RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4290
(135 letters)
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 29.2 bits (65), Expect = 0.45
Identities = 21/90 (23%), Positives = 31/90 (34%), Gaps = 23/90 (25%)
Query: 15 ELQEFFRSTLQLHLWEGQACFHNLELDLE--ALESLVPFHFVSGHINELRIKVPWTSLGS 72
+LQE F L D E LV F+ G+++ L V + +G
Sbjct: 32 QLQEQFNKIL-------PEPTEGFAADDEPTTPAELV-GKFL-GYVSSL---VEPSKVGQ 79
Query: 73 SS--VEVVIDTI--GYLSGIFECMAAIHAL 98
+ + + YL G IHAL
Sbjct: 80 FDQVLNLCLTEFENCYLEG-----NDIHAL 104
Score = 25.8 bits (56), Expect = 5.6
Identities = 21/104 (20%), Positives = 35/104 (33%), Gaps = 36/104 (34%)
Query: 21 RSTLQLHLWEGQACFH-NLELDLEALESLVP--FHFVSGHINELR------IKVPWTSLG 71
R L L H +LE L LVP F ++L+ + P
Sbjct: 7 RP-LTLS--------HGSLEHVL-----LVPTASFF---IASQLQEQFNKILPEPTEGFA 49
Query: 72 -----SSSVEVVIDTIGYLSGIFECMAAIHALNGRYATALQYAI 110
++ E+V +GY+S + E G++ L +
Sbjct: 50 ADDEPTTPAELVGKFLGYVSSLVEPSKV-----GQFDQVLNLCL 88
>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein,
RNA splicing, structural GENO joint center for
structural genomics, JCSG; HET: MSE; 1.80A {Mus
musculus} PDB: 1o0p_A 1opi_A
Length = 105
Score = 28.2 bits (63), Expect = 0.46
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 61 LRIKVPWTSLGSSSVEVVIDTIGYLSGIFECMAAIHALNGRY 102
I++P G + + S +F+C A+ L GR
Sbjct: 43 KSIEIPRPVDGVEVPGCGKIFVEFTS-VFDCQKAMQGLTGRK 83
>3gqv_A Enoyl reductase; medium-chain reductase (MDR superfamily), rossmann
fold, NAD binding, oxidoreductase; HET: NAP; 1.74A
{Aspergillus terreus} PDB: 3b6z_A* 3b70_A*
Length = 371
Score = 28.1 bits (63), Expect = 0.77
Identities = 8/42 (19%), Positives = 16/42 (38%)
Query: 69 SLGSSSVEVVIDTIGYLSGIFECMAAIHALNGRYATALQYAI 110
+ +++ +D I + C AAI G Y + +
Sbjct: 226 TYTKNNLRYALDCITNVESTTFCFAAIGRAGGHYVSLNPFPE 267
>2ehh_A DHDPS, dihydrodipicolinate synthase; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; 1.90A {Aquifex aeolicus}
Length = 294
Score = 27.8 bits (63), Expect = 1.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F E+D EAL +L+ FH +G
Sbjct: 13 FKEGEVDYEALGNLIEFHVDNG 34
>1o5k_A DHDPS, dihydrodipicolinate synthase; TM1521, structural genomics,
J protein structure initiative, joint center for
structural G lyase; HET: MCL; 1.80A {Thermotoga
maritima} SCOP: c.1.10.1 PDB: 3pb2_A 3pb0_A
Length = 306
Score = 27.3 bits (61), Expect = 1.6
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N ELDLE+ E LV + +G
Sbjct: 25 FKNGELDLESYERLVRYQLENG 46
>2vc6_A MOSA, dihydrodipicolinate synthase; DHDPS, TIM barrel, schiff
base, lyase; HET: MCL; 1.95A {Sinorhizobium meliloti}
Length = 292
Score = 27.2 bits (61), Expect = 1.7
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F + +D AL LV + G
Sbjct: 13 FADDRIDEVALHDLVEWQIEEG 34
>3m5v_A DHDPS, dihydrodipicolinate synthase; TIM barrel, csgid,
amino-acid biosynthesis, diaminopimelate biosynthesis,
lyase, lysine biosynthesis; HET: MSE; 1.80A
{Campylobacter jejuni} PDB: 3ler_A*
Length = 301
Score = 27.1 bits (61), Expect = 2.0
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N ++D ++ L+ +G
Sbjct: 20 FKNGKVDEQSYARLIKRQIENG 41
>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM,
RNA binding domain, ST genomics, joint center for
structural genomics, JCSG; HET: MSE; 1.23A {Homo
sapiens} PDB: 3us5_A 2dny_A
Length = 118
Score = 26.3 bits (58), Expect = 2.2
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 56 GHINELRIKVPWTSLGSSSVEVVIDTIGYLSGIFECMAAIHALNGRY 102
G +N + I + +V + + E AI ALNGR+
Sbjct: 50 GAVNRVIIYQEKQGEEEDAEIIVKIFVEFSI-ASETHKAIQALNGRW 95
>2yxg_A DHDPS, dihydrodipicolinate synthase; MJ0244, TIM
beta/alpha-barrel fold, structural genomics, NPPSFA;
2.20A {Methanocaldococcus jannaschii DSM2661}
Length = 289
