RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12057
(172 letters)
>1wsr_A Aminomethyltransferase; glycine-cleavage sytem; 2.00A {Homo
sapiens} PDB: 1wsv_A*
Length = 375
Score = 176 bits (449), Expect = 8e-55
Identities = 55/110 (50%), Positives = 70/110 (63%)
Query: 61 GKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSGCP 120
GKRRR FPGA +I Q+K V R+R GL G P+R I N ++G +TSGCP
Sbjct: 265 GKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCP 324
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHTP 170
SPSLKKN+AMGY+ YS+ G L V VR K+ V+KMPF+ +NY+T
Sbjct: 325 SPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTL 374
>3gir_A Aminomethyltransferase; glycine cleavage system, aminotransferase,
structural genomics; 1.60A {Bartonella henselae}
Length = 393
Score = 167 bits (426), Expect = 3e-51
Identities = 37/109 (33%), Positives = 55/109 (50%), Gaps = 1/109 (0%)
Query: 61 GKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTG-VPIRPGYEIFNANDQRVGAITSGC 119
K RE F GA ++ G SR R GL PIR G +F+ R+G +TSG
Sbjct: 283 PKNVREKAQFYGAKAFLESLQKGPSRCRVGLKPQTRQPIRAGAVLFDNEGNRIGVVTSGG 342
Query: 120 PSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYH 168
PS +AMGY+ A+ G E++ +R K++ + V +PF++ Y
Sbjct: 343 FGPSFDGPVAMGYVPVAWKVEGTEVFTELRGKKIALSVHSLPFVEQRYF 391
>1v5v_A Aminomethyltransferase; glycine-cleavage sytem, structural riken
structural genomics/proteomics initiative, RSGI; 1.50A
{Pyrococcus horikoshii} SCOP: b.44.2.1 d.250.1.1
Length = 401
Score = 130 bits (328), Expect = 7e-37
Identities = 30/102 (29%), Positives = 48/102 (47%), Gaps = 2/102 (1%)
Query: 69 GFPGASIIQSQIKSGVSRKRTGLTSTGVPI-RPGYEIFNANDQRVGAITSGCPSPSLKKN 127
F G + Q + GV RK I R GY+++ AN + +G +TSG SP L
Sbjct: 296 DFIGKDALLKQKERGVGRKLVHFKMIDKGIPREGYKVY-ANGEMIGEVTSGTLSPLLNVG 354
Query: 128 IAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNYHT 169
I + +++ Y+K G+E+ V +R +R PF +
Sbjct: 355 IGIAFVKEEYAKPGIEIEVEIRGQRKKAVTVTPPFYDPKKYG 396
>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 = 124 bits (315), Expect = 4e-35
Identities = 39/104 (37%), Positives = 59/104 (56%), Gaps = 4/104 (3%)
Query: 63 RRRETGGFPGASIIQSQIKSGVSRKRTGLTST--GVPIRPGYEIFNANDQRVGAITSGCP 120
+ ++ F G S++ Q ++G RK GL G+P R GYE+F N + VG +T+G
Sbjct: 263 KHKKESDFFGKSVLSEQKENGAKRKLVGLEMIEKGIP-RHGYEVF-QNGKSVGKVTTGTQ 320
Query: 121 SPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLK 164
SP+L KN+ + I+ S++G + V +R K V KV K PF K
Sbjct: 321 SPTLGKNVGLALIDSETSEIGTVVDVEIRKKLVKAKVVKTPFYK 364
>3ttg_A Putative aminomethyltransferase; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG; 2.00A
{Leptospirillum rubarum}
Length = 355
Score = 113 bits (284), Expect = 8e-31
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 8/101 (7%)
Query: 68 GGFPGASIIQSQIKSG-VSRKRTGLTSTGVPI-RPGYEIF---NANDQRVGAITSGCPSP 122
G + G + G ++R G G P + + + + G +T S
Sbjct: 258 GCYVGQEPVTRLKFQGHLNRSLAGFRLEGGPFPKMEFPVTLFNPKDGNEAGILTRTSSSD 317
Query: 123 SLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFL 163
L I +GYI+ +S+ G EL + V+V +PF+
Sbjct: 318 ILGSGIGLGYIKRNFSENGTELLL---PDAQLVRVHSLPFV 355
>1vlo_A Aminomethyltransferase; NP417381, tetrahydrofolat dependent) of
glycine cleavage system, structural genomics, protein
