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= psy1686
(448 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UK6|A Chain A, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|B Chain B, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|C Chain C, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|D Chain D, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|E Chain E, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|F Chain F, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|G Chain G, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|H Chain H, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|I Chain I, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|J Chain J, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|K Chain K, Crystal Structure Of The Tip48 (Tip49b) Hexamer
pdb|3UK6|L Chain L, Crystal Structure Of The Tip48 (Tip49b) Hexamer
Length = 368
Score = 409 bits (1051), Expect = e-114, Method: Compositional matrix adjust.
Identities = 205/359 (57%), Positives = 263/359 (73%), Gaps = 20/359 (5%)
Query: 3 AAAKVQEVREITRVERVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKE 62
A KV E+R++TR+ER+GAHSHIRGLGLDD+LEPR+ SQGMVGQL ARRAAGVVL MI+E
Sbjct: 6 ATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGMVGQLAARRAAGVVLEMIRE 65
Query: 63 EVVMVWPCVMCGRGKNPQKVKKISTATGREEEPDYDGWLAD------------VTKDLRC 110
+ ++ G+ + + A + + +T+ R
Sbjct: 66 GKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLEMSKTEALTQAFRR 125
Query: 111 PDGELQKRKTVVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWREEG 170
G ++ + VHTV+LHEIDVINSRT GFLALF+GDTGEI EVREQI+AKV EWREEG
Sbjct: 126 SIG-VRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEG 184
Query: 171 KAEIVPGVLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYSSPHGIP 230
KAEI+PGVLFIDEVHMLDIE FSFLNRALES+M+PV+I ATNRG+T+IRGT+Y SPHGIP
Sbjct: 185 KAEIIPGVLFIDEVHMLDIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQSPHGIP 244
Query: 231 IDLLDRMVIIPTQPYQDEEIQAILKIRL------MQTDGLRVLTKIALDTSLRYAIQLIT 284
IDLLDR++I+ T PY +++ + IL+IR M D VLT+I L+TSLRYAIQLIT
Sbjct: 245 IDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLIT 304
Query: 285 TASVVCRRRKATEICMEDIRKVYALFLDEGRSTQYLREHQNEYMFDSTVTGGAGDTKME 343
AS+VCR+RK TE+ ++DI++VY+LFLDE RSTQY++E+Q+ ++F+ + G DT +E
Sbjct: 305 AASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYMKEYQDAFLFNE-LKGETMDTSLE 362
Score = 94.4 bits (233), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 43/52 (82%), Positives = 47/52 (90%)
Query: 362 VHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWREEGHSE 413
VHTV+LHEIDVINSRT GFLALF+GDTGEI EVREQI+AKV EWREEG +E
Sbjct: 136 VHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAE 187
>pdb|2XSZ|D Chain D, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|E Chain E, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|F Chain F, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 378
Score = 387 bits (995), Expect = e-108, Method: Compositional matrix adjust.
Identities = 198/348 (56%), Positives = 249/348 (71%), Gaps = 20/348 (5%)
Query: 3 AAAKVQEVREITRVERVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKE 62
A KV E+R++TR+ER+GAHSHIRGLGLDD+LEPR+ SQG VGQL ARRAAGVVL I+E
Sbjct: 21 ATTKVPEIRDVTRIERIGAHSHIRGLGLDDALEPRQASQGXVGQLAARRAAGVVLEXIRE 80
Query: 63 EVVMVWPCVMCGRGKNPQKVKKISTATGREEEPDYDGWLAD------------VTKDLRC 110
+ ++ G+ + A + + +T+ R
Sbjct: 81 GKIAGRAVLIAGQPGTGKTAIAXGXAQALGPDTPFTAIAGSEIFSLEXSKTEALTQAFRR 140
Query: 111 PDGELQKRKT--VVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWRE 168
G K VVHTV+LHEIDVINSRT GFLALF+GDTGEI EVREQI+AKV EWRE
Sbjct: 141 SIGVRIKEGPPGVVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWRE 200
Query: 169 EGKAEIVPGVLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTAYSSPHG 228
EGKAEI+PGVLFIDEVH LDIE FSFLNRALES+ +PV+I ATNRG+T+IRGT+Y SPHG
Sbjct: 201 EGKAEIIPGVLFIDEVHXLDIESFSFLNRALESDXAPVLIXATNRGITRIRGTSYQSPHG 260
Query: 229 IPIDLLDRMVIIPTQPYQDEEIQAILKIR------LMQTDGLRVLTKIALDTSLRYAIQL 282
IPIDLLDR++I+ T PY +++ + IL+IR D VLT+I L+TSLRYAIQL
Sbjct: 261 IPIDLLDRLLIVSTTPYSEKDTKQILRIRCEEEDVEXSEDAYTVLTRIGLETSLRYAIQL 320
Query: 283 ITTASVVCRRRKATEICMEDIRKVYALFLDEGRSTQYLREHQNEYMFD 330
IT AS+VCR+RK TE+ ++DI++VY+LFLDE RSTQY +E+Q+ ++F+
Sbjct: 321 ITAASLVCRKRKGTEVQVDDIKRVYSLFLDESRSTQYXKEYQDAFLFN 368
Score = 95.1 bits (235), Expect = 7e-20, Method: Compositional matrix adjust.
