RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy1871
(139 letters)
>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 108
Score = 120 bits (303), Expect = 8e-37
Identities = 64/114 (56%), Positives = 80/114 (70%), Gaps = 7/114 (6%)
Query: 21 PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
PKKD S +P K GGK KKKKWSKGK ++K+NN VLFDKA+YDKLL E
Sbjct: 2 APKKDKAPPPSSKPAK-------SGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSE 54
Query: 81 VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG 134
VP YK ITPSV+SERL++ GSLAR+A+++L +G I+ V H +Q+IYTR T
Sbjct: 55 VPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVHSSQLIYTRATNA 108
>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation,
ribosome, ribosomal, ribosomal R ribosomal protein,
eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z
Length = 108
Score = 119 bits (299), Expect = 3e-36
Identities = 47/104 (45%), Positives = 68/104 (65%)
Query: 32 KQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSV 91
+Q K K +GGK KKKWSK ++D+ + V+ D+ YD++LKEVP Y+ ++ SV
Sbjct: 5 QQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSV 64
Query: 92 VSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGD 135
+ +RLK+ GSLAR AL L ++G+IK + KH Q IYTR T +
Sbjct: 65 LVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE 108
>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_8
Length = 143
Score = 111 bits (278), Expect = 1e-32
Identities = 33/111 (29%), Positives = 61/111 (54%), Gaps = 1/111 (0%)
Query: 27 KGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAY-K 85
K ++ Q + + + K KKKW+KGK +DK+N+ V +K + + ++ K
Sbjct: 3 KQPAAGQKKTKEAIAKAAQAKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGK 62
Query: 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136
++T S V E+LKV GSLAR+ + + + L+++V K+ Q +Y+ +
Sbjct: 63 VLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAKNGNQWVYSVIGGVKE 113
>2qc0_A Uncharacterized protein; NP_719793.1, uncharacterized protein,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.60A {Shewanella oneidensis}
PDB: 3eqx_A*
Length = 373
Score = 32.9 bits (75), Expect = 0.025
Identities = 10/72 (13%), Positives = 26/72 (36%), Gaps = 2/72 (2%)
Query: 48 KAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKAL 107
K + + + Q+ K +L++ + + E + A L
Sbjct: 275 KIAAARELIAHTTEYVRQQL--PKIYSHELVQVIFEQPYCRIQNLVESGLAKRQTASVYL 332
Query: 108 EELLQKGLIKQV 119
++L G++++V
Sbjct: 333 KQLCDIGVLEEV 344
>3ll5_A Gamma-glutamyl kinase related protein; alternate mevalonate
pathway, isopentenyl phsophate kinase, beta-alpha
sandwich fold; HET: MSE ADP IPE ATP IP8; 1.99A
{Thermoplasma acidophilum} PDB: 3lkk_A*
Length = 249
Score = 28.8 bits (65), Expect = 0.58
Identities = 13/80 (16%), Positives = 25/80 (31%), Gaps = 7/80 (8%)
Query: 43 GGSGGKAKKKKWSKGKVRDKLNNQVLFDK--ASYDKLLKEVP----AYKLITPSVVSERL 96
GGS G K ++ ++ + + + + L V + SV L
Sbjct: 49 GGSFGHIKAMEFGLPGPKNPRS-SIGYSIVHRDMENLDLMVIDAMIEMGMRPISVPISAL 107
Query: 97 KVRGSLARKALEELLQKGLI 116
+ G L + G +
Sbjct: 108 RYDGRFDYTPLIRYIDAGFV 127
>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 = 28.7 bits (63), Expect = 0.76
Identities = 12/82 (14%), Positives = 32/82 (39%), Gaps = 19/82 (23%)
Query: 61 DKLNNQVLFDKASYDKL----LKEVPAYKLIT--------PSVVSERL--KVRGSLARKA 106
DKL + ++S + L +++ + ++ P+++ + V S
Sbjct: 353 DKLTTII---ESSLNVLEPAEYRKM--FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV 407
Query: 107 LEELLQKGLIKQVVKHHAQVIY 128
+ +L + L+++ K I
Sbjct: 408 VNKLHKYSLVEKQPKESTISIP 429
>3k40_A Aromatic-L-amino-acid decarboxylase; PLP dependent protein, alpha
beta protein, alternative splicing, catecholamine
biosynthesis, lyase; HET: LLP; 1.75A {Drosophila
melanogaster}
Length = 475
Score = 28.2 bits (63), Expect = 1.00
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 88 TPSVVSERLKVRGSLARKALEELLQKGLI 116
SV SE ++RG+ KA+E+ + +GLI
Sbjct: 206 LRSVQSENHRMRGAALEKAIEQDVAEGLI 234
>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK,
