RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780591|ref|YP_003065004.1| aminomethyltransferase protein
(glycine cleavage) [Candidatus Liberibacter asiaticus str. psy62]
(273 letters)
>1vly_A SPOT PR51, unknown protein from 2D-PAGE; 1789265, B2898, unknown
protein from 2D-PAGE (SPOT PR51), structural genomics,
JCSG; HET: MSE; 1.30A {Escherichia coli} SCOP: b.44.2.1
d.250.1.1 PDB: 1nrk_A
Length = 338
Score = 82.0 bits (201), Expect = 1e-16
Identities = 43/294 (14%), Positives = 91/294 (30%), Gaps = 35/294 (11%)
Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65
L + + + G + ++Q +TADV + +A +GK+ + + +
Sbjct: 36 LDDWALATITGADSEKYMQGQVTADVSQMAEDQHLLAAHCDAKGKMWSNLRLFRDGDGFA 95
Query: 66 ILEIDRSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFSI--- 122
+E + L + + I + ++ Q + F +
Sbjct: 96 WIERRSVREPQLTELKKYAVFSKVTIAPDDERVLLGVAGFQARAALANLFSELPSKEKQV 155
Query: 123 ------------------------ADVLLHRTWGHNEKIASDIKTYHELRINHGIVDPNT 158
A + E ++ + + L I G +
Sbjct: 156 VKEGATTLLWFEHPAERFLIVTDEATANMLTDKLRGEAELNNSQQWLALNIEAGFPVID- 214
Query: 159 DFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIITGTDD-LPPSG 217
P + L GIS KGCY GQE+V+R + R ++ ++ G+ LP +G
Sbjct: 215 AANSGQFIPQATNLQALGGISFKKGCYTGQEMVARAKFRGANKRALWLLAGSASRLPEAG 274
Query: 218 SPILT----DDIEIGTL--GVVVGKKALAIARIDKVDHAIKKGMALTVHGVRVK 265
+ + GT+ V + + + + D + +
Sbjct: 275 EDLELKMGENWRRTGTVLAAVKLEDGQVVVQVVMNNDMEPDSIFRVRDDANTLH 328
>1pj5_A N,N-dimethylglycine oxidase; channelling, FAD binding, folate
binding, amine oxidase, oxidoreductase; HET: FAD; 1.61A
{Arthrobacter globiformis} SCOP: b.44.2.1 c.3.1.2
d.16.1.5 d.250.1.1 PDB: 1pj6_A* 1pj7_A* 3gsi_A*
Length = 830
Score = 56.8 bits (136), Expect = 5e-09
Identities = 36/198 (18%), Positives = 67/198 (33%), Gaps = 12/198 (6%)
Query: 75 DSLIDKLLFYKLRSNVIIEIQPINGVVLSWNQEHTFSNSSFIDERFSIADVLLHRTWGHN 134
D + L Y NV+I P+ + LS+ E + + D + D L
Sbjct: 622 DDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFG 681
Query: 135 EKIASDIKTYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRI 194
A + LR+ G TD P +A + + + K +IG+ +
Sbjct: 682 VIAAG-RAAFSSLRLEKGYRSWGTDMTTEHD-PFEAGLGFA--VKMAKESFIGKGALEGR 737
Query: 195 QHRNIIRK-RPMIITGTDDLPPSGSPILTDDIEIG-----TLGVVVGKKALAIARIDKVD 248
R+ R + I + P+ + +G G V K +A + +
Sbjct: 738 TEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVA-KPIAYSYLPG-T 795
Query: 249 HAIKKGMALTVHGVRVKA 266
++ + + G R+ A
Sbjct: 796 VSVGDSVDIEYFGRRITA 813
>2gag_A Heterotetrameric sarcosine oxidase alpha-subunit; flavoenzyme,
electron transfer, folate- methylating enzyme,
oxidoreductase; HET: NAD FAD FMN; 1.85A
{Stenotrophomonas maltophilia} PDB: 2gah_A* 1x31_A*
1vrq_A*
Length = 965
Score = 48.0 bits (113), Expect = 2e-06
Identities = 27/138 (19%), Positives = 48/138 (34%), Gaps = 18/138 (13%)
Query: 143 TYHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRK 202
T H LR G + D + P DA M+ + +S K +IG SR + RK
Sbjct: 815 TMHVLRAEKGFIIVGQDTDGTVT-PQDAGMEWV--VSKLKD-FIGNRSYSRADNAREDRK 870
Query: 203 R--PMIITGTDDLPPSGSPILTDD-IEIGTLGVVVG-----------KKALAIARIDKVD 248
+ ++ P G+ ++ D + + + G + +A I
Sbjct: 871 QLVSVLPVDKSLRLPEGAALVASDALASEGITPMEGWVTSSYDSPNLGRTFGLALIKNGR 930
Query: 249 HAIKKGMALTVHGVRVKA 266
+ I + + V V
Sbjct: 931 NRIGEVLKTPVGDQLVDV 948
>1yx2_A Aminomethyltransferase; glycine cleavage system T protein,
alpha-beta, beta-barrel, structural genomics, PSI,
protein structure initiative; 2.08A {Bacillus subtilis}
Length = 365
