RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5756
(360 letters)
>2zkr_n 60S ribosomal protein L5; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 297
Score = 343 bits (881), Expect = e-118
Identities = 168/227 (74%), Positives = 202/227 (88%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
MGFVKVVKNK YFKRYQVKF+RRREGKTDYYARKRL++QDKNKYNTPKYR+IVR +N+DI
Sbjct: 1 MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYV 164
CQ+AY+RIEGD I+C+ Y+HELPKYG+KVGLTNYAAAY TGLLLARRLL +D++Y
Sbjct: 61 ICQIAYARIEGDMIVCARYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G EVTG+E++VES+D PGAF CYLD GL +T+TG KVFGA+KGAVDGGL+IPHS KRF
Sbjct: 121 GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF 180
Query: 225 PGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSERV 271
PGYD+ESK+FNAE+HRKHI G +VA+YMR L EED++A+K+QFS+ +
Sbjct: 181 PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYI 227
>3u5e_D 60S ribosomal protein L5; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 3u5i_D 3izc_Q 3izs_Q
3o58_E 3o5h_E 3jyw_E 1s1i_E
Length = 297
Score = 337 bits (865), Expect = e-116
Identities = 129/225 (57%), Positives = 167/225 (74%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
M F K K+ Y R+Q F+RRREGKTDYY RKRL+ Q K KYNTPKYRL+VRF+NKDI
Sbjct: 1 MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYV 164
CQ+ S I GD ++ +AYSHELP+YGI GLTN+AAAYATGLL+ARR L+ L LD Y
Sbjct: 61 ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G EV GE E+V+ GP F+ +LD+GL +T+TGA+VFGA+KGA DGGL +PHS RF
Sbjct: 121 GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF 180
Query: 225 PGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
PG+D E+++ + E+ R +IFG HV++YM +L+++D+E F F
Sbjct: 181 PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKG 225
>4a17_M RPL5, 60S ribosomal protein L5; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_M 4a1c_M 4a1e_M
Length = 301
Score = 335 bits (860), Expect = e-115
Identities = 126/230 (54%), Positives = 168/230 (73%), Gaps = 5/230 (2%)
Query: 45 MGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDI 104
MGFVKV+K K YFKR+Q K++RRREG TDYYARKRLI+QDK+KYNTPKYRL+ R +N I
Sbjct: 1 MGFVKVLKTKAYFKRFQTKYRRRREGLTDYYARKRLIIQDKDKYNTPKYRLVARATNTRI 60
Query: 105 TCQVAYSRIEGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYV 164
Q+ Y+ ++ D ++C+A S+EL ++G+ GL +YAAAYATGLLLARRLLK + LD +Y
Sbjct: 61 IAQIVYATLKCDRVLCAADSYELKRFGVSTGLASYAAAYATGLLLARRLLKQIGLDTVYA 120
Query: 165 GCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRF 224
G T+V G F+V+ K F+ LD GL++T+TG +VFG +KGA DGG+NIPHS RF
Sbjct: 121 GQTKVDGAYFNVDEDQKEKKPFKAILDAGLVRTTTGNRVFGVLKGACDGGINIPHSESRF 180
Query: 225 PGY-----DNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
PGY + ES + E H+ IFG H+ YM+ L + +EAF++QFS+
Sbjct: 181 PGYVRASDEGESSKYKPEDHKARIFGKHIDAYMKHLKGQSNEAFQKQFSK 230
>3iz5_Q 60S ribosomal protein L5 (L18P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_Q
Length = 304
Score = 325 bits (834), Expect = e-111
Identities = 137/227 (60%), Positives = 172/227 (75%), Gaps = 4/227 (1%)
Query: 43 LEMGFVKVVKNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNK 102
L+ GFVK K YFKR+QVKFKRRR+GKTDY AR RL QDKNKYNTPKYR +NK
Sbjct: 3 LQGGFVKTQKTHAYFKRFQVKFKRRRQGKTDYRARIRLTNQDKNKYNTPKYR---FVTNK 59
Query: 103 DITCQVAYSRIEGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRL 162
DIT Q+ Y+ I GD ++ +AYSHELP+YG++VGLTNYAAAY TGLLLARR+L LD+
Sbjct: 60 DITAQIVYATIAGDIVMAAAYSHELPRYGLEVGLTNYAAAYCTGLLLARRVLTLRGLDQE 119
Query: 163 YVGCTEVTGEEFSVESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVK 222
Y G E TGE++ VE D FR LDVGL++T+TG +VFGA+KGA+DGGL+IPHS K
Sbjct: 120 YEGNVEATGEDYYVEPAD-ERRPFRALLDVGLIRTTTGNRVFGALKGALDGGLDIPHSDK 178
Query: 223 RFPGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
RF G+ + K +++IHRK+I+G HVA+YMR ++EE+ E F+ FSE
Sbjct: 179 RFAGFKKDEKQLDSDIHRKYIYGGHVADYMRSMAEEEPEKFQAHFSE 225
>1vq8_N 50S ribosomal protein L18P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.55.4.1 PDB: 1vq4_N*
1vq5_N* 1vq6_N* 1vq7_N* 1s72_N* 1vq9_N* 1vqk_N* 1vql_N*
1vqm_N* 1vqn_N* 1vqo_N* 1vqp_N* 1yhq_N* 1yi2_N* 1yij_N*
1yit_N* 1yj9_N* 1yjn_N* 1yjw_N* 2otj_N* ...