transcriptional regulator, structural genomi 2; 2.09A
{Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2
Length = 239
Score = 27.6 bits (62), Expect = 1.4
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 93 SERLKV-RGSLARKALEELLQKGLIKQV 119
+ +V + ++ K+LE L QKG I QV
Sbjct: 36 MAQFEVSKSTI-TKSLELLEQKGAIFQV 62
>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged
helix-TUR UTRA, DNA-binding, transcription regulation;
1.80A {Mycobacterium smegmatis}
Length = 248
Score = 27.2 bits (61), Expect = 1.5
Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 93 SERLKV-RGSLARKALEELLQKGLI 116
+E+ +V R ++ R+AL ELL G +
Sbjct: 43 AEQFEVARETV-RQALRELLIDGRV 66
>2ra5_A Putative transcriptional regulator; beta structure, UTRA domain,
structural genomics, PSI-2, protein structure
initiative; HET: SRT; 2.40A {Streptomyces coelicolor A3}
SCOP: d.190.1.2
Length = 247
Score = 27.2 bits (61), Expect = 1.9
Identities = 9/25 (36%), Positives = 18/25 (72%), Gaps = 2/25 (8%)
Query: 93 SERLKV-RGSLARKALEELLQKGLI 116
+ RL + R ++ R+A++ L+ KGL+
Sbjct: 47 AARLGLSRPTV-RQAIQSLVDKGLL 70
>2lrn_A Thiol:disulfide interchange protein; structural genomics,
thioredoxin-like, NEW YORK structural G research
consortium, oxidoreductase; NMR {Bacteroides SP}
Length = 152
Score = 26.5 bits (59), Expect = 2.1
Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 10/82 (12%)
Query: 50 KKKKWSKGKVRDKLN-NQVLFDKASYDKLLKE-----VPAYKLITPS--VVSERLKVRGS 101
+++ W K DK NQVL K +L+ P L+ P +V++ L RG
Sbjct: 73 REEDWKKAIEEDKSYWNQVLLQKDDVKDVLESYCIVGFPHIILVDPEGKIVAKEL--RGD 130
Query: 102 LARKALEELLQKGLIKQVVKHH 123
+E+ + HH
Sbjct: 131 DLYNTVEKFVNGAKEGHHHHHH 152
>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome
biogenesis, metal BIN protein; NMR {Pyrococcus
horikoshii}
Length = 165
Score = 26.4 bits (58), Expect = 2.6
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117
++ + TPSVV E ++ ++ LE L+ G +K
Sbjct: 20 FIQGIDIEGYTTPSVVEE---IKDRESKIFLESLISAGKVK 57
>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding,
transcription regulation, transcriptional regulator,
GNTR/HUTC family; 2.40A {Bacillus subtilis}
Length = 243
Score = 26.4 bits (59), Expect = 3.0
Identities = 8/28 (28%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 93 SERLKV-RGSLARKALEELLQKGLIKQV 119
+E+ + R ++ R+AL L+ +GL+ ++
Sbjct: 41 AEQFGISRMTV-RQALSNLVNEGLLYRL 67
>3eet_A Putative GNTR-family transcriptional regulator; structural
genomics, PSI-2, protein structure initiative; 1.97A
{Streptomyces avermitilis}
Length = 272
Score = 26.2 bits (58), Expect = 3.3
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 9/52 (17%)
Query: 93 SERLKV-RGSLARKALEELLQKGLIK-------QVVKHHAQVIYTRTTKGDD 136
E V A +A + L+ +GL++ V + R+ D
Sbjct: 60 REEYGVSDTV-ALEARKVLMAEGLVEGRSGSGTYVRERPVPRRVARSGYRPD 110
>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like,
hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8
d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X
Length = 301
Score = 26.3 bits (59), Expect = 3.4
Identities = 6/20 (30%), Positives = 12/20 (60%)
Query: 94 ERLKVRGSLARKALEELLQK 113
++K G ARK ++E+ +
Sbjct: 252 AKIKTIGIEARKDMQEMFEA 271
>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase,
wild type, viral protein; 2.38A {Sindbis virus} SCOP:
b.47.1.3 PDB: 1ld4_A 3j0f_A
Length = 264
Score = 26.3 bits (57), Expect = 3.7
Identities = 22/90 (24%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
Query: 21 PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
PP++ + K K +E AK K + ++ KL LFD + D +
Sbjct: 68 PPRQKKQAPKQPPKPKKPKPQEKKKKQPAKTKPGKRQRMALKLEADRLFDVKNED---GD 124
Query: 81 VPAYKLITPSVVSERLKVRGSLARKALEEL 110
V + L V + L V+G++ L +L
Sbjct: 125 VIGHALAMEGKVMKPLHVKGTIDHPVLSKL 154
>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA,
30S ribosome ASSE GTP-binding, nucleotide-binding; HET:
GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*
Length = 308
Score = 26.3 bits (59), Expect = 3.9
