RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 040022
(490 letters)
>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 = 252 bits (646), Expect = 1e-79
Identities = 77/424 (18%), Positives = 128/424 (30%), Gaps = 67/424 (15%)
Query: 70 AGSVRAKN-TMNIMLTNVLDAATGGLFYYLFGFAFAFGNPSNGFIGKHFFGLEAFPSPSF 128
A V N ++NI+ ++ +F +GF+ G G + L
Sbjct: 11 ARLVAQYNYSINILAMLLVGFGFLMVFVRRYGFSATTGTYLVVATGLPLYILLRANGIFG 70
Query: 129 DYGY-----FLYQWAFAIAAAGITSGSIAERTQFVAYLIYSSFLTGLVYPIVSHWFWSSD 183
+ FA+A I G++ R + Y + + F+ VY + +
Sbjct: 71 HALTPHSVDAVIYAEFAVATGLIAMGAVLGRLRVFQYALLALFIVP-VYLLNEWLVLD-N 128
Query: 184 GWASPTRTDNNLLFGSGVIDFAGSGVVHMVGGIAGLWGALIEGPRIGKFDHNDRPATMRG 243
G D AGS +H G GL ++ + +P
Sbjct: 129 AS----------GLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRA----QPIESDA 174
Query: 244 HSGTLVVLGTFLLWFGWYGFNPGSFVYILKTYGESGSYYGQWSAIGRTAITTTLAGCSAA 303
S +LG+ +LW W F + + +T + T LA C A
Sbjct: 175 TSDRFSMLGSMVLWLFWPSFATAI---------------VPFEQMPQTIVNTLLALCGAT 219
Query: 304 LTTLFGKRLIA-GHWNVTDVCNGLLGGFAAITGGCSVVDPWAAIICGFVAAWILIGC--- 359
L T F L G ++ D+ N L G AI C++V P A + G + I +
Sbjct: 220 LATYFLSALFHKGKASIVDMANAALAGGVAIGSVCNIVGPVGAFVIGLLGGAISVVGFVF 279
Query: 360 --NKLAEKFKYDDPLEAAQLHGGCGAWGVIFTGLFAKESYVNEVYPGKPGRPYGLFMGGG 417
L K K D LHG G G L
Sbjct: 280 IQPMLESKAKTIDTCGVHNLHGLPGLLGGFSAILIV------------------------ 315
Query: 418 GKLLAAHIVQILVITGWVSVTMGTLFWLLNKLKLLRISTDEEMAGMDLTSHGGLAYAYHD 477
+ A + I + + L+ + + ++ + L A
Sbjct: 316 PGIAVAQLTGIGITLALALIGGVIAGALIKLTGTTKQAYEDSHEFIHLAGPEDEHKAERL 375
Query: 478 DLDS 481
L++
Sbjct: 376 VLEA 379
>2b2h_A AMT-1, ammonium transporter; membrane protein, transport protein;
1.54A {Archaeoglobus fulgidus} PDB: 2b2f_A 2b2i_A 2b2j_A
Length = 399
Score = 249 bits (638), Expect = 2e-78
Identities = 120/440 (27%), Positives = 187/440 (42%), Gaps = 52/440 (11%)
Query: 40 VDTGYAIDNTYLLFSAYLVFVMQLGFAMLCAGSVRAKNTMNIMLTNVLDAATGGLFYYLF 99
+ G + ++L S LV +M G AG VR KN +N++ + + L + +
Sbjct: 1 MSDG---NVAWILASTALVMLMVPGVGFFYAGMVRRKNAVNMIALSFISLIITVLLWIFY 57
Query: 100 GFAFAFGNPSNGFIGK-HFFGLEAFPSPSFDYGYFLYQWAFAIAAAGITSGSIAERTQFV 158
G++ +FGN +G IG ++ L D + +YQ FA I + +IAER +
Sbjct: 58 GYSVSFGNDISGIIGGLNYALLSGVKGE--DLLFMMYQMMFAAVTIAILTSAIAERAKVS 115
Query: 159 AYLIYSSFLTGLVYPIVSHWFWSSDGWASPTRTDNNLLFGSGVIDFAGSGVVHMVGGIAG 218
++++ S+ VY +HW W GW L G +DFAG VVH+ G A
Sbjct: 116 SFILLSALWLTFVYAPFAHWLWG-GGW----------LAKLGALDFAGGMVVHISSGFAA 164
Query: 219 LWGALIEGPRIGKFDHNDRPATMRGHSGTLVVLGTFLLWFGWYGFNPGSFVYILKTYGES 278
L A+ G R G +++ P HS L ++G LLWFGW+GFN GS
Sbjct: 165 LAVAMTIGKRAGFEEYSIEP-----HSIPLTLIGAALLWFGWFGFNGGS----------- 208
Query: 279 GSYYGQWSAIGRTA---ITTTLAGCSAALTTLFGKRLIAGHWNVTDVCNGLLGGFAAITG 335
+A + T + A + I G + +G + G AAIT
Sbjct: 209 -----ALAANDVAINAVVVTNTSAAVAGFVWMVIGW-IKGKPGSLGIVSGAIAGLAAITP 262
Query: 336 GCSVVDPWAAIICGFVAAWILIGCNKLAEKFKYDDPLEAAQLHGGCGAWGVIFTGLFAKE 395
