RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 017570
(369 letters)
>1u7g_A Probable ammonium transporter; right handed helical bundle,
transmembrane helices, ammonia membrane protein, RH
protein, transport protein; HET: MSE BOG; 1.40A
{Escherichia coli} SCOP: f.44.1.1 PDB: 1u77_A* 1u7c_A*
1xqf_A 1xqe_A 2ns1_A* 2nop_A 2nmr_A 3c1g_A 3c1i_A*
3c1h_A* 2now_A 2npe_A 2npc_A 2npd_A 2npg_A 2npj_A
2nuu_A* 3c1j_A 2npk_A
Length = 385
Score = 246 bits (630), Expect = 6e-79
Identities = 100/321 (31%), Positives = 166/321 (51%), Gaps = 17/321 (5%)
Query: 18 PDWLNKGDSAWQMTASTLVGIQSMPGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICWVL 77
P +K D+A+ M + LV ++PG+ + Y +++ K ++ V FA V I WV+
Sbjct: 2 PAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVV 61
Query: 78 VCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVYFQ 137
Y +A G+ F+G + L + Y FQ
Sbjct: 62 YGYSLASGEGN-NFFG----NINWLMLKNIELTAVMG---------SIYQYIHVA---FQ 104
Query: 138 FTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWGGGFLYQWGVIDYSGG 197
+FA ITV L+ G++ R+ A + FV +WL SY A +WGGG L G +D++GG
Sbjct: 105 GSFACITVGLIVGALAERIRFPAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGG 164
Query: 198 YVIHVSSGIAGLTAAYWVGPRLKSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGAPYAAH 257
V+H+++ IAGL AY +G R+ KE F P+N+ ++ G +L++GW GFN G+ A+
Sbjct: 165 TVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTAN 224
Query: 258 IASSIAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSWAA 317
+++A +NT VA A ++L W + G PS++GA G + GLV +TP G + A
Sbjct: 225 EIAALAFVNTVVATAAAILGWIFGEWALRGLPSLLGACSGAIAGLVGVTPACGYIGVGGA 284
Query: 318 IVMGILSGSIPWVTMMILHKK 338
+++G+++G + +L +
Sbjct: 285 LIIGVVAGLAGLWGVTMLKRL 305
>2b2h_A AMT-1, ammonium transporter; membrane protein, transport protein;
1.54A {Archaeoglobus fulgidus} PDB: 2b2f_A 2b2i_A 2b2j_A
Length = 399
Score = 242 bits (619), Expect = 4e-77
Identities = 100/308 (32%), Positives = 161/308 (52%), Gaps = 27/308 (8%)
Query: 21 LNKGDSAWQMTASTLVGIQSM-PGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICWVLVC 79
++ G+ AW + ++ LV + M PG+ YA +V++K AVN + + ++ W+
Sbjct: 1 MSDGNVAWILASTALVML--MVPGVGFFYAGMVRRKNAVNMIALSFISLIITVLLWIFYG 58
Query: 80 YRMAFGDQLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVYFQFT 139
Y ++FG+ + G L L G + + + +Q
Sbjct: 59 YSVSFGNDISGIIG----GLNYALLSG-VKGEDLLF------------------MMYQMM 95
Query: 140 FAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWGGGFLYQWGVIDYSGGYV 199
FAA+T+ +L ++ R + +++ LWL F Y A LWGGG+L + G +D++GG V
Sbjct: 96 FAAVTIAILTSAIAERAKVSSFILLSALWLTFVYAPFAHWLWGGGWLAKLGALDFAGGMV 155
Query: 200 IHVSSGIAGLTAAYWVGPRLKSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGAPYAAHIA 259
+H+SSG A L A +G R ++ P+++ L L GA LLW GW GFNGG+ AA+
Sbjct: 156 VHISSGFAALAVAMTIGKRAGFEEYSIEPHSIPLTLIGAALLWFGWFGFNGGSALAANDV 215
Query: 260 SSIAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSWAAIV 319
+ A++ TN +AA + VW + I GKP +G V G + GL ITP AG V AIV
Sbjct: 216 AINAVVVTNTSAAVAGFVWMVIGWI-KGKPGSLGIVSGAIAGLAAITPAAGFVDVKGAIV 274
Query: 320 MGILSGSI 327
+G+++G +
Sbjct: 275 IGLVAGIV 282
>3b9w_A Ammonium transporter family; membrane protein, ammonia transport,
rhesus protein, transpo protein; HET: BOG; 1.30A
