RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030220
(181 letters)
>2fp4_A Succinyl-COA ligase [GDP-forming] alpha-chain, mitochondrial;
active site phosphohistidine residue; HET: NEP GTP;
2.08A {Sus scrofa} SCOP: c.2.1.8 c.23.4.1 PDB: 2fpg_A*
2fpi_A* 2fpp_A* 1euc_A* 1eud_A*
Length = 305
Score = 230 bits (589), Expect = 1e-76
Identities = 81/112 (72%), Positives = 93/112 (83%)
Query: 45 SAAASHPAVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVF 104
S AS ++VDKNT+VICQG TGK GTFH++QA+EYGT +VGG TP KGG HLGLPVF
Sbjct: 1 SYTASRKHLYVDKNTKVICQGFTGKQGTFHSQQALEYGTNLVGGTTPGKGGKTHLGLPVF 60
Query: 105 NSVAEAKAETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
N+V EAK +T A ASVIYVPPPFAAAAI EA++AE+ LVVCITEGIPQ DMV
Sbjct: 61 NTVKEAKEQTGATASVIYVPPPFAAAAINEAIDAEVPLVVCITEGIPQQDMV 112
>2nu8_A Succinyl-COA ligase [ADP-forming] subunit alpha; citric acid cycle,
heterotetramer, ligase, ATP-grAsp fold, R fold; HET:
COA; 2.15A {Escherichia coli} SCOP: c.2.1.8 c.23.4.1
PDB: 2nu9_A* 2nu7_A* 2nua_A* 2nu6_A* 2scu_A* 1jll_A*
1scu_A* 1jkj_A* 1cqj_A* 1cqi_A*
Length = 288
Score = 227 bits (582), Expect = 8e-76
Identities = 70/105 (66%), Positives = 84/105 (80%)
Query: 52 AVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAK 111
++ +DKNT+VICQG TG GTFH+EQAI YGTKMVGGVTP KGGT HLGLPVFN+V EA
Sbjct: 1 SILIDKNTKVICQGFTGSQGTFHSEQAIAYGTKMVGGVTPGKGGTTHLGLPVFNTVREAV 60
Query: 112 AETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
A T A ASVIYVP PF +I+EA++A + L++ ITEGIP DM+
Sbjct: 61 AATGATASVIYVPAPFCKDSILEAIDAGIKLIITITEGIPTLDML 105
>2yv1_A Succinyl-COA ligase [ADP-forming] subunit alpha; COA-binding
domain, structural genomics, NPPSFA; 1.70A
{Methanocaldococcus jannaschii}
Length = 294
Score = 227 bits (582), Expect = 1e-75
Identities = 59/105 (56%), Positives = 80/105 (76%)
Query: 52 AVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAK 111
+ +D+NT+ I QGITG+ G+FHT++ +E GTK+VGGVTP KGG G+PVF++V EA
Sbjct: 7 MILLDENTKAIVQGITGRQGSFHTKKMLECGTKIVGGVTPGKGGQNVHGVPVFDTVKEAV 66
Query: 112 AETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
ET ANASVI+VP PFA A+ EA++A ++L+V ITE IP HD +
Sbjct: 67 KETDANASVIFVPAPFAKDAVFEAIDAGIELIVVITEHIPVHDTM 111
>1oi7_A Succinyl-COA synthetase alpha chain; SCS, ligase, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; 1.23A {Thermus thermophilus} SCOP: c.2.1.8
c.23.4.1
Length = 288
Score = 225 bits (577), Expect = 4e-75
Identities = 58/104 (55%), Positives = 77/104 (74%)
Query: 53 VFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAKA 112
+ V++ TRV+ QGITG+ G FHT+Q + YGTK+V GVTP KGG E LG+PV+++V EA A
Sbjct: 2 ILVNRETRVLVQGITGREGQFHTKQMLTYGTKIVAGVTPGKGGMEVLGVPVYDTVKEAVA 61
Query: 113 ETKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
+ +AS+I+VP P AA A +EA A + L+V ITEGIP DMV
Sbjct: 62 HHEVDASIIFVPAPAAADAALEAAHAGIPLIVLITEGIPTLDMV 105
>2yv2_A Succinyl-COA synthetase alpha chain; COA-binding domain, ligase,
structural genomics, NPPSFA; 2.20A {Aeropyrum pernix}
Length = 297
Score = 224 bits (573), Expect = 2e-74
Identities = 60/106 (56%), Positives = 79/106 (74%), Gaps = 1/106 (0%)
Query: 52 AVFVDKNTRVICQGITGKNGTFHTEQAIEYGTKMVGGVTPKKGGTEHLGLPVFNSVAEAK 111
AV VD TRV+ QGITG+ G+FH + +EYGTK+V GVTP KGG+E G+PV++SV EA
Sbjct: 7 AVLVDSETRVLVQGITGREGSFHAKAMLEYGTKVVAGVTPGKGGSEVHGVPVYDSVKEAL 66
Query: 112 AE-TKANASVIYVPPPFAAAAIMEAMEAELDLVVCITEGIPQHDMV 156