VD AI+ G VA + K K D+ L+A +HG G WG + G+ A
Sbjct: 263 AAGFVDVKGAIVIGLVAGIVCYLAMDFRIKKKIDESLDAWAIHGIGGLWGSVAVGILANP 322
Query: 396 SYVNEVYPGKPGRPYGLFMGGGGKLLAAHIVQILVITGWVSVTMGTLFWLLNKLKLLRIS 455
Y + G +LL + ++ + T + + L ++ LR+S
Sbjct: 323 EVN----------GYAGLLFGNPQLLVSQLIAVASTTAYAFLVTLILAKAVDAAVGLRVS 372
Query: 456 TDEEMAGMDLTSHGGLAYAY 475
+ EE G+DL+ H +AY
Sbjct: 373 SQEEYVGLDLSQHEEVAYTL 392
>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 = 220 bits (562), Expect = 2e-67
Identities = 118/426 (27%), Positives = 180/426 (42%), Gaps = 56/426 (13%)
Query: 40 VDTGYAIDNTYLLFSAYLVFVMQL-GFAMLCAGSVRAKNTMNIMLTNVLDAATGGLFYYL 98
D DN +++ LV M + G A+ G +R KN ++++ + A + + +
Sbjct: 5 ADKA---DNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVV 61
Query: 99 FGFAFAFGNPSNGFIG--KHFF----GLEAFPSPSFDYGYFLYQWAFAIAAAGITSGSIA 152
+G++ A G N F G L A + Y + +Q +FA G+ G++A
Sbjct: 62 YGYSLASG-EGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALA 120
Query: 153 ERTQFVAYLIYSSFLTGLVYPIVSHWFWSSDGWASPTRTDNNLLFGSGVIDFAGSGVVHM 212
ER +F A LI+ L Y ++H W G L G +DFAG VVH+
Sbjct: 121 ERIRFPAVLIFVVVWLTLSYIPIAHMVWG-GGL----------LASHGALDFAGGTVVHI 169
Query: 213 VGGIAGLWGALIEGPRIGKFDHNDRPATMRGHSGTLVVLGTFLLWFGWYGFNPGSFVYIL 272
IAGL GA + G R+G +P H+ +V GT +L+ GW+GFN GS
Sbjct: 170 NAAIAGLVGAYLIGKRVGFGKEAFKP-----HNLPMVFTGTAILYIGWFGFNAGS----- 219
Query: 273 KTYGESGSYYGQWSAIGRTA---ITTTLAGCSAALTTLFGKRLIAGHWNVTDVCNGLLGG 329
+A A + T +A +A L +FG+ + G ++ C+G + G
Sbjct: 220 -----------AGTANEIAALAFVNTVVATAAAILGWIFGEWALRGLPSLLGACSGAIAG 268
Query: 330 FAAITGGCSVVDPWAAIICGFVAAWI-LIGCNKLAEKFKYDDPLEAAQLHGGCGAWGVIF 388
+T C + A+I G VA L G L + DDP + +HG CG G I
Sbjct: 269 LVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIM 328
Query: 389 TGLFAKESYVNEVYPGKPGRPYGLFMGGGGKLLAAHIVQILVITGWVSVTMGTLFWLLNK 448
TG+FA S G G G+ MG L + I + W V + L +
Sbjct: 329 TGIFAASSL------GGVGFAEGVTMGH---QLLVQLESIAITIVWSGVVAFIGYKLADL 379
Query: 449 LKLLRI 454
LR+
Sbjct: 380 TVGLRV 385
>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 = 198 bits (506), Expect = 5e-58
Identities = 68/402 (16%), Positives = 112/402 (27%), Gaps = 50/402 (12%)
Query: 90 ATGGLFYYLFGFAFAFGNPSNGFIGKHFFGLEAFPSPSFDYGYFLYQWAFAIAAAGITSG 149
+ G + L F + G+ HF L F +A+ + G
Sbjct: 92 SAVGFNFLLAAFGIQWALLMQGWF--HFLQDRYIVVGVE----NLINADFCVASVCVAFG 145
Query: 150 SIAERTQFVAYLIYSSFLTGLVYPIVSHWFWSSDGWASPTRTDNNLLFGSGVIDFAGSGV 209
++ + + LI + + + + LL V D GS
Sbjct: 146 AVLGKVSPIQLLIMT------FFQVTLFAVN---EFI--------LLNLLKVKDAGGSMT 188
Query: 210 VHMVGGIAGLWGALIEGPRIGKFDHNDRPATMRGHSGTLVVLGTFLLWFGWYGFNPGSFV 269
+H G GL I R + + S ++GT LW W FN
Sbjct: 189 IHTFGAYFGLTVTRILYRRNLEQSKERQN--SVYQSDLFAMIGTLFLWMYWPSFNSAI-- 244
Query: 270 YILKTYGESGSYYGQWSAIGRTAITTTLAGCSAALTTLFGKRLIAGHWNVTDVCNGLLGG 329
SY+G +LA C + G ++ + N L G
Sbjct: 245 ----------SYHGDSQHRAAINTYCSLAACVLTSVAISSALHKKGKLDMVHIQNATLAG 294
