RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12939
(413 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 = 76.3 bits (188), Expect = 2e-15
Identities = 17/92 (18%), Positives = 25/92 (27%), Gaps = 15/92 (16%)
Query: 175 YPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPP 234
Y + V + G+ D AGS A+H F + + R
Sbjct: 118 YLLNEWLVLDN-ASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRAQP----IES 172
Query: 235 PGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
S + GS+ LW F
Sbjct: 173 DATSDRFSM-----LGSMVLW-----LFWPSF 194
Score = 74.4 bits (183), Expect = 1e-14
Identities = 13/69 (18%), Positives = 19/69 (27%), Gaps = 5/69 (7%)
Query: 343 YPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPP 402
Y + V + G+ D AGS A+H F + + R
Sbjct: 118 YLLNEWLVLDN-ASGLTEGFQDSAGSIAIHAFGAYFGLGVSIALTTAAQRAQP----IES 172
Query: 403 PGHSLPVST 411
S S
Sbjct: 173 DATSDRFSM 181
Score = 62.8 bits (153), Expect = 5e-11
Identities = 22/92 (23%), Positives = 34/92 (36%), Gaps = 7/92 (7%)
Query: 65 GRPCWNFLFTVNAGLMGMVSVCAGANVFSMWSSLVIGLIAGPLYVA-----LRYLVIACG 119
G+ + + NA L G V++ + N+ + VIGL+ G + V L
Sbjct: 232 GKA--SIVDMANAALAGGVAIGSVCNIVGPVGAFVIGLLGGAISVVGFVFIQPMLESKAK 289
Query: 120 VDDPLDASAVHFGGGLWGVMSEPLFRRGGLIY 151
D +H GL G S L G +
Sbjct: 290 TIDTCGVHNLHGLPGLLGGFSAILIVPGIAVA 321
Score = 56.6 bits (137), Expect = 5e-09
Identities = 16/116 (13%), Positives = 29/116 (25%), Gaps = 19/116 (16%)
Query: 182 VWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLPG 241
V+ +K D G +H G +A L+ P I
Sbjct: 278 VFIQPMLESKAKTIDTCGVHNLHGLPGLLGGFSAILIVPGI------------------- 318
Query: 242 LLHNAVGAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAYPPS 297
+ G G +L I + L + + E + + +
Sbjct: 319 AVAQLTGIGITLALALIGGVIAGALIKLTGTTKQAYEDSHEFIHLAGPEDEHKAER 374
>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 = 65.3 bits (159), Expect = 1e-11
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 7/83 (8%)
Query: 173 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 232
+T+ V+ + ++ LN L D GS +H F ++ R R
Sbjct: 159 MTFFQVTLFAVNEFILLNLLKVKDAGGSMTIHTFGAYFGLTVTRILYRRNLEQSKER--Q 216
Query: 233 PPPGHSLPGLLHNAVGAGSIFLW 255
S + G++FLW
Sbjct: 217 NSVYQSDLFAM-----IGTLFLW 234
Score = 61.8 bits (150), Expect = 1e-10
Identities = 13/71 (18%), Positives = 23/71 (32%), Gaps = 2/71 (2%)
Query: 341 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 400
+T+ V+ + ++ LN L D GS +H F ++ R R
Sbjct: 159 MTFFQVTLFAVNEFILLNLLKVKDAGGSMTIHTFGAYFGLTVTRILYRRNLEQSKER--Q 216
Query: 401 PPPGHSLPVST 411
S +
Sbjct: 217 NSVYQSDLFAM 227
Score = 54.1 bits (130), Expect = 4e-08
Identities = 18/127 (14%), Positives = 31/127 (24%), Gaps = 12/127 (9%)
Query: 182 VWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPR--IGRFGNGRYSSPPPGHSL 239
V+ ++L D G +H G I + + +G
Sbjct: 327 VYLTPFLESRLHIQDTCGINNLHGIPGIIGGIVGAVTAASASLEVYGKEGLVHSFDFQGF 386