structure initiative; HET: MSE; 1.70A {Escherichia coli
K12} SCOP: b.44.2.1 d.250.1.1 PDB: 3a8j_A* 3a8i_A*
3a8k_A*
Length = 381
Score = 111 bits (281), Expect = 5e-30
Identities = 31/109 (28%), Positives = 48/109 (44%), Gaps = 10/109 (9%)
Query: 62 KRRRETGGFPGASIIQSQIKSGVSRKRTGLTST--GVPIRPGYEIFN---ANDQRVGAIT 116
F G ++ Q + G K GL T GV R + +Q G IT
Sbjct: 268 AWEPADRDFIGREALEVQREHGT-EKLVGLVMTEKGVL-RNELPVRFTDAQGNQHEGIIT 325
Query: 117 SGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKS 165
SG SP+L +IA+ + G V++R++ + VKVTK F+++
Sbjct: 326 SGTFSPTLGYSIALARVPEGI---GETAIVQIRNREMPVKVTKPVFVRN 371
>3tfi_A GCVT-like aminomethyltransferase protein; demethylase, THF; 1.60A
{Candidatus pelagibacter ubique} PDB: 3tfh_A 3tfj_A*
Length = 369
Score = 108 bits (272), Expect = 6e-29
Identities = 21/96 (21%), Positives = 44/96 (45%), Gaps = 2/96 (2%)
Query: 70 FPGASIIQSQIKSGVSRKRTGLTSTGVPI-RPGYE-IFNANDQRVGAITSGCPSPSLKKN 127
F G ++ G +K G+ I G + I++ N+ +G + S C SP +K
Sbjct: 274 FLGKEKLKEIKLKGPQKKLRGVKIDIKEISLTGSKNIYDENNNVIGELRSACYSPHFQKV 333
Query: 128 IAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFL 163
I + I+ ++ + +++ D ++ V +PF+
Sbjct: 334 IGIAMIKKSHWEASQGFKIQINDNTINGNVCDLPFI 369
>1wos_A Aminomethyltransferase; T-protein; 1.84A {Thermotoga maritima}
SCOP: b.44.2.1 d.250.1.1 PDB: 1woo_A* 1wop_A* 1wor_A
Length = 364
Score = 106 bits (266), Expect = 5e-28
Identities = 32/101 (31%), Positives = 45/101 (44%), Gaps = 5/101 (4%)
Query: 69 GFPGASIIQSQIKSGVSRKRTGLTST--GVPIRPGYEIFNANDQRVGAITSGCPSPSLKK 126
F G + K V RK L + + R GYE+ N +RVG ITSG SP+L K
Sbjct: 263 DFVGKEALLKA-KEKVERKLVALELSGKRIA-RKGYEVLK-NGERVGEITSGNFSPTLGK 319
Query: 127 NIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPFLKSNY 167
+IA+ + + V K V+ V K PF + +
Sbjct: 320 SIALALVSKSVKIGDQLGVVFPGGKLVEALVVKKPFYRGSV 360
>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 = 62.8 bits (153), Expect = 3e-12
Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 4/101 (3%)
Query: 64 RRETGGFPGASIIQSQIKSGVSRKRTGLT-STGVPIRPGYE-IFNANDQRVGAITSGCPS 121
+ F G ++ + + +R+ LT G I G E +F +Q VG +TS
Sbjct: 722 KMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVF-YKEQAVGYVTSAAYG 780
Query: 122 PSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKVTKMPF 162
++ K IA Y+ P VG + + +R+ VT+ P
Sbjct: 781 YTVAKPIAYSYL-PGTVSVGDSVDIEYFGRRITATVTEDPL 820
>2gag_A Heterotetrameric sarcosine oxidase alpha-subunit; flavoenzyme,
electron transfer, folate-ME enzyme, oxidoreductase;
HET: NAD FAD FMN; 1.85A {Stenotrophomonas maltophilia}
PDB: 2gah_A* 1x31_A* 1vrq_A* 3ad7_A* 3ad8_A* 3ad9_A*
3ada_A*
Length = 965
Score = 56.5 bits (136), Expect = 5e-10
Identities = 15/65 (23%), Positives = 27/65 (41%)
Query: 98 IRPGYEIFNANDQRVGAITSGCPSPSLKKNIAMGYIEPAYSKVGVELWVRVRDKRVDVKV 157
+ G +TS SP+L + + I+ +++G L V D+ VDV V
Sbjct: 891 VASDALASEGITPMEGWVTSSYDSPNLGRTFGLALIKNGRNRIGEVLKTPVGDQLVDVVV 950
Query: 158 TKMPF 162
++
Sbjct: 951 SETVL 955
>3qwd_A ATP-dependent CLP protease proteolytic subunit; caseinolytic
protease, serin-protease, hydrolase; 2.10A
{Staphylococcus aureus subsp} PDB: 3v5e_A 3v5i_A 3sta_V
3st9_A
Length = 203
Score = 26.7 bits (60), Expect = 3.1
Identities = 10/17 (58%), Positives = 10/17 (58%), Gaps = 4/17 (23%)
Query: 49 AMDIYSRLL----IFPG 61