AE + N S+++VP PFA A+ EA++A + LVV ITEGIP HD +
Sbjct: 67 AEHPEINTSIVFVPAPFAPDAVYEAVDAGIRLVVVITEGIPVHDTM 112
>3mwd_B ATP-citrate synthase; ATP-grAsp, phosphohistidine, organic acid,
lyase, transferas; HET: CIT; 2.10A {Homo sapiens} PDB:
3mwe_B*
Length = 334
Score = 176 bits (448), Expect = 5e-55
Identities = 23/118 (19%), Positives = 46/118 (38%), Gaps = 13/118 (11%)
Query: 52 AVFVDKNTRVICQGITGK--NGTFHTEQAIEY-GTKMVGGVTPKKG--------GTEHLG 100
++T+ I G+ + G + + V P G G + +
Sbjct: 4 TTLFSRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEIL 63
Query: 101 LPVFNSVAEA-KAETKANASVIYVPPPFAAAAIMEAME-AELDLVVCITEGIPQHDMV 156
+PVF ++A+A + + + + + A + ME M A++ + I EGIP+
Sbjct: 64 IPVFKNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTR 121
>3pff_A ATP-citrate synthase; phosphohistidine, organic acid, ATP-grAsp,
lyase, transferas; HET: TLA ADP; 2.30A {Homo sapiens}
Length = 829
Score = 170 bits (431), Expect = 1e-49
Identities = 33/174 (18%), Positives = 59/174 (33%), Gaps = 19/174 (10%)
Query: 2 ARQALAKLIGSIGSRRPSTASSVSHYRLSSSAAPAAHSRNYGSSAAASH------PAVFV 55
L GS + PS +S S R A + S
Sbjct: 434 TANFLLNASGSTSTPAPSRTASFSESRADEVAPAKKAKPAMPQDSVPSPRSLQGKSTTLF 493
Query: 56 DKNTRVICQGITGKN--GTFHTEQAIEY-GTKMVGGVTPKKG--------GTEHLGLPVF 104
++T+ I G+ + G + + V P G G + + +PVF
Sbjct: 494 SRHTKAIVWGMQTRAVQGMLDFDYVCSRDEPSVAAMVYPFTGDHKQKFYWGHKEILIPVF 553
Query: 105 NSVAEA-KAETKANASVIYVPPPFAAAAIMEAME-AELDLVVCITEGIPQHDMV 156
++A+A + + + + + A + ME M A++ + I EGIP+
Sbjct: 554 KNMADAMRKHPEVDVLINFASLRSAYDSTMETMNYAQIRTIAIIAEGIPEALTR 607
>3dmy_A Protein FDRA; predicted actyl-COA synthetase, nysgrc, PSI-II, STRU
genomics, protein structure initiative; 2.07A
{Escherichia coli}
Length = 480
Score = 113 bits (284), Expect = 5e-30
Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 77 QAIEYGTKMVGGVTPKKGGTEHL-GLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEA 135
Q +E K + G ++ L + ++S + AN ++I V +AA +A
Sbjct: 2 QQLEEALK---QLAQGSGSSQALTQVRRWDSACQK--LPDANLALISVAGEYAAELANQA 56
Query: 136 MEAELDLVVCITEGIPQHDMV 156
++ L+ V+ ++ + D +
Sbjct: 57 LDRNLN-VMMFSDNVTLEDEI 76
>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 = 34.6 bits (79), Expect = 0.014
Identities = 38/207 (18%), Positives = 60/207 (28%), Gaps = 77/207 (37%)
Query: 2 ARQALAKLIGSIGSRRPSTASSVSHYR--------LSS-SAAPAAHSRNYGSSAAASHPA 52
+ + L++L R A + L + S P ++Y S S P
Sbjct: 191 SAETLSEL-----IRTTLDAEK--VFTQGLNILEWLENPSNTP---DKDYLLSIPISCPL 240
Query: 53 VFVDKNTRVICQGITGKNGTFHTEQAIEYG-TKMVGGVTPK------KGGTEHL-GLPVF 104
+ G+ Q Y T + G TP KG T H GL
Sbjct: 241 I-----------GVI---------QLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT- 279
Query: 105 NSVAEAKAETKAN-----------------ASVIYVPPPFAAAAIMEAMEAELDLVVCIT 147
+VA A+ ++ + P +I+E
Sbjct: 280 -AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLEN-------N 331
Query: 148 EGIPQHDM--VINFTRVNIL-LVAFLN 171
EG+P M + N T+ + V N
Sbjct: 332 EGVPSP-MLSISNLTQEQVQDYVNKTN 357
Score = 30.8 bits (69), Expect = 0.29
Identities = 24/127 (18%), Positives = 38/127 (29%), Gaps = 26/127 (20%)
Query: 27 YRLSSSA------APAAHSRNYGSSAAASHPAVFVDKNTRVICQGITGKNGTFHTE--QA 78
Y+ S +A A YG S V N + G+ G E A
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILD-----IVINNPVNLTIHFGGEKGKRIRENYSA 1690
Query: 79 IEYGTKMVGGVTPKK---GGTEHLGLPVFNSVAEAKAETKANASVIYVPPP--FAAA-AI 132
