RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8195
(192 letters)
>2g6v_A Riboflavin biosynthesis protein RIBD; RIBD APO structure,
structural genomics, structural proteomi europe, spine,
hydrolase, oxidoreductase; 2.60A {Escherichia coli} PDB:
2obc_A* 2o7p_A*
Length = 402
Score = 304 bits (781), Expect = e-104
Identities = 88/192 (45%), Positives = 127/192 (66%), Gaps = 8/192 (4%)
Query: 1 MTLALQQAKLSI-NSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNA--AAQGY 57
M AL+ A+ + PNP VGCVIVK+ I+ GY + G HAE+ AL A A+G
Sbjct: 34 MARALKLAQRGRFTTHPNPNVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKAKG- 92
Query: 58 DVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGIS 117
+T Y+TLEPCS+ G TPPC +ALI +G+ +V+ ++ DPNP V+G+G+ +L AGI
Sbjct: 93 ----ATAYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQDPNPQVAGRGLYRLQQAGID 148
Query: 118 VKQGLMQKEAYEINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSH 177
V GLM EA ++N GF RM+ G P++++K+ +SLD +T++ + SQWITS ++R D
Sbjct: 149 VSHGLMMSEAEQLNKGFLKRMRTGFPYIQLKLGASLDGRTAMASGESQWITSPQARRDVQ 208
Query: 178 IWRARSCAILTG 189
+ RA+S AILT
Sbjct: 209 LLRAQSHAILTS 220
>2b3z_A Riboflavin biosynthesis protein RIBD; alpha/beta/alpha, deaminase
domain and reductase domain, hydrolase, oxidoreductase;
2.41A {Bacillus subtilis} SCOP: c.71.1.2 c.97.1.2 PDB:
2d5n_A* 3ex8_A*
Length = 373
Score = 303 bits (778), Expect = e-104
Identities = 79/192 (41%), Positives = 117/192 (60%), Gaps = 4/192 (2%)
Query: 1 MTLALQQAKLSINS-SPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDV 59
M LAL AK NP VG V+VK+ +I+ G G HAE+ A+ A G
Sbjct: 18 MKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMA---GAHA 74
Query: 60 YNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISVK 119
+ +Y+TLEPCS++G TPPC E +I SGIK+V +A+ DPNPLV+G+G++ + AGI V+
Sbjct: 75 EGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVR 134
Query: 120 QGLMQKEAYEINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIW 179
+G++ +A +N F M+ G+P+V +K A+SLD K + S+WITS+ +R D+ +
Sbjct: 135 EGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQY 194
Query: 180 RARSCAILTGKN 191
R +IL G
Sbjct: 195 RKTHQSILVGVG 206
>2hxv_A Diaminohydroxyphosphoribosylaminopyrimidine deami
amino-6-(5-phosphoribosylamino)uracil...;
oxidoreductase, structural genomics; HET: NDP; 1.80A
{Thermotoga maritima} SCOP: c.71.1.2 c.97.1.2
Length = 360
Score = 296 bits (761), Expect = e-102
Identities = 77/192 (40%), Positives = 117/192 (60%), Gaps = 3/192 (1%)
Query: 1 MTLALQQAKLSI-NSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDV 59
M A++ AK + +PNP VG V+VK+ RII+ G+ GG HAE A+ +A +G D+
Sbjct: 18 MKRAIELAKKGLGRVNPNPPVGAVVVKDGRIIAEGFHPYFGGPHAERMAIESARKKGEDL 77
Query: 60 YNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISVK 119
+T+ +TLEPC + G TPPCT+ +I+SGIK V+I DPNP VSG GV + + GI V
Sbjct: 78 RGATLIVTLEPCDHHGKTPPCTDLIIESGIKTVVIGTRDPNP-VSGNGVEKFRNHGIEVI 136
Query: 120 QGLMQKEAYEINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIW 179