Query: 240 PG-------LLHNAVGAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEG---LDITKH 289
G G +L I+ L L + E ++ +
Sbjct: 387 NGDWTARTQGKFQIYGLLVTLAMALMGGIIVGLILRLPFWGQPSDENCFEDAVYWEMPEG 446
Query: 290 NEIAYPP 296
N Y P
Sbjct: 447 NSTVYIP 453
>2b2h_A AMT-1, ammonium transporter; membrane protein, transport protein;
1.54A {Archaeoglobus fulgidus} PDB: 2b2f_A 2b2i_A 2b2j_A
Length = 399
Score = 63.8 bits (156), Expect = 2e-11
Identities = 35/94 (37%), Positives = 43/94 (45%), Gaps = 16/94 (17%)
Query: 173 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 232
Y +HW+W GWL KLG DFAG VH+ +G + A +G R G YS
Sbjct: 127 FVYAPFAHWLWGG-GWLAKLGALDFAGGMVVHISSGFAALAVAMTIGKRAGF---EEYSI 182
Query: 233 PPPGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
P HS+P +GA LW F FGF
Sbjct: 183 EP--HSIP---LTLIGAA--LLW-----FGWFGF 204
Score = 59.9 bits (146), Expect = 4e-10
Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 341 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 400
Y +HW+W GWL KLG DFAG VH+ +G + A +G R G YS
Sbjct: 127 FVYAPFAHWLWGG-GWLAKLGALDFAGGMVVHISSGFAALAVAMTIGKRAGF---EEYSI 182
Query: 401 PPPGHSLP 408
P HS+P
Sbjct: 183 EP--HSIP 188
Score = 53.0 bits (128), Expect = 7e-08
Identities = 26/123 (21%), Positives = 44/123 (35%), Gaps = 17/123 (13%)
Query: 187 GWLNKLGYSDFAGSGAVHLFAG------TCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLP 240
+ K + + A+H G + G FGN +
Sbjct: 288 DFRIKKKIDESLDAWAIHGIGGLWGSVAVGILANPEVNGYAGLLFGNPQL---------- 337
Query: 241 GLLHNAVGAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAYPPSAWN 300
L+ + S ++ + IL + LRV S EE GLD+++H E+AY +
Sbjct: 338 -LVSQLIAVASTTAYAFLVTLILAKAVDAAVGLRVSSQEEYVGLDLSQHEEVAYTLEHHH 396
Query: 301 NFH 303
+ H
Sbjct: 397 HHH 399
Score = 49.1 bits (118), Expect = 1e-06
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 81 GMVSVCAGANVFSMWSSLVIGLIAGPL---YVALRYLVIACGVDDPLDASAVHFGGGLWG 137
G+ ++ A + ++VIGL+AG + + R +D+ LDA A+H GGLWG
Sbjct: 256 GLAAITPAAGFVDVKGAIVIGLVAGIVCYLAMDFRIKK---KIDESLDAWAIHGIGGLWG 312
Query: 138 VM------SEPLFRRGGLIYGITD 155
+ + + GL++G
Sbjct: 313 SVAVGILANPEVNGYAGLLFGNPQ 336
>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 = 62.3 bits (152), Expect = 8e-11
Identities = 30/92 (32%), Positives = 41/92 (44%), Gaps = 16/92 (17%)
Query: 175 YPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPP 234
Y ++H VW G L G DFAG VH+ A + AYL+G R+G G+ + P
Sbjct: 140 YIPIAHMVWGG-GLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGF---GKEAFKP 195
Query: 235 PGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
H+LP + G L+ FGF
Sbjct: 196 --HNLPMVF---TGTA--ILY-----IGWFGF 215
Score = 59.9 bits (146), Expect = 5e-10
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 343 YPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPP 402
Y ++H VW G L G DFAG VH+ A + AYL+G R+G G+ + P