Length = 187
Score = 223 bits (570), Expect = 8e-73
Identities = 65/220 (29%), Positives = 90/220 (40%), Gaps = 53/220 (24%)
Query: 56 YFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRIEG 115
RY+V +RRRE +TDY+ R RL+ + K RL+ R SNK + Q+ G
Sbjct: 3 TGPRYKVPMRRRREARTDYHQRLRLL-------KSGKPRLVARKSNKHVRAQLVTLGPNG 55
Query: 116 DHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLARRLLKNLNLDRLYVGCTEVTGEEFS 175
D + SA+S +L +YG + N +AY TGLL R +
Sbjct: 56 DDTLASAHSSDLAEYGWEAPTGNMPSAYLTGLLAGLRAQE-------------------- 95
Query: 176 VESVDKGPGAFRCYLDVGLMKTSTGAKVFGAMKGAVDGGLNIPHSVKRFPGYDNESKDFN 235
G LD+GL + G+KVF +GA+D GL+IPH+ +
Sbjct: 96 -------AGVEEAVLDIGLNSPTPGSKVFAIQEGAIDAGLDIPHNDDVLADWQ------- 141
Query: 236 AEIHRKHIFGLHVAEYMRQLSEE------DDEAFKRQFSE 269
G H+AEY QL E D F E
Sbjct: 142 ------RTRGAHIAEYDEQLEEPLYSGDFDAADLPEHFDE 175
>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 = 36.4 bits (83), Expect = 0.015
Identities = 51/382 (13%), Positives = 106/382 (27%), Gaps = 142/382 (37%)
Query: 9 DSSLLQSLQTCDLPFGLRCPEKRVFRSLKSFFKPLEMGFVKVVKNKQYFKRYQVKFKRRR 68
++L+ LQ L + + + S +++ + + +R K +
Sbjct: 195 PETVLEMLQK--LLYQIDPN----WTSRSDHSSNIKLRIHSI---QAELRRL---LKSKP 242
Query: 69 EGKTDYYARKRLI---VQDKNKYNTPKYRLIVR-FSNKDITCQV---------------- 108
Y L+ VQ+ F +++C++
Sbjct: 243 ------YENCLLVLLNVQNAK---------AWNAF---NLSCKILLTTRFKQVTDFLSAA 284
Query: 109 AYSRIEGDHI-----------ICSAY----SHELPKYGIKVG---LTNYAAAYATGLLLA 150
+ I DH + Y +LP+ + L+ A + GL
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
Query: 151 RRLLKNLNLDRLYVGCTEVTGEEFSVESVDKGPGAFR-CYLDVGLMKTSTGAKVFGAMKG 209
K++N D+L T + E S+ ++ P +R + + VF
Sbjct: 345 DNW-KHVNCDKL----TTII--ESSLNVLE--PAEYRKMFDRLS---------VF--PPS 384
Query: 210 AVDGGLNIPHSVKRFPGYDNESKDFNAEIHRKHIFGLHVAEYMRQLSEEDDEAFKRQFSE 269
A +IP + L + + + D + +
Sbjct: 385 A-----HIPTIL------------------------LSL--IWFDVIKSDVMVVVNKLHK 413
Query: 270 RVGGWGTLSEQLGMTKSSFKCEKLWI--VYFCVGI-GENLACLHDISCRLYKLRKKIKNS 326
+ + K + I +Y + + EN LH Y + K +
Sbjct: 414 Y-----------SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSD 462
Query: 327 NFPPTLHAKSPTMSYDGPVHNH 348
+ P D ++H
Sbjct: 463 DLIPP--------YLDQYFYSH 476
>3r8s_O 50S ribosomal protein L18; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
3fik_O 2wwq_O 3oat_O* 3oas_O* 3ofd_O 3ofc_O 3ofr_O*
3ofz_O* 3og0_O 3ofq_O 3r8t_O 3i1n_O 1p85_M 1p86_M 1vs8_O
1vs6_O 2aw4_O 2awb_O 1vt2_O 2i2v_O ...