+G++++E ++ F + + + P+V +K AS+LD K + + S+WIT + R H
Sbjct: 137 EGVLEEEVKKLCEFFITYVTKKRPFVALKYASTLDGKIADHRGDSKWITD-KLRFKVHEM 195
Query: 180 RARSCAILTGKN 191
R A+L G
Sbjct: 196 RNIYSAVLVGAG 207
>2hvw_A Deoxycytidylate deaminase; 3-layer (alpha-beta)-sandwich,
protein-liand complex, hydrolase; HET: DCP DDN; 1.67A
{Streptococcus mutans} PDB: 2hvv_A*
Length = 184
Score = 92.4 bits (230), Expect = 5e-24
Identities = 34/139 (24%), Positives = 54/139 (38%), Gaps = 30/139 (21%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGY-------------------TKSPGG 41
M A +K S + VG V+VK RII+ GY
Sbjct: 46 MANAELISKRS--TCNRAYVGAVLVKNNRIIATGYNGGVADTDNCDDVGHEMEDGHCIRT 103
Query: 42 NHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNP 101
HAE++AL+ A +G N+ +Y+T PC CT+AL+++G+KK+
Sbjct: 104 VHAEMNALIQCAKEGISANNTEIYVTHFPCI------NCTKALLQAGVKKITYNTAYRI- 156
Query: 102 LVSGKGVAQLISAGISVKQ 120
+ + + Q
Sbjct: 157 --HPFAIELMTQKEVEYVQ 173
>1p6o_A Cytosine deaminase; hydrolase, dimer, inhibitor bound; 1.14A
{Saccharomyces cerevisiae} SCOP: c.97.1.2 PDB: 1ox7_A
1rb7_A 1ysd_A 1ysb_A 2o3k_A 1uaq_A
Length = 161
Score = 81.9 bits (203), Expect = 3e-20
Identities = 33/145 (22%), Positives = 53/145 (36%), Gaps = 20/145 (13%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEK--RIISCGY-----TKSPGGNHAEIDALLNAA 53
M +A ++A L P +G ++ K ++ G+ S H EI L N
Sbjct: 18 MDIAYEEAALGYKEGGVP-IGGCLINNKDGSVLGRGHNMRFQKGSATL-HGEISTLENCG 75
Query: 54 AQG-YDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLI 112
++T+Y TL PC CT A+I GI + ++ N KG L
Sbjct: 76 RLEGKVYKDTTLYTTLSPCDM------CTGAIIMYGIPRCVVGENVNF---KSKGEKYLQ 126
Query: 113 SAGISVKQGLMQKEAYEINIGFFSR 137
+ G + + +I F
Sbjct: 127 TRGH-EVVVVDDERCKKIMKQFIDE 150
>2azn_A HTP reductase, putative 5-amino-6-(5-phosphoribosylamino)uracil;
oxidoreductase; HET: MA5 NAP EPE; 2.70A
{Methanocaldococcus jannaschii} SCOP: c.71.1.2
Length = 219
Score = 79.8 bits (198), Expect = 6e-19
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 1/51 (1%)
Query: 141 GIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIWRARSCAILTGKN 191
P++ + +LD K + NN S+ I+ +E H RA I+ G
Sbjct: 2 KKPYIISNVGMTLDGKLATINNDSR-ISCEEDLIRVHKIRANVDGIMVGIG 51
>2w4l_A DCMP deaminse, deoxycytidylate deaminase; pyrimidine metabolism,
nucleotide biosynthesis, zinc, hexamer, hydrolase,
metal-binding, phosphoprotein; 2.10A {Homo sapiens}
Length = 178
Score = 78.6 bits (194), Expect = 8e-19
Identities = 41/159 (25%), Positives = 68/159 (42%), Gaps = 37/159 (23%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIV-KEKRIISCGY-----------------------T 36
M +A A+ S PN +VG IV E +I+ GY T
Sbjct: 17 MAVAFLSAQRS--KDPNSQVGACIVNSENKIVGIGYNGMPNGCSDDVLPWRRTAENKLDT 74
Query: 37 KSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAI 96
K P HAE++A++N DV ++Y+ L PC+ C + +I++GIK+VI
Sbjct: 75 KYPYVCHAELNAIMNKN--LTDVKGCSMYVALFPCNE------CAKLIIQAGIKEVIFMS 126
Query: 97 NDPNPLVSGKGVAQLIS-AGISVKQGLMQKEAYEINIGF 134
+ + L + AG++ ++ + +I I F
Sbjct: 127 DKYHDSDEATAARLLFNMAGVTFRK--FIPKCSKIVIDF 163