Sbjct: 140 YIPIAHMVWGG-GLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGF---GKEAFKP 195
Query: 403 PGHSLP 408
H+LP
Sbjct: 196 --HNLP 199
Score = 51.5 bits (124), Expect = 2e-07
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 81 GMVSVCAGANVFSMWSSLVIGLIAGPL-YVALRYLVIACGVDDPLDASAVHFGGGLWGVM 139
G+V V + +L+IG++AG + L VDDP D VH G+ G +
Sbjct: 268 GLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCI 327
Query: 140 SEPLF 144
+F
Sbjct: 328 MTGIF 332
>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 = 46.6 bits (110), Expect = 1e-05
Identities = 91/495 (18%), Positives = 145/495 (29%), Gaps = 179/495 (36%)
Query: 8 RF-GHKHSQISQSHLEGFCAICDKGL--FLKRFDRGN---CNCYGLIVPKSKREGRQDRL 61
+F G+ S + S + F + + L F + GN L+ + L
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 62 --------GLCGRPCWNF----LFT-VNAGLMGMVSVCAG-----------ANVFSMWSS 97
+ RP LF V G +V++ G +++ +
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHV 182
Query: 98 LVIGLI--AGPLYVALRYLVIACGVDDPLDASAVHFGGGL----WGVMSEPLFRRGGLIY 151
LV LI + L L+ LDA F GL W + P Y
Sbjct: 183 LVGDLIKFSAET---LSELI-----RTTLDAE-KVFTQGLNILEW--LENPS-NTPDKDY 230
Query: 152 GITDDAVKVTSTNKQTSP--LPGITYPIVSHWVWSDEGWLNKLGYS--DFAG--SGA-VH 204
++ P P I ++H+V + LG++ + GA H
Sbjct: 231 LLS-------------IPISCPLIGVIQLAHYVVT----AKLLGFTPGELRSYLKGATGH 273
Query: 205 ---LFAGTC--------SFIAAYLMGPR----IG-----RFGNGRYSSPPP--------- 235
L SF + IG + N +S PP
Sbjct: 274 SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPN---TSLPPSILEDSLEN 330
Query: 236 GHSLP-------GLLHNAV------------GAGSIFLWSLT---TSFILFGF---LY-L 269
+P L V + + SL + ++ G LY L
Sbjct: 331 NEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEI-SLVNGAKNLVVSGPPQSLYGL 389
Query: 270 INMLR---VPSTEEIEGLDITK--HNE-----------IAYPPSAWNNFHAKHMLP-NDH 312
LR PS GLD ++ +E +A P FH+ ++P +D
Sbjct: 390 NLTLRKAKAPS-----GLDQSRIPFSERKLKFSNRFLPVASP------FHSHLLVPASDL 438
Query: 313 IMIDVLNHN-----TDARVKV--TSTNK-----QTSPLPGITYPIVSHWV-WSDEGWLNK 359
I D++ +N D ++ V T S I I+ V W +
Sbjct: 439 INKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWET---TTQ 495
Query: 360 LGYS---DFAGSGAV 371
+ DF G G
Sbjct: 496 FKATHILDF-GPGGA 509
Score = 33.9 bits (77), Expect = 0.12
Identities = 28/164 (17%), Positives = 52/164 (31%), Gaps = 45/164 (27%)
Query: 121 DDPLDASAVHFGG-----------------GLWG-VMSEPLFRRGG-----LIYGITDDA 157
++P++ +HFGG + G + +E +F+ +
Sbjct: 1667 NNPVNL-TIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGL 1725
Query: 158 VKVTSTNKQTSPLPGITYPIVS---HWVWSDEGWLNKLGYSDFAG-S-G---AVHLFAGT 209
+ T Q P +T ++ +G + FAG S G A+ A
Sbjct: 1726 LSATQ-FTQ----PALT--LMEKAAFEDLKSKGLIPADAT--FAGHSLGEYAALASLADV 1776
Query: 210 CSFI-AAYLMGPRIGRFGNGRYSSPPPGHSLPGLLHNAVGAGSI 252
S ++ R G G S G++ A+ G +
Sbjct: 1777 MSIESLVEVVFYR-GMTMQVAVPRDELGRSNYGMI--AINPGRV 1817
>1bwd_A ADT, protein (inosamine-phosphate amidinotransferase);
