RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4124
(99 letters)
>1gy6_A Nuclear transport factor 2; 1.6A {Rattus norvegicus} SCOP: d.17.4.2
PDB: 1a2k_A 1oun_A 1ar0_A 1u5o_A 1ask_A 1gy5_A 1jb5_A
1jb4_A 1jb2_A 1qma_A
Length = 127
Score = 82.6 bits (204), Expect = 4e-22
Identities = 37/126 (29%), Positives = 56/126 (44%), Gaps = 36/126 (28%)
Query: 5 LNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF--- 61
P +E IG F+Q YY LFD+ R L +Y + S +T+EG Q QG I+EK
Sbjct: 3 DKPIWEQIGSSFIQHYYQLFDN--DRTQLGAIYI-DASCLTWEGQQFQGKAAIVEKLSSL 59
Query: 62 ------------------------------NCDDDPPHAYSQIFVLKPLGASFYCQHDIF 91
D+DP + Q+F+LK + ++ C +D+F
Sbjct: 60 PFQKIQHSITAQDHQPTPDSCIISMVVGQLKADEDPIMGFHQMFLLKNINDAWVCTNDMF 119
Query: 92 RLGIHD 97
RL +H+
Sbjct: 120 RLALHN 125
>1gy7_A Nuclear transport factor 2; protein transport; 1.6A {Saccharomyces
cerevisiae} SCOP: d.17.4.2 PDB: 1gyb_A
Length = 125
Score = 76.0 bits (187), Expect = 2e-19
Identities = 36/124 (29%), Positives = 50/124 (40%), Gaps = 38/124 (30%)
Query: 5 LNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKFNC- 63
++ + + + F Q YY FD R L N+Y S +TFE QLQGA I+EK
Sbjct: 1 MSLDFNTLAQNFTQFYYNQFD--TDRSQLGNLYR-NESMLTFETSQLQGAKDIVEKLVSL 57
Query: 64 ----------------------------------DDDPPHAYSQIFVLKPLGASFYCQHD 89
++ P +SQ+F L P G S+Y +D
Sbjct: 58 PFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPDGNSYYVFND 117
Query: 90 IFRL 93
IFRL
Sbjct: 118 IFRL 121
>1zo2_A NTF2, nuclear transport factor 2; structural genomics, structural
genomics consortium, SGC, transport protein; 1.60A
{Cryptosporidium parvum} SCOP: d.17.4.2
Length = 129
Score = 75.4 bits (185), Expect = 3e-19
Identities = 41/129 (31%), Positives = 52/129 (40%), Gaps = 37/129 (28%)
Query: 1 MSSQLNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEK 60
S LNP ++ IGK FVQ YY F RP L +Y S +T+E Q QG I+ K
Sbjct: 3 QSINLNPQFDQIGKQFVQHYYQTFQ--TNRPALGGLYG-PQSMLTWEDTQFQGQANIVNK 59
Query: 61 FN---------------------------------CDDDPPHAYSQIFVLKPLGA-SFYC 86
FN DD P +SQ+F L P G F
Sbjct: 60 FNSLNFQRVQFEITRVDCQPSPNNGSIVFVTGDVRIDDGQPLKFSQVFNLMPSGNGGFMI 119
Query: 87 QHDIFRLGI 95
+D+FRL +
Sbjct: 120 FNDLFRLNL 128
>3ujm_A Rasputin; NTF2-like fold, RAS signaling, signaling protein; HET:
EPE; 2.74A {Drosophila melanogaster}
Length = 120
Score = 68.3 bits (167), Expect = 1e-16
Identities = 25/119 (21%), Positives = 43/119 (36%), Gaps = 36/119 (30%)
Query: 8 AYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKFN----- 62
++ ++G+ FV+QYY L + +L YN +S++ E + G +I +
Sbjct: 2 SHMSVGREFVRQYYTLLNK--APNHLHRFYNHNSSYIHGESKLVVGQREIHNRIQQLNFN 59
Query: 63 ----------------------------CDDDPPHAYSQIFVLKPLGA-SFYCQHDIFR 92
D P ++Q FVL +Y +DIFR
Sbjct: 60 DCHAKISQVDAQATLGNGVVVQVTGELSNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFR 118
>3nv0_B NTF2-related export protein; NTF2-like domain, beta sheet
heterodimer interface, nucleopo binding pocket, water
