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= 012486
(462 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
Length = 727
Score = 95.9 bits (237), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 88/385 (22%), Positives = 153/385 (39%), Gaps = 76/385 (19%)
Query: 102 KDKFVVVSYNILGVENALKHPDLYDKVPPKFLKWERRKKLIREEMSSYNASILCLQEVDH 161
K F V+SYN L A P +Y P L W+ R+ ++E++ SY++ +LCLQEV+
Sbjct: 392 KRTFTVLSYNTLCQHYAT--PKMYRYTPSWALSWDYRRNKLKEQILSYDSDLLCLQEVES 449
Query: 162 --FDDL-DDLLQMDGFRGVYKART---------GDANDGCAIFWKEKLFTLLHQENIEFQ 209
F++ LL G+ G++ A+ DGC IF+K F L+ ++ ++F
Sbjct: 450 KTFEEYWVPLLDKHGYTGIFHAKARAKTMHSKDSKKVDGCCIFFKRDQFKLITKDAMDFS 509
Query: 210 NFGLRHNVAQLCVLKMNXXXXXXXXXXXXXXXXXXXXXXXGNI--HVLFNPNRGDIKLGQ 267
++H Q +N + H+ ++P D+K Q
Sbjct: 510 GAWMKHKKFQRTEDYLNRAMNKDNVALFLKLQHIPSGDTIWAVTTHLHWDPKFNDVKTFQ 569
Query: 268 IRLFL---------EKAYKLSQEWGGIPVLLAGDLNSSPNSALYQFLASSELDVCQHDRR 318
+ + L E ++ Q+ PVL+ GD NS NSA+Y+ + + + + Q
Sbjct: 570 VGVLLDHLETLLKEETSHNFRQDIKKFPVLICGDFNSYINSAVYELINTGRVQIHQE--- 626
Query: 319 HISGQFAKCRDIDFQKRNSTSDWISISRPLLYQWTDVELRLATGCEGVTELQHQLNLCSA 378
RD + + S H L L S+
Sbjct: 627 ------GNGRDFGYMSEKNFS-------------------------------HNLALKSS 649
Query: 379 YFGIPGSHRTRDNLGEPLATSYHSKFMGTVDYIWHTEELVPVR-VLETLPVNILRRNGGL 437
Y + +GE T++ F +DYIW + + VR +L + + + G
Sbjct: 650 Y----------NCIGELPFTNFTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGF 699
Query: 438 PSERWGSDHLALVCELAFANNGDGT 462
P++++ SDH+ L+ F G+
Sbjct: 700 PNDKFPSDHIPLLARFEFMKTNTGS 724
>pdb|3NGQ|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain
Length = 398
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 104/407 (25%), Positives = 166/407 (40%), Gaps = 86/407 (21%)
Query: 89 RQW-TFSSRDLSKFKDKFVVVSYNILGVENALKHPDLYDKVPPKFLKWERRKKLIREEMS 147
R W T RD F V+ YN+L + A + LY P L WE RKK I EE+
Sbjct: 15 RPWITLKERDQILPSASFTVMCYNVLCDKYATRQ--LYGYCPSWALNWEYRKKGIMEEIV 72
Query: 148 SYNASILCLQEVD---HFDDLDDLLQMDGFRGVY--KARTGDAN-------DGCAIFWKE 195
+ +A I+ LQEV+ +F L+ G+ G + K+R + DGCAIF+K
Sbjct: 73 NCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKT 132
Query: 196 KLFTLLHQENIEFQNFGL---------------RHNVAQLCVLKMNXXXXXXXXXXXXXX 240
+ FTL+ + +EF + + N+ VL+++
Sbjct: 133 EKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVH--KELFGAGMKPIH 190
Query: 241 XXXXXXXXXGNIHVLFNPNRGDIKLGQIRLF-------LEKAYKL----SQEWGGIPVLL 289
N H+ ++P D+KL Q +F LEKA + + IP++L
Sbjct: 191 AADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVL 250
Query: 290 AGDLNSSPNSALYQFLASSELDVCQHDRRHISGQFAKC-RDIDFQKRNSTSDWISISRPL 348
DLNS P+S + ++L++ + D + + ++ +C + +N +S
Sbjct: 251 CADLNSLPDSGVVEYLSNGGVADNHKDFKEL--RYNECLMNFSCNGKNGSS--------- 299
Query: 349 LYQWTDVELRLATGCEGVTELQHQLNLCSAYFGIPGSHRTRDNLGEPLATSYHSKFMGTV 408
EG + H L SAY +NL T+Y F G +
Sbjct: 300 ---------------EG--RITHGFQLKSAY---------ENNLMP--YTNYTFDFKGVI 331
Query: 409 DYIWHTEELVPVR-VLETLPVNILRRNG--GLPSERWGSDHLALVCE 452
DYI++++ + V VL L L N G P SDH +L+ +
Sbjct: 332 DYIFYSKTHMNVEGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQ 378
>pdb|3NGN|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Amp