Score = 26.7 bits (60), Expect = 2.3
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N E+D + LE + F +G
Sbjct: 13 FKNKEVDFDGLEENINFLIENG 34
>2rfg_A Dihydrodipicolinate synthase; beta barrel, amino-acid
biosynthesis, diaminopimelate biosyn lyase, lysine
biosynthesis, schiff base; 1.50A {Hahella chejuensis}
Length = 297
Score = 26.3 bits (59), Expect = 3.0
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N ++D +AL LV + G
Sbjct: 13 FINGQVDEKALAGLVDWQIKHG 34
>3a5f_A Dihydrodipicolinate synthase; TIM barrel, enzyme, amino-acid
biosynthesis, cytoplasm, diaminopimelate biosynthesis,
lyase; HET: KPI; 1.19A {Clostridium botulinum A} PDB:
3bi8_A* 3ird_A*
Length = 291
Score = 26.5 bits (59), Expect = 3.1
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N +D + L L+ +H S
Sbjct: 14 FTNTGVDFDKLSELIEWHIKSK 35
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 25.6 bits (56), Expect = 3.4
Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 6/47 (12%)
Query: 56 GHINELRIKVPWTSLGSSSVEVVIDTIGYLSGIFECMAAIHALNGRY 102
G + E+ + +V V + A+ LN R+
Sbjct: 52 GEVEEMNVCDNLGDHLVGNVYVKFRREE------DAEKAVIDLNNRW 92
>3daq_A DHDPS, dihydrodipicolinate synthase; lysine biosynthesis,
amino-ACI biosynthesis, diaminopimelate biosynthesis,
lyase, schiff B; 1.45A {Staphylococcus aureus} PDB:
3di1_A 3di0_A
Length = 292
Score = 26.3 bits (59), Expect = 3.9
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F N +++LEAL++ V F +
Sbjct: 15 FTNNKVNLEALKAHVNFLLENN 36
>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint
center for struc genomics, JCSG, protein structure
initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus
musculus} PDB: 2lq5_A
Length = 114
Score = 25.4 bits (56), Expect = 5.0
Identities = 6/13 (46%), Positives = 11/13 (84%)
Query: 90 ECMAAIHALNGRY 102
+AA++AL+GR+
Sbjct: 67 AAIAAVNALHGRW 79
>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1
domain, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 112
Score = 25.1 bits (55), Expect = 6.0
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 90 ECMAAIHALNGRY 102
E I L+GR+
Sbjct: 76 EADYCIQTLDGRW 88
>3fi7_A LMO1076 protein; listeria monocytogenes, autolysin, N
acetylglucosaminidase, peptidoglycan hydrolase,
autoinhibition, GH73, hydrolase; 2.35A {Undefined}
Length = 183
Score = 25.5 bits (56), Expect = 6.4
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 93 AAIHALNGRYATALQYAILLVPI 115
A L GRYAT YA L +
Sbjct: 151 DATAWLQGRYATDNTYASKLNTL 173
>3t37_A Probable dehydrogenase; BET alpha beta fold, ADP binding,
oxidoreductase; HET: FAD; 2.19A {Mesorhizobium loti}
Length = 526
Score = 25.5 bits (57), Expect = 6.7
Identities = 4/59 (6%), Positives = 12/59 (20%), Gaps = 16/59 (27%)
Query: 13 VAELQEFFRST---------LQLHLWEGQACFHNLELDLEALESLVPFHFVSGHINELR 62
+E + R+ + + + E+ + S
Sbjct: 329 HSESMAYMRADSFTAAGQPEIVVG-------CGVAPIVSESFPAPAAGSAYSLLFGITH 380
>2r91_A 2-keto-3-deoxy-(6-phospho-)gluconate aldolase; TIM barrel,
thermophilic, lyase; 2.00A {Thermoproteus tenax} PDB:
2r94_A
Length = 286
Score = 25.2 bits (56), Expect = 8.6
Identities = 6/22 (27%), Positives = 7/22 (31%)
Query: 35 FHNLELDLEALESLVPFHFVSG 56
F LD E + V G
Sbjct: 11 FRGGRLDPELFANHVKNITSKG 32
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
0.323 0.135 0.425
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,041,485
Number of extensions: 112713
Number of successful extensions: 242
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 27
Length of query: 135
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 51
Effective length of database: 4,356,429
Effective search space: 222177879
Effective search space used: 222177879
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (23.8 bits)