Score = 44.1 bits (103), Expect = 4e-05
Identities = 50/316 (15%), Positives = 96/316 (30%), Gaps = 51/316 (16%)
Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65
+S+ ++V G ++ FLQ ++T DV L A+ +A+ P G + LI + E+ +
Sbjct: 52 VSHMGEVEVSGNDSLSFLQRLMTNDVSALTPGRAQYTAMCYPDGGTVDDLLIYQKGENRY 111
Query: 66 ILEIDRSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSWNQEH--------------TFS 111
+L I+ S D + + + I ++ +
Sbjct: 112 LLVINASNIDKDLAWMKEHAAGDVQIDNQSDQIALLAVQGPKAEAILKNLTDADVSALKP 171
Query: 112 NSSFIDERFSIADVLLHRT-------------WGHNEKIASDIK--------------TY 144
+ + S L+ RT I I
Sbjct: 172 FAFIDEADISGRKALISRTGYTGEDGYEIYCRSDDAMHIWKKIIDAGDAYGLIPCGLGAR 231
Query: 145 HELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRP 204
LR I + + + + G+ V+S + RK
Sbjct: 232 DTLRFEANIPLYGQEL--TRDITPIEAGIGFAVKHKKESDFFGKSVLSEQKENGAKRKLV 289
Query: 205 MIITGTDDLPPSGSPILTDDIEIGTL-----GVVVGKKALAIARIDKVDHAIKKGMALTV 259
+ +P G + + +G + +G K + +A ID I + + +
Sbjct: 290 GLEMIEKGIPRHGYEVFQNGKSVGKVTTGTQSPTLG-KNVGLALIDSETSEIGTVVDVEI 348
Query: 260 HGVRVKASF--PHWYK 273
VKA +YK
Sbjct: 349 RKKLVKAKVVKTPFYK 364
>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 = 43.8 bits (103), Expect = 4e-05
Identities = 39/191 (20%), Positives = 60/191 (31%), Gaps = 80/191 (41%)
Query: 108 HTFSNSSFIDERF--SIADVL--LHRTWGHNEKIASDIKTYHELRINHGIVD-------- 155
T+ + A+ L L RT D + G+ +
Sbjct: 178 QTYH--VLV-GDLIKFSAETLSELIRT-------TLDAEKVF----TQGL-NILEWLENP 222
Query: 156 ---PNTDFLPST-I-FPHDALMDLLNG-ISLTKGCYIGQEVVSRI--QHRNIIRKRPMII 207
P+ D+L S I P L G I L Y+ V +++ +R +
Sbjct: 223 SNTPDKDYLLSIPISCP-------LIGVIQLAH--YV---VTAKLLGFTPGELRSY---L 267
Query: 208 TGTDDLPPSG-SPILTDDIEIGTLGVVVGKKALAIARIDK----VDHAIKKGMALTVH-- 260
G +G S G+V A+AIA D K A+TV
Sbjct: 268 KGA-----TGHSQ-----------GLVT---AVAIAETDSWESFFVSVRK---AITVLFF 305
Query: 261 -GVRVKASFPH 270
GVR ++P+
Sbjct: 306 IGVRCYEAYPN 316
Score = 27.6 bits (61), Expect = 2.8
Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 18/93 (19%)
Query: 7 SNQSFIKVC-GKSAIPFLQAIITADVLTLPY---KIARGSAILTPQGKILLYFLISKIEE 62
SN I + G+ A F Q L Y ++ + + L +I+ Y +E
Sbjct: 1805 SNYGMIAINPGRVAASFSQE-------ALQYVVERVGKRTGWLV---EIVNY----NVEN 1850
Query: 63 DTFILEIDRSKRDSLIDKLLFYKLRSNVIIEIQ 95
++ D D++ + L F KL+ IIE+Q
Sbjct: 1851 QQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQ 1883
>1v5v_A Aminomethyltransferase; glycine-cleavage sytem, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; 1.50A {Pyrococcus horikoshii} SCOP:
b.44.2.1 d.250.1.1
Length = 401
Score = 41.8 bits (97), Expect = 2e-04
Identities = 26/137 (18%), Positives = 50/137 (36%), Gaps = 17/137 (12%)
Query: 143 TYHELRINHGIVDPNTDFLPSTIFPHDALM------DLLNGISLTKGCYIGQEVVSRIQH 196
LR+ G + + D +L I K +IG++ + + +
Sbjct: 250 ARDTLRLEAGYTLYGNETKELQLLSTDIDEVTPLQANLEFAIYWDKD-FIGKDALLKQKE 308
Query: 197 RNIIRKRPMIITGTDDLPPSGSPILTDDIEIGTL-----GVVVGKKALAIARIDKVDHAI 251
R + RK +P G + + IG + ++ + IA + + ++A
Sbjct: 309 RGVGRKLVHFKMIDKGIPREGYKVYANGEMIGEVTSGTLSPLLN-VGIGIAFVKE-EYA- 365
Query: 252 KKGMALTVH--GVRVKA 266
K G+ + V G R KA
Sbjct: 366 KPGIEIEVEIRGQRKKA 382
>1wsr_A Aminomethyltransferase; glycine-cleavage sytem; 2.00A {Homo
sapiens} PDB: 1wsv_A*
Length = 375
Score = 30.8 bits (68), Expect = 0.31
Identities = 39/309 (12%), Positives = 93/309 (30%), Gaps = 50/309 (16%)
Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65
+S+ K+ G + +++++ D+ L S G IL +++ E
Sbjct: 53 VSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHL 112