{Nitrosomonas europaea} PDB: 3bhs_A 3b9y_A* 3b9z_A*
Length = 407
Score = 172 bits (438), Expect = 3e-50
Identities = 49/277 (17%), Positives = 95/277 (34%), Gaps = 22/277 (7%)
Query: 53 KKKWAVNSAFMVLYAFAAVLICWVLVCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPE 112
+ +++N M+L F +++ + G L+ G L +
Sbjct: 16 QYNYSINILAMLLVGFGFLMVFVRRYGFSATTGTYLVVATGLPLYILLR----------- 64
Query: 113 STHEVDGKTVTTEPFYAMATLVYFQFTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFS 172
+ + FA T ++ G+VLGR+ + + L+++
Sbjct: 65 ------ANGIFGHALTPHSVDAVIYAEFAVATGLIAMGAVLGRLRVFQYALLA-LFIVPV 117
Query: 173 YTVGAFSLWGGGFLYQWGVIDYSGGYVIHVSSGIAGLTAAYWVGPRL-KSDKERFPPNNV 231
Y + + + G D +G IH GL + + ++ +
Sbjct: 118 YLLNEWLVLDNASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRAQPIESDATSD 177
Query: 232 LLMLAGAGLLWMGWSGFNGGAPYAAHIASSIAILNTNVAAATSLLVWTCL-DVIFFGKPS 290
+ G+ +LW+ W F I+NT +A + L L + GK S
Sbjct: 178 RFSMLGSMVLWLFWPSFATAI--VPFEQMPQTIVNTLLALCGATLATYFLSALFHKGKAS 235
Query: 291 VIGAVQGMMTGLVCITPGAGLVQSWAAIVMGILSGSI 327
++ + G V I +V A V+G+L G+I
Sbjct: 236 IVDMANAALAGGVAIGSVCNIVGPVGAFVIGLLGGAI 272
>3hd6_A Ammonium transporter RH type C; ammonia, channel, rhesus,
glycoprotein, membran structural genomics, PSI-2,
protein structure initiative; HET: BOG; 2.10A {Homo
sapiens}
Length = 490
Score = 136 bits (343), Expect = 4e-36
Identities = 41/198 (20%), Positives = 72/198 (36%), Gaps = 13/198 (6%)
Query: 136 FQFTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWGGGFLYQWGVIDYS 195
F +V + G+VLG+++ + V F++ L V D
Sbjct: 131 INADFCVASVCVAFGAVLGKVSPIQLLIMTFFQ------VTLFAVNEFILLNLLKVKDAG 184
Query: 196 GGYVIHVSSGIAGLTAAYWVGPRL---KSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGA 252
G IH GLT + R +++ + L + G LWM W FN
Sbjct: 185 GSMTIHTFGAYFGLTVTRILYRRNLEQSKERQNSVYQSDLFAMIGTLFLWMYWPSFNSAI 244
Query: 253 PYAAHIASSIAILNTNVAAATSLLVWTCLDVIF--FGKPSVIGAVQGMMTGLVCI-TPGA 309
Y + A +NT + A +L + GK ++ + G V + T
Sbjct: 245 SYHGD-SQHRAAINTYCSLAACVLTSVAISSALHKKGKLDMVHIQNATLAGGVAVGTAAE 303
Query: 310 GLVQSWAAIVMGILSGSI 327
++ + A+++G + G I
Sbjct: 304 MMLMPYGALIIGFVCGII 321
>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 = 40.0 bits (93), Expect = 0.001
Identities = 62/426 (14%), Positives = 121/426 (28%), Gaps = 157/426 (36%)
Query: 5 PIP----IAYQQ-------ELPAVPDWLNKGD---SAWQMTASTL--VGIQSMPGLLIIY 48
+P Q LP + D + ++ L V P + +
Sbjct: 21 LVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQF 80
Query: 49 ASIVKKK-WAVNSAFMV---LYAFAAVLIC----------WVLVCYRMAFGDQLLPFWGK 94
++ + ++ ++A AA L+ ++ Y A PF K
Sbjct: 81 DQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKK 140
Query: 95 GAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAM-----ATLVYFQ-----F-TFAAI 143
AL + G A+ A+ T YF+ + T+ +
Sbjct: 141 SNSALFRAVGEGNAQ-----------------LVAIFGGQGNTDDYFEELRDLYQTYHVL 183
Query: 144 --TVILLAGSVLGR---------------MNIRAWM---AFVPLWLMFSYTVGA-FSLWG 182
+I + L +NI W+ + P Y + S
Sbjct: 184 VGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK---DYLLSIPIS-CP 239
Query: 183 GGFLYQWG-------VIDYSGGYVIHVSSGIAG--------------------------- 208
+ Q ++ ++ G + G G
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKA 299
Query: 209 LTAAYWVGPRLKSDKERFPPNNV---LL-------------MLAGAGL----LWMGWSGF 248
