RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2056
(220 letters)
>3a2q_A 6-aminohexanoate-cyclic-dimer hydrolase; alpha/beta fold, nylon
degradation; 1.80A {Arthrobacter SP} PDB: 3a2p_A
Length = 493
Score = 73.8 bits (182), Expect = 1e-15
Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 16/92 (17%)
Query: 122 TNQLLLNSAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVD 181
+ L A A L+R+ ++S +++EA I ++ VNP +NAV+ F A E++
Sbjct: 2 SKVDLWQDATAQAELVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELA- 60
Query: 182 ILLAASTKSVEEIGRDTPLLGVPLTVKESVAV 213
P GVP +K+ V
Sbjct: 61 ---------------SGPFAGVPYLLKDLTVV 77
>3ppm_A Fatty-acid amide hydrolase 1; protein-inhibitor complex, FAAH,
oxazole, oxadiazole, endoca degradation, membrane
protein; HET: JG1 1DO; 1.78A {Rattus norvegicus} PDB:
2wj2_A* 3k7f_A* 3k83_A* 3k84_A* 3lj6_A* 3lj7_A 3oj8_A*
2wj1_A* 3pr0_A* 2wap_A* 1mt5_A* 2vya_A* 3qk5_A* 3qj8_A*
3qj9_A* 3qkv_A*
Length = 573
Score = 71.4 bits (175), Expect = 9e-15
Identities = 17/107 (15%), Positives = 41/107 (38%), Gaps = 16/107 (14%)
Query: 109 RSLSYRHKPLPPITNQLLLN-SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNAVVD 167
+++ P + ++ LL + +++ ++S V ++ + +VN N V
Sbjct: 51 KAVQRFRLQNPDLDSEALLTLPLLQLVQKLQSGELSPEAVFFTYLGKAWEVNKGTNCVTS 110
Query: 168 ERFNLALEEAKQVDILLAASTKSVEEIGRDTPLLGVPLTVKESVAVK 214
+ + ++ R L GVP+++KE + K
Sbjct: 111 YLTDCETQLSQ---------------APRQGLLYGVPVSLKECFSYK 142
>3ip4_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, ATP-binding, nucleotide-bindi protein
biosynthesis; 1.90A {Staphylococcus aureus subsp} PDB:
2df4_A 2dqn_A* 2g5h_A 2g5i_A* 2f2a_A
Length = 485
Score = 62.2 bits (152), Expect = 1e-11
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVDILLAAST 188
S + LI+ K++ VV+ I + +P + + + A+++A+++D L A
Sbjct: 7 SVENLLTLIKDKKIKPSDVVKDIYDAIEETDPTIKSFLALDKENAIKKAQELDELQAKD- 65
Query: 189 KSVEEIGRDTPLLGVPLTVKESVAVK 214
+ G L G+P+ +K+++
Sbjct: 66 ---QMDG---KLFGIPMGIKDNIITN 85
>2dc0_A Probable amidase; structural genomics, NPPSFA, national project on
protein structural and functional analyses; 2.00A
{Thermus thermophilus}
Length = 434
Score = 60.3 bits (147), Expect = 5e-11
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 8/86 (9%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVDILLAAST 188
+ L+ T + + + ++E + R + NA+ A +EA + L
Sbjct: 2 DLLEAKRLLETGRTTPLALLEEALERAKAFQD-RNALAYLDEEAARKEALALTEELRRG- 59
Query: 189 KSVEEIGRDTPLLGVPLTVKESVAVK 214
+ G PL G+PLTVK+ VK
Sbjct: 60 ---QVRG---PLHGLPLTVKDLFPVK 79
>3h0l_A Glutamyl-tRNA(Gln) amidotransferase subunit A; multi protein
complex, ligase, protein biosynthesis; HET: ADP; 2.30A
{Aquifex aeolicus} PDB: 3h0m_A 3h0r_A*
Length = 478
Score = 59.1 bits (144), Expect = 2e-10
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 13/86 (15%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVDILLAAST 188
S + L++ +VS +VVE+F R Q + A + + AL++A+ +
