RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4310
(203 letters)
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 223 bits (571), Expect = 2e-71
Identities = 147/179 (82%), Positives = 168/179 (93%)
Query: 24 MGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFS 83
MGDIEGLIDKVNELKLDDNE LIEK+KHGQFTLRDMYEQFQNIMKMGPFSQI+GMIPGF
Sbjct: 297 MGDIEGLIDKVNELKLDDNEALIEKLKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFG 356
Query: 84 QDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKE 143
DF+SKG+EQESMARLK+LMTIMDSMND ELD+ DGAK+FSKQ GRI RVA+G+GV+ ++
Sbjct: 357 TDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRD 416
Query: 144 VKDLISQYTKFAAVVKKMGGIKGLFKGGDITKNVNQTQMMKLNQQMAKMMDPRVLHQMG 202
V++L++QYTKFA +VKKMGGIKGLFKGGD++KNV+Q+QM KLNQQMAKMMDPRVLH MG
Sbjct: 417 VQELLTQYTKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMG 475
>1mfq_C SRP54, signal recognition particle 54KDA protein; RNA-protein
complex, A-minor motif, 3-helix junction, signaling
protein/RNA complex; HET: CCC; 3.10A {Homo sapiens}
SCOP: a.36.1.1
Length = 129
Score = 149 bits (379), Expect = 7e-47
Identities = 95/126 (75%), Positives = 111/126 (88%)
Query: 43 EELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRL 102
KHGQFTLRDMYEQFQNIMKMGPFSQI+GMIPGF DF+SKG+EQESMARLK+L
Sbjct: 4 SHHHHHHKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKL 63
Query: 103 MTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMG 162
MTIMDSMND ELD+ DGAK+FSKQ GRI RVA+G+GV+ ++V++L++QYTKFA +VKKMG
Sbjct: 64 MTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMG 123
Query: 163 GIKGLF 168
GIKGLF
Sbjct: 124 GIKGLF 129
>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding,
signal recognition particle, GTP-binding, RNA-binding;
2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B
Length = 432
Score = 144 bits (366), Expect = 1e-41
Identities = 44/140 (31%), Positives = 74/140 (52%), Gaps = 6/140 (4%)
Query: 24 MGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFS 83
MGD+E L++K ++ + EE I+ I G+FTL ++ Q + I MG +I+ MIPGF
Sbjct: 295 MGDLESLLEKAEDMVDEKTEESIDAIMRGKFTLNELMTQLEAIENMGSMKKILSMIPGFG 354
Query: 84 QDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKE 143
+ K + A++K+ I+ SM E +N K RI R+A+G+G TE +
Sbjct: 355 GA-MPKELSHLTEAKIKKYKVIISSMTKEERENPKIIK-----ASRIRRIARGSGTTEND 408
Query: 144 VKDLISQYTKFAAVVKKMGG 163
V++++ Y + K+
Sbjct: 409 VREVLRYYETTKNAIDKLHH 428
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 138 bits (350), Expect = 2e-39
Identities = 57/152 (37%), Positives = 84/152 (55%), Gaps = 10/152 (6%)
Query: 24 MGDIEGLIDKVNEL--KLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPG 81
+GDI+GL++K EL +++ EE IE+ G+FTL+DMY Q + + KMGP QI+ MIPG
Sbjct: 296 LGDIQGLLEKFKELEKEVEIKEEDIERFLRGKFTLKDMYAQLEAMRKMGPLKQILRMIPG 355
Query: 82 FSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTE 141
L RLK+ IMDSM + EL N + RI R+A+G+G +
Sbjct: 356 LGYS-LPDDVISIGEERLKKFKVIMDSMTEEELLNPEIIN-----YSRIKRIARGSGTST 409
Query: 142 KEVKDLISQYTKFAAVVKKM--GGIKGLFKGG 171
K+VK+L+ QY + + K M + L +
Sbjct: 410 KDVKELLDQYRQMKKLFKSMNKRQLSRLARRF 441
>1qb2_A SRP54, human signal recognition particle 54 KD protein;
alpha-helix, helix-turn-helix, signaling protein; 2.10A