+T +++G R E +P ++ +L ML+ + L + +
Sbjct: 300 ITVLFFIGVR---CYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 249 NGGAPYAAHIASSIAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPG 308
N P + I+++N A +L+V + G P ++ G+ L
Sbjct: 357 NSHLPAGKQV--EISLVN----GAKNLVV-S-------GPPQ---SLYGLNLTLRKAKAP 399
Query: 309 AGLVQS 314
+GL QS
Sbjct: 400 SGLDQS 405
Score = 30.4 bits (68), Expect = 1.2
Identities = 42/209 (20%), Positives = 62/209 (29%), Gaps = 91/209 (43%)
Query: 47 IYASIVKKKWAVNSA--FMV------LYAFAAVLICWVLVCYRMAFGDQLLPFWGKGAPA 98
+ S+V N A +V LY L R A K
Sbjct: 366 VEISLV------NGAKNLVVSGPPQSLYGLNLTL--------RKA----------KAPSG 401
Query: 99 LGQKYLVGRARVPESTHEVDGKTV---TTEPF----YAMAT------LVYFQFTFAA--- 142
L Q +R+P S ++ PF A+ LV +F A
Sbjct: 402 LDQ------SRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDI 455
Query: 143 -ITVI---------LLAGSVLGRMNIRAWMAFVPL-W---LMFSYTVGAFSLWGGGFLYQ 188
I V +L+GS+ R I + +P+ W F T
Sbjct: 456 QIPVYDTFDGSDLRVLSGSISER--IVDCIIRLPVKWETTTQFKAT-------------- 499
Query: 189 WGVIDY-SGGYVIHVSSGIAGLTAAYWVG 216
++D+ GG +SG+ LT G
Sbjct: 500 H-ILDFGPGG-----ASGLGVLTHRNKDG 522
>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 = 32.9 bits (74), Expect = 0.20
Identities = 13/77 (16%), Positives = 30/77 (38%), Gaps = 21/77 (27%)
Query: 288 KPSVIGAVQGMMTGLVCITPGAGLVQSWAAI-------VMGILSGSIPWVTMMILHKKCS 340
+P+ + G+ G+G ++W A+ V + I W+ + + +
Sbjct: 148 RPAKNVLIDGV--------LGSG--KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET 197
Query: 341 LLQQVSFTFLKLFYFLT 357
+L+ + KL Y +
Sbjct: 198 VLEML----QKLLYQID 210
>2xov_A Rhomboid protease GLPG; membrane protein, hydrolase, intramembrane
protease; HET: BNG; 1.65A {Escherichia coli} PDB:
2ic8_A* 2nrf_A 2xtu_A* 2irv_A* 3b45_A* 2o7l_A* 2xow_A*
3txt_A* 2xtv_A* 3b44_A*
Length = 181
Score = 28.8 bits (65), Expect = 1.7
Identities = 13/66 (19%), Positives = 20/66 (30%), Gaps = 3/66 (4%)
Query: 194 YSGGYVIHVSSGIAGLTAAYWV-GPRLKSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGA 252
+SG + +S + L W+ G R ++ L W F
Sbjct: 102 FSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDL--FGMSM 159
Query: 253 PYAAHI 258
AHI
Sbjct: 160 ANGAHI 165
>2d7t_H Anti polyhydroxybutyrate antibody FV, heavy chain; plastic, immune
system; 1.70A {Homo sapiens}
Length = 139
Score = 27.5 bits (62), Expect = 3.9
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 237 GAGLLWMGW-SGFNGGAPYA 255
G GL +MGW + +G YA
Sbjct: 42 GQGLEYMGWINPKSGDTNYA 61
>1txk_A OPGG, glucans biosynthesis protein G; beta-sandwich, biosynthetic
protein; 2.50A {Escherichia coli} SCOP: b.1.18.2
b.30.5.9
Length = 498
Score = 28.6 bits (64), Expect = 4.3
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 5/43 (11%)
Query: 205 GIAGLTAAYWVGPRLKSDKERFPPN----NVLLMLAGAG-LLW 242
G+A LT+ + GP S + P N L + AG G +W
Sbjct: 225 GVAPLTSMFLFGPNQPSPANNYRPELHDSNGLSIHAGNGEWIW 267
>3fe3_A MAP/microtubule affinity-regulating kinase 3; serine/threonine
protein kinase, MARK;PAR-1, UBA domai TAK1;P78;MARK3,
ATP-binding; 1.90A {Homo sapiens} PDB: 2qnj_A 1y8g_A*
1zmw_A 1zmu_A 1zmv_A 2wzj_A 2r0i_A 2hak_A 3iec_A
Length = 328
Score = 28.0 bits (63), Expect = 4.5
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 7/40 (17%)