pdb|3NGO|A Chain A, Crystal Structure Of The Human Cnot6l Nuclease Domain In
Complex With Poly(A) Dna
Length = 398
Score = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 104/407 (25%), Positives = 166/407 (40%), Gaps = 86/407 (21%)
Query: 89 RQW-TFSSRDLSKFKDKFVVVSYNILGVENALKHPDLYDKVPPKFLKWERRKKLIREEMS 147
R W T RD F V+ YN+L + A + LY P L WE RKK I EE+
Sbjct: 15 RPWITLKERDQILPSASFTVMCYNVLCDKYATRQ--LYGYCPSWALNWEYRKKGIMEEIV 72
Query: 148 SYNASILCLQEVD---HFDDLDDLLQMDGFRGVY--KARTGDAN-------DGCAIFWKE 195
+ +A I+ LQEV+ +F L+ G+ G + K+R + DGCAIF+K
Sbjct: 73 NCDADIISLQEVETEQYFTLFLPALKERGYDGFFSPKSRAKIMSEQERKHVDGCAIFFKT 132
Query: 196 KLFTLLHQENIEFQNFGL---------------RHNVAQLCVLKMNXXXXXXXXXXXXXX 240
+ FTL+ + +EF + + N+ VL+++
Sbjct: 133 EKFTLVQKHTVEFNQVAMANSDGSEAMLNRVMTKDNIGVAVVLEVH--KELFGAGMKPIH 190
Query: 241 XXXXXXXXXGNIHVLFNPNRGDIKLGQIRLF-------LEKAYKL----SQEWGGIPVLL 289
N H+ ++P D+KL Q +F LEKA + + IP++L
Sbjct: 191 AADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPLVL 250
Query: 290 AGDLNSSPNSALYQFLASSELDVCQHDRRHISGQFAKC-RDIDFQKRNSTSDWISISRPL 348
DLNS P+S + ++L++ + D + + ++ +C + +N +S
Sbjct: 251 CADLNSLPDSGVVEYLSNGGVADNHKDFKEL--RYNECLMNFSCNGKNGSS--------- 299
Query: 349 LYQWTDVELRLATGCEGVTELQHQLNLCSAYFGIPGSHRTRDNLGEPLATSYHSKFMGTV 408
EG + H L SAY +NL T+Y F G +
Sbjct: 300 ---------------EG--RITHGFQLKSAY---------ENNLMP--YTNYTFDFKGVI 331
Query: 409 DYIWHTEELVPV-RVLETLPVNILRRNG--GLPSERWGSDHLALVCE 452
DYI++++ + V VL L L N G P SDH +L+ +
Sbjct: 332 DYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPHIPSDHFSLLTQ 378
>pdb|2ZIR|B Chain B, Crystal Structure Of Rat Protein Farnesyltransferase
Complexed With A Benzofuran Inhibitor And Fpp
pdb|2ZIS|B Chain B, Crystal Structure Of Rat Protein Farnesyltransferase
Complexed With A Bezoruran Inhibitor And Fpp
Length = 440
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 287 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 316
>pdb|1O1R|B Chain B, Structure Of Fpt Bound To Ggpp
pdb|1O1S|B Chain B, Structure Of Fpt Bound To Isoprenoid Analog 3b
pdb|1O1T|B Chain B, Structure Of Fpt Bound To The Cvim-Fpp Product
pdb|3EU5|B Chain B, Crystal Structure Of Ftase(Alpha-Subunit; Beta-Subunit
Delta C10) In Complex With Biotingpp
pdb|4GTM|B Chain B, Ftase In Complex With Bms Analogue 11
pdb|4GTO|B Chain B, Ftase In Complex With Bms Analogue 14
pdb|4GTP|B Chain B, Ftase In Complex With Bms Analogue 16
pdb|4GTQ|B Chain B, Ftase In Complex With Bms Analogue 12
pdb|4GTR|B Chain B, Ftase In Complex With Bms Analogue 13
Length = 427
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|3PZ4|B Chain B, Crystal Structure Of Ftase(Alpha-Subunit; Beta-Subunit
Delta C10) In Complex With Bms3 And Lipid Substrate Fpp
Length = 426
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 283 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 312
>pdb|3EUV|B Chain B, Crystal Structure Of Ftase(Alpha-Subunit; Beta-Subunit
Delta C10, W102t, Y154t) In Complex With Biotingpp
Length = 427
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|2H6G|B Chain B, W102t Protein Farnesyltransferase Mutant Complexed With A
Geranylgeranylated Ddptasacvls Peptide Product At 1.85a
Resolution