>1wkq_A Guanine deaminase; domain SWAP, the cytidine deaminase superfamily,
substrate specificity, structural plasticity, hydrolase;
1.17A {Bacillus subtilis} SCOP: c.97.1.2 PDB: 1tiy_A
Length = 164
Score = 75.5 bits (186), Expect = 1e-17
Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 12/105 (11%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLNAAA-- 54
+ A+ A +N+ G VIVK+ II+ G N HAE+ A+ A
Sbjct: 15 LKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVL 74
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDP 99
Y + + +Y + EPC P C A+ + K V A
Sbjct: 75 GAYQLDDCILYTSCEPC------PMCLGAIYWARPKAVFYAAEHT 113
>2p4g_A Hypothetical protein; pyrimidine reductase-like protein, structural
genomics, JOIN for structural genomics, JCSG; 2.30A
{Corynebacterium diphtheriae}
Length = 270
Score = 76.8 bits (189), Expect = 2e-17
Identities = 11/61 (18%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 129 EINIGFFSRMQRGIPWVRMKIASSLDNKTSLYNNSSQWITSKESRNDSHIWRARSCAILT 188
+I G P R +S++ +L + S + + + R + AI+
Sbjct: 20 QIVYGALPLTTINEPECRAIAITSINGSATL-SGVSGPMGDQTDADLLIQLRGWADAIVV 78
Query: 189 G 189
G
Sbjct: 79 G 79
>1z3a_A TRNA-specific adenosine deaminase; tRNA adenosine deaminase, dimer,
zinc, metalloenzyme, structural genomics, PSI, protein
structure initiative; 2.03A {Escherichia coli} SCOP:
c.97.1.2 PDB: 3ocq_A
Length = 168
Score = 73.7 bits (182), Expect = 5e-17
Identities = 44/156 (28%), Positives = 69/156 (44%), Gaps = 30/156 (19%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLNAAA-- 54
M AL AK + + P VG V+V R+I G+ + G + HAEI AL
Sbjct: 13 MRHALTLAKRAWDEREVP-VGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVM 71
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKG-----VA 109
Q Y + ++T+Y+TLEPC C A+I S I +V+ D K +
Sbjct: 72 QNYRLIDATLYVTLEPC------VMCAGAMIHSRIGRVVFGARDA------KTGAAGSLM 119
Query: 110 QLISAG-----ISVKQGLMQKEAYEINIGFFSRMQR 140
++ + + +G++ E + FF RM+R
Sbjct: 120 DVLHHPGMNHRVEITEGILADECAALLSDFF-RMRR 154
>1wwr_A TRNA adenosine deaminase TADA; homodimer, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, hydrolase; 1.80A {Aquifex aeolicus} SCOP:
c.97.1.2
Length = 171
Score = 73.7 bits (182), Expect = 5e-17
Identities = 34/105 (32%), Positives = 50/105 (47%), Gaps = 13/105 (12%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLNAAA-- 54
+ +AL++AK + P VG +IVKE IIS + HAE+ A+ A
Sbjct: 27 LKVALREAKRAFEKGEVP-VGAIIVKEGEIISKAHNSVEELKDPTAHAEMLAIKEACRRL 85
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDP 99
+ +Y+TLEPC C+ AL+ S I+KVI + D
Sbjct: 86 NTKYLEGCELYVTLEPC------IMCSYALVLSRIEKVIFSALDK 124
>2nx8_A TRNA-specific adenosine deaminase; TAD, hydrolase; 2.00A
{Streptococcus pyogenes serotype M6}
Length = 179
Score = 73.8 bits (182), Expect = 6e-17
Identities = 40/157 (25%), Positives = 74/157 (47%), Gaps = 32/157 (20%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGY-----TKSPGGNHAEIDALLNAAA- 54
M AL++++ S+ + P +GCVIVK+ II G+ + HAE+ A+ A A
Sbjct: 20 MQEALKESEKSLQKAEIP-IGCVIVKDGEIIGRGHNAREESNQAIM-HAEMMAINEANAH 77