A DIYSRLL I G
Sbjct: 17 AYDIYSRLLKDRIIMLG 33
>1y7o_A ATP-dependent CLP protease proteolytic subunit; hydrolase; 2.51A
{Streptococcus pneumoniae} SCOP: c.14.1.1
Length = 218
Score = 26.4 bits (59), Expect = 4.1
Identities = 8/17 (47%), Positives = 9/17 (52%), Gaps = 4/17 (23%)
Query: 49 AMDIYSRLL----IFPG 61
+ DIYSRLL I
Sbjct: 35 SYDIYSRLLKDRIIMLT 51
>3p2l_A ATP-dependent CLP protease proteolytic subunit; structural
genomics, center for structural genomics of infec
diseases, csgid; 2.29A {Francisella tularensis subsp}
Length = 201
Score = 26.3 bits (59), Expect = 4.1
Identities = 9/17 (52%), Positives = 10/17 (58%), Gaps = 4/17 (23%)
Query: 49 AMDIYSRLL----IFPG 61
A DIYSRLL +F
Sbjct: 20 AFDIYSRLLKERIVFLN 36
>1yg6_A ATP-dependent CLP protease proteolytic subunit; endopeptidase
CLP, caseinolytic protease, protease TI, heat shock
protein F21.5, hydrolase; 1.90A {Escherichia coli}
SCOP: c.14.1.1 PDB: 1tyf_A 2fzs_A* 3mt6_R 1yg8_A 3hln_A
2zl2_A 2zl0_A 2zl4_A 2zl3_A 3tt7_A* 3tt6_A 3ktg_A
3kth_A 3kti_A* 3ktj_A* 3ktk_A* 3q7h_A
Length = 193
Score = 26.3 bits (59), Expect = 4.7
Identities = 9/17 (52%), Positives = 10/17 (58%), Gaps = 4/17 (23%)
Query: 49 AMDIYSRLL----IFPG 61
+ DIYSRLL IF
Sbjct: 16 SFDIYSRLLKERVIFLT 32
>2f6i_A ATP-dependent CLP protease, putative; structural genomics,
structural genomics conso SGC, hydrolase; 2.45A
{Plasmodium falciparum} SCOP: c.14.1.1
Length = 215
Score = 26.4 bits (59), Expect = 4.9
Identities = 2/17 (11%), Positives = 4/17 (23%), Gaps = 4/17 (23%)
Query: 49 AMDIYSRLL----IFPG 61
D+ I+
Sbjct: 29 KKDVKLFFFKKRIIYLT 45
>1tg6_A Putative ATP-dependent CLP protease proteolytic S; mitochondrial
CLPP, CLP/HSP 100, ATP-dependent protease, HYD; HET:
FME; 2.10A {Homo sapiens} SCOP: c.14.1.1
Length = 277
Score = 26.2 bits (58), Expect = 5.8
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 49 AMDIYSRLL 57
A DIYSRLL
Sbjct: 72 AYDIYSRLL 80
>1dkq_A Phytase; histidine acid phosphatase fold, hydrolase; HET: IHP;
2.05A {Escherichia coli} SCOP: c.60.1.2 PDB: 1dkp_A*
1dkm_A 1dkn_A 1dko_A 1dkl_A
Length = 410
Score = 26.1 bits (56), Expect = 7.8
Identities = 20/163 (12%), Positives = 45/163 (27%), Gaps = 23/163 (14%)
Query: 1 MSCPWTVVWVLISIHNM--CFKFQPIAWLSTHSMAIKTSSVNTILLELFLAMDIYSRLLI 58
++ ++ +L I + W L + LL
Sbjct: 207 LTGAVSLASMLTEIFLLQQAQGMPEPGWGRITDSHQ--------WNTLLSLHNAQFYLLQ 258
Query: 59 FPGKRRRETGGFPGASIIQSQIKSGVSRKRTGLTSTGVPIRPGYEIFNANDQRVGAITSG 118
+ R IK+ ++ + GV + +D + +
Sbjct: 259 RTPEVARSRATPLL-----DLIKTALTPHPPQKQAYGVTLPTSVLFIAGHDTNLANLGG- 312
Query: 119 CPSPSLK-KNIAMGYIE--PAYSKVGVELWVRVRDKRVDVKVT 158
+L+ G + P ++ E W R+ D ++V+
Sbjct: 313 ----ALELNWTLPGQPDNTPPGGELVFERWRRLSDNSQWIQVS 351
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
0.322 0.136 0.422
Gapped
Lambda K H
0.267 0.0785 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,589,116
Number of extensions: 141240
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 167
Number of HSP's successfully gapped: 18
Length of query: 172
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 85
Effective length of database: 4,272,666
Effective search space: 363176610
Effective search space used: 363176610
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: 54 (24.5 bits)