Length = 437
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|1FT1|B Chain B, Crystal Structure Of Protein Farnesyltransferase At 2.25
Angstroms Resolution
pdb|1FPP|B Chain B, Protein Farnesyltransferase Complex With Farnesyl
Diphosphate
pdb|1QBQ|B Chain B, Structure Of Rat Farnesyl Protein Transferase Complexed
With A Cvim Peptide And Alpha-Hydroxyfarnesylphosphonic
Acid.
pdb|1D8D|B Chain B, Co-Crystal Structure Of Rat Protein Farnesyltransferase
Complexed With A K-Ras4b Peptide Substrate And Fpp
Analog At 2.0a Resolution
pdb|1D8E|B Chain B, Zinc-Depleted Ftase Complexed With K-Ras4b Peptide
Substrate And Fpp Analog.
pdb|1JCR|B Chain B, Crystal Structure Of Rat Protein Farnesyltransferase
Complexed With The Non-Substrate Tetrapeptide Inhibitor
Cvfm And Farnesyl Diphosphate Substrate
pdb|1JCS|B Chain B, Crystal Structure Of Rat Protein Farnesyltransferase
Complexed With The Peptide Substrate Tkcvfm And An
Analog Of Farnesyl Diphosphate
pdb|1KZO|B Chain B, Protein Farnesyltransferase Complexed With Farnesylated
K-Ras4b Peptide Product And Farnesyl Diphosphate
Substrate Bound Simultaneously
pdb|1KZP|B Chain B, Protein Farnesyltransferase Complexed With A Farnesylated
K-Ras4b Peptide Product
pdb|1O5M|B Chain B, Structure Of Fpt Bound To The Inhibitor Sch66336
pdb|1SA5|B Chain B, Rat Protein Farnesyltransferase Complexed With Fpp And
Bms- 214662
pdb|1TN7|B Chain B, Protein Farnesyltransferase Complexed With A Tc21 Peptide
Substrate And A Fpp Analog At 2.3a Resolution
pdb|1TN8|B Chain B, Protein Farnesyltransferase Complexed With A H-Ras Peptide
Substrate And A Fpp Analog At 2.25a Resolution
pdb|3DPY|B Chain B, Protein Farnesyltransferase Complexed With Fpp And Caged
Tkcvim Substrate
pdb|3E30|B Chain B, Protein Farnesyltransferase Complexed With Fpp And
Ethylene Diamine Inhibitor 4
pdb|3E32|B Chain B, Protein Farnesyltransferase Complexed With Fpp And
Ethylenediamine Scaffold Inhibitor 2
pdb|3E33|B Chain B, Protein Farnesyltransferase Complexed With Fpp And
Ethylenediamine Scaffold Inhibitor 7
pdb|3E34|B Chain B, Protein Farnesyltransferase Complexed With Fpp And
Ethylenediamine-Scaffold Inhibitor 10
pdb|3KSL|B Chain B, Structure Of Fpt Bound To Datfp-Dh-Gpp
pdb|3KSQ|B Chain B, Discovery Of C-Imidazole Azaheptapyridine Fpt Inhibitors
Length = 437
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|1JCQ|B Chain B, Crystal Structure Of Human Protein Farnesyltransferase
Complexed With Farnesyl Diphosphate And The
Peptidomimetic Inhibitor L-739,750
pdb|1LD7|B Chain B, Co-Crystal Structure Of Human Farnesyltransferase With
Farnesyldiphosphate And Inhibitor Compound 66
pdb|1LD8|B Chain B, Co-Crystal Structure Of Human Farnesyltransferase With
Farnesyldiphosphate And Inhibitor Compound 49
pdb|1MZC|B Chain B, Co-Crystal Structure Of Human Farnesyltransferase With
Farnesyldiphosphate And Inhibitor Compound 33a
pdb|1SA4|B Chain B, Human Protein Farnesyltransferase Complexed With Fpp And
R115777
pdb|1S63|B Chain B, Human Protein Farnesyltransferase Complexed With L-778,123
And Fpp
pdb|1TN6|B Chain B, Protein Farnesyltransferase Complexed With A Rap2a Peptide