Query: 55 -QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKG-----V 108
+ + ++T+++T+EPC C+ A+ + I VI ++ K +
Sbjct: 78 EGNWRLLDTTLFVTIEPC------VMCSGAIGLARIPHVIYGASNQ------KFGGVDSL 125
Query: 109 AQLISAG-----ISVKQGLMQKEAYEINIGFFSRMQR 140
Q+++ + V++GL+ + I FF R R
Sbjct: 126 YQILTDERLNHRVQVERGLLAADCANIMQTFF-RQGR 161
>2b3j_A TRNA adenosine deaminase; mixed alpha-beta, protein-RNA complex,
RNA stem-loop, hydrol complex; HET: P5P; 2.00A
{Staphylococcus aureus subsp} SCOP: c.97.1.2
Length = 159
Score = 72.9 bits (180), Expect = 7e-17
Identities = 38/152 (25%), Positives = 67/152 (44%), Gaps = 20/152 (13%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLNAAA-- 54
MTLA+++AK + P +G +I K+ +I+ + HAE A+ AA
Sbjct: 11 MTLAIEEAKKAAQLGEVP-IGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIERAAKVL 69
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKGVAQLISA 114
+ + T+Y+TLEPC C ++ S I +V+ +DP SG + L+
Sbjct: 70 GSWRLEGCTLYVTLEPC------VMCAGTIVMSRIPRVVYGADDPKGGCSG-SLMNLLQQ 122
Query: 115 G-----ISVKQGLMQKEAYEINIGFFSRMQRG 141
V +G++++ + FF + R
Sbjct: 123 SNFNHRAIVDKGVLKEACSTLLTTFF-KNLRA 153
>2a8n_A Cytidine and deoxycytidylate deaminase; RNA editing, RNA binding
protein; 1.60A {Agrobacterium tumefaciens} SCOP:
c.97.1.2
Length = 144
Score = 72.1 bits (178), Expect = 1e-16
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 13/105 (12%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSPGGN----HAEIDALLNAAA-- 54
M LAL +A+ + P +G V+V + R+I+ ++ N HAEI + A
Sbjct: 8 MELALVEARSAGERDEVP-IGAVLVLDGRVIARSGNRTRELNDVTAHAEIAVIRMACEAL 66
Query: 55 QGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDP 99
+ + +Y+TLEPC C A+ + I+++ DP
Sbjct: 67 GQERLPGADLYVTLEPC------TMCAAAISFARIRRLYYGAQDP 105
>3dh1_A TRNA-specific adenosine deaminase 2; zinc-binding protein, TRA tRNA
processing, hydrolase, structural genomics, structural
consortium, SGC; 2.80A {Homo sapiens}
Length = 189
Score = 71.9 bits (177), Expect = 3e-16
Identities = 35/167 (20%), Positives = 57/167 (34%), Gaps = 44/167 (26%)
Query: 1 MTLALQQAK--LSINSSPNPRVGCVIVKEKRIISCGY-----TKSPGGNHAEIDALLNAA 53
M A+ AK L P VGC++V ++ G TK+ HAE+ A+
Sbjct: 30 MEEAMHMAKEALENTEVP---VGCLMVYNNEVVGKGRNEVNQTKNATR-HAEMVAIDQVL 85
Query: 54 AQGYDVY--------NSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSG 105
++ +Y+T+EPC C AL I V+ +
Sbjct: 86 DWCRQSGKSPSEVFEHTVLYVTVEPC------IMCAAALRLMKIPLVVYGCQNE------ 133
Query: 106 KG-----VAQLISAG-------ISVKQGLMQKEAYEINIGFFSRMQR 140
+ V + SA G +EA E+ F+ + +
Sbjct: 134 RFGGCGSVLNIASADLPNTGRPFQCIPGYRAEEAVEMLKTFY-KQEN 179
>2g84_A Cytidine and deoxycytidylate deaminase zinc-bindi; zinc-binding
region, structural genomics, PSI, protein structure
initiative; 1.40A {Nitrosomonas europaea} SCOP: c.97.1.2
Length = 197
Score = 71.8 bits (176), Expect = 5e-16
Identities = 32/163 (19%), Positives = 56/163 (34%), Gaps = 29/163 (17%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEK--RIISCGYTKSPGGN----HAEIDALLNAAA 54