Identities = 44/53 (83%), Positives = 48/53 (90%)
Query: 361 VVHTVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQISAKVTEWREEGHSE 413
VVHTV+LHEIDVINSRT GFLALF+GDTGEI EVREQI+AKV EWREEG +E
Sbjct: 153 VVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAE 205
>pdb|2XSZ|A Chain A, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|B Chain B, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
pdb|2XSZ|C Chain C, The Dodecameric Human Ruvbl1:ruvbl2 Complex With Truncated
Domains Ii
Length = 367
Score = 209 bits (533), Expect = 2e-54, Method: Compositional matrix adjust.
Identities = 128/361 (35%), Positives = 204/361 (56%), Gaps = 46/361 (12%)
Query: 4 AAKVQEVREITRVERVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKEE 63
+K++EV+ T+ +R+ +HSH++GLGLD+S ++ + G+VGQ AR A GV++ +IK +
Sbjct: 14 GSKIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSK 73
Query: 64 VVMVWPCVMCGRGKNPQKVKKISTATGREEE--------PDYDG--WLADVTK------- 106
++ G P K + A +E P + ++ K
Sbjct: 74 KXAGRAVLLAG----PPGTGKTALALAIAQELGSKVPFCPXVGSEVYSTEIKKTEVLXEN 129
Query: 107 -----DLRCPDGELQKRKTVVHTVTLHEIDVINSRTHGFLALFAG-------DTGEITPE 154
LR +G ++ VTLH++DV N+R G + + EIT +
Sbjct: 130 FRRAIGLRIKEGP----PGIIQDVTLHDLDVANARPQGGQDILSXXGQLXKPKKTEITDK 185
Query: 155 VREQISAKVTEWREEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRG 214
+R +I+ V ++ ++G AE+VPGVLF+DEVH LDIECF++L+RALES ++P+VI A+NRG
Sbjct: 186 LRGEINKVVNKYIDQGIAELVPGVLFVDEVHXLDIECFTYLHRALESSIAPIVIFASNRG 245
Query: 215 VTKIRGTA-YSSPHGIPIDLLDRMVIIPTQPYQDEEIQAILKIRLMQTDGLRV------- 266
IRGT +SPHGIP+DLLDR+ II T Y +E + I+KIR QT+G+ +
Sbjct: 246 NCVIRGTEDITSPHGIPLDLLDRVXIIRTXLYTPQEXKQIIKIR-AQTEGINISEEALNH 304
Query: 267 LTKIALDTSLRYAIQLITTASVVCRRRKATEICMEDIRKVYALFLDEGRSTQYLREHQNE 326
L +I T+LRY++QL+T A+++ + I E + ++ LF D S + L + Q++
Sbjct: 305 LGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDK 364
Query: 327 Y 327
Y
Sbjct: 365 Y 365
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 7/60 (11%)
Query: 361 VVHTVTLHEIDVINSRTHGFLALFAG-------DTGEITPEVREQISAKVTEWREEGHSE 413
++ VTLH++DV N+R G + + EIT ++R +I+ V ++ ++G +E
Sbjct: 145 IIQDVTLHDLDVANARPQGGQDILSXXGQLXKPKKTEITDKLRGEINKVVNKYIDQGIAE 204
>pdb|2C9O|A Chain A, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|B Chain B, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
pdb|2C9O|C Chain C, 3d Structure Of The Human Ruvb-Like Helicase Ruvbl1
Length = 456
Score = 189 bits (480), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 100/233 (42%), Positives = 152/233 (65%), Gaps = 16/233 (6%)
Query: 111 PDGELQKRKTVVHTVTLHEIDVINSRTHG-------FLALFAGDTGEITPEVREQISAKV 163
P G++ K+K ++ VTLH++DV N+R G L EIT ++R +I+ V
Sbjct: 224 PKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKTEITDKLRGEINKVV 283
Query: 164 TEWREEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESEMSPVVITATNRGVTKIRGTA- 222
++ ++G AE+VPGVLF+DEVHMLDIECF++L+RALES ++P+VI A+NRG IRGT
Sbjct: 284 NKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNRGNCVIRGTED 343
Query: 223 YSSPHGIPIDLLDRMVIIPTQPYQDEEIQAILKIRLMQTDGLRV-------LTKIALDTS 275
+SPHGIP+DLLDR++II T Y +E++ I+KIR QT+G+ + L +I T+
Sbjct: 344 ITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIR-AQTEGINISEEALNHLGEIGTKTT 402
Query: 276 LRYAIQLITTASVVCRRRKATEICMEDIRKVYALFLDEGRSTQYLREHQNEYM 328
LRY++QL+T A+++ + I E + ++ LF D S + L + Q++YM
Sbjct: 403 LRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYM 455
Score = 61.6 bits (148), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 47/69 (68%)
Query: 6 KVQEVREITRVERVGAHSHIRGLGLDDSLEPRKVSQGMVGQLQARRAAGVVLGMIKEEVV 65
K++EV+ T+ +R+ +HSH++GLGLD+S ++ + G+VGQ AR A GV++ +IK + +
Sbjct: 2 KIEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKM 61
Query: 66 MVWPCVMCG 74
++ G
Sbjct: 62 AGRAVLLAG 70
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 47/84 (55%), Gaps = 7/84 (8%)