streptomycin; 3.10A {Streptomyces griseus} SCOP:
d.126.1.2
Length = 348
Score = 29.5 bits (64), Expect = 1.9
Identities = 24/147 (16%), Positives = 42/147 (28%), Gaps = 15/147 (10%)
Query: 4 PVRFRFGHKHSQISQSHLEGFCAICDKGLFLKRFDRGNCNCYGLIVPKSKREGRQDRLGL 63
+ + +H++ GL L R N + +
Sbjct: 211 GDTYTVHPCRKLYASTHVDSTIVPLRPGLVLTNPSRVNDENMPDFLRSWEN--------- 261
Query: 64 CGRPCWNFLFTVNAGLMGMVSVCAGANVFSMWSSLVIGLIAGPLYVALRYLVIACGVD-D 122
C + G SV G N+ + L + AL L+ G++
Sbjct: 262 --ITCPELVDIGFTGDKPHCSVWIGMNLLVVRPDLAV---VDRRQTALIRLLEKHGMNVL 316
Query: 123 PLDASAVHFGGGLWGVMSEPLFRRGGL 149
PL + GG + + + R G L
Sbjct: 317 PLQLTHSRTLGGGFHCATLDVRRTGAL 343
>1jdw_A L-arginine\:glycine amidinotransferase; creatine biosynthesis,
catalytic triad, reaction mechanism, novel fold,
fivefold pseudosymmetry; 1.90A {Homo sapiens} SCOP:
d.126.1.2 PDB: 2jdw_A 3jdw_A* 4jdw_A* 8jdw_A 5jdw_A
6jdw_A* 1jdx_A* 7jdw_A 9jdw_A* 2jdx_A
Length = 423
Score = 29.1 bits (63), Expect = 2.8
Identities = 21/131 (16%), Positives = 37/131 (28%), Gaps = 16/131 (12%)
Query: 20 HLEGFCAICDKGLFLKRFDRGNCNCYGLIVPKSKREGRQDRLGLCGRPCWNFLFTVNAGL 79
H++ I G+ L DR + P W
Sbjct: 303 HIDATFNIIGPGIVLSNPDRPCHQIDLFKKAGWTIITPPTPIIPDDHPLW---------- 352
Query: 80 MGMVSVCAGANVFSMWSSLVIGLIAGPLYVALRYLVIACGVD-DPLDASAVHFGGGLWGV 138
M S NV + V+ V ++ + G+ ++ + GG +
Sbjct: 353 --MSSKWLSMNVLMLDEKRVM---VDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHC 407
Query: 139 MSEPLFRRGGL 149
+ + RRG L
Sbjct: 408 WTCDVRRRGTL 418
>3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich,
DNA-binding, transcription regulation; HET: MES; 1.83A
{Citrobacter freundii} PDB: 3kot_A
Length = 219
Score = 28.4 bits (64), Expect = 3.2
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 2/26 (7%)
Query: 121 DDPLDASAVHFGGGLW-GVMSEPLFR 145
+ LD + +GGG W ++ L
Sbjct: 56 AEGLDY-TIRYGGGAWHDTDAQYLCS 80
>3bzc_A TEX; helix-turn-helix, helix-hairpin-helix, S1 domain, YQGF domain,
transcription, RNA binding protein; 2.27A {Pseudomonas
aeruginosa} SCOP: a.60.2.6 a.60.2.6 a.294.1.1 b.40.4.5
c.55.3.13 PDB: 3bzk_A 2oce_A
Length = 785
Score = 28.3 bits (64), Expect = 6.1
Identities = 9/10 (90%), Positives = 10/10 (100%)
Query: 121 DDPLDASAVH 130
D+PLDASAVH
Sbjct: 564 DNPLDASAVH 573
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 0.141 0.465
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 6,749,743
Number of extensions: 414133
Number of successful extensions: 834
Number of sequences better than 10.0: 1
Number of HSP's gapped: 819
Number of HSP's successfully gapped: 32
Length of query: 413
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 317
Effective length of database: 4,021,377
Effective search space: 1274776509
Effective search space used: 1274776509
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 (21.9 bits)
S2: 58 (26.0 bits)