{Homo sapiens} SCOP: a.36.1.1 PDB: 1ry1_W* 2go5_W
Length = 109
Score = 128 bits (324), Expect = 7e-39
Identities = 85/109 (77%), Positives = 101/109 (92%)
Query: 53 QFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDG 112
QFTLRDMYEQFQNIMKMGPFSQI+GMIPGF DF+SKG+EQESMARLK+LMTIMDSMND
Sbjct: 1 QFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQ 60
Query: 113 ELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKM 161
ELD+ DGAK+FSKQ GRI RVA+G+GV+ ++V++L++QYTKFA +VKKM
Sbjct: 61 ELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKM 109
>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition
particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A
{Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A
Length = 433
Score = 126 bits (319), Expect = 8e-35
Identities = 41/143 (28%), Positives = 78/143 (54%), Gaps = 10/143 (6%)
Query: 24 MGDIEGLIDKVNE-LKLDDNEELIEKIK--HGQFTLRDMYEQFQNIMKMGPFSQIMGMIP 80
MGDIE +++KV + D ++ +E + G+ TLRD+Y Q + KMGP S+++ IP
Sbjct: 295 MGDIESILEKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIP 354
Query: 81 GFSQDFLSKGSEQESMA--RLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAG 138
G + +Q + +++R + ++SM EL+N + R+ R+A+G+G
Sbjct: 355 GLGIMLPTPSEDQLKIGEEKIRRWLAALNSMTYKELENPNIID-----KSRMRRIAEGSG 409
Query: 139 VTEKEVKDLISQYTKFAAVVKKM 161
+ +EV++L+ Y ++K +
Sbjct: 410 LEVEEVRELLEWYNNMNRLLKMV 432
>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA
binding protein, hydrolase, gtpas; HET: GCP; 3.94A
{Escherichia coli} PDB: 2j28_9
Length = 433
Score = 86.4 bits (215), Expect = 3e-20
Identities = 41/142 (28%), Positives = 66/142 (46%), Gaps = 8/142 (5%)
Query: 24 MGDIEGLIDKVNE-LKLDDNEELIEKIKHGQ-FTLRDMYEQFQNIMKMGPFSQIMGMIPG 81
MGD+ LI+ + + E+L K+K G F L D EQ + + MG + +MG +PG
Sbjct: 297 MGDVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLRQMKNMGGMASLMGKLPG 356
Query: 82 FSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTE 141
Q Q L R+ I++SM E R ++ R R+A G+G+
Sbjct: 357 MGQ-IPDNVKSQMDDKVLVRMEAIINSMTMKE---RAKPEIIKGS--RKRRIAAGSGMQV 410
Query: 142 KEVKDLISQYTKFAAVVKKMGG 163
++V L+ Q+ ++KKM
Sbjct: 411 QDVNRLLKQFDDMQRMMKKMKK 432
>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M
domain, RNA-binding, signal sequence-binding,
helix-turn-helix, protein targeting; 3.20A {Thermus
aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB:
2iy3_A
Length = 425
Score = 81.8 bits (203), Expect = 1e-18
Identities = 42/144 (29%), Positives = 72/144 (50%), Gaps = 17/144 (11%)
Query: 24 MGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82
MGD+ L +KV + + ++ +L D +Q QN+ ++GPFS+I+G++PG
Sbjct: 294 MGDVASLAEKVRAAGLEAEAPKSAKE-----LSLEDFLKQMQNLKRLGPFSEILGLLPGV 348
Query: 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEK 142
Q K E+ +KRL I+ SM E R ++ R R+A+G+G + +
Sbjct: 349 PQG--LKVDEKA----IKRLEAIVLSMTPEE---RKDPRIL--NGSRRKRIAKGSGTSVQ 397
Query: 143 EVKDLISQYTKFAAVVKKMGGIKG 166
EV I + + A++K + KG
Sbjct: 398 EVNRFIKAFEEMKALMKSLEKKKG 421
>2jqe_A SRP54, signal recognition 54 kDa protein; AF54, structure,
solution, signaling protein; NMR {Archaeoglobus
fulgidus}
Length = 119
Score = 75.7 bits (187), Expect = 3e-18
