RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 021591
(310 letters)
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 293
Score = 282 bits (724), Expect = 2e-95
Identities = 66/251 (26%), Positives = 110/251 (43%), Gaps = 6/251 (2%)
Query: 58 ASRKFSTTILTPDSSEGAFPSDLLLK---KTVLTPDITIGLHQDLVIPVTNFFNEDKGFM 114
S F ++ L S +L T + + +P+ NF E G
Sbjct: 9 LSLSFFSSSLFSSKSRNFSSKPILKLPSSSHSQTSLSLSIKSELIPLPILNFSGEKVGET 68
Query: 115 VLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGT 174
L + ++HR + L +++GT ST T +EV G G+KP+ QK TGRAR G+
Sbjct: 69 FLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGS 128
Query: 175 LRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTK 234
P GG + GPKPR IK+NKK RRL L A+++ ++ KTK
Sbjct: 129 QGSPLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAVGNSFVVEEFAENFEKPKTK 188
Query: 235 FIVNYYNQM--ENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVM 292
+ + + +K L + E ++ + +N+ + +L LN++ +L + LV
Sbjct: 189 DFIAAMQRWGLDPAEKSLFFLMD-LVENVEKSGRNIRTLKLLTPRSLNLFDVLNAEKLVF 247
Query: 293 SRDAVNKIVDR 303
+ + + R
Sbjct: 248 TEGTIQYLNQR 258
>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
RNA, 23S ribosomal subunit, ribosome recycling factor,
RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
Length = 201
Score = 278 bits (713), Expect = 8e-95
Identities = 70/197 (35%), Positives = 114/197 (57%), Gaps = 2/197 (1%)
Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
+ + + ++ F + ++H+VV A +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6 KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65
Query: 168 GRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE 227
GRAR G+++ P +R G +P+ H+ K+NKK+ R LK LS + +L+V E
Sbjct: 66 GRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFS 125
Query: 228 VPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSILQH 287
V + KTK + M + VL+ G + E L LA +NLH V+V + G++ S++
Sbjct: 126 VEAPKTKLLAQKLKDM-ALEDVLIITGE-LDENLFLAARNLHKVDVRDATGIDPVSLIAF 183
Query: 288 DTLVMSRDAVNKIVDRM 304
D +VM+ DAV ++ + +
Sbjct: 184 DKVVMTADAVKQVEEML 200
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
1pny_C 1vor_F 1vou_F ...
Length = 205
Score = 274 bits (703), Expect = 2e-93
Identities = 75/189 (39%), Positives = 115/189 (60%), Gaps = 5/189 (2%)
Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
++ + ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG
Sbjct: 14 TIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRS 73
Query: 177 GPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFI 236
P F GG GPKPRS+ L ++VR+LGL +A+++R GKL+ + ++ KTK
Sbjct: 74 VPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKLVAVDGFDIADAKTKNF 133
Query: 237 VNYYNQM--ENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSR 294
+++ Q + T+KVLL E + A +N+ +V+VLP G+NVY IL+HD LV+
Sbjct: 134 ISWAKQNGLDGTEKVLLVTD---DENTRRAARNVSWVSVLPVAGVNVYDILRHDRLVIDA 190
Query: 295 DAVNKIVDR 303
A+ + +
Sbjct: 191 AALEIVEEE 199
>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
2wro_F 2wrr_F 2x9s_F 2x9u_F ...
