RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5052
(172 letters)
>1tv8_A MOAA, molybdenum cofactor biosynthesis protein A; TIM barrel,
ligand binding protein; HET: SAM; 2.20A {Staphylococcus
aureus} SCOP: c.1.28.3 PDB: 1tv7_A* 2fb3_A* 2fb2_A*
Length = 340
Score = 257 bits (660), Expect = 5e-87
Identities = 60/170 (35%), Positives = 93/170 (54%), Gaps = 3/170 (1%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
AGL IN+SLD + ++ I R + +L ID A +G N+KVNVV+ K ND
Sbjct: 116 YDAGLRRINVSLDAIDDTLFQSINNRNIKATTILEQIDYATSIGL-NVKVNVVIQKGIND 174
Query: 61 DEILDFVLLTRDRPIDVRFIEYMPF-SGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAP 119
D+I+ + +D+ I++RFIE+M + N W+ +K++ EMLT I++
Sbjct: 175 DQIIPMLEYFKDKHIEIRFIEFMDVGNDNGWDFSKVVTKDEMLTMIEQHFEIDPVEPKYF 234
Query: 120 NDTSKAYKVPEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTE 169
+ +K Y+ + Q G ITS+++ FC TC R RL +DG CLF +
Sbjct: 235 GEVAKYYRHKDNGVQFGLITSVSQSFCSTCTRARLSSDGKFYGCLFATVD 284
>2z2u_A UPF0026 protein MJ0257; metal binding protein; 2.40A
{Methanocaldococcus jannaschii}
Length = 311
Score = 50.7 bits (120), Expect = 4e-08
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 7/96 (7%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG--WSRVLAGIDLAVQLGYDNLKVNVVVMKNFN 59
+K + ISLD D Y I K W +L +D+ + + +++ +N
Sbjct: 172 EKIEPTQLYISLDAYDLDSYRRICGGKKEYWESILNTLDILKEKKRT--CIRTTLIRGYN 229
Query: 60 DDEILDFVLLTRDRPIDVRFIEYMPFSGNQWNNTKI 95
DD IL FV L DV FIE + ++ ++
Sbjct: 230 DD-ILKFVELYER--ADVHFIELKSYMHVGYSQKRL 262
>3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet
cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation,
beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga
maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A*
Length = 348
Score = 37.2 bits (86), Expect = 0.001
Identities = 21/103 (20%), Positives = 43/103 (41%), Gaps = 1/103 (0%)
Query: 1 YKKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
+K+AG D + +T P + + + L + +LGY+ ++V +
Sbjct: 148 WKEAGADRYLLRHETANPVLHRKLRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTI 207
Query: 61 DEILDFVLLTRDRPID-VRFIEYMPFSGNQWNNTKIMPFSEML 102
D+++D +L ++ D V ++P N K F+ L
Sbjct: 208 DDLVDDLLFLKEHDFDMVGIGPFIPHPDTPLANEKKGDFTLTL 250
>3can_A Pyruvate-formate lyase-activating enzyme; structural genomics,
pyruvate-formate lyase-activating enzym MCSG,
APC20359.1; 1.80A {Bacteroides vulgatus atcc 8482}
Length = 182
Score = 30.7 bits (70), Expect = 0.16
Identities = 11/82 (13%), Positives = 27/82 (32%), Gaps = 4/82 (4%)
Query: 6 LDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDDE--I 63
+ + I L ++ ++ +L I + + + + +++ N DE I
Sbjct: 55 CELLLIDLKSMDSTVHQTFCDVPN-ELILKNIRRVAEADF-PYYIRIPLIEGVNADEKNI 112
Query: 64 LDFVLLTRDRPIDVRFIEYMPF 85
P I +P+
Sbjct: 113 KLSAEFLASLPRHPEIINLLPY 134
>3n0w_A ABC branched chain amino acid family transporter, periplasmic
ligand binding protein...; receptor family ligand
binding region; HET: MSE; 1.88A {Burkholderia
xenovorans}
Length = 379