Identities = 37/117 (31%), Positives = 63/117 (53%), Gaps = 5/117 (4%)
Query: 47 EKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIM 106
++ G FTL+D+Y+Q + + KMGP +I M+P + + + ++K+ IM
Sbjct: 3 GTMEKGTFTLKDIYKQIEAMNKMGPVRKIFEMLPFGLGLKVDNDVMEMTQEKMKKFRVIM 62
Query: 107 DSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMGG 163
DSM + EL N + RI R+A G+G + +EVK+L++ Y ++KKM
Sbjct: 63 DSMTEEELLNPKIID-----SSRIRRIAIGSGTSPQEVKELLNYYKTMKNLMKKMKK 114
>1hq1_A Signal recognition particle protein; protein-RNA complex, double
helix, tetraloop, internal loop, SRP, ribonucleoprotein;
HET: CCC; 1.52A {Escherichia coli} SCOP: a.36.1.1 PDB:
3lqx_A* 2pxb_A 2pxd_A 2pxe_A 2pxf_A 2pxk_A 2pxl_A 2pxp_A
2pxq_A 2pxt_A 2pxu_A 2pxv_A
Length = 105
Score = 54.8 bits (133), Expect = 2e-10
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 6/109 (5%)
Query: 54 FTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGE 113
F L D EQ + + MG + +MG +PG Q Q L R+ I++SM E
Sbjct: 2 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQ-IPDNVKSQMDDKVLVRMEAIINSMTMKE 60
Query: 114 LDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMG 162
+ K R R+A G+G+ ++V L+ Q+ ++KKM
Sbjct: 61 RAKPEIIK-----GSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMMKKMK 104
>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 = 5e-04
Identities = 32/223 (14%), Positives = 63/223 (28%), Gaps = 49/223 (21%)
Query: 19 CGICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQ-FTLRDMYEQFQNIMKMGPFSQIMG 77
G + ++ + + K+D I + + + E Q + QI
Sbjct: 161 SGKTWVA-LDVCLSYKVQCKMDFK---IFWLNLKNCNSPETVLEMLQKL-----LYQIDP 211
Query: 78 M-IPGFSQDFLSKGSEQESMARLKRLMT---------IMDSMNDGE----LDN------- 116
K A L+RL+ ++ ++ + + +
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLT 271
Query: 117 -RDGA---KLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAA-----VVKK-----MG 162
R L + T I+ +T EVK L+ +Y V +
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331
Query: 163 GIKGLFKGGDIT-KNVNQTQMMKLNQQMA---KMMDPRVLHQM 201
I + G T N KL + +++P +M
Sbjct: 332 IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374
>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 = 31.6 bits (71), Expect = 0.20
Identities = 26/146 (17%), Positives = 46/146 (31%), Gaps = 29/146 (19%)
Query: 36 ELKLDD----NEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMG-MIPGFSQDFLS-- 88
DD EL+ K + + K+G F Q++ + F +L
Sbjct: 47 GFAADDEPTTPAELVGKFL--GYVSSLVEPS-----KVGQFDQVLNLCLTEFENCYLEGN 99
Query: 89 ---------KGSEQESMARLKRLMTI---MDSMNDGELDNRDGAKLF-SKQTGRITRVAQ 135
++ + K L+ M D + + LF + G VA
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAI 159
Query: 136 --GAGVTEKEVKDLISQYTKFAAVVK 159
G G T+ ++L Y + +V
Sbjct: 160 FGGQGNTDDYFEELRDLYQTYHVLVG 185
Score = 30.8 bits (69), Expect = 0.38
Identities = 25/135 (18%), Positives = 41/135 (30%), Gaps = 37/135 (27%)
Query: 73 SQIMGMIPGFSQDFLSKGSEQESMAR--LKRLMTIMD---------SMNDGELDN-RDGA 120
SQ GM G D + A+ R D S+ D ++N +
Sbjct: 1626 SQEQGM--G--MDLY----KTSKAAQDVWNR----ADNHFKDTYGFSILDIVINNPVNLT 1673
Query: 121 KLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMGGIKGLFKG--GDITKNVN 178
F + G+ R A + E V + F + + F+ G + +
Sbjct: 1674 IHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSY--TFRSEKGLL----S 1727