Length = 210
Score = 272 bits (698), Expect = 2e-92
Identities = 87/205 (42%), Positives = 120/205 (58%), Gaps = 10/205 (4%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
IPV + G LA D I ++ VVRWQLAKR++GT STKT EV+ +G+K
Sbjct: 9 IPVLSP----SGRRELAAD-LPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63
Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKL 220
W QK TGRARHG + P F GG + GPKPR ++ L KKVR+ GL +A++ RA EGKL
Sbjct: 64 IWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKL 123
Query: 221 LVFEDLEVPSHKTKFIVNYYNQM--ENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVG 278
L+ E + KTK + + + + ++ VLL G +E ++ A +NL +V L G
Sbjct: 124 LLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTG---NELVRRAARNLPWVVTLAPEG 180
Query: 279 LNVYSILQHDTLVMSRDAVNKIVDR 303
LNVY I++ + LVM DA +R
Sbjct: 181 LNVYDIVRTERLVMDLDAWEVFQNR 205
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
c.22.1.1
Length = 225
Score = 271 bits (694), Expect = 1e-91
Identities = 86/221 (38%), Positives = 130/221 (58%), Gaps = 18/221 (8%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
+ + N E G + ++ VF++ D++ R V QL+ R+ GT STKT EVSG G+K
Sbjct: 3 VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62
Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKL 220
PW QK TGRARHG++R P +R G +HGPKPR + KLNKK+++L L+ ALS + E KL
Sbjct: 63 PWPQKHTGRARHGSIRSPIWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKL 122
Query: 221 LVFEDLEVPSHKTKFIVNYYNQME-NTKKVLLCDGGC--IHEKLKLATQNLHYVNVLPS- 276
LV +DL++ KTK + ++ + KK L+ + +KL+ +NL V V+ +
Sbjct: 123 LVLDDLKLERPKTKSLKEILQNLQLSDKKTLIVLPWKEEGYMNVKLSGRNLPDVKVIIAD 182
Query: 277 --------------VGLNVYSILQHDTLVMSRDAVNKIVDR 303
GLNV+ +L++D LV++RD V+KI +
Sbjct: 183 NPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEEV 223
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
ribosomal protein L3; mitochondrial ribosome, large
ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
taurus} PDB: 3iy9_D
Length = 175
Score = 256 bits (657), Expect = 7e-87
Identities = 71/175 (40%), Positives = 105/175 (60%), Gaps = 3/175 (1%)
Query: 131 HRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPK 190
H+V WQ ++ TKT +EV G G+KPW QKGTGRARHG++R P +RGG HGP+
Sbjct: 1 HQVAMWQKNFKRISYAKTKTRAEVRGGGRKPWPQKGTGRARHGSIRSPLWRGGGVAHGPR 60
Query: 191 -PRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKV 249
P S+ L KVR LGLK+AL+ + A+ L + + LE+P+ +++ + V
Sbjct: 61 GPTSYYYMLPMKVRALGLKVALTVKLAQDDLHIMDSLELPTGDPQYLTELAHYRRWGDSV 120
Query: 250 LLCDGGC--IHEKLKLATQNLHYVNVLPSVGLNVYSILQHDTLVMSRDAVNKIVD 302
LL D + + + AT L N++P+VGLNV+S+L+H TLV++ V + D
Sbjct: 121 LLVDLTHEEMPQSIVEATSRLKTFNLIPAVGLNVHSMLKHQTLVLTLPTVAFLED 175
>1vq8_C 50S ribosomal protein L4E; 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.22.1.1 PDB: 1k73_E*
1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E*
1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C
1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ...
Length = 246
Score = 154 bits (391), Expect = 7e-46
Identities = 57/249 (22%), Positives = 98/249 (39%), Gaps = 51/249 (20%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHS-----TKTISEVS 155