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 94 ERLKVRGSLARKALEELLQK 113
+RLK G AR+ LE +L +
Sbjct: 261 QRLKEIGKRARQELELILGR 280
>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote
initiative, RSGI, structural genomics, hydrolase; HET:
GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8
d.52.3.1
Length = 301
Score = 25.9 bits (58), Expect = 4.3
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 94 ERLKVRGSLARKALEELLQK 113
++K G RK LE LL K
Sbjct: 251 RKIKEIGQATRKQLEALLGK 270
>2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.52.7.1
Length = 129
Score = 25.4 bits (56), Expect = 4.4
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 93 SERLKVRGSLARKALEELLQKGLIKQ 118
RL+ L KAL +LL + Q
Sbjct: 12 HARLRALNGLLYKALTDLLCTPEVSQ 37
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.5 bits (55), Expect = 6.0
Identities = 4/21 (19%), Positives = 11/21 (52%)
Query: 94 ERLKVRGSLARKALEELLQKG 114
+RL+ + ++ +E +K
Sbjct: 96 KRLQELDAASKVMEQEWREKA 116
>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural
GE PSI-2, protein structure initiative, midwest center
for STR genomics, MCSG; 2.09A {Listeria innocua}
Length = 236
Score = 25.3 bits (56), Expect = 6.9
Identities = 7/28 (25%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 93 SERLKV-RGSLARKALEELLQKGLIKQV 119
E R ++ R+A++ L+++GL+ +
Sbjct: 40 QEIYSSSRTTI-RRAVDLLVEEGLVVRK 66
>3k9t_A Putative peptidase; structural genomics, joint center for ST
genomics, JCSG, protein structure initiative, PSI-2,
aminop hydrolase; 2.37A {Clostridium acetobutylicum}
Length = 435
Score = 25.7 bits (55), Expect = 7.1
Identities = 5/27 (18%), Positives = 12/27 (44%)
Query: 93 SERLKVRGSLARKALEELLQKGLIKQV 119
+ + + + A + L + L+K V
Sbjct: 409 AYKSGMEFRRIKYAADALYRVELLKLV 435
>1ku9_A Hypothetical protein MJ223; putative transcription factor,
homodimeric winged-helix fold, structural genomics, PSI;
2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36
Length = 152
Score = 25.0 bits (54), Expect = 8.0
Identities = 9/43 (20%), Positives = 19/43 (44%)
Query: 92 VSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG 134
+ E LK+ +L++L + G +++V + Y G
Sbjct: 47 IMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDG 89
>1pix_A Glutaconyl-COA decarboxylase A subunit; biotin-dependent ION
pump, carboxyltransferase, lyase; 2.20A
{Acidaminococcus fermentans} SCOP: c.14.1.4 c.14.1.4
Length = 587
Score = 25.4 bits (56), Expect = 8.7
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 38 QKKKEGGSGGKAKKKKWSKGK--VRDKLNNQVLFDKASY 74
Q KE GKA +G+ ++ L + S+
Sbjct: 40 QLIKEAQEAGKADADVNKRGELTALQRIE--KLVEPGSW 76
>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein
structure initiative; 2.20A {Thermoplasma acidophilum
dsm 1728} SCOP: a.4.5.28 b.43.5.2
Length = 230
Score = 25.1 bits (54), Expect = 9.1
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG 134
E +T S +++ L + A + + +L + G I + V I T KG
Sbjct: 18 EAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTV-TKRGQILNITEKG 74
>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance
repressor, structura genomics, joint center for
structural genomics, JCSG; 2.20A {Streptococcus suis}
Length = 142
Score = 24.6 bits (54), Expect = 9.8
Identities = 9/32 (28%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 87 ITPSVVSERLKV-RGSLARKALEELLQKGLIK 117
+ + ERL++ R ++ R L+ L + G I
Sbjct: 46 LHQLALQERLQIDRAAVTR-HLKLLEESGYII 76
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
0.309 0.128 0.353
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,000,011
Number of extensions: 106899
Number of successful extensions: 370
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 52
Length of query: 139
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 55
Effective length of database: 4,356,429
Effective search space: 239603595
Effective search space used: 239603595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 52 (23.7 bits)