mediated interface; 1.84A {Caenorhabditis elegans}
Length = 154
Score = 68.9 bits (168), Expect = 2e-16
Identities = 20/126 (15%), Positives = 34/126 (26%), Gaps = 41/126 (32%)
Query: 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF---- 61
+ K F+ YY + D +R + +Y + S + G + G I E
Sbjct: 30 DEELCNESKKFMDVYYDVMD--RKREKIGFLYT-QVSNAVWNGNPINGYDSICEFMKALP 86
Query: 62 ----------------------------------NCDDDPPHAYSQIFVLKPLGASFYCQ 87
D D A++Q +L + +
Sbjct: 87 STQHDIQSLDAQRLPEGVTGDMSGGMLLNVAGAVTVDGDSKRAFTQTLLLGVEDGKYKVK 146
Query: 88 HDIFRL 93
D FR
Sbjct: 147 SDRFRY 152
>3q90_A RAS GTPase-activating protein-binding protein 1; structural
genomics, structural genomics consortium, SGC, NT (A+B
proteins); 1.70A {Homo sapiens}
Length = 140
Score = 64.5 bits (157), Expect = 6e-15
Identities = 27/135 (20%), Positives = 46/135 (34%), Gaps = 47/135 (34%)
Query: 3 SQLNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQ--------LQGA 54
P+ +G+ FV+QYY L + Q P++++ + + S G+ + G
Sbjct: 3 VMEKPSPLLVGREFVRQYYTLLN---QAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQ 59
Query: 55 VKIMEKFN---------------------------------CDDDPPHAYSQIFVLKPLG 81
+I K ++ + Q FVL P G
Sbjct: 60 KEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEG 119
Query: 82 A---SFYCQHDIFRL 93
+ FY +DIFR
Sbjct: 120 SVANKFYVHNDIFRY 134
>1jkg_A P15; NTF2-like domain, transport protein; 1.90A {Homo sapiens}
SCOP: d.17.4.2 PDB: 1jn5_A
Length = 140
Score = 60.7 bits (147), Expect = 2e-13
Identities = 19/123 (15%), Positives = 33/123 (26%), Gaps = 44/123 (35%)
Query: 12 IGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQLQGAVKIMEKF---------- 61
+ FV YY D +R L +Y T+ + + G + G + E F
Sbjct: 16 AAEEFVNVYYTTMD--KRRRLLSRLYM-GTATLVWNGNAVSGQESLSEFFEMLPSSEFQI 72
Query: 62 ---------------------------NCDDDPPHAYSQIFVLKP----LGASFYCQHDI 90
+ + ++Q F+L + D
Sbjct: 73 SVVDCQPVHDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQASPSNTVWKIASDC 132
Query: 91 FRL 93
FR
Sbjct: 133 FRF 135
>2qiy_A UBP3-associated protein BRE5; deubiquitylation, ubiquitin-specific
processing proteases(UB NTF2, protein-protein
recognition; 1.69A {Saccharomyces cerevisiae} SCOP:
d.17.4.2 PDB: 1zx2_A
Length = 154
Score = 59.0 bits (142), Expect = 1e-12
Identities = 23/145 (15%), Positives = 38/145 (26%), Gaps = 57/145 (39%)
Query: 3 SQLNPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSFMTFEGIQ------------ 50
+ + + I F+Q YY L Y T+ +T Q
Sbjct: 5 ASMGVTVQDICFAFLQNYYERMR--TDPSKLAYFYA-STAELTHTNYQSKSTNEKDDVLP 61
Query: 51 ---LQGAVKIMEKFN-------------------------------------CDDDPPHA 70
+ G I + F+ P +
Sbjct: 62 TVKVTGRENINKFFSRNDAKVRSLKLKLDTIDFQYTGHLHKSILIMATGEMFWTGTPVYK 121
Query: 71 YSQIFVLKPL--GASFYCQHDIFRL 93
+ Q F+L P G++F +DI R
Sbjct: 122 FCQTFILLPSSNGSTFDITNDIIRF 146
>1of5_A MRNA export factor MEX67; nuclear protein, repeat, leucine- rich
repeat, nuclear transport; 2.8A {Saccharomyces
cerevisiae} SCOP: d.17.4.2