+ + G + L DVF+ P+R D+I + VR A R+Q S +T +E
Sbjct: 3 ATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61
Query: 156 GTGK-KPWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSA 213
G+G+ + K GRAR R PQ G + H PK + ++ LN K R+L ++ AL+A
Sbjct: 62 GSGRGQAHVPKLDGRAR----RVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAA 117
Query: 214 RAAEGKLL----VFEDLEVP---------SHKTKFIVNYYNQMENTKKVLLCDGGCI--- 257
A + F+ EVP KT+ +V+ ++ + D I
Sbjct: 118 TADADLVADRGHEFDRDEVPVVVSDDFEDLVKTQEVVSLLEALDVHADIDRADETKIKAG 177
Query: 258 -------------------HEKLKLATQNLHYVNVLPSVGLNVYSILQHDTL----VMSR 294
++ A +NL +V + +N + V +
Sbjct: 178 QGSARGRKYRRPASILFVTSDEPSTAARNLAGADVATASEVNTEDLAPGGAPGRLTVFTE 237
Query: 295 DAVNKIVDR 303
A+ ++ +R
Sbjct: 238 SALAEVAER 246
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 132 bits (332), Expect = 4e-36
Identities = 48/253 (18%), Positives = 74/253 (29%), Gaps = 53/253 (20%)
Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG-----THSTKTISEVS 155
+ V + E + VF PIR DI+H V ++Q +T +E
Sbjct: 6 VTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSAESW 65
Query: 156 GTGKKPW---RQKGTGRARHGT-LRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIA 210
GTG+ R G G R G G RGG K R +K+N +R A
Sbjct: 66 GTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYATASA 125
Query: 211 LSARAAEGKL--------------LVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGC 256
++A A + LV KTK V + +L
Sbjct: 126 IAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSK 185
Query: 257 IH-------------------------EKLKLATQNLHYVNVLPSVGLNVYSILQH---- 287
+ A +N+ V LN+ +
Sbjct: 186 KLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLG 245
Query: 288 DTLVMSRDAVNKI 300
++ + A K+
Sbjct: 246 RFVIWTEAAFTKL 258
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 128 bits (322), Expect = 2e-34
Identities = 50/262 (19%), Positives = 80/262 (30%), Gaps = 59/262 (22%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGT-- 157
V + + L VF PIR DI+H+V R+Q + + +G
Sbjct: 9 VHDAKEANKQTATKLTLP-AVFTAPIRTDIVHKVFTDLNKNRKQASGVKISTRGTAGMGH 67
Query: 158 ----------GKKPWRQKGTGRARHGT-LRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRL 205
+ R G+G R G G Q R G K R ++N +R
Sbjct: 68 SAESWGTGRAVARIPRVGGSGTHRSGQAAFGNQCRKGRMFAPLKTYRRVHRRVNVNQKRH 127
Query: 206 GLKIALSARAAEGKL--------------LVFEDLEVPSHKTKFIV-------------- 237
+ AL+A A + VF+D KTK V
Sbjct: 128 AVAAALAASALVPLVFARGHRISNVQELPYVFDDSVESYEKTKQAVAFLKRVGAYDDVLR 187
Query: 238 ------------NYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSI- 284
N+ ++ L G L A +N+ V+V LN+ +
Sbjct: 188 VAETKALRAGQGKLRNRRYKLRRGPLVVYGNEKSTLTRALRNIPGVDVCNVNRLNLLQLA 247
Query: 285 ---LQHDTLVMSRDAVNKIVDR 303
++ + A K+ +
Sbjct: 248 PGGHVGRFIIWTESAFKKLNEI 269
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 117 bits (293), Expect = 3e-30
Identities = 49/242 (20%), Positives = 78/242 (32%), Gaps = 54/242 (22%)
Query: 119 DVFDVPIRKDIIHRVVRWQLAKRQQ-------GTHSTKTISEVSGTG-KKPWRQKGTGRA 170
+VF P+R D++ V R ++Q H T S +G + R G G
Sbjct: 30 EVFRAPLRPDVVRFVHRLLSCNKRQPYAVSRRAGHQTSAESWGTGRAVSRIPRVPGGGTH 89
Query: 171 RHGTLR-GPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAEGKL-------- 220
R G G RGG K R ++N +RR+ + AL+A + +