Query: 330 FAAI-TGGCSVVDPWAAIICGFVAAWILIGCNK-----LAEKFKYDDPLEAAQLHGGCGA 383
A+ T ++ P+ A+I GFV I L + D LHG G
Sbjct: 295 GVAVGTAAEMMLMPYGALIIGFVCGIISTLGFVYLTPFLESRLHIQDTCGINNLHGIPGI 354
Query: 384 WGVIFTGLFAKESYVNEVYPGKPGRPYGLFMGGG----GKLLAAHIVQILVITGWVSVTM 439
G I + A + + + G I +LV +
Sbjct: 355 IGGIVGAVTAASASLEVYGKEGLVHSFDFQGFNGDWTARTQGKFQIYGLLVTLAMALMGG 414
Query: 440 GTLFWLLNKLKLLRISTDEEM---AGMDLTSHGGLAYAYHDD 478
+ +L + S + ++ Y D
Sbjct: 415 IIVGLILRLPFWGQPSDENCFEDAVYWEMPEGNSTVYIPEDP 456
>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 = 34.3 bits (78), Expect = 0.12
Identities = 51/318 (16%), Positives = 78/318 (24%), Gaps = 126/318 (39%)
Query: 52 LFSAYLVFVMQLGFAMLCAGSVRAKN--TMNIMLTNVLDAATGGLFYYLFG-----FAFA 104
L +L +V L V + +L L YL G A
Sbjct: 60 LVGKFLGYVSSL---------VEPSKVGQFDQVLNLCLTEFENC---YLEGNDIHALAAK 107
Query: 105 FGNPSNGFIGKHFFGLEAF-------------PSPSFDYGYFLYQWAFAIAAAGITSGSI 151
++ + K ++ + S S A A
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS----------ALFRAVG------- 150
Query: 152 AERTQFVA------------------YLIYSSFLTGLVYPIVSHWFWSSDGWASPTRTDN 193
Q VA Y Y + L+ T D
Sbjct: 151 EGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAET-LSEL----IRTTLDA 205
Query: 194 NLLFGSGVIDFAGSGVVHMVGGIAGLWGALIEGPRIGKFDHNDRP-------ATMRGHSG 246
+F G ++ W +E P ++ P + S
Sbjct: 206 EKVFTQG-LNILE-------------W---LENP-------SNTPDKDYLLSIPI---SC 238
Query: 247 TLVVLGTFLLWFGWY-------GFNPGSFVYILKTYGESGSYYGQWSAIGRTAITTT--- 296
L+ ++ Y GF PG LK G +G G +A+ A T +
Sbjct: 239 PLI----GVIQLAHYVVTAKLLGFTPGELRSYLK--GATGHSQGLVTAVA-IAETDSWES 291
Query: 297 -LAGCSAALTTLF--GKR 311
A+T LF G R
Sbjct: 292 FFVSVRKAITVLFFIGVR 309
Score = 31.6 bits (71), Expect = 0.80
Identities = 23/124 (18%), Positives = 36/124 (29%), Gaps = 58/124 (46%)
Query: 3 ALACSASNLS-----PLL---------------GGATNATAAA---------------EY 27
ALA A +S ++ G +N A +Y
Sbjct: 1769 ALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQY 1828
Query: 28 ICGRFEAVSNKFVDTGYAI--DNTYLLFSAYLVFVMQLGFAMLCAGSVRAKNTMNIMLTN 85
+ R + V+ I N +V AG +RA +T +TN
Sbjct: 1829 VVERVGKRTGWLVE----IVNYN-----VENQQYV--------AAGDLRALDT----VTN 1867
Query: 86 VLDA 89
VL+
Sbjct: 1868 VLNF 1871
Score = 28.1 bits (62), Expect = 7.9
Identities = 22/94 (23%), Positives = 29/94 (30%), Gaps = 33/94 (35%)
Query: 148 SGSIAERTQFVAYLIYSSFLTGLVYPIVSHWFWSSDGWASPTRTDNN----LLFGSGVID 203
SGSI+ER + I + P+ W T T L FG G
Sbjct: 472 SGSISER---IVDCI-------IRLPV--KW---------ETTTQFKATHILDFGPGGA- 509
Query: 204 FAGSGVVHMVGGIA-GLWGALIEGPRIGKFDHND 236
SG+ + G +I G D N
Sbjct: 510 ---SGLGVLTHRNKDGTGVRVIVA---GTLDINP 537
>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 = 33.7 bits (76), Expect = 0.16
Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 15/60 (25%)
Query: 410 YGLFMGGGGK-LLAAHIVQILVITG-------WVSV----TMGTLFWLLNKLKLLRISTD 457
G + G GK +A + + W+++ + T+ +L KL L +I +