+ + T + G + +K EH F S + T P A
Sbjct: 1691 MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSAT-QFTQ------PALTLMEKAA 1743
Query: 133 MEAMEAE 139
E ++++
Sbjct: 1744 FEDLKSK 1750
Score = 26.2 bits (57), Expect = 9.6
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 8/60 (13%)
Query: 121 IYVPPP--FAAAAIMEAMEAELDLVVCITEGIPQHDMVINFTRVNILLVAFLNFIMKLTR 178
+ VP F A+ + E L TEG D T L+ FL ++ L
Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEP---TEGFAADD---EPTTPAELVGKFLGYVSSLVE 73
>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 = 32.2 bits (72), Expect = 0.050
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 13/34 (38%)
Query: 3 RQALAKLIGSIGSRRPSTASSVSHYRLSSSAAPA 36
+QAL KL +S+ Y + +APA
Sbjct: 19 KQALKKL-----------QASLKLY--ADDSAPA 39
Score = 31.8 bits (71), Expect = 0.056
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 109 EAKAETKANASV-IYVPPPFAAAAIMEAME 137
E +A K AS+ +Y A AI ME
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>2vt3_A REX, redox-sensing transcriptional repressor REX; transcriptional
regulation, redox poise; HET: ATP; 2.0A {Bacillus
subtilis} PDB: 2vt2_A*
Length = 215
Score = 32.2 bits (73), Expect = 0.057
Identities = 22/88 (25%), Positives = 35/88 (39%), Gaps = 5/88 (5%)
Query: 55 VDKNTRVICQGITGKNGT--FHTEQAIEYGTKMVGG--VTPKKGGTEHLGLPVFNSVAEA 110
D+ T VI G+ G GT H TK+ + K GTE G+PV+N
Sbjct: 82 QDEMTDVILIGV-GNLGTAFLHYNFTKNNNTKISMAFDINESKIGTEVGGVPVYNLDDLE 140
Query: 111 KAETKANASVIYVPPPFAAAAIMEAMEA 138
+ + +++ VP A + +
Sbjct: 141 QHVKDESVAILTVPAVAAQSITDRLVAL 168
>3epo_A Thiamine biosynthesis protein THIC; alpha-beta barrel, SAM
superfamily, biosynthetic protein; HET: MP5; 2.10A
{Caulobacter crescentus} PDB: 3epm_A* 3epn_A*
Length = 612
Score = 30.5 bits (69), Expect = 0.28
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 81 YGTKMVGGVTPKKGGTEHLGLPVFNSVAE 109
+GT M+ VTPK EHLGLP + V
Sbjct: 468 FGTAMLCYVTPK----EHLGLPDRDDVKT 492
>2duw_A Putative COA-binding protein; ligand binding protein; NMR
{Klebsiella pneumoniae}
Length = 145
Score = 28.9 bits (65), Expect = 0.58
Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 89 VTPKKGGTEHLGLPVFNSVAEAKAETKANASVIYVPPPFAAAAIMEAMEA 138
V+PK G LG + ++A+ + ++ A EA+
Sbjct: 46 VSPKVAGKTLLGQQGYATLADVPEKVD--MVDVFRNSEAAWGVAQEAIAI 93
>1ual_A TRNA (guanine-N(1)-)-methyltransferase; spout class, TRMD,
tRNA(M1G37)methyltrans tRNA modification; HET: SAH;
1.80A {Haemophilus influenzae} SCOP: c.116.1.4 PDB:
1uak_A* 1uaj_A* 1uam_A* 3axz_A* 1p9p_A*
Length = 274
Score = 25.6 bits (57), Expect = 9.6
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 102 PVFNSVAEAKAETKANASVIYVPP---PFAAAAIME-AMEAELDLV 143
P+ +++ AKA A VIY+ P + E A +L LV
Sbjct: 86 PLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILV 131
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
0.318 0.130 0.372
Gapped
Lambda K H
0.267 0.0562 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,748,559
Number of extensions: 161462
Number of successful extensions: 396
Number of sequences better than 10.0: 1
Number of HSP's gapped: 378
Number of HSP's successfully gapped: 29
Length of query: 181
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 93
Effective length of database: 4,244,745
Effective search space: 394761285
Effective search space used: 394761285
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.0 bits)