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= 003880
(789 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FQD|A Chain A, Crystal Structure Of The S. Pombe Rat1-Rai1 Complex
Length = 899
Score = 563 bits (1450), Expect = e-160, Method: Compositional matrix adjust.
Identities = 330/819 (40%), Positives = 444/819 (54%), Gaps = 79/819 (9%)
Query: 2 GVPAFYRWLAEKYPLVVADVIEEEPVVI-DGVKIPVDTSKPNPNGLEYDNLYLDMNGIIH 60
GVPA +R L+ K+ V+ VIE + DG +I D S PNPNG+E DNLYLD NGI+H
Sbjct: 5 GVPALFRLLSRKFAKVITPVIEAPTEKLPDGTEIEPDLSLPNPNGVECDNLYLDXNGIVH 64
Query: 61 PCFHPEDRPAPTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQXXXXXX 120
PC HPEDRPAP T DE +F+Y DR+ VRPR+LL++AIDGVAPRAK NQQ
Sbjct: 65 PCSHPEDRPAPETEDEXXVAVFEYTDRILAXVRPRQLLFIAIDGVAPRAKXNQQRSRRFR 124
Query: 121 XXXXXXXXXXXXXXXXXXXXXXXXKLPPK-SDSQVFDSNVITPGTEFMAVLSIALQYYIH 179
+ + + +DSN ITPGT F L+ +L+YYI
Sbjct: 125 SSREAALKEEELQAFIEEAKQQGIPIDENATKKKSWDSNCITPGTPFXDTLAKSLRYYII 184
Query: 180 LRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIML 239
+LN+DP W ++ ILSDA+VPGEGEHKI ++R QR P YDPNT H +YGLDADLI L
Sbjct: 185 NKLNSDPCWRNVRFILSDASVPGEGEHKIXEFIRSQRVKPEYDPNTHHVVYGLDADLIXL 244
Query: 240 ALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVP- 298
LATHE HF +LRE VF Q G E + K D+ + VP
Sbjct: 245 GLATHEPHFRVLREDVFF-----------QQGSTKKTKEERLGIK--RLDDVSETNKVPV 291
Query: 299 KKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIRE 358
KKP+ +L++ LREYL+ E +PN PF DLE +DD++F FFVGNDFLPH+P+L+IR+
Sbjct: 292 KKPFIWLNVSILREYLEVELYVPNLPFPFDLERAIDDWVFFIFFVGNDFLPHLPSLDIRD 351
Query: 359 GAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAVGSYEDRIF----QKRARLHQR 414
GA+ L +++ GGYLT +L R E + AVG+ ED IF Q+ R ++
Sbjct: 352 GAVERLTEIWRASLPHXGGYLTLDGSVNLARAEVILSAVGNQEDDIFKRLKQQEDRRNEN 411
Query: 415 HAERIKREKAQARRG--DDV---------------------------EPLAQPDSLVPVS 445
+ R +RE Q D+V + + D+ PV
Sbjct: 412 YRRRQQRESNQESESYVDNVVIQRSVETQSTEVVTSSKSTSVDTKPPKKTQKIDAPAPVD 471
Query: 446 RFHGSRLASGPSPSPYQQSECVGRLDNGKGTSGRPHKVPRLS--SGATIGAAIVEAE--- 500
+ S S S + R N G S V ++ + + + A +V E
Sbjct: 472 LVNLSEKTSNRSLGATNRELINNRAANRLGLSREAAAVSSVNKLAASALKAQLVSNETLQ 531
Query: 501 -----------------NSFETDPQXXXXXXXXXXXXXXRDKSDAFNSDNPEEDKVKLGE 543
+S E+ + K+ +N D V+L E
Sbjct: 532 NVPLEDSIASSSAYEDTDSIESSTPVVHPIDTKVSNVGQKRKAPDSTEENENTDTVRLYE 591
Query: 544 PGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPF 603
PG++ERYYE+KF+ +P+E E+ R + V Y GLCWV+ YYY+G SW W+YPYHYAPF
Sbjct: 592 PGYRERYYEQKFHI-SPDEPEKIR-EAVKHYVHGLCWVLLYYYQGCPSWTWYYPYHYAPF 649
Query: 604 ASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTD 663
A+D KDL ++ FEL PFKP+ QLLGV P+AS + LPE + L TD NS I DFYP +
Sbjct: 650 AADFKDLASIDVKFELNQPFKPYEQLLGVLPAASKNNLPEKLQTLXTDENSEIIDFYPEN 709
Query: 664 FEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLSHPL 723
F +D+NGK++ WQG+A LPFIDE RLL+ V KI LTEEE++RN + +LF+ HP
Sbjct: 710 FTIDLNGKKFEWQGVALLPFIDENRLLNAVSKIYPQLTEEESKRNEDGSTLLFISEHHP- 768
Query: 724 SASIYTLDEHCKQLKIKERVEVKERLNPELSDGMNGYIS 762
E KQL K+R +L+ + + G+ G ++
Sbjct: 769 -----XFSELVKQLYSKKRQGKPLKLSGKXAHGLFGKVN 802
>pdb|3PIE|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIF|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
Length = 1155
Score = 274 bits (701), Expect = 1e-73, Method: Compositional matrix adjust.
