RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780172|ref|YP_003064585.1| general L-amino acid transport
system permease protein [Candidatus Liberibacter asiaticus str. psy62]
(386 letters)
>3dhw_A D-methionine transport system permease protein METI;
ABC-transporter, methionine uptake transporter, membrane
protein, amino-acid transport; 3.70A {Escherichia coli
K12} SCOP: f.58.1.1
Length = 217
Score = 61.3 bits (148), Expect = 3e-10
Identities = 42/210 (20%), Positives = 89/210 (42%), Gaps = 8/210 (3%)
Query: 172 SLWGGLLVTLVISFFGIIISMPLGILLALGRNSNI---PVLRYACITFIELFRGVPLVTV 228
+W L +T V FFG +I +P+G+LL + R I L + +FR +P + +
Sbjct: 12 GVWETLAMTFVSGFFGFVIGLPVGVLLYVTRPGQIIANAKLYRTVSAIVNIFRSIPFIIL 71
Query: 229 LFMASIMLPLFLPDTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGL 288
L + L A++ ++ A+ +IA ++ L I G EA+ ++G
Sbjct: 72 LVWMIPFTRVI---VGTSIGLQAAIVPLTVGAAPFIARMVENALLEIPTGLIEASRAMGA 128
Query: 289 SYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIINMFDLLGIVRVNFSESTWISS 348
+ +Q +R +++P+ + ++ T I L S++ + L I +
Sbjct: 129 TPMQIVRKVLLPEALPGLVNAATITLITLVGYSAMGGAVGAGGLGQIGYQYGYIGYNATV 188
Query: 349 VTPTTGLIFIGFVFWIFCFSISLYSVFIEK 378
+ T L+ + + ++ F+ + +
Sbjct: 189 M--NTVLVLLVILVYLIQFAGDRIVRAVTR 216
>3d31_C Sulfate/molybdate ABC transporter, permease protein; ATP-binding,
nucleotide-binding, membrane, transmembrane, transport
protein; 3.00A {Methanosarcina acetivorans} SCOP:
f.58.1.1
Length = 295
Score = 61.2 bits (148), Expect = 4e-10
Identities = 39/265 (14%), Positives = 90/265 (33%), Gaps = 21/265 (7%)
Query: 113 MAQRWRPILVFLTGSILLTPMLIPSFPRKFLNSILLFGLFPIFSFFVLYGGLGLS----- 167
M + R F + + + +L+ + LF + + S
Sbjct: 24 MKAKNRKTRKFEPLTFVFSFLLLV---------LFLFIFLTLSNMIFEQITEDFSGLVKA 74
Query: 168 IVETSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFR------ 221
S+ + ++L F ++++ LG + + I++
Sbjct: 75 AGNRSVISSIFLSLYAGFLATLLALLLGAPTGYILARFDFPGKRLVESIIDVPVVVPHTV 134
Query: 222 -GVPLVTVLFMASIMLPLFLPDTWDVDKLLRALLGVSAFASAYIAEVLRGGLQSISKGQF 280
G+ L+TV ++ D L ++ + + Y+A R G +S+
Sbjct: 135 AGIALLTVFGSRGLIGEPLESYIQFRDALPGIVVAMLFVSMPYLANSAREGFKSVDPRLE 194
Query: 281 EAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISIINMFDLLGIVRVNF 340
AA SLG + + +P + ++ G V T+ + + I+ + ++G +
Sbjct: 195 NAARSLGAPLWKAFFFVTLPLSARYLLIGSVMTWARAISEFGAVVILAYYPMVGPTLIYD 254
Query: 341 SESTWISSVTPTTGLIFIGFVFWIF 365
++ S + ++ I IF
Sbjct: 255 RFISYGLSASRPIAVLLILVTLSIF 279
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 48.8 bits (116), Expect = 2e-06
Identities = 56/306 (18%), Positives = 86/306 (28%), Gaps = 129/306 (42%)
Query: 139 PRKFLNSILL-------FGLFPIFS--------F------FVLYGGLGLSIVETSLWGGL 177
K NS L L IF F + Y L +++ S
Sbjct: 137 FDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFS--AET 194
Query: 178 LVTL------VISFFG----II-------------------ISMPL-GIL-LALGRNSNI 206
L L F I+ IS PL G++ LA
Sbjct: 195 LSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA------- 247
Query: 207 PVLRYACIT----------FIELFRGVP-----LVTVLFMASIMLPLFLPDTWD-----V 246
Y +T +G LVT + +A D+W+ V
Sbjct: 248 ---HY-VVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAET-------DSWESFFVSV 296
Query: 247 DKLLRAL--LGV---SAFASAYIAEVLRGGLQ-SISKGQFEAANSLGLSYLQKMRLIIMP 300
K + L +GV A+ + + + L+ S+ E S LS + +
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSI---LEDSLENN--EGVPSPMLS----ISNLTQE 347