Score = 29.3 bits (66), Expect = 0.57
Identities = 6/30 (20%), Positives = 10/30 (33%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
FS L + K + L+ + K
Sbjct: 186 FSSYLLQAKASGAQLIVSTSGGAANINIMK 215
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 29.3 bits (65), Expect = 0.80
Identities = 16/79 (20%), Positives = 30/79 (37%), Gaps = 19/79 (24%)
Query: 64 LDFVLLTRDRPIDVRFIEYMPFSGNQWNNTKI----MPF----SEMLTKIKEAHPDLL-- 113
L F L + R+ E + N ++ ++ + F + L + EA DLL
Sbjct: 225 LRFALFDDE-----RYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVV 279
Query: 114 ----TLENAPNDTSKAYKV 128
L + + S+ Y+
Sbjct: 280 DEAHHLVWSEDAPSREYQA 298
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.1 bits (64), Expect = 0.96
Identities = 26/174 (14%), Positives = 52/174 (29%), Gaps = 34/174 (19%)
Query: 14 DTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDDEILD--FV---- 67
+ L+ + Y+F+ S + + + +ND+++ V
Sbjct: 85 EVLRIN-YKFL-----MSP-IKTEQRQPSMMTRMYIEQRDRL--YNDNQVFAKYNVSRLQ 135
Query: 68 -------LLTRDRPIDVRFIEYMPFSGNQW------NNTKI---MPFSEMLTKIKEAHPD 111
L RP I+ + SG W + K+ M F +K +
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP 195
Query: 112 LLTLENAPNDTSKAYKVPEFKGQVGFITSMTEHFCGTCNRLR-LMADGSLKVCL 164
LE + P + + +++ LR L+ + CL
Sbjct: 196 ETVLEMLQKLLYQI--DPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247
>3i09_A Periplasmic branched-chain amino acid-binding Pro; type I
periplasmic binding protein, structural genomics, JOI
for structural genomics; HET: MSE CIT; 1.80A
{Burkholderia mallei}
Length = 375
Score = 28.5 bits (64), Expect = 1.3
Identities = 11/30 (36%), Positives = 15/30 (50%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
FS L + + + +L L NA DT A K
Sbjct: 184 FSSFLLQAQSSKAQILGLANAGGDTVNAIK 213
>3db3_A E3 ubiquitin-protein ligase UHRF1; cell cycle, DNA damage, DNA
repair, tandem tudor domains, LI metal binding, DNA
replication; HET: M3L; 2.40A {Homo sapiens} PDB: 3db4_A
2l3r_A*
Length = 161
Score = 27.7 bits (61), Expect = 1.3
Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 8/73 (10%)
Query: 43 LGYDNLKVNVVVMKNFNDDEIL------DFVLLTRDRPIDVRFIEYMPFSG-NQWNNTKI 95
+ + +L+V VVM N+N D D + + R + G + N+ +I
Sbjct: 88 IKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRI 147
Query: 96 MPFSEMLTKIKEA 108
+ E+ KI+
Sbjct: 148 IFVDEVF-KIERP 159
>3td9_A Branched chain amino acid ABC transporter, peripl amino
acid-binding protein; leucine binding, structural
genomics; HET: MSE PHE; 1.90A {Thermotoga maritima}
Length = 366
Score = 28.0 bits (63), Expect = 1.5
Identities = 5/16 (31%), Positives = 8/16 (50%)
Query: 98 FSEMLTKIKEAHPDLL 113
FS L+ +PD +
Sbjct: 193 FSAQLSVAMSFNPDAI 208
>3u0h_A Xylose isomerase domain protein; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, TIM barrel;
2.30A {Alicyclobacillus acidocaldarius subsp}
Length = 281
Score = 27.8 bits (62), Expect = 1.7
Identities = 17/120 (14%), Positives = 40/120 (33%), Gaps = 17/120 (14%)
Query: 2 KKAGL--DSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFN 59