Sbjct: 6 SLSELRELLKRGEVSPKEVVESFYDRYNQTEEKVKAYITPLYGKALKQAESLK------- 58
Query: 189 KSVEEIGRDTPLLGVPLTVKESVAVK 214
R+ PL G+P+ VK+++ V+
Sbjct: 59 ------ERELPLFGIPIAVKDNILVE 78
>1m22_A Peptide amidase, PAM; eleven-stranded beta sheet, covered double
layers of alpha helices on TOP and bottom, hydrolase;
HET: EPE; 1.40A {Stenotrophomonas maltophilia} SCOP:
c.117.1.1 PDB: 1m21_A*
Length = 503
Score = 54.1 bits (131), Expect = 6e-09
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 15/91 (16%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVN---PMLNAV--VDERFNLALEEAKQVDIL 183
+ ++ + +A++ RI ++ P L AV ++ AL+EA + D
Sbjct: 12 DVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPD---ALKEAAERDRE 68
Query: 184 LAASTKSVEEIGRDTPLLGVPLTVKESVAVK 214
G PL G+PL +K+++
Sbjct: 69 RRDG----RLRG---PLHGIPLLLKDNINAA 92
>3kfu_E Glutamyl-tRNA(Gln) amidotransferase subunit A; ASPRS, gatcab,
ATP-binding, aminoacyl-tRNA synthetase, ligas
nucleotide-binding, protein biosynthesis, ligase-RNA
comple; HET: H2U 5MU PSU; 3.00A {Thermus thermophilus}
Length = 471
Score = 52.9 bits (128), Expect = 2e-08
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 19/88 (21%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNA--VVDERFNLALEEAKQVDILLAA 186
A + + +VS ++V +A++ R+++++P L A ++ER LEEA+ VD
Sbjct: 2 LAHEIRARVARGEVSPLEVAQAYLKRVQELDPGLGAFLSLNER---LLEEAEAVD----- 53
Query: 187 STKSVEEIGRDTPLLGVPLTVKESVAVK 214
PL G+ + VK+++A +
Sbjct: 54 ---------PGLPLAGLVVAVKDNIATR 72
>2gi3_A Glutamyl-tRNA(Gln) amidotransferase subunit A; TM1272, structural
genomics, joint center for structura genomics, JCSG;
HET: MSE MPD; 1.80A {Thermotoga maritima} SCOP:
c.117.1.1 PDB: 3al0_A*
Length = 476
Score = 49.1 bits (118), Expect = 4e-07
Identities = 10/79 (12%), Positives = 32/79 (40%), Gaps = 20/79 (25%)
Query: 136 LIRTKQVSCVKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVDILLAASTKSVEEIG 195
++ + K+ + + I++++P + A + R N+++E+
Sbjct: 15 CLKLSEEEREKLPQLSLETIKRLDPHVKAFISVRENVSVEKKG----------------- 57
Query: 196 RDTPLLGVPLTVKESVAVK 214
G+P+ +K+++
Sbjct: 58 ---KFWGIPVAIKDNILTL 73
>1o9p_A Malonamidase E2; malonate; 1.8A {Bradyrhizobium japonicum} SCOP:
c.117.1.1 PDB: 1o9o_A 1obl_A 1och_A 1obk_A 1obi_A
1o9q_A* 1obj_A 1o9n_A 1ock_A 1ocl_A 1ocm_A
Length = 414
Score = 44.4 bits (106), Expect = 9e-06
Identities = 11/82 (13%), Positives = 22/82 (26%), Gaps = 24/82 (29%)
Query: 129 SAQKTALLIRTKQVSCVKVVEAFITRIRQVNPMLNA--VVDERFNLALEEAKQVDILLAA 186
S I T ++S + I ++A D+ + +
Sbjct: 3 SLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKS--ARAQASG-------- 52
Query: 187 STKSVEEIGRDTPLLGVPLTVK 208
PL G+ + +K
Sbjct: 53 ------------PLRGIAVGIK 62
>3a1k_A Amidase; AS family enzyme, hydrolase; 2.17A {Rhodococcus SP} PDB:
3a1i_A
Length = 521
Score = 44.2 bits (105), Expect = 2e-05
Identities = 14/99 (14%), Positives = 33/99 (33%), Gaps = 4/99 (4%)
Query: 119 PPITNQLLLNSAQKTALLIRTKQVSCVKVVEAFIT---RIRQVNPMLNAVVDERFNLALE 175