Sbjct: 90 RAGQGAFGNMCRGGRMFAPTKTWRKWHRRVNVHLRRVAVASALAATSVPSLVLARGHRIE 149
Query: 221 ------LVFEDLEVPSHKTKFIVN--------------------------YYNQMENTKK 248
LV D KT + N+ +K
Sbjct: 150 TVPELPLVISDSAESIEKTSQAIKILKQVGAYADAEKAKDSVGIRPGKGKMRNRRYINRK 209
Query: 249 VLLCDGGCIHEKLKLATQNLHYVNVLPSVGLNVYSIL----QHDTLVMSRDAVNKIVDRM 304
L G K+ A +NL V+V LN+ + ++ + A K+ +
Sbjct: 210 GPLIVYGTEGSKIVKAFRNLPGVDVANVERLNLLDLAPGGHLGRFVIWTESAFKKLEEVY 269
Query: 305 HT 306
T
Sbjct: 270 GT 271
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 110 bits (276), Expect = 1e-27
Identities = 45/260 (17%), Positives = 74/260 (28%), Gaps = 53/260 (20%)
Query: 100 VIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQG---------THSTKT 150
+I V + E G V VF PIR DI++ V +Q S ++
Sbjct: 7 LISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQTSAES 66
Query: 151 ISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKI 209
+ P + G G RGG K R ++N +R +
Sbjct: 67 WGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKRYAICS 126
Query: 210 ALSARAAEGKL--------------LVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGG 255
AL+ + + LV ED KTK V +++ +
Sbjct: 127 ALACLSLPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIKKVYAS 186
Query: 256 ---------------------CI----HEKLKLATQNLHYVNVLPSVGLNVYSI----LQ 286
CI + A + + +L LN+ +
Sbjct: 187 QRMRAGKGKMRNRRRIQRRGPCIIYNEDNGIIKAFRKHPGITLLNVSKLNILKLAPGGHV 246
Query: 287 HDTLVMSRDAVNKIVDRMHT 306
+ + A K+ D T
Sbjct: 247 GRFCIWTESAFRKLDDLYGT 266
>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 = 56.2 bits (135), Expect = 6e-09
Identities = 49/176 (27%), Positives = 72/176 (40%), Gaps = 52/176 (29%)
Query: 35 PP-DLYV---------ACSGDNLFPLKSGLSFLASRK--FST---TILTPDSSEGAFPSD 79
PP LY A SG + +S + F + RK FS + +P F S
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLD----QSRIPF-SERKLKFSNRFLPVASP------FHSH 430
Query: 80 LL------LKKTVLTPDITIGLHQDLVIPVTNFFN-EDKGFMVLAGDVFDVPIRKDIIHR 132
LL + K ++ +++ +D+ IPV + F+ D VL+G + + I II
Sbjct: 431 LLVPASDLINKDLVKNNVSFN-AKDIQIPVYDTFDGSD--LRVLSGSISER-IVDCIIRL 486
Query: 133 VVRWQLAKRQQGTHSTKTI-----SEVSGTGKKPWRQK-GTGRAR---HGTL-RGP 178
V+W+ + + TH I SG G R K GTG R GTL P
Sbjct: 487 PVKWETTTQFKATH----ILDFGPGGASGLGVLTHRNKDGTG-VRVIVAGTLDINP 537
Score = 37.0 bits (85), Expect = 0.009
Identities = 49/313 (15%), Positives = 79/313 (25%), Gaps = 117/313 (37%)
Query: 7 RRLLRRFG-SFSAFGRYESPSLT-------SRSIRSPPDLYVACSGDNLFPLK-SGLSFL 57
+G S +LT + IR + Y A + + K
Sbjct: 1651 NHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIR---ENYSAMIFETIVDGKLKTEKIF 1707
Query: 58 ASRKFSTTILTPDSSEGAFPSDLLLKKTVLT-PDIT---IGLHQDL----VIPVTNFFNE 109
+T T S +G LL T T P +T +DL +IP F
Sbjct: 1708 KEINEHSTSYTFRSEKG------LLSATQFTQPALTLMEKAAFEDLKSKGLIPADATF-- 1759
Query: 110 DKGFMVLAG-------------DVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSG 156
AG DV + + ++ VV R
Sbjct: 1760 -------AGHSLGEYAALASLADVMSI---ESLV-EVVF----YR--------------- 1789
Query: 157 TGKKPWRQKGTGRARHGTL-RGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARA 215
G + R R M P A +++ + +
Sbjct: 1790 -----------GMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQ---YVVERVGK 1835