M L+ + +I + P + + +I+ G + G HAEI AL A A
Sbjct: 32 MGYVLELVRANIAADGGP-FAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQA 90
Query: 55 Q-------GYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPLVSGKG 107
+ + + + EPC C A+I SG++ ++ A + G
Sbjct: 91 KLDTHDLSADGLPACELVTSAEPC------VMCFGAVIWSGVRSLVCAARSDDVEAIGFD 144
Query: 108 VAQLISA--------GISVKQGLMQKEAYEINIGFFSRMQRGI 142
GI+V GL++ A + + I
Sbjct: 145 EGPRPENWMGGLEARGITVTTGLLRDAACALLREYN-ACNGVI 186
>1vq2_A DCMP deaminase, deoxycytidylate deaminase; hydrolase; HET: DDN;
2.20A {Enterobacteria phage T4} SCOP: c.97.1.2
Length = 193
Score = 63.8 bits (155), Expect = 4e-13
Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 9/94 (9%)
Query: 43 HAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPNPL 102
HAE++A+L AA G + +T+Y+TL PC C +A+ +SGIKK++
Sbjct: 104 HAELNAILFAAENGSSIEGATMYVTLSPCPD------CAKAIAQSGIKKLVYCETYDKNK 157
Query: 103 VSGKGVAQLISAGISVKQGLMQKEAYEINIGFFS 136
+ L +AGI V + +K ++N +
Sbjct: 158 PGWDDI--LRNAGIEVFN-VPKKNLNKLNWENIN 188
Score = 41.1 bits (96), Expect = 5e-05
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVIVKEKRIISCGYTKSP-GGNH 43
+ +A ++ S + +VG VI K RIIS GY SP GG +
Sbjct: 7 LQIAYLVSQES--KCCSWKVGAVIEKNGRIISTGYNGSPAGGVN 48
>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 = 55.1 bits (132), Expect = 2e-09
Identities = 37/203 (18%), Positives = 64/203 (31%), Gaps = 71/203 (34%)
Query: 24 IVKEKRIISCGY-----TKSPGGNHAEIDALLNAAA------------QG---------- 56
+VK K +I K P + AL A QG
Sbjct: 116 LVKTKELIKNYITARIMAKRPFDKKSN-SALFRAVGEGNAQLVAIFGGQGNTDDYFEELR 174
Query: 57 --YDVYNSTV--YI-----TLEPCSYFGYTPPCTEALIKSGIKKVIIAINDPN--PLVSG 105
Y Y+ V I TL T E + G+ ++ + +P+ P
Sbjct: 175 DLYQTYHVLVGDLIKFSAETLSELI---RTTLDAEKVFTQGL-NILEWLENPSNTP---- 226
Query: 106 KGVAQLISAGISVKQ-GLMQKEAYEI---NIG-----FFSRMQ------RGIPWVRMKIA 150
L+S IS G++Q Y + +G S ++ +G+ + IA
Sbjct: 227 -DKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV-TAVAIA 284
Query: 151 SSLDNKTSLYNNSSQ------WI 167
+ D+ S + + + +I
Sbjct: 285 ET-DSWESFFVSVRKAITVLFFI 306
>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 = 34.8 bits (79), Expect = 0.015
Identities = 26/163 (15%), Positives = 50/163 (30%), Gaps = 40/163 (24%)
Query: 46 IDALLNAAAQGYDVYNSTVYITLEPCSY-FGYTPPCTEALIKSGIKKVIIA-----INDP 99
LL+ + + V L +Y F +P TE S + ++ I ND
Sbjct: 68 FWTLLSKQEEMVQKFVEEV---LRI-NYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN 123
Query: 100 NPL----VS-GKGVAQLISA--------GISV-------KQGLMQKEAYEI--NIGFFSR 137
VS + +L A + + K + A ++ + +
Sbjct: 124 QVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWV----ALDVCLSYKVQCK 179
Query: 138 MQRGIPWVRM----KIASSLDNKTSLYNNSSQWITSKESRNDS 176
M I W+ + + L+ L TS+ + +
Sbjct: 180 MDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSN 222
>3g8q_A Predicted RNA-binding protein, contains thump domain; cytidine
deaminase, ferredoxin-like domain; 2.40A {Methanopyrus
kandleri}
Length = 278
Score = 34.3 bits (78), Expect = 0.015