Query: 66 ILEID---RSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLS---------------WNQE 107
+ + K +L+ + + ++ ++ +L+ +
Sbjct: 113 YVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLR 172
Query: 108 HTFSNSSFIDERFSIADVLLHRT------------------------WGHNEKIASDIKT 143
+S + E F ++ + R + E + +
Sbjct: 173 KLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAA 232
Query: 144 YHELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKR 203
LR+ G+ D T +L L + G +V+ + R+R
Sbjct: 233 RDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAMDFPGAKVIVPQLKGRVQRRR 292
Query: 204 PMIITGTDDLPPSGSPILTDDIEIGTLGVVVG------KKALAIARIDKVDHAIKKGMAL 257
++ + + + +IGT V G KK +A+ + + +
Sbjct: 293 VGLMCEGAPMRAHSPILNMEGTKIGT--VTSGCPSPSLKKNVAMGYVPCEYSRPGTMLLV 350
Query: 258 TVHGVRVKA 266
V + A
Sbjct: 351 EVRRKQQMA 359
>1ee0_A 2-pyrone synthase; polyketide synthase, thiolase fold, transferase;
HET: CAA; 2.05A {Gerbera hybrid cultivar} SCOP: c.95.1.2
c.95.1.2 PDB: 1qlv_A
Length = 402
Score = 29.7 bits (66), Expect = 0.79
Identities = 17/103 (16%), Positives = 33/103 (32%), Gaps = 12/103 (11%)
Query: 161 LPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIIT-GTDDLPPSGSP 219
P D ++ ++ +E RI + I+KR + +T P+
Sbjct: 31 TPPNCVAQADYADYYFRVTKSEHMVDLKEKFKRICEKTAIKKRYLALTEDYLQENPTMCE 90
Query: 220 ILTDDI---------EIGTLGVVVGKKALAIARIDK--VDHAI 251
+ + + LG KA+ + K + H I
Sbjct: 91 FMAPSLNARQDLVVTGVPMLGKEAAVKAIDEWGLPKSKITHLI 133
>1l5j_A Aconitate hydratase 2; molecular recognition, RNA binding, citric
acid cycle, heat- like domain, lyase; HET: TRA; 2.40A
{Escherichia coli} SCOP: a.118.15.1 c.8.2.1 c.83.1.1
Length = 865
Score = 28.0 bits (62), Expect = 2.7
Identities = 15/57 (26%), Positives = 22/57 (38%)
Query: 208 TGTDDLPPSGSPILTDDIEIGTLGVVVGKKALAIARIDKVDHAIKKGMALTVHGVRV 264
T TDDL P+ DI + L ++ + V IK+ AL G +
Sbjct: 177 TNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPL 233
>2efj_A 3,7-dimethylxanthine methyltransferase; SAM-dependant
methyltransferase, SAH, theobromine; HET: SAH 37T; 2.00A
{Coffea canephora} PDB: 2eg5_A*
Length = 384
Score = 26.9 bits (59), Expect = 5.8
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 192 SRIQHRNIIRKRPMIITGTDDLPPSGSPILTDDIEIGTLGVVVGKKALAIARIDKVDHAI 251
S +IR +P++ +L + P + ++G LG G + + + +I
Sbjct: 22 SSYN-LFLIRVKPVLEQCIQELLRANLPNINKCFKVGDLGCASGPNTFST--VRDIVQSI 78
Query: 252 KK 253
K
Sbjct: 79 DK 80
>3oit_A OS07G0271500 protein; type III polyketide synthases, transferase;
2.00A {Oryza sativa}
Length = 387
Score = 26.7 bits (58), Expect = 6.4
Identities = 14/99 (14%), Positives = 33/99 (33%), Gaps = 10/99 (10%)
Query: 160 FLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPM-----IITGTDDLP 214
P + + D ++ + ++ RI +++R + +++ +
Sbjct: 19 ANPPNCVTQEEIPDFYFRVTNSDHLTALKDKFKRICQEMGVQRRYLHHTEEMLSAHPEFV 78
Query: 215 PSGSPILTDDIEIGT-----LGVVVGKKALAIARIDKVD 248
+P L ++I L KKA+A D
Sbjct: 79 DRDAPSLDARLDIAADAVPELAAEAAKKAIAEWGRPAAD 117
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
0.323 0.140 0.410
Gapped
Lambda K H
0.267 0.0501 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,450,464
Number of extensions: 117448
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 18
Length of query: 273
Length of database: 5,693,230
Length adjustment: 91
Effective length of query: 182
Effective length of database: 3,487,026
Effective search space: 634638732
Effective search space used: 634638732
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (25.9 bits)