPNIDRVGDMQSD 256
R ++ E G + G + ++ G+ I C K +G GG IP N++ + + D
Sbjct: 135 LQREYFHMRPEEDGATMFGPIEITEQTKRGERNIHCQKDVGEGGYQIPFNVENIEFQKHD 194
Query: 257 AMFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVD 316
A I+ +E Y RL E+ F + I+V KGQP +TR +++M EL +PV D
Sbjct: 195 ASMIIAIETGGMYARLMENGFDEAYNAILVHLKGQPARSTRRIIKRMNEELGIPVAVFTD 254
Query: 317 SDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDLDKYKIPEQCRLPMTEQDIK 376
DP+ +I + G+ ++ S + TP K+LG++PSD+ +Y++ +TEQD+
Sbjct: 255 GDPWSYRIYASVAYGAIKSAHLSEFMATPAAKFLGLQPSDIVEYELSTD---KLTEQDVS 311
Query: 377 TGKDLLEEDFVKKNPGWVEELNLMVKTKQKAEIQALSSFGFQYLSEVYLPLKLQQ 431
+ L + + + W E++ L + +KAE QA + G +++EVYLP +L++
Sbjct: 312 ALRSELSDPRFESDY-WKEQIQLQLDIGKKAEQQAFAGKGLDFVTEVYLPNRLKE 365
>pdb|3AKF|A Chain A, Crystal Structure Of Exo-1,5-Alpha-L-Arabinofuranosidase
pdb|3AKG|A Chain A, Crystal Structure Of Exo-1,5-Alpha-L-Arabinofuranosidase
Complexed With Alpha-1,5-L-Arabinofuranobiose
pdb|3AKH|A Chain A, Crystal Structure Of Exo-1,5-Alpha-L-Arabinofuranosidase
Complexed With Alpha-1,5-L-Arabinofuranotriose
pdb|3AKI|A Chain A, Crystal Structure Of Exo-1,5-Alpha-L-Arabinofuranosidase
Complexed With Alpha-L-Arabinofuranosyl Azido
Length = 468
Score = 34.3 bits (77), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 8/60 (13%)
Query: 125 VPELDRIVLKDKTTLRPFASLSTVRKSTITVKILSLIHQLCLRNIHVTKRDLFYTDVKLF 184
VPE DRIVL+ TTL+ L+T ++TI K H + H+ ++ + D K +
Sbjct: 38 VPEYDRIVLRRATTLQ---GLATAPETTIWTK-----HASGVMGAHIWAPEIHFIDGKWY 89
>pdb|2XUB|A Chain A, Human Rpc62 Subunit Structure
pdb|2XV4|S Chain S, Structure Of Human Rpc62 (Partial)
Length = 534
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 32/151 (21%), Positives = 58/151 (38%), Gaps = 18/151 (11%)
Query: 203 CTRSSLNVIAAEKGVVVGRLIFSDNGDMIDCTKMGMGGK-----AIPPNIDRVGDMQSDA 257
C+R L ++ + + + ++SD G++I ++ + GK + DR+ + D
Sbjct: 79 CSRV-LRMLRYPRYIYTTKTLYSDTGELI-VEELLLNGKLTMSAVVKKVADRLTETMEDG 136
Query: 258 MFILLVEKDAAYIRLAEDRFYNRFPCIIVTAKGQPDVATRLFLRKMKMELKLPVLALVDS 317
+ E ++RLA+ F R P + T P L + +
Sbjct: 137 KTMDYAEVSNTFVRLADTHFVQRCPSVPTTENSD-----------PGPPPPAPTLVINEK 185
Query: 318 DPYGLKILSVYGCGSKNMSYDSANLTTPDIK 348
D Y + LS+ G G + S D P K
Sbjct: 186 DMYLVPKLSLIGKGKRRRSSDEDAAGEPKAK 216
>pdb|3G6N|A Chain A, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
pdb|3G6N|B Chain B, Crystal Structure Of An Efpdf Complex With Met-Ala-Ser
Length = 191
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 4/50 (8%)
Query: 352 IRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVK--KNPGWVEELNL 399
IR + ++ ++ LP++E+DI GK++LE F+K ++P EEL+L
Sbjct: 12 IREGNPTLREVAKEVSLPLSEEDISLGKEMLE--FLKNSQDPIKAEELHL 59
>pdb|3CMD|A Chain A, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
pdb|3CMD|B Chain B, Crystal Structure Of Peptide Deformylase From