P + + L +T ++ +++ + + Q+ A+
Sbjct: 5 RPDDKAIDAAARHYGITLDKTARLEWPALIDGALGSYDVVDQLYADEATPPTTSREHAVP 64
Query: 176 EAKQVDILLAASTKSVEEIGRDTPLLGVPLTVKESVAVK 214
A + + L A + D L G + +K++V V
Sbjct: 65 SASE-NPLSAWYVTTSIPPTSDGVLTGRRVAIKDNVTVA 102
>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 = 38.5 bits (89), Expect = 0.001
Identities = 43/280 (15%), Positives = 83/280 (29%), Gaps = 85/280 (30%)
Query: 2 LSYVISAFVCYNSKIFSKGNVFSTLIKYLMWFGVRLLLILIWPLTRIRSL--SY---RH- 55
L+ ++ F + ++ + +LL L + + L +Y R
Sbjct: 84 LNLCLTEF---ENCYLEGNDIHA--------LAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 56 --KPLPPITNQLLLNSAQK-----TAL-------------LIRTKQVFSTLIKYLMWFGV 95
+P +N L + + A+ L Q + L+ L+ F
Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSA 192
Query: 96 RLLLILIWPLTRIRSLSYRH-----------KPLPPITNQLLLNSAQKTALLIRTKQVSC 144
L LI + + P + L S + LI Q++
Sbjct: 193 ETLSELIRTTLDAEKV-FTQGLNILEWLENPSNTPD---KDYLLSIPISCPLIGVIQLAH 248
Query: 145 VKVVEAFITRIRQVNPMLNAVVDERFNLALEEAKQVDILLA---ASTKSVEE-------- 193
V ++ P + A ++ ++ A A T S E
Sbjct: 249 YVVT----AKLLGFTP---GELRSYLKGATGHSQ--GLVTAVAIAETDSWESFFVSVRKA 299
Query: 194 ------IG----RDTPLLGVPLT-VKESVAV--KVPAPMV 220
IG P +P + +++S+ VP+PM+
Sbjct: 300 ITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
>2hq2_A Putative heme/hemoglobin transport protein; heme oxygenase,
structural repeat; HET: HEM; 1.45A {Escherichia coli}
SCOP: e.62.1.1 PDB: 1u9t_A
Length = 354
Score = 28.4 bits (63), Expect = 1.9
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 105 LTRIRSLSYRHKPLP-PITNQLL---LNSAQKTAL--LIRTKQVSCVKVVEAFITRIRQV 158
LTR ++ + L ++N L L SAQ+ ++ CV++ + ++ +
Sbjct: 216 LTRQQAFNLVADDLACKVSNSALAQILESAQQDGNEIMVFVGNRGCVQIFTGVVEKVVPM 275
Query: 159 NPMLNAVVDERFNLALEEAK 178
LN + + F L L E
Sbjct: 276 KGWLN-IFNPTFTLHLLEES 294
>2j0p_A HEMS, hemin transport protein HEMS; conformational changes, HAEM,
iron, trans ION transport, proteobacteria, iron
transport; HET: HEM 12P; 1.7A {Yersinia enterocolitica}
SCOP: e.62.1.1 PDB: 2j0r_A*
Length = 345
Score = 28.0 bits (62), Expect = 2.5
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 7/80 (8%)
Query: 105 LTRIRSLSYRHKPLP-PITNQLL---LNSAQKTAL--LIRTKQVSCVKVVEAFITRIRQV 158
LTR ++ L + N L LN AQ+ +I CV++ I ++
Sbjct: 207 LTRQQAFRAVGNDLAYQVDNSSLTQLLNIAQQEQNEIMIFVGNRGCVQIFTGMIEKVTPH 266
Query: 159 NPMLNAVVDERFNLALEEAK 178
+N V ++RF L L E
Sbjct: 267 QDWIN-VFNQRFTLHLIETT 285
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
0.326 0.138 0.404
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,126,271
Number of extensions: 176731
Number of successful extensions: 330
Number of sequences better than 10.0: 1
Number of HSP's gapped: 315
Number of HSP's successfully gapped: 17
Length of query: 220
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,188,903
Effective search space: 544557390
Effective search space used: 544557390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.1 bits)