Identities = 154/413 (37%), Positives = 224/413 (54%), Gaps = 65/413 (15%)
Query: 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIH 60
MG+P F+ +++E++P + +IDG +IP E+DNLYLDMN I+H
Sbjct: 1 MGIPKFFHFISERWPQISQ--------LIDGSQIP-----------EFDNLYLDMNSILH 41
Query: 61 PCFHPEDRPAPTTF--DEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQXXXX 118
C H + + +EV+ +F YID LF ++P++ YMAIDGVAPRAKMNQQ
Sbjct: 42 NCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQTFYMAIDGVAPRAKMNQQRARR 101
Query: 119 XXXXXXXXXXXXXXXXXXXXXXXXXXKLPPKSDSQVFDSNVITPGTEFMAVLSIALQYYI 178
+LP + FDSN ITPGTEFMA L+ L+Y+I
Sbjct: 102 FRTAMDAEKALQKAIENGD-------ELPK---GEPFDSNAITPGTEFMAKLTENLKYFI 151
Query: 179 HLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238
H ++ ND W+ +KVI S VPGEG+HKIM Y+R R Y+PNTRHC+YGLDADLI+
Sbjct: 152 HDKITNDTRWQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLII 211
Query: 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEV-VV 297
L L+TH+ HF +LRE V F ++ V +
Sbjct: 212 LGLSTHDHHFCLLREEV-------------------------------TFGKRSSSVKTL 240
Query: 298 PKKPYQFLHIWTLREYLDYEFR--IPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLE 355
+ + LH+ LREYL EF + FE D E ++DDFIF+ F +GNDFLP++P L
Sbjct: 241 ETQNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLH 300
Query: 356 IREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAVGSYEDRIFQKR 408
+++GA +L+ +K+ + + GY+ + K +L R +++ + +E F+K+
Sbjct: 301 LKKGAFPVLLQTFKEALQHMDGYINEQGKINLARFSIWLKYLSDFEYLNFEKK 353
Score = 160 bits (405), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 74/174 (42%), Positives = 111/174 (63%), Gaps = 4/174 (2%)
Query: 546 WKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFAS 605
WK++YY++K + + ++ K++ Y GL WV++YYY G SW W+Y YHYAP S
Sbjct: 491 WKDQYYKDKLDFSINDT--DSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRIS 548
Query: 606 D-LKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDF 664
D +K +DQ NI F G PFKPF QL+ V P S + +P YR LM D +SPI DFYP +
Sbjct: 549 DVIKGIDQ-NIEFHKGQPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEV 607
Query: 665 EVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVL 718
E+D+NGK W+ + K+ F+D+ RL++ + + L+ +E +RNS D++F+
Sbjct: 608 ELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAKLSPDEKKRNSFGTDLIFIF 661
>pdb|2Y35|A Chain A, Crystal Structure Of Xrn1-Substrate Complex
Length = 1140
Score = 271 bits (694), Expect = 7e-73, Method: Compositional matrix adjust.