Query: 216 AEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCI----HEK-LKLATQNLHY 270
G L+ E IVN YN + + L T L++
Sbjct: 1836 RTGWLV-----E--------IVN-YN----------VENQQYVAAGDLRALDTVTNVLNF 1871
Query: 271 VNV--LPSVGLNV 281
+ + + + L
Sbjct: 1872 IKLQKIDIIELQK 1884
>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 = 39.5 bits (91), Expect = 0.001
Identities = 48/306 (15%), Positives = 90/306 (29%), Gaps = 84/306 (27%)
Query: 18 AFGRYESPSLTSRSIR-SPPDL-YVACSGDNLFPLKSGLSFLAS--RKFSTTI-----LT 68
E SL + + P DL + + P + LS +A R T +
Sbjct: 297 TLTPDEVKSLLLKYLDCRPQDLPREVLTTN---PRR--LSIIAESIRDGLATWDNWKHVN 351
Query: 69 PDSSEGAFPSDLLLKKTVLTPDITIGLHQDLVIPVTNFFNED-----KGFMVL-AGDVFD 122
D S L VL P + L + F ++ +
Sbjct: 352 CDKLTTIIESSL----NVLEPAEYRKMFDRLSV-----FPPSAHIPTILLSLIWFDVIKS 402
Query: 123 VPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTL----RGP 178
+ +++++ ++ L ++Q ST +I + K + A H ++ P
Sbjct: 403 DVM--VVVNKLHKYSLVEKQP-KESTISIPSIYLELKVKLENE---YALHRSIVDHYNIP 456
Query: 179 QFRGGTTMHGPKPRS--------HAIK-------------------LNKKVRRLGLKIAL 211
+ + P H L +K+R
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDS----- 511
Query: 212 SARAAEGKLL-VFEDLEVPSHKTKFIV---NYYNQMENTKKVLL--CDGGCIHEK----L 261
+A A G +L + L+ +K +I Y ++ N L + I K L
Sbjct: 512 TAWNASGSILNTLQQLKF--YK-PYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLL 568
Query: 262 KLATQN 267
++A
Sbjct: 569 RIALMA 574
Score = 33.7 bits (76), Expect = 0.079
Identities = 39/284 (13%), Positives = 81/284 (28%), Gaps = 79/284 (27%)
Query: 90 DITIGLHQ----DLVIPVTNFFNEDKGFM--------VLAGDVFD-VPIRKDIIHRVVR- 135
D G HQ D++ + F ++ +L+ + D + + KD + +R
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRL 67
Query: 136 -WQLAKRQQGTHSTKTISEVSGTGKKPW---------RQKGTGRARHGTLRGPQFRGG-- 183
W L + + E + RQ + R +
Sbjct: 68 FWTL--LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQV 125
Query: 184 -TTMHGPKPRSHAIKLNKKVRRL--GLKIALSARAAEGK----LLVFEDLEV-------- 228
+ + + + +KL + + L + + GK L V +V
Sbjct: 126 FAKYNVSRLQPY-LKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184
Query: 229 ----------PSHKTKFIVNYYNQMENTKKVLLCDGGC--------IHEKLKLATQNLHY 270
P + + Q++ D I +L+ ++ Y
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSR-SDHSSNIKLRIHSIQAELRRLLKSKPY 243
Query: 271 VNVLPSVGL---NVYS--ILQH-D----TLVMSRDAVNKIVDRM 304
N L L NV + + L+ +R ++ D +
Sbjct: 244 ENCL----LVLLNVQNAKAWNAFNLSCKILLTTRFK--QVTDFL 281
Score = 27.5 bits (60), Expect = 6.8
Identities = 14/90 (15%), Positives = 29/90 (32%), Gaps = 20/90 (22%)
Query: 229 PSHKTKFIVNYYNQMENTKKVLLCDGGCIHE---KLKLATQNLHYVNVLPSVGLNVY--- 282
PS T+ + +++ N +V + KL+ A L P+ + +
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELR-----PAKNVLIDGVL 159
Query: 283 ----SILQHDTLVMSRDAVNKIVDRMHTPI 308
+ + D K+ +M I
Sbjct: 160 GSGKTWVALDVC---LS--YKVQCKMDFKI 184
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 32.6 bits (73), Expect = 0.071
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 8/36 (22%)
Query: 51 KSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTV 86
K L L + S + DS+ P+ L +K T+
Sbjct: 19 KQALKKLQA---SLKLYADDSA----PA-LAIKATM 46
>3gbx_A Serine hydroxymethyltransferase; structural genomics, IDP01011,