++ GL ++ + L+ + + S + L +LG + V + + +
Sbjct: 57 QRRGLVLANLGLPLNLYDSEP----VFLRELSLLPDRARLCARLGARS--VTAFLWPSMD 110
Query: 60 DDEILDFVLLTRD--------RPIDVRF-IEYMPFSGNQWNNTKIMPFSEMLTKIKEAHP 110
++ + L R P+ +R +EY+ + + L EA
Sbjct: 111 EEPVRYISQLARRIRQVAVELLPLGMRVGLEYVGPHHLRHRRYPFVQSLADLKTFWEAIG 170
>3ipc_A ABC transporter, substrate binding protein (amino; venus flytrap
domain, transport protein; 1.30A {Agrobacterium
tumefaciens} PDB: 3ip5_A 3ip6_A 3ip7_A 3ip9_A 3ipa_A
Length = 356
Score = 27.6 bits (62), Expect = 1.9
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 98 FSEMLTKIKEAHPDLL 113
FS +++K+KEA ++
Sbjct: 182 FSALISKMKEAGVSII 197
>3ask_A E3 ubiquitin-protein ligase UHRF1; histone reader modules,
epigenetic regulation, trimethylaion of lysine residue,
ligase-DNA binding protein; HET: M3L; 2.90A {Homo
sapiens}
Length = 226
Score = 27.4 bits (60), Expect = 2.0
Identities = 21/115 (18%), Positives = 36/115 (31%), Gaps = 9/115 (7%)
Query: 43 LGYDNLKVNVVVMKNFNDDEIL------DFVLLTRDRPIDVRFIEYMPFSGNQWNNTKIM 96
+ + +L+V VVM N+N D D + + R + G+ N +
Sbjct: 71 IKWQDLEVGQVVMLNYNPDNPKERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRI 130
Query: 97 PFSEMLTKIKEAHPDLLTLENAPNDTSKAYKVPEFKGQVGFITSMTEHFCGTCNR 151
F + + KI+ ++N S K V C C
Sbjct: 131 IFVDEVFKIERPGEGSPMVDNPMRRKSGPS-CKHCKDDVN--RLCRVCACHLCGG 182
>1usg_A Leucine-specific binding protein; leucine-binding protein, X-RAY
crystallography, protein structure, ABC transport
systems, transport protein; 1.53A {Escherichia coli}
SCOP: c.93.1.1 PDB: 1usi_A* 1usk_A 2lbp_A 1z15_A 1z16_A
1z17_A 1z18_A 2liv_A
Length = 346
Score = 27.6 bits (62), Expect = 2.0
Identities = 4/16 (25%), Positives = 11/16 (68%)
Query: 98 FSEMLTKIKEAHPDLL 113
FS ++ ++K+ + D +
Sbjct: 182 FSALIARLKKENIDFV 197
>3hut_A Putative branched-chain amino acid ABC transporter; extracellular
ligand-binding receptor,transport protein; 1.93A
{Rhodospirillum rubrum atcc 11170}
Length = 358
Score = 27.6 bits (62), Expect = 2.2
Identities = 3/16 (18%), Positives = 10/16 (62%)
Query: 98 FSEMLTKIKEAHPDLL 113
F +++ +I++ P +
Sbjct: 183 FDDVIDEIEDEAPQAI 198
>3h5l_A Putative branched-chain amino acid ABC transporter; structural
genomics, PSI-2, protein structure initiative; 1.70A
{Ruegeria pomeroyi}
Length = 419
Score = 27.5 bits (61), Expect = 2.6
Identities = 3/16 (18%), Positives = 8/16 (50%)
Query: 98 FSEMLTKIKEAHPDLL 113
+ L K++ P ++
Sbjct: 208 WGPTLAKLRADPPAVI 223
>3t7v_A Methylornithine synthase PYLB; TIM-barrel fold, mutase,
[4Fe-4S]-cluster, SAM, lysine, transferase; HET: SAM
MD0; 1.50A {Methanosarcina barkeri}
Length = 350
Score = 26.9 bits (60), Expect = 4.1
Identities = 7/46 (15%), Positives = 18/46 (39%)
Query: 1 YKKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYD 46
++ G + + + +T + Y + + + + A Q GY
Sbjct: 158 AREKGANFLALYQETYDTELYRKLRVGQSFDGRVNARRFAKQQGYC 203
>3snr_A Extracellular ligand-binding receptor; structural genomics,
APC102214, PSI-biology, midwest center structural
genomics, MCSG; HET: MSE TYR PHE; 1.49A