Vre-E.Faecium
Length = 196
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 4/50 (8%)
Query: 352 IRPSDLDKYKIPEQCRLPMTEQDIKTGKDLLEEDFVK--KNPGWVEELNL 399
IR + ++ ++ LP++E+DI GK++LE F+K ++P EEL+L
Sbjct: 17 IREGNPTLREVAKEVSLPLSEEDISLGKEMLE--FLKNSQDPIKAEELHL 64
>pdb|2VKZ|G Chain G, Structure Of The Cerulenin-Inhibited Fungal Fatty Acid
Synthase Type I Multienzyme Complex
pdb|2VKZ|H Chain H, Structure Of The Cerulenin-Inhibited Fungal Fatty Acid
Synthase Type I Multienzyme Complex
pdb|2VKZ|I Chain I, Structure Of The Cerulenin-Inhibited Fungal Fatty Acid
Synthase Type I Multienzyme Complex
pdb|3HMJ|G Chain G, Saccharomyces Cerevisiae Fas Type I
pdb|3HMJ|H Chain H, Saccharomyces Cerevisiae Fas Type I
pdb|3HMJ|I Chain I, Saccharomyces Cerevisiae Fas Type I
pdb|2UV8|G Chain G, Crystal Structure Of Yeast Fatty Acid Synthase With
Stalled Acyl Carrier Protein At 3.1 Angstrom Resolution
pdb|2UV8|H Chain H, Crystal Structure Of Yeast Fatty Acid Synthase With
Stalled Acyl Carrier Protein At 3.1 Angstrom Resolution
pdb|2UV8|I Chain I, Crystal Structure Of Yeast Fatty Acid Synthase With
Stalled Acyl Carrier Protein At 3.1 Angstrom Resolution
Length = 2051
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/61 (21%), Positives = 34/61 (55%), Gaps = 1/61 (1%)
Query: 298 LFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLTTPDIKWLGIRPSDL 357
+++ ++ +P++ + S Y ++ L++ G G ++ S + T +K+LG++P +
Sbjct: 652 IYVNPFMLQWGIPLIKELRSKGYPIQFLTI-GAGVPSLEVASEYIETLGLKYLGLKPGSI 710
Query: 358 D 358
D
Sbjct: 711 D 711
>pdb|3GVP|A Chain A, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|B Chain B, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|C Chain C, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
pdb|3GVP|D Chain D, Human Sahh-Like Domain Of Human Adenosylhomocysteinase 3
Length = 435
Score = 29.3 bits (64), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 19/85 (22%)
Query: 284 IIVTAKGQPDVATRLFLRKMKMELKLPVLALVDSDPYGLKILSVYGCGSKNMSYDSANLT 343
I++T G +V TR L +MK V G N D A+L
Sbjct: 278 IVITCTGNKNVVTREHLDRMKNSC------------------IVCNMGHSNTEIDVASLR 319
Query: 344 TPDIKWLGIRPSDLDKYKIPEQCRL 368
TP++ W +R S +D P+ R+
Sbjct: 320 TPELTWERVR-SQVDHVIWPDGKRI 343
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 0.136 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,117,080
Number of Sequences: 62578
Number of extensions: 425907
Number of successful extensions: 860
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 845
Number of HSP's gapped (non-prelim): 15
length of query: 435
length of database: 14,973,337
effective HSP length: 102
effective length of query: 333
effective length of database: 8,590,381
effective search space: 2860596873
effective search space used: 2860596873
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)