serine hydroxymethyltransfera salmonella typhimurium.;
HET: MSE; 1.80A {Salmonella typhimurium} PDB: 1dfo_A*
3g8m_A* 1eqb_A*
Length = 420
Score = 31.0 bits (71), Expect = 0.52
Identities = 12/31 (38%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 172 HGTLRGPQFRGGTTMHGPKPRSHAIKLNKKV 202
H TL GP RGG + KLN V
Sbjct: 231 HKTLAGP--RGGLILAKGGDEELYKKLNSAV 259
>1iye_A Branched-chain amino acid aminotransferase; hexamer, PLP; HET: PGU;
1.82A {Escherichia coli} SCOP: e.17.1.1 PDB: 1i1l_A*
1i1m_A* 1iyd_A* 1i1k_A* 1a3g_A*
Length = 309
Score = 28.7 bits (65), Expect = 2.1
Identities = 18/66 (27%), Positives = 28/66 (42%), Gaps = 20/66 (30%)
Query: 39 YVA-CSGDNLFPLKSGLSFLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLHQ 97
Y++ +G+NLF +K G + TP + A P +T D I L +
Sbjct: 191 YISEGAGENLFEVKDG-----------VLFTPPFTSSALPG--------ITRDAIIKLAK 231
Query: 98 DLVIPV 103
+L I V
Sbjct: 232 ELGIEV 237
>2dkj_A Serine hydroxymethyltransferase; PLP dependent enzyme, structural
genomics; HET: PLP; 1.15A {Thermus thermophilus}
Length = 407
Score = 27.5 bits (62), Expect = 5.7
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 172 HGTLRGPQFRGGTTMHGPKPRSHAIKLNKKV 202
H TLRGP RGG + +++K +
Sbjct: 225 HKTLRGP--RGGLIL--SNDPELGKRIDKLI 251
>3ecd_A Serine hydroxymethyltransferase 2; ssgcid, decode, bupsa00008A,
one-carbon metabolism, pyridoxa phosphate, structural
genomics; 1.60A {Burkholderia pseudomallei}
Length = 425
Score = 27.2 bits (61), Expect = 6.9
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 172 HGTLRGPQFRGGTTMHGPKPRSHAIKLNKKV 202
H TLRGP RGG + A K+N V
Sbjct: 234 HKTLRGP--RGGFVL--TNDEEIAKKINSAV 260
>2vi8_A Serine hydroxymethyltransferase; SHMT, E53Q, FTHF, enzyme memory,
pyridoxal phosphate, one-carbon metabolism,
PLP-dependent enzymes; HET: PLP; 1.67A {Bacillus
stearothermophilus} PDB: 2vi9_A* 2via_A* 2vib_A* 1kkj_A*
1kkp_A* 1kl1_A* 1kl2_A* 1yjs_A* 2w7f_A* 2w7d_A* 2w7e_A*
2w7g_A* 2w7h_A* 1yjz_A* 1yjy_A* 2vgu_A* 2vgs_A* 2vgt_A*
2vgv_A* 2vgw_A* ...
Length = 405
Score = 27.1 bits (61), Expect = 9.1
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 5/31 (16%)
Query: 172 HGTLRGPQFRGGTTMHGPKPRSHAIKLNKKV 202
H TLRGP RGG + + A +++K +
Sbjct: 225 HKTLRGP--RGGMILCQEQ---FAKQIDKAI 250
>2vx2_A Enoyl-COA hydratase domain-containing protein 3; isomerase, fatty
acid metabolism, transit peptide, lipid Met crontonase,
mitochondrion, CAsp; 2.3A {Homo sapiens}
Length = 287
Score = 26.8 bits (60), Expect = 10.0
Identities = 7/30 (23%), Positives = 10/30 (33%), Gaps = 3/30 (10%)
Query: 49 PLKSGLSFLASRKFSTTILTPDSSEG--AF 76
L + S+ + D EG AF
Sbjct: 249 DLGTAYYL-TSQAMVDNLALRDGQEGITAF 277
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
0.321 0.137 0.402
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,669,923
Number of extensions: 276427
Number of successful extensions: 519
Number of sequences better than 10.0: 1
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 27
Length of query: 310
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 217
Effective length of database: 4,105,140
Effective search space: 890815380
Effective search space used: 890815380
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: 57 (26.3 bits)