Length = 116
Score = 32.1 bits (74), Expect = 0.067
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 6/68 (8%)
Query: 90 TPKYRLIVRFSNKDITCQVAYSRI--EGDHIICSAYSHELPKYGIKVGLTNYAAAYATGL 147
RL+V + + I QV I G ++ +A + E N AA A G
Sbjct: 20 LGATRLVVHRTPRHIYAQV----IAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGK 75
Query: 148 LLARRLLK 155
+A R L+
Sbjct: 76 AVAERALE 83
>2zjr_L 50S ribosomal protein L18; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.55.4.1 PDB: 1sm1_M* 2zjp_L* 2zjq_L
1nkw_M 3cf5_L* 3dll_L* 3pio_L* 3pip_L* 1nwy_M* 1nwx_M*
1xbp_M* 1pnu_M 1pny_M 1vor_P 1vou_P 1vow_P 1voy_P 1vp0_P
Length = 114
Score = 30.6 bits (70), Expect = 0.21
Identities = 20/90 (22%), Positives = 31/90 (34%), Gaps = 15/90 (16%)
Query: 71 KTDYYARKRLIVQDKNKY---NTPKYRLIVRFSNKDITCQVAYSRI--EGDHIICSAYSH 125
T R++L + K + + + RL V S+K I Q+ I + +A S
Sbjct: 2 ATATTIRRKLRTRRKVRTTTAASGRLRLSVYRSSKHIYAQI----IDDSRGQTLAAASSA 57
Query: 126 ELPKYGIKVGLTNYAAAYATGLLLARRLLK 155
L A A G LA +
Sbjct: 58 ALKSGN------KTDTAAAVGKALAAAAAE 81
>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 161
Score = 31.2 bits (71), Expect = 0.24
Identities = 16/66 (24%), Positives = 25/66 (37%), Gaps = 8/66 (12%)
Query: 94 RLIVRFSNKDITCQVAYSRI--EGDHIICSAYSHE--LPKYGIKVGLTNYAAAYATGLLL 149
RL V SNK + QV I H + SA + + + + A G ++
Sbjct: 67 RLCVFRSNKHLYVQV----IDDSKMHTLASASTMQKSISEELDYSSSPTIEVAKKVGEVI 122
Query: 150 ARRLLK 155
A L+
Sbjct: 123 ASACLE 128
>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
stearothermophilus} SCOP: c.55.4.1
Length = 120
Score = 30.6 bits (70), Expect = 0.28
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 94 RLIVRFSNKDITCQVAYSRI--EGDHIICSAYSHELPKYGIKVGLTNYAAAYATGLLLAR 151
RL V SNK I Q+ I I SA + + ++G+ N AA G L+A+
Sbjct: 30 RLSVFRSNKHIYAQI----IDDTKSATIVSASTLD-KEFGLDST-NNIEAAKKVGELVAK 83
Query: 152 RLLKN 156
R L+
Sbjct: 84 RALEK 88
>3v2d_S 50S ribosomal protein L18; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
1vsp_M 2hgj_R 2hgq_R 2hgu_R 1vsa_M 2j03_S 2jl6_S 2jl8_S
2v47_S 2v49_S 2wdi_S 2wdj_S 2wdl_S 2wdn_S 2wh2_S 2wh4_S
2wrj_S 2wrl_S 2wro_S 2wrr_S ...