Identities = 153/412 (37%), Positives = 220/412 (53%), Gaps = 64/412 (15%)
Query: 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIH 60
MGVP F+R+++E+YP ++++ E IP E+DNLYLDMNGI+H
Sbjct: 1 MGVPKFFRYISERYP-CLSELAREHC-------IP-----------EFDNLYLDMNGIVH 41
Query: 61 PCFHPEDRPAPTTFDE--VFQCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQXXXX 118
C HP+D +E +FQ +F+Y+D+LF +++P++L ++++DGVAPRAKMNQQ
Sbjct: 42 NCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDGVAPRAKMNQQRSRR 101
Query: 119 XXXXXXXXXXXXXXXXXXXXXXXXXXKLPPKSDSQVFDSNVITPGTEFMAVLSIALQYYI 178
+ + FDSN ITPGTEFM L L+ ++
Sbjct: 102 FRTAREAEQQEAKAAQRGEL-----------REHERFDSNCITPGTEFMVRLQEGLRAFL 150
Query: 179 HLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238
+++ DP W++ VILS PGEGEHKIM Y+R + P YDPNTRHCLYGLDA LI+
Sbjct: 151 KTKISTDPLWQRCTVILSGQEAPGEGEHKIMDYIRYMKTQPDYDPNTRHCLYGLDAALII 210
Query: 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVP 298
L L THE+HF +LRE V +F V
Sbjct: 211 LGLCTHELHFVVLREEV-------------------------------KFGRNVKRTSVE 239
Query: 299 KKPYQFLHIWTLREYLDYEF-RIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIR 357
+ + LH+ LREYL+ EF + ++D+ ++DD++ M F VGNDF+PH+P L I
Sbjct: 240 ETRFFLLHLGLLREYLELEFDALRTDEHKLDIAQLIDDWVLMGFLVGNDFIPHLPCLHIS 299
Query: 358 EGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAVGSYEDRIFQKRA 409
A+ LL Y + LGG + + K +LRR++ FI A+ E F++ A
Sbjct: 300 SNALPLLYRTYIGIYPTLGGNINENGKLNLRRLQIFISALTEVELDHFKEHA 351
Score = 163 bits (413), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 74/164 (45%), Positives = 103/164 (62%), Gaps = 3/164 (1%)
Query: 545 GWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFA 604
+K +Y KF + +E +++ Y L WV+ YYY GV SW W+YP+HY PF
Sbjct: 413 NYKRNFYRNKFKR---DPNDELIEELCHHYVNALQWVLDYYYRGVQSWDWYYPFHYTPFI 469
Query: 605 SDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDF 664
SDLK+++Q I+F +G PF PF QLL V P+AS+ LP Y LM P SP+++FYP +F
Sbjct: 470 SDLKNIEQVEIAFHMGTPFLPFQQLLAVLPAASAKLLPVAYHDLMLLPTSPLAEFYPLEF 529
Query: 665 EVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRN 708
E D+NGK++ W+ + +PFIDE RLL + E L+ EE RN
Sbjct: 530 ESDLNGKKHDWEAVVLIPFIDEGRLLAAMLPCEAQLSLEERERN 573
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 34.3 bits (77), Expect = 0.25, Method: Composition-based stats.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEV 295
KCF CG+ GH+A NC KR + ++G ++
Sbjct: 14 KCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQM 46
>pdb|2OMK|A Chain A, Structure Of The Bacteroides Thetaiotaomicron Thiamin
Pyrophosphokinase
pdb|2OMK|B Chain B, Structure Of The Bacteroides Thetaiotaomicron Thiamin
Pyrophosphokinase
Length = 231
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 27/126 (21%), Positives = 52/126 (41%), Gaps = 5/126 (3%)
Query: 323 PPFEIDLECIVD-DFIFMCFFVGNDFLP--HMPTLEIREGAINLLMAVYKKEFRALGGYL 379
P E+ L + + F+ C N+++ H P + I +G + L+ YKK F ++ +
Sbjct: 43 PAHELPLRLLAEAQFVVCCXXAANEYISRGHTPDVIIGDG--DSLLPEYKKRFSSIILQI 100
Query: 380 TDGSKPSLRRVEHFIQAVGSYEDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPD 439
+D + H++Q+ G + I + I R G +V +
Sbjct: 101 SDQETNDQTKAVHYLQSKGIRKIAIVGATGKREDHTLGNISLLVEYMRSGMEVRTVTDYG 160
Query: 440 SLVPVS 445
+ +PVS
Sbjct: 161 TFIPVS 166
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH+A NC +A RK G
Sbjct: 14 KCFNCGKEGHIAKNC--RAPRKKG 35
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH+A NC +A RK G
Sbjct: 14 KCFNCGKEGHIAKNC--RAPRKKG 35
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH+A NC +A RK G
Sbjct: 14 KCFNCGKEGHIAKNC--RAPRKKG 35
>pdb|3V4S|A Chain A, Crystal Structure Of Adp-atp Complex Of Purk:
N5-carboxyaminoimidazole Ribonucleotide Synthetase
pdb|3V4S|B Chain B, Crystal Structure Of Adp-atp Complex Of Purk:
N5-carboxyaminoimidazole Ribonucleotide Synthetase
Length = 387
Score = 32.7 bits (73), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 250 ILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWT 309
+LR+V G C+L HL E KA+RK G + D + V + + LHIW
Sbjct: 329 VLRQVNRLTG----CYL-----HLYGKEEAKAQRKMGHVNILNDNIEVALEKAKSLHIWD 379
Query: 310 LREYL 314
+E L
Sbjct: 380 HQEQL 384