Query: 301 QVIKRVIPGIVNTFIGLFKDSSL-ISIINMFDLLGIVRVNF-----SES-----TWISSV 349
QV V N+ L + IS++N G N +S +
Sbjct: 348 QVQDYV--NKTNSH--LPAGKQVEISLVN-----G--AKNLVVSGPPQSLYGLNLTLRKA 396
Query: 350 TPTTGL 355
+GL
Sbjct: 397 KAPSGL 402
Score = 47.2 bits (112), Expect = 5e-06
Identities = 85/434 (19%), Positives = 128/434 (29%), Gaps = 195/434 (44%)
Query: 2 IDSCKEFPYVRKRLLQP--SLPP----VYQRG--IIAWIHKNFFGTP-KDILLTALI--- 49
I E L V+ +G I+ W+ N TP KD LL+ I
Sbjct: 188 IKFSAE-------TLSELIRTTLDAEKVFTQGLNILEWLE-NPSNTPDKDYLLSIPISCP 239
Query: 50 -ICLL-L--FSI--------PGIIHWVFLDAVWIGSNRTVCTTVSQGGI------QPDGW 91
I ++ L + + PG + +L T SQG + + D W
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTPGELR-SYLKGA---------TGHSQGLVTAVAIAETDSW 289
Query: 92 ----NAACWA-----FIYDRYEQFIFGNYPMAQRWRPILVFLTGSILL----------TP 132
+ A FI R + YP L SIL +P
Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEA----YP--------NTSLPPSILEDSLENNEGVPSP 337
Query: 133 ML-IPSFPRKFL-------NSILLFGLFP----IF-SF------FVLYGGLGLSIVETSL 173
ML I + ++ + NS L P + S V+ G S+
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHL-----PAGKQVEISLVNGAKNLVV-SGPPQSLY---- 387
Query: 174 WGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLFMAS 233
GL +TL P G+ S IP F E R +
Sbjct: 388 --GLNLTLR------KAKAPSGL-----DQSRIP--------FSE--RKLKFSNR----- 419
Query: 234 IMLPLFLPDTWDVDKLLRALLGVSA-FASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQ 292
FLP V++ F S + A+ L L
Sbjct: 420 -----FLP--------------VASPFHSHLL----------------VPASDLINKDLV 444
Query: 293 KMRLIIMPQVIKRVIPGIVNTFIGLFKD-----SSLI-SIINMFDLLGIVR--VNFSEST 344
K + + I+ IP + +TF G D S+ I++ I+R V + +T
Sbjct: 445 KNNVSFNAKDIQ--IP-VYDTFDG--SDLRVLSGSISERIVDC-----IIRLPVKWETTT 494
Query: 345 WISSVTPTTGLI-F 357
T ++ F
Sbjct: 495 ----QFKATHILDF 504
>2r6g_F Maltose transport system permease protein MALF; ABC transporter,
catalytic intermediate, E. coli maltose transporter,
MBP; HET: MAL ATP; 2.80A {Escherichia coli K12} SCOP:
e.70.1.1 f.58.1.1 PDB: 3fh6_F
Length = 514
Score = 37.8 bits (87), Expect = 0.004
Identities = 27/173 (15%), Positives = 61/173 (35%), Gaps = 16/173 (9%)
Query: 171 TSLWGGLLVTLVISFFGIIISMPLGILLALGRNSNIPVLRYACITFIELFRGVPLVTVLF 230
+ T+V S + +++ +G++LA + + L VP +
Sbjct: 275 KPFLAIFVWTVVFSLITVFLTVAVGMVLACLVQWEALRGKAVYRVLLILPYAVPSFISIL 334
Query: 231 MASIMLPLFLPDTWDVDKLLRAL----------------LGVSAFASAYIAEVLRGGLQS 274
+ + + + L + + + Y+ + G L++
Sbjct: 335 IFKGLFNQSFGEINMMLSALFGVKPAWFSDPTTARTMLIIVNTWLGYPYMMILCMGLLKA 394
Query: 275 ISKGQFEAANSLGLSYLQKMRLIIMPQVIKRVIPGIVNTFIGLFKDSSLISII 327
I +EA+ G Q I +P +IK + P ++ +F F + LI ++
Sbjct: 395 IPDDLYEASAMDGAGPFQNFFKITLPLLIKPLTPLMIASFAFNFNNFVLIQLL 447
>1cii_A Colicin IA; bacteriocin, ION channel formation, transmembrane
protein; 3.00A {Escherichia coli} SCOP: f.1.1.1 h.4.3.1
Length = 602
Score = 34.1 bits (77), Expect = 0.052
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 169 VETSLWGGLLVTLVISFFGIIISMPLGIL 197
ET + G LV F I+ LGI+
Sbjct: 549 TETIIAGNAATALVALVFSILTGSALGII 577
>3kvh_A Protein syndesmos; NUDT16-like, NUDT16L1, nudix, RNA regulation,
RNA-binding, structural genomics consortium, SGC, RNA
degradation; 1.70A {Homo sapiens}
Length = 214
Score = 29.4 bits (66), Expect = 1.4
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 90 GWNAACWAFIYDRYEQFIFGNYPM 113
GW+ +C A +Y +FG PM