Query: 337 AGDTKMEVDKFVQCPDGELQKRKTVVHTVTLHEIDVINSRTHG-------FLALFAGDTG 389
A + +E +++V P G++ K+K ++ VTLH++DV N+R G L
Sbjct: 210 ATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMGQLMKPKKT 269
Query: 390 EITPEVREQISAKVTEWREEGHSE 413
EIT ++R +I+ V ++ ++G +E
Sbjct: 270 EITDKLRGEINKVVNKYIDQGIAE 293
>pdb|2QMW|A Chain A, The Crystal Structure Of The Prephenate Dehydratase (Pdt)
From Staphylococcus Aureus Subsp. Aureus Mu50
pdb|2QMW|B Chain B, The Crystal Structure Of The Prephenate Dehydratase (Pdt)
From Staphylococcus Aureus Subsp. Aureus Mu50
Length = 267
Score = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 1/36 (2%)
Query: 299 CMEDIRKVYALFLDEGRSTQYLREHQNEYMF-DSTV 333
+ DI+KVY++ ++T Y+ +HQ +Y + DST+
Sbjct: 97 SISDIKKVYSIAPAISQTTNYIHQHQFDYDYVDSTI 132
>pdb|2FK6|A Chain A, Crystal Structure Of Rnase ZTRNA(THR) COMPLEX
Length = 320
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 91 REEEPDYDGWL-ADVTKDLRCPDGELQKRKTVVHTVTLHEIDVINSR------THGFLAL 143
R +E D G L ADV K++ P G + ++ TVTL + +IN G +
Sbjct: 148 RVQEKDVPGSLKADVLKEMNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVV 207
Query: 144 FAGDT 148
F+GDT
Sbjct: 208 FSGDT 212
>pdb|4GCW|A Chain A, Crystal Structure Of Rnase Z In Complex With Precursor
Trna(Thr)
Length = 320
Score = 29.3 bits (64), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 91 REEEPDYDGWL-ADVTKDLRCPDGELQKRKTVVHTVTLHEIDVINSR------THGFLAL 143
R +E D G L ADV K++ P G + ++ TVTL + +IN G +
Sbjct: 148 RVQEKDVPGSLKADVLKEMNIPPGPVYQKIKKGETVTLEDGRIINGNDFLEPPKKGRSVV 207
Query: 144 FAGDT 148
F+GDT
Sbjct: 208 FSGDT 212
>pdb|3SBP|A Chain A, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|B Chain B, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|C Chain C, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|D Chain D, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|E Chain E, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|F Chain F, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|G Chain G, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBP|H Chain H, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form
pdb|3SBQ|A Chain A, Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal
Form
pdb|3SBQ|B Chain B, Pseudomonas Stutzeri Nitrous Oxide Reductase, P65 Crystal
Form
pdb|3SBR|A Chain A, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|B Chain B, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|C Chain C, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|D Chain D, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|E Chain E, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|F Chain F, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|G Chain G, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
pdb|3SBR|H Chain H, Pseudomonas Stutzeri Nitrous Oxide Reductase, P1 Crystal
Form With Substrate
Length = 638
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 124 TVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQIS 160
TVT+ ID I +HGF+ + G + EI+P+ I+
Sbjct: 569 TVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSIT 605
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 364 TVTLHEIDVINSRTHGFLALFAGDTGEITPEVREQIS 400
TVT+ ID I +HGF+ + G + EI+P+ I+
Sbjct: 569 TVTITNIDQIEDVSHGFVVVNHGVSMEISPQQTSSIT 605
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 0.135 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,853,846
Number of Sequences: 62578
Number of extensions: 533616
Number of successful extensions: 1260
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1235
Number of HSP's gapped (non-prelim): 24
length of query: 448
length of database: 14,973,337
effective HSP length: 102
effective length of query: 346
effective length of database: 8,590,381
effective search space: 2972271826
effective search space used: 2972271826
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)