Length = 112
Score = 29.8 bits (68), Expect = 0.43
Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 12/87 (13%)
Query: 71 KTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAYSRI--EGDHIICSAYSHELP 128
+ Y R++ V+++ K T + RL V S K I Q+ I E + SA S L
Sbjct: 3 RLTAYERRKFRVRNRIK-RTGRLRLSVFRSLKHIYAQI----IDDEKGVTLVSASSLAL- 56
Query: 129 KYGIKVGLTNYAAAYATGLLLARRLLK 155
K+ A G LA + L
Sbjct: 57 ----KLKGNKTEVARQVGRALAEKALA 79
>2llk_A Cyclin-D-binding MYB-like transcription factor 1; helix bundle,
SGC, structural genomics consortium, NESG, NOR
structural genomics consortium; NMR {Homo sapiens}
Length = 73
Score = 27.2 bits (60), Expect = 1.7
Identities = 8/56 (14%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 239 HRKHIFGLHVAEYMRQLSEEDDEAFKRQFSERVGGWGTLSEQLGMTKSSFKCEKLW 294
+ ++ + + E+ E K + W T+ LG +S+ +
Sbjct: 12 ENLYFQ--GDRNHVGKYTPEEIEKLKELRIKHGNDWATIGAALG--RSASSVKDRC 63
>3ndn_A O-succinylhomoserine sulfhydrylase; seattle structural genomics
center for infectious disease, S mycobacterium, PLP,
schiff base; HET: LLP; 1.85A {Mycobacterium
tuberculosis}
Length = 414
Score = 29.5 bits (67), Expect = 1.8
Identities = 6/29 (20%), Positives = 13/29 (44%), Gaps = 9/29 (31%)
Query: 115 GDHIICSA---------YSHELPKYGIKV 134
GD ++ + S LP++G++
Sbjct: 120 GDRLVAARSLFGSCFVVCSEILPRWGVQT 148
>2rfv_A Methionine gamma-lyase; pyridoxal-5'-phosphate, PLP-dependent
enzyme; HET: LLP; 1.35A {Citrobacter freundii} PDB:
1y4i_A* 3jwa_A* 3jw9_A* 3jwb_A* 3mkj_A*
Length = 398
Score = 29.0 bits (66), Expect = 2.5
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 9/29 (31%)
Query: 115 GDHIICS--AY-------SHELPKYGIKV 134
GDHI+ + Y SH +PK+GI V
Sbjct: 103 GDHIVSASAIYGCTHAFLSHSMPKFGINV 131
>3g85_A Transcriptional regulator (LACI family); transcription regulator,
PSI-II, structural genomics structure initiative; 1.84A
{Clostridium acetobutylicum atcc 824}
Length = 289
Score = 28.7 bits (65), Expect = 2.6
Identities = 4/28 (14%), Positives = 10/28 (35%), Gaps = 3/28 (10%)
Query: 204 FGAMKGAVDGGLNIPH--SVKRFPGYDN 229
G + ++IP + G ++
Sbjct: 201 LGVISVLNKRQISIPDDIEIVAI-GMND 227
>3nng_A Uncharacterized protein; F5_F8_TYPE_C domain, NESG, structural
genomics, PSI-2, prote structure initiative; 2.18A
{Bacteroides fragilis}
Length = 168
Score = 28.2 bits (62), Expect = 2.9
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 41 KPLEMGFVKVVKNKQYFKRYQVK---FKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIV 97
+P+ + V K Y Y ++ K R+EG+T++ R++ K P+Y I
Sbjct: 70 RPVTLTGFSVTKQSAYGSGYNLRSAEIKVRKEGETEWVTYPRVLTFRNFKGADPQYAAIE 129
>3evs_C Bone morphogenetic protein receptor type-1B; ligand-receptor
complex, cystin-knot ligand, three-finger to (receptor);
2.10A {Mus musculus}
Length = 119
Score = 27.5 bits (60), Expect = 3.0
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 325 NSNFPPTLHAKSPTMSYDGPVH 346
N + PTL DGP+H
Sbjct: 96 NKDLHPTLPPLKDRDFVDGPIH 117
>2eab_A Alpha-fucosidase; glycoside hydrolase; 1.12A {Bifidobacterium
bifidum} PDB: 2eac_A* 2ead_A* 2eae_A*
Length = 899
Score = 28.8 bits (63), Expect = 3.8
Identities = 21/117 (17%), Positives = 29/117 (24%), Gaps = 15/117 (12%)