Length = 221
Score = 34.0 bits (77), Expect = 0.003
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSF 43
N A F + L+D+ R L+N+Y+ ++ F
Sbjct: 7 NDALGQSSTDFATNFLNLWDN--NREQLLNLYSPQSQF 42
>1q40_B MEX67, mRNA export factor MEX67; NTF2-fold, nuclear export,
translation; 1.95A {Candida albicans} SCOP: d.17.4.2
Length = 219
Score = 33.6 bits (76), Expect = 0.004
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSF 43
+ + F+ Y L+D R L+ +Y E+ F
Sbjct: 10 DEDSRNLATNFIANYLKLWDA--NRSELMILYQNESQF 45
>1jkg_B TAP; NTF2-like domain, transport protein; 1.90A {Homo sapiens}
SCOP: d.17.4.2 PDB: 1jn5_B 1go5_A
Length = 250
Score = 32.7 bits (74), Expect = 0.009
Identities = 10/38 (26%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 6 NPAYEAIGKGFVQQYYALFDDPAQRPNLINMYNTETSF 43
+++ F+QQYYA++D R L++ Y+
Sbjct: 11 TENLKSLVLHFLQQYYAIYDSG-DRQGLLDAYHDGACC 47
>3nv0_A Nuclear RNA export factor 2; NTF2-like domain, beta sheet
heterodimer interface, nucleopo binding pocket, water
mediated interface; 1.84A {Caenorhabditis elegans}
Length = 205
Score = 31.6 bits (71), Expect = 0.020
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 6 NPAYEAIGKGFVQQYYALFDDPA---QRPNLINMYNTETSFMTF 46
+ + + F+ YY ++D R L++ Y+T S T
Sbjct: 9 SDEVRTLVEEFIITYYKIYDGADGQQTRKQLLDAYDTNNSTFTH 52
>2d9z_A Protein kinase C, NU type; PH domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 129
Score = 26.9 bits (59), Expect = 0.94
Identities = 5/56 (8%), Positives = 20/56 (35%)
Query: 34 INMYNTETSFMTFEGIQLQGAVKIMEKFNCDDDPPHAYSQIFVLKPLGASFYCQHD 89
+ ++ E+ ++ I L ++I + + + F + ++ +
Sbjct: 36 LTLFQNESGSKYYKEIPLSEILRISSPRDFTNISQGSNPHCFEIITDTMVYFVGEN 91
>2coa_A Protein kinase C, D2 type; protein kinase D2, PH domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
b.55.1.1
Length = 125
Score = 26.1 bits (57), Expect = 1.5
Identities = 9/58 (15%), Positives = 20/58 (34%)
Query: 32 NLINMYNTETSFMTFEGIQLQGAVKIMEKFNCDDDPPHAYSQIFVLKPLGASFYCQHD 89
I ++ T+ ++ I L + + N PP F + A+++
Sbjct: 34 KCITLFQNNTTNRYYKEIPLSEILTVESAQNFSLVPPGTNPHCFEIVTANATYFVGEM 91
>3e77_A Phosphoserine aminotransferase; SERC, PLP, structural genomi
structural genomics consortium, SGC, amino-acid
biosynthesi aminotransferase; HET: PLP; 2.50A {Homo
sapiens}
Length = 377
Score = 26.0 bits (58), Expect = 2.5
Identities = 10/34 (29%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 36 MYNTETSF------MTFEGIQLQGAVKIMEKFNC 63
+YNT F + E I+ G MEK +
Sbjct: 246 LYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSS 279
>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 = 26.0 bits (56), Expect = 2.8
Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 55 VKIMEKFNCDDDPPHAYSQI------FVLKPLGASFYCQH-DIFRLGI 95
+K + + CD+DP Y ++ F+ K ++ D+ R+ +
Sbjct: 527 LKFYKPYICDNDP--KYERLVNAILDFLPKIEENLICSKYTDLLRIAL 572
>3m5u_A Phosphoserine aminotransferase; alpha-beta half sandwich, csgid,
amino-acid biosynthesis, cytoplasm, pyridoxal phosphate;