Query: 73 ICWVLVCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPE 112
I + LV LPF G+ L ++ L G+ R+P
Sbjct: 203 ILYTLVSGS-------LPFDGQNLKELRERVLRGKYRIPF 235
>2b7k_A SCO1 protein; metallochaperone, cytochrome C oxidase, metal binding
protein; 1.80A {Saccharomyces cerevisiae} SCOP:
c.47.1.10 PDB: 2b7j_A
Length = 200
Score = 27.8 bits (62), Expect = 4.5
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 118 DGKTVTTEPFYAMATLVYFQFTF 140
G T + +++YF F+
Sbjct: 30 YGNEFTEKNLLGKFSIIYFGFSN 52
>1chu_A Protein (L-aspartate oxidase); flavoenzyme, NAD biosynthesis, FAD,
oxidoreductase; 2.20A {Escherichia coli} SCOP: a.7.3.1
c.3.1.4 d.168.1.1 PDB: 1knr_A* 1knp_A*
Length = 540
Score = 28.4 bits (64), Expect = 4.8
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 199 VIHVSSGIAGLTAAYWVGPRLK 220
V+ + SG AGL+ A + + +
Sbjct: 11 VLIIGSGAAGLSLALRLADQHQ 32
>3byv_A Rhoptry kinase; malaria, transferase, structural genomics,
structural genomics consortium, SGC; 1.80A {Toxoplasma
gondii} PDB: 2w1z_A
Length = 377
Score = 28.0 bits (62), Expect = 4.9
Identities = 7/36 (19%), Positives = 11/36 (30%), Gaps = 2/36 (5%)
Query: 78 VCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPES 113
V Y + D LP A + +P+
Sbjct: 302 VIYWIWCAD--LPITKDAALGGSEWIFRSCKNIPQP 335
>2ggt_A SCO1 protein homolog, mitochondrial; copper chaperone, Cu-binding
protein, mitochondrial assembly factor, redox, nickel,
disuplhide, mitochondrion; 2.40A {Homo sapiens} SCOP:
c.47.1.10 PDB: 2gqk_A 2gql_A 2gqm_A 2gt5_A 2gt6_A 2gvp_A
2hrf_A 2hrn_A 1wp0_A
Length = 164
Score = 27.3 bits (61), Expect = 5.7
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 118 DGKTVTTEPFYAMATLVYFQFTF 140
G+ T + + L+YF FT
Sbjct: 12 TGERKTDKDYLGQWLLIYFGFTH 34
>2rli_A SCO2 protein homolog, mitochondrial; copper protein, thioredoxin
fold, metal transport, structural genomics,
spine2-complexes; NMR {Homo sapiens}
Length = 171
Score = 27.3 bits (61), Expect = 5.8
Identities = 7/23 (30%), Positives = 9/23 (39%)
Query: 118 DGKTVTTEPFYAMATLVYFQFTF 140
G+ F L+YF FT
Sbjct: 15 RGRARCKADFRGQWVLMYFGFTH 37
>3lh2_H FV 4E10 heavy chain; epitope-scaffold, immune system; 2.65A {Homo
sapiens} PDB: 3h3p_H 3lhp_H 2xtj_D
Length = 137
Score = 26.4 bits (59), Expect = 7.9
Identities = 8/20 (40%), Positives = 8/20 (40%), Gaps = 1/20 (5%)
Query: 237 GAGLLWMGW-SGFNGGAPYA 255
G GL WMG YA
Sbjct: 44 GRGLEWMGGVIPLLTITNYA 63
>3u6r_H Antibody 1:7 (heavy chain); IG-like domain, neutralizing single
chain FV, immune system; 2.67A {Homo sapiens}
Length = 149
Score = 26.4 bits (59), Expect = 9.9
Identities = 7/20 (35%), Positives = 7/20 (35%), Gaps = 1/20 (5%)
Query: 237 GAGLLWMGW-SGFNGGAPYA 255
G G WMG YA
Sbjct: 45 GQGPEWMGNIIPVYNTPNYA 64
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 0.451
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,853,256
Number of extensions: 359060
Number of successful extensions: 930
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 45
Length of query: 369
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 274
Effective length of database: 4,049,298
Effective search space: 1109507652
Effective search space used: 1109507652
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: 58 (26.1 bits)