RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026839
(232 letters)
>1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY
crystallography, putative translation factor, PSI,
protein structure initiative; 1.40A {Escherichia coli}
SCOP: d.115.1.1 PDB: 1kk9_A
Length = 206
Score = 154 bits (393), Expect = 1e-47
Identities = 44/185 (23%), Positives = 84/185 (45%), Gaps = 6/185 (3%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 87
+A++ ++ G VI PTD+ Y C A+ RI I+ + D+S+++
Sbjct: 18 NQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDGHNFTLMCRDLSELST 77
Query: 88 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 147
++ D++ L+ + PG T +L + + L ++IG+RVP + + + L
Sbjct: 78 YSFVDNVAFRLMKNNTPGNYTFILKGTKEV-PRRLLQEKRKTIGMRVPSNPIAQALLEAL 136
Query: 148 ESALALTSANLTGQPSSVSVKD--FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFK 205
+ TS L G + S + + L ++ + GG G+ +TV+DLT
Sbjct: 137 GEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGG--YLGQKPTTVIDLTD-DTPV 193
Query: 206 ILRPG 210
++R G
Sbjct: 194 VVREG 198
>1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural
genomics; NMR {Methanothermobacterthermautotrophicus}
SCOP: d.115.1.1
Length = 208
Score = 153 bits (389), Expect = 7e-47
Identities = 65/195 (33%), Positives = 101/195 (51%), Gaps = 8/195 (4%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 87
EEAI ++ G ++ PTDT+YG +A +AV R++ +KGR P++ICV V +I R
Sbjct: 17 EEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGRSPHKPVSICVSCVDEIPR 76
Query: 88 FAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGL 147
F+ L++ +LPGP TVVL R + + + G +G+RVPD R IA
Sbjct: 77 FSRPSGDAMELMERILPGPYTVVLER--NELIPDVITGGSSRVGIRVPDDEICRRIAARF 134
Query: 148 ESALALTSANLTGQPSSVSVKDFENLWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKIL 207
+ TSAN++G+P S +++ + V D G STV+DLT ++L
Sbjct: 135 --PVTATSANISGKPPSPRLEEIVRDLDAVDLVLDAGDCLDM-EPSTVIDLTV-NPPRVL 190
Query: 208 RPGSAKEETIAILEK 222
R G + +L +
Sbjct: 191 RRGKGPLD--PVLLR 203
>1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5,
PSI, protein structure initiative, midwest center for
structural genomics; 2.00A {Escherichia coli} SCOP:
d.115.1.1
Length = 188
Score = 123 bits (311), Expect = 2e-35
Identities = 49/185 (26%), Positives = 72/185 (38%), Gaps = 11/185 (5%)
Query: 28 EEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGDVSDINR 87
AI L +VIA PT+ ++G CD S AV R+ E+K R L + + +
Sbjct: 11 AAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANYEQLKP 70
Query: 88 FAVTDHLP---HGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIA 144
+ L + S PGPVT V + + L +S+ VRV D V +
Sbjct: 71 YIDDTMLTDVQRETIFSRWPGPVTFVFPA--PATTPRWLTGRFDSLAVRVTDHPLVVALC 128
Query: 145 RGLESALALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDLTRLGK 203
+ L TSANL+G P +V + V G S + D G
Sbjct: 129 QAYGKPLVSTSANLSGLPPCRTVDEVRAQFGAAFPVV-PGETGGRLNP-SEIRDALT-G- 184
Query: 204 FKILR 208
++ R
Sbjct: 185 -ELFR 188
>2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5
domain, structural genomics, NPPSFA; HET: AMP; 1.80A
{Sulfolobus tokodaii} PDB: 3aje_A* 4e1b_A*
Length = 352
Score = 126 bits (320), Expect = 3e-35
Identities = 52/201 (25%), Positives = 91/201 (45%), Gaps = 10/201 (4%)
Query: 22 ATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICVGD 81
+ A ++ G +A PT+T+YG +A A +I++ K R +PL + + D
Sbjct: 12 PEIDKIKIAADVIRNGGTVAFPTETVYGLGANAFDGNACLKIFQAKNRPVDNPLIVHIAD 71
Query: 82 VSDINRFAVT-DHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFV 140