Identities = 18/82 (21%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 12 INSSPNPRVGCVIVKEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPC 71
+N P V +++ I++ + HAE + +DV V++T PC
Sbjct: 16 LNEIPKRTVTAALLEGGEIVA---VEEADDEHAE-----RKLVRRHDVEGKVVFVTARPC 67
Query: 72 SYFGYTPPCTEALIKSGIKKVI 93
Y C L ++G+ V+
Sbjct: 68 LY------CARELAEAGVAGVV 83
>1r5t_A Cytidine deaminase; zinc dependent deaminase, RNA editing,
apobec-1 related protein, hydrolase; 2.00A
{Saccharomyces cerevisiae} SCOP: c.97.1.1
Length = 142
Score = 29.4 bits (66), Expect = 0.40
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 6/66 (9%)
Query: 19 RVGCVIVKEKRIISCG----YTKSPGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSYF 74
RVGC I+ +I G AE A++ G+ + I +
Sbjct: 33 RVGCSILTNNDVIFTGANVENASYSNCICAERSAMIQVLMAGHRSGWKCMVICGDSED-- 90
Query: 75 GYTPPC 80
PC
Sbjct: 91 QCVSPC 96
>3b8f_A Putative blasticidin S deaminase; cytidine deaminase, structural
genomics, MCSG, protein structure initiative; 1.90A
{Bacillus anthracis}
Length = 142
Score = 28.4 bits (63), Expect = 0.93
Identities = 9/42 (21%), Positives = 11/42 (26%)
Query: 39 PGGNHAEIDALLNAAAQGYDVYNSTVYITLEPCSYFGYTPPC 80
E A+L A V +S S PC
Sbjct: 48 STELCMETGAILEAHKFQKKVTHSICLARENEHSELKVLSPC 89
>2h3h_A Sugar ABC transporter, periplasmic sugar-binding protein; glucose
binding protein, periplasmic binding protein, GBP; HET:
BGC; 1.70A {Thermotoga maritima} PDB: 2qvc_A* 3c6q_B*
Length = 313
Score = 28.2 bits (63), Expect = 1.7
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
E+ I G+ + IA +DP ++ + + + GI V
Sbjct: 51 ESFIAEGVNGIAIAPSDPTAVIP--TIKKALEMGIPV 85
>3g1w_A Sugar ABC transporter; sugar-binding protein, bacillus halod target
11229F, transport protein, structural genomics; 2.02A
{Bacillus halodurans c-125}
Length = 305
Score = 27.7 bits (62), Expect = 2.6
Identities = 9/37 (24%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
E I + I+ DP L + + + AGI +
Sbjct: 55 EQAIAKNPAGIAISAIDPVELTD--TINKAVDAGIPI 89
>3nhv_A BH2092 protein; alpha-beta protein, structural genomics, PSI-2,
protein STRU initiative, northeast structural genomics
consortium, NESG; 2.50A {Bacillus halodurans} PDB:
3o3w_A
Length = 144
Score = 26.7 bits (59), Expect = 3.4
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 26 KEKRIISCGYTKSPGGNHAEIDALLNAAAQGYDVYN 61
KEK II+ Y P N A A A G+ V
Sbjct: 71 KEKVIIT--YCWGPACNGATK-AAAKFAQLGFRVKE 103
>2uzh_A 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; ISPF,
lyase, mycobacteria, complex with CDP; HET: CDP IPE;
2.2A {Mycobacterium smegmatis}
Length = 165
Score = 26.3 bits (59), Expect = 4.9
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 43 HAEIDALLNAAAQG 56
HA DALL+AA G
Sbjct: 47 HALCDALLSAAGLG 60
>3mqd_A Beta-ketoacyl synthase; ssgcid, ALS collaborative crystallography,
beta-ketoacyl SYN brucella melitensis, fragments of
LIFE; HET: 3MQ; 1.25A {Brucella melitensis biovar
abortus} PDB: 3lrf_A* 3u0e_A* 3u0f_A*
Length = 428
Score = 26.7 bits (60), Expect = 5.2
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 1 MTLALQQAKLSINSSPNPRVGCVI 24