>pdb|3Q2O|A Chain A, Crystal Structure Of Purk: N5-Carboxyaminoimidazole
Ribonucleotide Synthetase
pdb|3Q2O|B Chain B, Crystal Structure Of Purk: N5-Carboxyaminoimidazole
Ribonucleotide Synthetase
pdb|3QFF|A Chain A, Crystal Structure Of Adp Complex Of Purk:
N5-Carboxyaminoimidazole Ribonucleotide Synthetase
pdb|3QFF|B Chain B, Crystal Structure Of Adp Complex Of Purk:
N5-Carboxyaminoimidazole Ribonucleotide Synthetase
pdb|3R5H|A Chain A, Crystal Structure Of Adp-Air Complex Of Purk:
N5-Carboxyaminoimidazole Ribonucleotide Synthetase
pdb|3R5H|B Chain B, Crystal Structure Of Adp-Air Complex Of Purk:
N5-Carboxyaminoimidazole Ribonucleotide Synthetase
Length = 389
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 250 ILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWT 309
+LR+V G C+L HL E KA+RK G + D + V + + LHIW
Sbjct: 329 VLRQVNRLTG----CYL-----HLYGKEEAKAQRKMGHVNILNDNIEVALEKAKSLHIWD 379
Query: 310 LREYL 314
+E L
Sbjct: 380 HQEQL 384
>pdb|4DLK|A Chain A, Crystal Structure Of Atp-ca++ Complex Of Purk: N5-
Carboxyaminoimidazole Ribonucleotide Synthetase
pdb|4DLK|B Chain B, Crystal Structure Of Atp-ca++ Complex Of Purk: N5-
Carboxyaminoimidazole Ribonucleotide Synthetase
Length = 380
Score = 32.7 bits (73), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 31/65 (47%), Gaps = 9/65 (13%)
Query: 250 ILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWT 309
+LR+V G C+L HL E KA+RK G + D + V + + LHIW
Sbjct: 323 VLRQVNRLTG----CYL-----HLYGKEEAKAQRKMGHVNILNDNIEVALEKAKSLHIWD 373
Query: 310 LREYL 314
+E L
Sbjct: 374 HQEQL 378
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 32.7 bits (73), Expect = 0.88, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH A NC +A RK G
Sbjct: 4 KCFNCGKEGHTARNC--RAPRKKG 25
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 32.7 bits (73), Expect = 0.88, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH A NC +A RK G
Sbjct: 3 KCFNCGKEGHTARNC--RAPRKKG 24
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 32.7 bits (73), Expect = 0.88, Method: Composition-based stats.
Identities = 14/24 (58%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 263 KCFLCGQPGHLAANCEGKAKRKAG 286
KCF CG+ GH A NC +A RK G
Sbjct: 3 KCFNCGKEGHTARNC--RAPRKKG 24
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 264 CFLCGQPGHLAANCEGKAKRKAGEFDEK 291
C+ CG PGH A C KRK+G E+
Sbjct: 7 CYTCGSPGHYQAQC--PKKRKSGNSRER 32
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 30.4 bits (67), Expect = 3.9, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 263 KCFLCGQPGHLAANCEG 279
KCF CG+ GH+A NC
Sbjct: 2 KCFNCGKEGHIARNCRA 18
>pdb|2OUG|A Chain A, Crystal Structure Of The Rfah Transcription Factor At 2.1a
Resolution
pdb|2OUG|B Chain B, Crystal Structure Of The Rfah Transcription Factor At 2.1a
Resolution
pdb|2OUG|C Chain C, Crystal Structure Of The Rfah Transcription Factor At 2.1a
Resolution
pdb|2OUG|D Chain D, Crystal Structure Of The Rfah Transcription Factor At 2.1a
Resolution
Length = 162
Score = 30.4 bits (67), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 32/114 (28%), Positives = 50/114 (43%), Gaps = 10/114 (8%)
Query: 598 YHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPIS 657
Y + F ++ N + + H F F + PSA H L + K + DP +P
Sbjct: 54 YLFVEFDPEVIHTTTINATRGVSH-FVRFGASPAIVPSAVIHQLSVYKPKDIVDPATP-- 110
Query: 658 DFYPTDFEVDMNGKRYSWQGIAKLPFIDEAR---LLDEV-KKIEHTLTEEEARR 707
YP D + G +Q I P EAR LL+ + K+I+H++ E R+
Sbjct: 111 --YPGDKVIITEGAFEGFQAIFTEP-DGEARSMLLLNLINKEIKHSVKNTEFRK 161
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 0.139 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,032,908
Number of Sequences: 62578
Number of extensions: 1107862
Number of successful extensions: 2337
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2294
Number of HSP's gapped (non-prelim): 36
length of query: 789
length of database: 14,973,337
effective HSP length: 107
effective length of query: 682
effective length of database: 8,277,491
effective search space: 5645248862
effective search space used: 5645248862
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: 55 (25.8 bits)