Query: 179 QTQMMKLNQQMAKMM 193
TQ Q A +
Sbjct: 1728 ATQ----FTQPA-LT 1737
>1dul_A Signal recognition particle protein (fifty-four homolog);
protein-RNA complex, double helix, tetraloop, internal
loop, SRP, ribonucleoprotein; HET: CCC; 1.80A
{Escherichia coli} SCOP: a.36.1.1 PDB: 2xkv_C
Length = 69
Score = 27.5 bits (62), Expect = 0.64
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 99 LKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVV 158
L R+ I++SM E + K R R+A G+G+ ++V L+ Q+ ++
Sbjct: 12 LVRMEAIINSMTMKERAKPEIIK-----GSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMM 66
Query: 159 KKM 161
KKM
Sbjct: 67 KKM 69
>1deq_A Fibrinogen (alpha chain); coiled-coil, blood clotting; 3.50A {Bos
taurus} SCOP: i.9.1.1
Length = 390
Score = 28.7 bits (63), Expect = 1.5
Identities = 18/100 (18%), Positives = 41/100 (41%), Gaps = 18/100 (18%)
Query: 19 CGICCMGDIEGLIDKVNELKLDDNEELIEKIKH----GQFTLRDMYEQFQNIMKMGPFSQ 74
C C ++GLID+V++ D I K++ Q +D +NI+++
Sbjct: 48 CPSGCR--MKGLIDEVDQ----DFTSRINKLRDSLFNYQKNSKDSNTLTKNIVEL----- 96
Query: 75 IMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGEL 114
M F++ + + ++ L+ + I+ ++
Sbjct: 97 ---MRGDFAKANNNDNTFKQINEDLRSRIEILRRKVIEQV 133
>3u4q_B ATP-dependent helicase/deoxyribonuclease subunit; helicase, nuclease,
double strand DNA repair, protein-DNA CO hydrolase-DNA
complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_B*
Length = 1166
Score = 28.2 bits (62), Expect = 2.3
Identities = 9/79 (11%), Positives = 25/79 (31%), Gaps = 7/79 (8%)
Query: 26 DIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMG---MIPGF 82
+ + L V +E E+I G+ ++ + + F + +
Sbjct: 1084 EFDLLTKHVRRT----FQEAGEQITDGRVSIEPYKMKNKTPCTYCAFKSVCQFDESLEEN 1139
Query: 83 SQDFLSKGSEQESMARLKR 101
L ++ + +K+
Sbjct: 1140 EYRPLKAEKDKTILEWIKK 1158
>1nya_A Calerythrin; EF-hand, metal binding protein; NMR {Saccharopolyspora
erythraea} SCOP: a.39.1.5
Length = 176
Score = 27.4 bits (61), Expect = 2.6
Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 5/62 (8%)
Query: 93 QESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYT 152
+ RLK+ D +G L+ D F K+ I A G EV+ L + +
Sbjct: 3 AIASDRLKKRFDRWDFDGNGALERAD----FEKEAQHIAE-AFGKDAGAAEVQTLKNAFG 57
Query: 153 KF 154
Sbjct: 58 GL 59
>3khe_A Calmodulin-like domain protein kinase isoform 3; calcium dependent
kinase, structural genomics, structural GE consortium,
SGC, ATP-binding; 1.95A {Toxoplasma gondii}
Length = 191
Score = 26.5 bits (59), Expect = 5.4
Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 88 SKGSEQESMARLKRLMTIMDSMNDGELDN---RDGAKLFSKQTGRITRVAQGAGVTEKEV 144
SK + E L ++ +D+ DG+LD +G + + G + E EV
Sbjct: 31 SKLTTLEETKELTQIFRQLDNNGDGQLDRKELIEGYRKLMQWKGDTVS-DLDSSQIEAEV 89
Query: 145 KDLISQ 150
++
Sbjct: 90 DHILQS 95
>3dwl_F Actin-related protein 2/3 complex subunit 4; propellor,
actin-binding, ATP-binding, cytoskeleton, nucleot
binding, WD repeat; HET: ATP; 3.78A {Schizosaccharomyces
pombe}
Length = 168
Score = 26.1 bits (57), Expect = 6.4
Identities = 27/107 (25%), Positives = 43/107 (40%), Gaps = 13/107 (12%)
Query: 27 IEGLIDKVN---ELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFS 83
IE ++ V +K D E I K QF L E F I++ P + G+