{Rhodopseudomonas palustris} PDB: 3uk0_A* 3t23_A*
3ukj_A* 3tx6_A*
Length = 362
Score = 26.5 bits (59), Expect = 5.3
Identities = 4/16 (25%), Positives = 8/16 (50%)
Query: 98 FSEMLTKIKEAHPDLL 113
+ K+ A+PD +
Sbjct: 179 VAGQALKLVAANPDAI 194
>3sg0_A Extracellular ligand-binding receptor; structural genomics,
PSI-biology; HET: 173; 1.20A {Rhodopseudomonas
palustris} PDB: 4dqd_A*
Length = 386
Score = 26.2 bits (58), Expect = 5.9
Identities = 4/16 (25%), Positives = 7/16 (43%)
Query: 98 FSEMLTKIKEAHPDLL 113
+ + KI PD +
Sbjct: 203 VTGQVLKIIATKPDAV 218
>3i45_A Twin-arginine translocation pathway signal protei; structural
genomics; 1.36A {Rhodospirillum rubrum}
Length = 387
Score = 26.2 bits (58), Expect = 6.1
Identities = 5/30 (16%), Positives = 11/30 (36%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
+ +++A P+ L D K +
Sbjct: 188 AGPTVQALQQAEPEGLFNVLFGADLPKFVR 217
>3lop_A Substrate binding periplasmic protein; protein structure initiative
II(PSI II), NYSGXRC, structural genomics; 1.55A
{Ralstonia solanacearum}
Length = 364
Score = 26.2 bits (58), Expect = 6.5
Identities = 3/30 (10%), Positives = 9/30 (30%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
+ K+ A + L ++ +
Sbjct: 185 VGPAVDKLLAADVQAIFLGATAEPAAQFVR 214
>4evq_A Putative ABC transporter subunit, substrate-bindi component;
structural genomics, PSI-biology, midwest center for
structu genomics; HET: MSE PHB; 1.40A {Rhodopseudomonas
palustris} PDB: 4evr_A
Length = 375
Score = 25.7 bits (57), Expect = 8.4
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
F L +I PD + + K K
Sbjct: 195 FQSALAEIASLKPDCVYAFFSGGGALKFIK 224
>3eaf_A ABC transporter, substrate binding protein; PSI2, NYSGXRC,
substrate binding P structural genomics, protein
structure initiative; 2.00A {Aeropyrum pernix}
Length = 391
Score = 25.9 bits (57), Expect = 9.0
Identities = 3/16 (18%), Positives = 7/16 (43%)
Query: 98 FSEMLTKIKEAHPDLL 113
+ ++ A PD +
Sbjct: 188 AERIAREMLAADPDYV 203
>4f06_A Extracellular ligand-binding receptor; PSI-biology, MCSG, midwest
center for structural genomics, transporter; HET: MSE
PHB; 1.30A {Rhodopseudomonas palustris} PDB: 4evs_A*
Length = 371
Score = 25.8 bits (57), Expect = 9.1
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 9/48 (18%)
Query: 81 EYMPFSGNQWNNTKIMPFSEMLTKIKEAHPD-LLTLENAPNDTSKAYK 127
MP S F ++ +IK + D + T A T K
Sbjct: 174 VRMPLSTTD--------FGPIMQRIKNSGADMIFTFLPAGPPTLGFVK 213
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.321 0.139 0.414
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,692,979
Number of extensions: 156538
Number of successful extensions: 433
Number of sequences better than 10.0: 1
Number of HSP's gapped: 429
Number of HSP's successfully gapped: 31
Length of query: 172
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 85
Effective length of database: 4,272,666
Effective search space: 363176610
Effective search space used: 363176610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.6 bits)