Query: 239 HRKHIFGLHVAEYMRQLSEEDDEAFKRQFSERVGGWGTLSEQLGMTKSSFKCEKLWIVYF 298
H H+ GL + + + E +A K R L G W
Sbjct: 679 HMSHLLGLFPGDLITIDNSEYMDAAKTSLRYRCFKGNVLQSNTGWAIGQRIN--SW---- 732
Query: 299 CVGIGENLACLHDISCRLYKLRKKIKNSNFPPTLHAKSPTMSYDGPVHNHGLRAEMS 355
A D Y+L + + L DG N EM
Sbjct: 733 --------ARTGD-GNTTYQLVELQLKNAMYANLFDYHAPFQIDGNFGNTSGVDEML 780
>1e5e_A MGL, methionine gamma-lyase; methionine biosynthesis, PLP-dependent
enzymes, C-S gamma lyase; HET: PPJ; 2.18A {Trichomonas
vaginalis} SCOP: c.67.1.3 PDB: 1e5f_A*
Length = 404
Score = 28.3 bits (64), Expect = 4.0
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 12/39 (30%)
Query: 115 GDHIICS--AY-------SHELPKYGIK---VGLTNYAA 141
GDH+I Y H L K+GI+ +
Sbjct: 101 GDHLISDECLYGCTHALFEHALTKFGIQVDFINTAIPGE 139
>1gc0_A Methionine gamma-lyase; pyridoxal-5'-phosphate; HET: LLP; 1.70A
{Pseudomonas putida} SCOP: c.67.1.3 PDB: 1gc2_A* 1pg8_A*
1ukj_A* 2o7c_A*
Length = 398
Score = 27.9 bits (63), Expect = 5.2
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 12/39 (30%)
Query: 115 GDHIICS--AY-------SHELPKYGIK---VGLTNYAA 141
GD ++ Y H + ++G+K V + + A
Sbjct: 104 GDEVLLGNTLYGCTFAFLHHGIGEFGVKLRHVDMADLQA 142
>1qgn_A Protein (cystathionine gamma-synthase); methionine biosynthesis,
pyridoxal 5'-phosphate, gamma-famil; HET: PLP; 2.90A
{Nicotiana tabacum} SCOP: c.67.1.3 PDB: 1i41_A* 1i48_A*
1i43_A*
Length = 445
Score = 28.0 bits (63), Expect = 5.3
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 12/39 (30%)
Query: 115 GDHIICS--AY-------SHELPKYGIK---VGLTNYAA 141
G HI+ + Y LPK GI + + A
Sbjct: 153 GGHIVTTTDCYRKTRIFIETILPKMGITATVIDPADVGA 191
>1ytm_A Phosphoenolpyruvate carboxykinase [ATP], phosphoenolpyruvate;
domain closure, nucleotide binding; HET: ATP; 2.20A
{Anaerobiospirillum succiniciproducens} PDB: 1yvy_A
Length = 532
Score = 28.1 bits (63), Expect = 5.7
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 5/48 (10%)
Query: 63 KFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAY 110
+ + + + K L V D RL +RF +VA+
Sbjct: 94 AWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRF-----VMEVAW 136
>3ri6_A O-acetylhomoserine sulfhydrylase; PYR 5'-phosphate,
gamma-elimination, direct sulfhydrylation, CY
metabolism, protein thiocarboxylate, TR; 2.20A
{Wolinella succinogenes}
Length = 430
Score = 27.9 bits (63), Expect = 5.8
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 9/29 (31%)
Query: 115 GDHIICSAY---------SHELPKYGIKV 134
GD ++ + LP +GI+V
Sbjct: 121 GDSVVTTDRLFGHTLSLFQKTLPSFGIEV 149
>2olr_A Phosphoenolpyruvate carboxykinase; carbon dioxide, lyase; HET: ATP;
1.60A {Escherichia coli K12} SCOP: c.91.1.1 c.109.1.1
PDB: 1k3c_A* 1k3d_A* 1aq2_A* 2olq_A* 1os1_A* 2pxz_X*
1ayl_A* 2py7_X* 1oen_A 1ylh_A* 1ygg_A*
Length = 540
Score = 27.8 bits (62), Expect = 5.9
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 63 KFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAY 110
++ + T + KRL V D P RL VRF +VA+
Sbjct: 101 TWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRF-----ITEVAW 143
>1j3b_A ATP-dependent phosphoenolpyruvate carboxykinase; adenosine
triphosphate, T thermophilus; 2.00A {Thermus
thermophilus} SCOP: c.91.1.1 c.109.1.1 PDB: 1xkv_A*