HET: MES; 2.15A {Campylobacter jejuni}
Length = 361
Score = 25.1 bits (56), Expect = 4.4
Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 36 MYNTETSF------MTFEGIQLQGAVKIMEKFN 62
++NT +F + + + QG + + + N
Sbjct: 234 LFNTPPTFAIYMFNLEMDWLLNQGGLDKVHEKN 266
>1w23_A Phosphoserine aminotransferase; pyridoxal-5'-phosphate; HET: PGE
PLP EPE; 1.08A {Bacillus alcalophilus} SCOP: c.67.1.4
PDB: 2bhx_A* 2bi1_A* 2bi2_A* 2bi3_A* 2bi5_A* 2bi9_A*
2bia_A* 2bie_A* 2big_A*
Length = 360
Score = 25.1 bits (56), Expect = 4.8
Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 36 MYNTETSF------MTFEGIQLQGAVKIMEKFN 62
+YNT +F + I+ G + + K N
Sbjct: 235 LYNTPPTFSIYMLRNVLDWIKDLGGAEAIAKQN 267
>2c0r_A PSAT, phosphoserine aminotransferase; pyridoxal-5'-phosphate,
pyridine serine biosynthesis, amino-acid biosynthesis,
pyridoxal phosphate; HET: PLP; 1.2A {Bacillus circulans}
SCOP: c.67.1.4 PDB: 1bt4_A* 1w3u_A*
Length = 362
Score = 24.8 bits (55), Expect = 5.3
Identities = 8/33 (24%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 36 MYNTETSF------MTFEGIQLQGAVKIMEKFN 62
+YNT SF + I+ +G ++ +++ N
Sbjct: 236 LYNTPPSFGIYMVNEVLKWIEERGGLEGVQQAN 268
>3qm2_A Phosphoserine aminotransferase; structural genomics, center for
structural genomics of infec diseases, csgid; 2.25A
{Salmonella enterica subsp} PDB: 1bjn_A* 1bjo_A* 3qbo_A*
Length = 386
Score = 24.8 bits (55), Expect = 5.4
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 36 MYNTETSF------MTFEGIQLQGAVKIMEKFN 62
M+NT +F + F+ ++ QG V M K N
Sbjct: 261 MFNTPPTFAWYLSGLVFKWLKAQGGVAAMHKIN 293
>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase;
2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A*
2anb_A* 2anc_A 2f3r_A* 2f3t_A*
Length = 219
Score = 24.8 bits (55), Expect = 5.8
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 8/34 (23%)
Query: 46 FEGIQLQGAVKIMEKFNCDDDPPHAYSQIFVLKP 79
+ I QGA +I +K PHA S IF+L P
Sbjct: 113 LD-IDWQGAQQIRQKM------PHARS-IFILPP 138
>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for
structural genomics of infec diseases, csgid, putative
guanylate kinase; HET: MSE; 2.05A {Listeria
monocytogenes}
Length = 208
Score = 24.0 bits (53), Expect = 10.0
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 7/31 (22%)
Query: 49 IQLQGAVKIMEKFNCDDDPPHAYSQIFVLKP 79
I++QGA+++ + P IF+ P
Sbjct: 106 IEVQGAMQVRKAM------PEGIF-IFLTPP 129
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 0.139 0.426
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,518,856
Number of extensions: 74538
Number of successful extensions: 149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 35
Length of query: 99
Length of database: 6,701,793
Length adjustment: 65
Effective length of query: 34
Effective length of database: 4,886,928
Effective search space: 166155552
Effective search space used: 166155552
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: 51 (23.7 bits)