Sbjct: 63 IESSVNSVRFSIRIKQVDEIERILVRKFMQF-LMGRAESFF-ILRRKP-------VQGYD 113
Query: 84 QDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRI 130
FL E M + K + I++ M + + + + KLF R+
Sbjct: 114 ISFLITNYHTEEMLKHKLVDFIIEFMEEVDAEISE-MKLFLNGRARL 159
>2yqu_A 2-oxoglutarate dehydrogenase E3 component; lipoamide dehydrogenase,
2-oxoglutarate dehydrogenase comple pyruvate
dehydrogenase complex; HET: FAD; 1.70A {Thermus
thermophilus} PDB: 2eq7_A*
Length = 455
Score = 26.3 bits (59), Expect = 7.1
Identities = 7/21 (33%), Positives = 10/21 (47%), Gaps = 1/21 (4%)
Query: 155 AAVVKKM-GGIKGLFKGGDIT 174
VV+ G++ LFK I
Sbjct: 85 DKVVQANTQGVEFLFKKNGIA 105
>1dxl_A Dihydrolipoamide dehydrogenase; oxidoreductase, multienzyme complex
protein, pyruvate dehydrogenase complex, glycine
decarboxylase complex; HET: FAD; 3.15A {Pisum sativum}
SCOP: c.3.1.5 c.3.1.5 d.87.1.1
Length = 470
Score = 26.3 bits (59), Expect = 8.5
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 1/21 (4%)
Query: 155 AAVVKKM-GGIKGLFKGGDIT 174
V + GI+GLFK +T
Sbjct: 92 DKAVSNLTRGIEGLFKKNKVT 112
>3r6q_A Aspartase; aspartate ammonia lyase, lyase; 2.40A {Bacillus SP} PDB:
1j3u_A 3r6v_A 3r6y_A
Length = 468
Score = 26.3 bits (59), Expect = 8.5
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 42 NEELIEKIKHGQFTLRDMYEQFQNIMKMG 70
+LIE K+ Q ++F ++KMG
Sbjct: 157 LNQLIETTKYMQQEFMKKADEFAGVIKMG 185
>3q4o_A Uncharacterized protein MJ0754; ferritin-like protein, four-helix
bundle, metal binding, DIN center, unknown function;
HET: B3P; 1.34A {Methanocaldococcus jannaschii} PDB:
3q4q_A* 3q4r_A* 3q4n_A
Length = 196
Score = 25.7 bits (56), Expect = 9.4
Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 24/102 (23%)
Query: 57 RDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTI------MDSMN 110
RD+Y N K+ F I SEQ M +K L+ + + +
Sbjct: 43 RDVYLTLYNKWKLQIFKNI-------------AESEQTHMDAVKYLLEKYNIPDPVKNDS 89
Query: 111 DGELDNRDGAKLFSK--QTGRITRVA---QGAGVTEKEVKDL 147
G N +L+ K + G + V GA + + ++ DL
Sbjct: 90 IGVFSNPKFEELYKKLVEKGDKSEVDALKVGATIEDLDIADL 131
>1jsw_A L-aspartase, L-aspartate ammonia-lyase; amino acid ammonia-lyase;
HET: BGC; 2.70A {Escherichia coli} SCOP: a.127.1.1
Length = 478
Score = 25.9 bits (58), Expect = 9.5
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 43 EELIEKIKHGQFTLRDMYEQFQNIMKMG 70
+L++ I + +FQ+I+KMG
Sbjct: 161 IKLVDAINQLREGFERKAVEFQDILKMG 188
>1v59_A Dihydrolipoamide dehydrogenase; 2-oxoacid dehydroganese complex,
pyruvate dehydrogenase complex; HET: FAD NAD; 2.20A
{Saccharomyces cerevisiae} SCOP: c.3.1.5 c.3.1.5
d.87.1.1 PDB: 1jeh_A*
Length = 478
Score = 25.9 bits (58), Expect = 9.8
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 155 AAVVKKM-GGIKGLFKGGDIT 174
VK++ GGI+ LFK +T
Sbjct: 92 DDAVKQLTGGIELLFKKNKVT 112
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 0.138 0.395
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,038,857
Number of extensions: 180250
Number of successful extensions: 794
Number of sequences better than 10.0: 1
Number of HSP's gapped: 769
Number of HSP's successfully gapped: 69
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
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: 55 (25.3 bits)