Sbjct: 19 GWSHSCHAMLYAANPGQLFGRIPM 42
>1p1j_A Inositol-3-phosphate synthase; 1L-MYO-inositol 1-phosphate, NADH,
isomerase, rossmann fold; HET: NAI; 1.70A {Saccharomyces
cerevisiae} SCOP: c.2.1.3 d.81.1.3 PDB: 1jkf_A* 1la2_A*
1p1f_A 1jki_A* 1p1i_A* 1p1h_A* 1p1k_A* 1rm0_A*
Length = 533
Score = 28.7 bits (64), Expect = 2.3
Identities = 8/42 (19%), Positives = 13/42 (30%), Gaps = 7/42 (16%)
Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135
D Y + I + S+L TP++I
Sbjct: 411 SKVAMDEYYSELMLGGHNR-----ISIHNVCEDSLLATPLII 447
>1vko_A Inositol-3-phosphate synthase; CE21227, structural genomics, JCSG,
protein structure initiative, PSI; HET: NAD; 2.30A
{Caenorhabditis elegans} SCOP: c.2.1.3 d.81.1.3
Length = 537
Score = 28.3 bits (63), Expect = 2.9
Identities = 9/42 (21%), Positives = 14/42 (33%), Gaps = 7/42 (16%)
Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135
D Y IF +V T S+L +P++
Sbjct: 413 SKRAMDEYICSIFMGGKQT-----FVVHNTCEDSLLASPLIY 449
>2c1l_A Restriction endonuclease; BFII, domain fusion, hydrolase; HET: TAR
TLA SRT MES; 1.9A {Bacillus firmus}
Length = 358
Score = 27.6 bits (61), Expect = 4.5
Identities = 11/46 (23%), Positives = 20/46 (43%)
Query: 338 VNFSESTWISSVTPTTGLIFIGFVFWIFCFSISLYSVFIEKTLHKG 383
+ E+ W+S+ TP G +++ F + + Y F E G
Sbjct: 20 IGMLENVWVSNHTPGEGTLYLISGFSNYNGGVRFYETFTEHINQGG 65
>1u1i_A INO1, MIPS, MYO-inositol-1-phosphate synthase; NAD cofactor, metal
IONS, isomerase; HET: NAD; 1.90A {Archaeoglobus fulgidus
dsm 4304} SCOP: c.2.1.3 d.81.1.3
Length = 392
Score = 27.5 bits (61), Expect = 4.9
Identities = 5/42 (11%), Positives = 11/42 (26%), Gaps = 7/42 (16%)
Query: 96 WAFIYDRYEQFIFGNYPMAQRWRPILVFLTG--SILLTPMLI 135
+D F M +I+ P+++
Sbjct: 305 NKTAFDFVHFKGFLGKLMK-----FYFIWDAIDAIVAAPLIL 341
>3bjx_A Halocarboxylic acid dehalogenase DEHI; plasmid, hydrolase; 2.30A
{Pseudomonas putida}
Length = 311
Score = 27.6 bits (61), Expect = 5.5
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 222 GVPLVTVLFMASIMLPLFLPDTWD 245
VP V P +LP W
Sbjct: 46 RVPWVAFGCRVLATFPGYLPLAWR 69
>2ci1_A NG, NG-dimethylarginine dimethylaminohydrolase 1; NOS regulation,
S-nitrosylation, zinc, MMA, ADMA, acetylation,
metal-binding; HET: KOR CIT; 1.08A {Bos taurus} PDB:
2c6z_A* 2ci3_A 2ci4_A 2ci5_A* 2ci6_A 2ci7_A 2jaj_A*
2jai_A*
Length = 275
Score = 27.4 bits (60), Expect = 5.9
Identities = 16/110 (14%), Positives = 35/110 (31%), Gaps = 7/110 (6%)
Query: 192 MPLGILLALGRNSNIPVLRYACITFIEL-FRGVPLVTVLFMASIMLPLFLPDTWDVDKLL 250
+ L + +N TF + VP+V L + S P+ +
Sbjct: 127 TGREFFVGLSKRTNQRGAEILADTFKDYAVSTVPVVDALHLKSFCSMAG-PNLIAIGSSE 185
Query: 251 RALLGVSAFASAYIAEVLRGGLQSISKGQFEAANSLGLSYLQKMRLIIMP 300
A + + ++ ++ AAN + L+ K +++
Sbjct: 186 SAQKAL-----KIMQQMSDHRYDKLTVPDDTAANCIYLNIPSKGHVLLHR 230
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.331 0.147 0.466
Gapped
Lambda K H
0.267 0.0568 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 3,435,076
Number of extensions: 160834
Number of successful extensions: 604
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 39
Length of query: 386
Length of database: 5,693,230
Length adjustment: 94
Effective length of query: 292
Effective length of database: 3,414,294
Effective search space: 996973848
Effective search space used: 996973848
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 58 (26.5 bits)