Sbjct: 156 DG--VLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKL-LYQIDPN 212
Score = 29.4 bits (65), Expect = 3.6
Identities = 63/434 (14%), Positives = 113/434 (26%), Gaps = 145/434 (33%)
Query: 146 ITSGSIAERTQFVAYL-------IYSSFLTGLV---YPIVSHWFWSSDGWASPTR----- 190
I S T + + + F+ ++ Y + S + R
Sbjct: 55 IMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYK----FLMSP--IKTEQRQPSMM 108
Query: 191 -----TDNNLLFGSGVIDFAGSGVVHMVGGIAGLWGALIEGPRIGKFDH------NDRPA 239
+ L+ + FA V R+ + RPA
Sbjct: 109 TRMYIEQRDRLYNDNQV-FAKYNV-----------------SRLQPYLKLRQALLELRPA 150
Query: 240 T------MRGHSG--TLV--VLGTF----LLWFG--WYGFN----PGSFVYILKT-YGES 278
+ G SG + V ++ + F W P + + +L+ +
Sbjct: 151 KNVLIDGVLG-SGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209
Query: 279 GSYYGQWSAIGRTAITTTLAGCSAALTTLFGKR------LI------AGHWNVTDV-CNG 325
+ S I + A L L + L+ A WN ++ C
Sbjct: 210 DPNWTSRSDHSSN-IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKI 268
Query: 326 LLGGFAAITGGCSVVDPWAAII----------CGF--------VAAWILIGCNKLAEKFK 367
LL T V D +A + ++ L +
Sbjct: 269 LL-----TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVL 323
Query: 368 YDDPLE----AAQLHGGCGAWGVIFTGLFAK-----ESYVNEVYPGKPGRPY---GLFMG 415
+P A + G W K ES +N + P + + + +F
Sbjct: 324 TTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPP 383
Query: 416 GGGKLLAAHI-VQILVITGWVSVTMGTLFWLLNKLK---LLRISTDEEMAGMDLTSHGGL 471
AHI +L + W V + ++NKL L+ E
Sbjct: 384 S------AHIPTILLSLI-WFDVIKSDVMVVVNKLHKYSLVEKQPKES------------ 424
Query: 472 AYAYHD-DLDSTQK 484
+ L+ K
Sbjct: 425 TISIPSIYLELKVK 438
Score = 28.3 bits (62), Expect = 8.7
Identities = 12/64 (18%), Positives = 18/64 (28%), Gaps = 11/64 (17%)
Query: 112 FIGKHFFGLEA------FPSPSFDYGYFLYQWAFAIAAAGITSGSIAERTQFVAYL-IYS 164
IG H +E F D+ FL Q I + + L Y
Sbjct: 476 HIGHHLKNIEHPERMTLFRMVFLDFR-FLEQ---KIRHDSTAWNASGSILNTLQQLKFYK 531
Query: 165 SFLT 168
++
Sbjct: 532 PYIC 535
>1ev7_A Type IIE restriction endonuclease NAEI; APO-NAEI, topoisomerase,
helix- turn-helix, CAP, hydrolase; 2.38A {Lechevalieria
aerocolonigenes} SCOP: c.52.1.9 PDB: 1iaw_A
Length = 317
Score = 28.9 bits (64), Expect = 3.7
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 223 LIEGPRIGKFDHNDRPATMRGHSGTLV 249
L +G R G+++ + T + H GTLV
Sbjct: 43 LYDGQRTGRWNFDQLHKTEKTHMGTLV 69
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
0.324 0.141 0.457
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,107,069
Number of extensions: 520673
Number of successful extensions: 1384
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1344
Number of HSP's successfully gapped: 24
Length of query: 490
Length of database: 6,701,793
Length adjustment: 97
Effective length of query: 393
Effective length of database: 3,993,456
Effective search space: 1569428208
Effective search space used: 1569428208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.5 bits)