Substrate And A Fpp Analog At 1.8a Resolution
pdb|2H6F|B Chain B, Protein Farnesyltransferase Complexed With A Farnesylated
Ddptasacvls Peptide Product At 1.5a Resolution
pdb|2F0Y|B Chain B, Crystal Structure Of Human Protein Farnesyltransferase
Complexed With Farnesyl Diphosphate And Hydantoin
Derivative
pdb|2IEJ|B Chain B, Human Protein Farnesyltransferase Complexed With Inhibitor
Compound Stn-48 And Fpp Analog At 1.8a Resolution
pdb|3E37|B Chain B, Protein Farnesyltransferase Complexed With Bisubstrate
Ethylenediamine Scaffold Inhibitor 5
Length = 437
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|2H6I|B Chain B, W102tY365F PROTEIN FARNESYLTRANSFERASE DOUBLE MUTANT
COMPLEXED WITH A Geranylgeranylated Ddptasacvls Peptide
Product At 3.0a
Length = 437
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|2H6H|B Chain B, Y365f Protein Farnesyltransferase Mutant Complexed With A
Farnesylated Ddptasacvls Peptide Product At 1.8a
Length = 437
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 284 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 313
>pdb|1FT2|B Chain B, Co-Crystal Structure Of Protein Farnesyltransferase
Complexed With A Farnesyl Diphosphate Substrate
Length = 401
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 263 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 292
>pdb|1N95|B Chain B, Aryl Tetrahydrophyridine Inhbitors Of Farnesyltranferase:
Glycine, Phenylalanine And Histidine Derivatives
pdb|1N9A|B Chain B, Farnesyltransferase Complex With Tetrahydropyridine
Inhibitors
pdb|1NI1|B Chain B, Imidazole And Cyanophenyl Farnesyl Transferase Inhibitors
Length = 402
Score = 30.8 bits (68), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 263 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 292
>pdb|1NL4|B Chain B, Crystal Structure Of Rat Farnesyl Transferase In Complex
With A Potent Biphenyl Inhibitor
pdb|2BED|B Chain B, Structure Of Fpt Bound To Inhibitor Sch207736
pdb|2R2L|B Chain B, Structure Of Farnesyl Protein Transferase Bound To Pb-93
Length = 401
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 262 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 291
>pdb|1N94|B Chain B, Aryl Tetrahydropyridine Inhbitors Of Farnesyltransferase:
Glycine, Phenylalanine And Histidine Derivates
pdb|1X81|B Chain B, Farnesyl Transferase Structure Of Jansen Compound
Length = 397
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 174 FRGVYKARTGDANDGCAIFWKEKLFTLLHQ 203
F G ++ R DGC FW+ L LLH+
Sbjct: 263 FEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 292
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 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,202,197
Number of Sequences: 62578
Number of extensions: 511385
Number of successful extensions: 844
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 816
Number of HSP's gapped (non-prelim): 20
length of query: 462
length of database: 14,973,337
effective HSP length: 102
effective length of query: 360
effective length of database: 8,590,381
effective search space: 3092537160
effective search space used: 3092537160
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)