+ + A + + PGP+T VL + + + K + GL+++ VR+P
Sbjct: 72 FNQLFEVAKDIPDKVLEIAQIVWPGPLTFVLKK--TERVPKEVTAGLDTVAVRMPAHPIA 129
Query: 141 RVIARGLESALALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAG--STVVD 197
+ R +A SANL +PS +D +L R + DGG + G ST+++
Sbjct: 130 LQLIRESGVPIAAPSANLATRPSPTKAEDVIVDLNGRVDVIIDGG--HTF-FGVESTIIN 186
Query: 198 LTRLGKFKILRPGSAKEETIA 218
+T +LRPG E +
Sbjct: 187 VTV-EPPVLLRPGPFTIEELK 206
>3vth_A Hydrogenase maturation factor; carbamoyltransfer, maturation of
[NIFE]-hydrogenase, carbamoylphosphate, iron, HYPE; HET:
APC AP2; 2.00A {Thermoanaerobacter tengcongensis} PDB:
3vti_A
Length = 761
Score = 107 bits (269), Expect = 5e-27
Identities = 39/193 (20%), Positives = 79/193 (40%), Gaps = 5/193 (2%)
Query: 20 RPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAICV 79
+ + +ALK GK++A+ + A +A EAV + K R P A+ +
Sbjct: 198 EGCFDDEIKCVAKALKEGKIVAIKGIGGFHLAVNALDDEAVATLRRRKKRYGK-PFAVMM 256
Query: 80 GDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNF 139
DV ++ ++ + LL S P+ ++ +GE L K + L+++GV +P +
Sbjct: 257 RDVEEVKKYCIVSPEEERLLLS-QRRPIVLLKKKGEK--LAKGIADDLDTLGVMLPYAPI 313
Query: 140 VRVIARGLESALALTSANLTGQPSSVSVKD-FENLWERCACVYDGGVLPSGRAGSTVVDL 198
++ ++ + +TS N++ +P ++ E L + R +V
Sbjct: 314 HYLLMEEIDFPIVMTSGNVSEEPICKDNEEALEKLKDIADVFLLNNRDIVNRIDDSVTSF 373
Query: 199 TRLGKFKILRPGS 211
+ I R
Sbjct: 374 NAGAERIIRRARG 386
>3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A
{Streptococcus mutans}
Length = 295
Score = 99.7 bits (248), Expect = 3e-25
Identities = 24/195 (12%), Positives = 48/195 (24%), Gaps = 18/195 (9%)
Query: 19 VRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKGRKHTSPLAIC 78
+ E G VI PT Y + + R +E K R P +
Sbjct: 39 IHWDGNLSQEGFEIVKGEGGVIVCPTKVGYI--IMTSDKKGLERKFEAKKRNRNKPGVVL 96
Query: 79 VGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVL---------------SRGESSNLEKSL 123
G + ++ A + + G +
Sbjct: 97 CGSMEELRALAQLTPEIDAFYQKHWDEDILLGCILPWKAEAYEKLKAYGDGREELMTDIR 156
Query: 124 NPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKD-FENLWERCACVYD 182
I V + + + +SAN +G+ + V+ E + V +
Sbjct: 157 GTSCFVIKFGVAGEQIAKEMWEKEGRMVYASSANPSGKGNRGKVEGIGERIESMVDLVIE 216
Query: 183 GGVLPSGRAGSTVVD 197
+ ++
Sbjct: 217 ADDYVASIQPDKTIE 231
>3ttc_A HYPF, transcriptional regulatory protein; Zn finger, nucleotide
binding, hydrogenase maturation factor transferase; HET:
ADP; 1.86A {Escherichia coli} PDB: 3tsp_A* 3tsu_A*
3ttf_A* 3ttd_A 3tsq_A
Length = 657
Score = 102 bits (255), Expect = 3e-25
Identities = 44/175 (25%), Positives = 72/175 (41%), Gaps = 14/175 (8%)
Query: 9 QVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYGFACDACSSEAVNRIYEIKG 68
+ + EA + AI LK G ++A+ + ACDA +S AV + K
Sbjct: 98 YLEWVSHGE--HAEQEAALQAAIAQLKMGNIVAIKGIGGFHLACDARNSNAVATLRARKH 155
Query: 69 RKHTSPLAICVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNLEKSLNPGLE 128
R PLA+ + + A LL + P V++ + L + PGL
Sbjct: 156 RPA-KPLAVMLPVADGLPDAA------RQLLTT--PAAPIVLVDKKYVPELCDDIAPGLN 206
Query: 129 SIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSVKDFENLWERCACVYDG 183
+GV +P + ++ + L+ L +TS NL+G+P E E + DG
Sbjct: 207 EVGVMLPANPLQHLLLQELQCPLVMTSGNLSGKP---PAISNEQALEDLQGIADG 258
>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 = 47.4 bits (112), Expect = 2e-06
Identities = 39/222 (17%), Positives = 67/222 (30%), Gaps = 89/222 (40%)
Query: 4 SLENGQ------VSVENKAGLVRPATEAHAEEAIQALKTGKVIAV-------------PT 44
SLEN + +S+ L + + + + L GK + + P
Sbjct: 327 SLENNEGVPSPMLSIS---NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPP 383