2pc9_A*
Length = 529
Score = 27.7 bits (62), Expect = 6.7
Identities = 11/48 (22%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 63 KFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLIVRFSNKDITCQVAY 110
F+ + Y + + L VQD +YRL VR + +
Sbjct: 82 AFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRV-----VTESPW 124
>2cb1_A O-acetyl homoserine sulfhydrylase; PLP enzyme, lyase, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; HET: LLP; 2.0A {Thermus
thermophilus}
Length = 412
Score = 27.5 bits (62), Expect = 7.3
Identities = 5/29 (17%), Positives = 9/29 (31%), Gaps = 9/29 (31%)
Query: 115 GDHIICSAY---------SHELPKYGIKV 134
GD ++ + L G+ V
Sbjct: 95 GDEVVAAKGLFGQTIGLFGQVLSLMGVTV 123
>2ctz_A O-acetyl-L-homoserine sulfhydrylase; crystal, O-acetyl homoserine
sulfhydrase, structural genomic structural
genomics/proteomics initiative; HET: PLP; 2.60A {Thermus
thermophilus} SCOP: c.67.1.3
Length = 421
Score = 27.5 bits (62), Expect = 7.6
Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 9/29 (31%)
Query: 115 GDHIICSAY---------SHELPKYGIKV 134
GD+I+ + L + GI+V
Sbjct: 97 GDNIVSTPNLYGGTFNQFKVTLKRLGIEV 125
>1pff_A Methionine gamma-lyase; homocysteine; 2.50A {Trichomonas vaginalis}
SCOP: c.67.1.3
Length = 331
Score = 27.5 bits (62), Expect = 7.6
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 9/29 (31%)
Query: 115 GDHIICS--AY-------SHELPKYGIKV 134
GDH+I Y H+L K+G++V
Sbjct: 37 GDHLISDDCLYGCTHALFEHQLRKFGVEV 65
>3acz_A Methionine gamma-lyase; L-methionine; HET: LLP; 1.97A {Entamoeba
histolytica} PDB: 3aej_A* 3ael_A* 3aem_A* 3aen_A*
3aeo_A* 3aep_A*
Length = 389
Score = 27.5 bits (62), Expect = 8.6
Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 12/39 (30%)
Query: 115 GDHIICS--AY-------SHELPKYGIK---VGLTNYAA 141
GDH+I Y +H LP++GI+ + ++
Sbjct: 98 GDHLIAGDTLYGCTVSLFTHWLPRFGIEVDLIDTSDVEK 136
>2f96_A Ribonuclease T; RNAse, RNT, RNAse T, tRNA hydrolase, SAD, PS
protein structure initiative, midwest center for
structural genomics; 2.09A {Pseudomonas aeruginosa}
SCOP: c.55.3.5
Length = 224
Score = 27.0 bits (60), Expect = 9.8
Identities = 3/16 (18%), Positives = 4/16 (25%)
Query: 147 LLLARRLLKNLNLDRL 162
LA L +
Sbjct: 164 ATLAGLAYGQTVLAKA 179
>3jyw_F 60S ribosomal protein L7(A); eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
1s1i_F
Length = 213
Score = 26.7 bits (58), Expect = 9.9
Identities = 2/45 (4%), Positives = 3/45 (6%)
Query: 52 KNKQYFKRYQVKFKRRREGKTDYYARKRLIVQDKNKYNTPKYRLI 96
A L+
Sbjct: 9 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGLV 53
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 0.138 0.419
Gapped
Lambda K H
0.267 0.0499 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,563,835
Number of extensions: 334773
Number of successful extensions: 712
Number of sequences better than 10.0: 1
Number of HSP's gapped: 703
Number of HSP's successfully gapped: 36
Length of query: 360
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 265
Effective length of database: 4,049,298
Effective search space: 1073063970
Effective search space used: 1073063970
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: 58 (26.7 bits)