Query: 45 DTLYGFACD-----ACSSEAVNRIYEIKGRK--------------HT------------- 72
+LYG A S +RI RK H+
Sbjct: 384 QSLYGLNLTLRKAKAPSGLDQSRI-PFSERKLKFSNRFLPVASPFHSHLLVPASDLINKD 442
Query: 73 ----------SPLAICVGDV---SDINRFAVTDHLPHGLLDSLLPGPV----------T- 108
+ I V D SD+ R ++ + ++D ++ PV T
Sbjct: 443 LVKNNVSFNAKDIQIPVYDTFDGSDL-R-VLSGSISERIVDCIIRLPVKWETTTQFKATH 500
Query: 109 -VVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLES 149
+ G +S L + + GVRV ++A L+
Sbjct: 501 ILDFGPGGASGLGVLTHRNKDGTGVRV-------IVAGTLDI 535
>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 = 43.3 bits (101), Expect = 4e-05
Identities = 34/298 (11%), Positives = 84/298 (28%), Gaps = 101/298 (33%)
Query: 5 LENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDTLYG--------FACDACS 56
L N V K + R +A+ L+ K + + G A D C
Sbjct: 119 LYND-NQVFAKYNVSRLQPYLKLRQALLELRPAKNV-----LIDGVLGSGKTWVALDVCL 172
Query: 57 SEAV-----NRIYEIK-GRK--------------------------HTSPLAICVGDVSD 84
S V +I+ + H+S + + + +
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232
Query: 85 -INRFAVTDHLPHGLL-----------DSLLPGPVTVVLSRGES---------------S 117
+ R + + LL ++ ++ +R +
Sbjct: 233 ELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLD 292
Query: 118 NLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQPSSVSV-----KDFEN 172
+ +L P E + ++ + + L LT P +S+ +D
Sbjct: 293 HHSMTLTPD-EVKSL------LLKYLDCRPQD---LPREVLTTNPRRLSIIAESIRDGLA 342
Query: 173 LWERCACVYDGGVLPSGRAGSTVVDLTRLGKFKILRPGSAKE--ETIAILEKHSLVEE 228
W+ + + +T+++ + +L P ++ + +++ + +
Sbjct: 343 TWDN----WK---HVNCDKLTTIIESS----LNVLEPAEYRKMFDRLSVFPPSAHIPT 389
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.4 bits (62), Expect = 1.2
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 6/31 (19%)
Query: 198 LTRL-GKFKILRPGSAKEETIAILEKHSLVE 227
L +L K+ SA +AI + +E
Sbjct: 22 LKKLQASLKLYADDSAP--ALAI---KATME 47
Score = 26.8 bits (58), Expect = 4.1
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 32 QALKTGKVIAVPTDTLYGFACDACSSEAVNRIYE 65
QALK K+ +L +A D+ + A+ E
Sbjct: 20 QALK--KL----QASLKLYADDSAPALAIKATME 47
>3rg9_A Bifunctional dihydrofolate reductase-thymidylate; oxidoreductase,
oxidoreductase-oxidoreductase inhibitor complex; HET:
NDP WRA; 2.00A {Trypanosoma brucei rhodesiense} PDB:
3qfx_A*
Length = 240
Score = 27.9 bits (62), Expect = 2.2
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 3/51 (5%)
Query: 103 LPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALAL 153
L + VVLSR + + P D V GLE AL +
Sbjct: 97 LSNRLNVVLSRSATKEQLLAGIPDPIKRAEAANDVVAV---NGGLEDALRM 144
>2wpn_B Periplasmic [nifese] hydrogenase, large subunit,
selenocysteine-containing; metal-binding,
oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
2.04A {Desulfovibrio vulgaris}
Length = 495
Score = 28.3 bits (63), Expect = 2.2
Identities = 8/36 (22%), Positives = 12/36 (33%)
Query: 118 NLEKSLNPGLESIGVRVPDSNFVRVIARGLESALAL 153
+L +G S R +AR E+ L
Sbjct: 351 DLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYML 386
>2gy5_A Angiopoietin-1 receptor; ligand-binding domain, transferase; HET:
NAG NDG; 2.90A {Homo sapiens} PDB: 2gy7_B*
Length = 423
Score = 27.7 bits (61), Expect = 3.2
Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 78 CVGDVSDINRFAVTDHLPHGLLDSLLPGPVTVVLSRGESSNL 119
C G V T + S LP +T+ + +G++ N+
Sbjct: 80 CEGRVRGEAIRIRTMKMRQQA--SFLPATLTMTVDKGDNVNI 119
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A 2a5t_A*
1pb8_A 1pb9_A
Length = 292
Score = 27.3 bits (60), Expect = 3.9
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 27 AEEAIQALKTGKVIAVPTDT--LYGFACDACSSEAVNRIYE 65
A EAIQA++ K+ A D+ L A C ++
Sbjct: 206 AAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFF 246
>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein,
calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides}
PDB: 3syk_A 3zuh_A*
Length = 309
Score = 27.4 bits (60), Expect = 3.9
Identities = 13/92 (14%), Positives = 28/92 (30%), Gaps = 4/92 (4%)
Query: 5 LENGQVSVENKAGLVR---PATEAHAEEAIQALKTGKVIAVPTDTLY-GFACDACSSEAV 60
+ G + + LV T +E ++ G + LY EA+
Sbjct: 97 VRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAMGGVLFIDEAYYLYRPDNERDYGQEAI 156
Query: 61 NRIYEIKGRKHTSPLAICVGDVSDINRFAVTD 92
+ ++ + I G + F ++
Sbjct: 157 EILLQVMENNRDDLVVILAGYADRMENFFQSN 188
>3irm_A Bifunctional dihydrofolate reductase-thymidylate; DHFR-TS
antifolate complex, methyltransfe multifunctional
enzyme, NADP; HET: 1CY; 2.10A {Trypanosoma cruzi} PDB:
3inv_A* 3irn_A* 3iro_A* 2h2q_A* 3cl9_A* 3clb_A* 3hbb_A*
3kjs_A*
Length = 521
Score = 27.5 bits (61), Expect = 4.9
Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 7/66 (10%)
Query: 103 LPGPVTVVLSRGESSNLEKSLNPGLESIGVRVPDSNFVRVIARGLESALALTSANLTGQP 162
LPG + VVLS ++ P E + + GLE AL L L
Sbjct: 91 LPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIV---AVNGGLEQALRL----LASPN 143
Query: 163 SSVSVK 168
+ S++
Sbjct: 144 YTPSIE 149
>2yjp_A Putative ABC transporter, periplasmic binding Pro amino acid;
transport protein, solute-binding protein; 2.26A
{Neisseria gonorrhoeae}
Length = 291
Score = 26.6 bits (59), Expect = 7.2
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 29 EAIQALKTGKVIAVPTDT--LYGFA 51
E ALK G+ +A+ D L+ +A
Sbjct: 196 ETFDALKDGRGVALAHDNALLWAWA 220
>2fqx_A Membrane lipoprotein TMPC; ABC transport system, ligand-binding
protein, guanosine, TP0319, transport protein; HET: GMP;
1.70A {Treponema pallidum} PDB: 2fqw_A* 2fqy_A*
Length = 318
Score = 26.6 bits (59), Expect = 7.6
Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 1 MAFSLENGQVSVENKAGLVRPATEAHAEEAIQALKTGKVIAVPTDT 46
+ F LE+ V + + + A + + + + I VP +
Sbjct: 269 IMFGLEDKAVGIPEENPNLSSAVMEKIRSFEEKIVSKE-IVVPVRS 313
>2v25_A Major cell-binding factor; antigen, adhesin, aspartate, glutamate,
transport, ABC transport, virulence factor, receptor;
1.49A {Campylobacter jejuni}
Length = 259
Score = 26.2 bits (58), Expect = 8.8
Identities = 7/25 (28%), Positives = 9/25 (36%), Gaps = 2/25 (8%)
Query: 29 EAIQALKTGKVIAVPTD--TLYGFA 51
AL +V A D L G+
Sbjct: 184 SIKAALDAKRVDAFSVDKSILLGYV 208
>1xt8_A Putative amino-acid transporter periplasmic solut protein; ABC
transport, cysteine uptake; 2.00A {Campylobacter jejuni}
SCOP: c.94.1.1
Length = 292
Score = 26.2 bits (58), Expect = 9.4
Identities = 6/25 (24%), Positives = 10/25 (40%), Gaps = 2/25 (8%)
Query: 29 EAIQALKTGKVIAVPTD--TLYGFA 51
E AL + A+ D L+ +
Sbjct: 185 ETFAALMDKRGDALSHDNTLLFAWV 209
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
0.315 0.132 0.377
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,478,618
Number of extensions: 210335
Number of successful extensions: 572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 556
Number of HSP's successfully gapped: 30
Length of query: 232
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 142
Effective length of database: 4,188,903
Effective search space: 594824226
Effective search space used: 594824226
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.5 bits)