M A+ A L+ N R G ++
Sbjct: 100 MDQAIADAGLTEEEVSNERTGIIM 123
>1iv3_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase;
isoprenoid, non-mevalonate, riken structural
genomics/proteomics initiative, RSGI; 1.52A {Thermus
thermophilus} SCOP: d.79.5.1 PDB: 1iv2_A 1iv4_A* 1iv1_A
Length = 152
Score = 25.9 bits (58), Expect = 5.9
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 43 HAEIDALLNAAAQG 56
HA DALL+A G
Sbjct: 42 HALTDALLSAYGLG 55
>3f0d_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; ssgcid, niaid,
isoprene biosynthe lyase, metal-binding, structural
genomics; 1.20A {Burkholderia pseudomallei} PDB: 3f0e_A
3f0f_A* 3f0g_A* 3ieq_A* 3iew_A* 3jvh_A* 3k14_A* 3k2x_A*
3ke1_A* 3mbm_A* 3p0z_A* 3p10_A* 3q8h_A* 3qhd_A* 3ikf_A*
3ike_A*
Length = 183
Score = 26.0 bits (58), Expect = 5.9
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 43 HAEIDALLNAAAQG 56
HA DAL AAA G
Sbjct: 65 HAITDALFGAAALG 78
>1t0a_A 2C-methyl-D-erythritol 2,4-cyclodiphosphate synth; mixed alpha
beta, homotrimer, synthase, lyase; HET: FPP; 1.60A
{Shewanella oneidensis} SCOP: d.79.5.1 PDB: 1vh8_A*
1vha_A* 1jn1_A 3fpi_A* 3f6m_A*
Length = 159
Score = 25.9 bits (58), Expect = 6.0
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 43 HAEIDALLNAAAQG 56
HA DA+L A A G
Sbjct: 44 HAISDAILGAMALG 57
>1gx1_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase;
isoprenoid, lyase, isoprene biosynthesis; HET: CDP;
1.8A {Escherichia coli} SCOP: d.79.5.1 PDB: 1h47_A*
1h48_A* 3ern_A* 3eor_A* 3elc_A* 3esj_A* 3fba_A* 2amt_A*
1knj_A* 1knk_A 1u3l_A* 1u3p_A 1u40_A* 1u43_A* 1jy8_A*
2gzl_A* 1yqn_A* 3ghz_A* 3t80_A*
Length = 160
Score = 25.9 bits (58), Expect = 6.1
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 43 HAEIDALLNAAAQG 56
HA DALL AAA G
Sbjct: 43 HALTDALLGAAALG 56
>3re3_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; structural
genomics, center for structural genomics of infec
diseases, csgid; 2.65A {Francisella tularensis subsp}
Length = 162
Score = 25.9 bits (58), Expect = 6.2
Identities = 7/14 (50%), Positives = 8/14 (57%)
Query: 43 HAEIDALLNAAAQG 56
HA DA+L A G
Sbjct: 48 HALCDAILGALGLG 61
>2pmp_A 2-C-methyl-D-erythritol 2,4-cyclodiphosphate SYNT; plant enzymes,
MEP pathway, isoprenoid proteins, CMP, zinc IONS,
lyase; HET: C5P; 2.30A {Arabidopsis thaliana}
Length = 160
Score = 25.9 bits (58), Expect = 6.8
Identities = 5/14 (35%), Positives = 7/14 (50%)
Query: 43 HAEIDALLNAAAQG 56
H +DA+L A
Sbjct: 45 HCVVDAILGALGLP 58
>1tjy_A Sugar transport protein; protein-ligand complex, signaling protein;
HET: PAV; 1.30A {Salmonella typhimurium} SCOP: c.93.1.1
PDB: 1tm2_A 3t95_A* 3ejw_A*
Length = 316
Score = 25.8 bits (57), Expect = 8.6
Identities = 5/37 (13%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
+ G +I++ P+ L + + + G+ +
Sbjct: 54 NNFVNQGYDAIIVSAVSPDGLCP--ALKRAMQRGVKI 88
>3gbv_A Putative LACI-family transcriptional regulator; NYSGXRC, PSI-II,
11231J, structur genomics, protein structure initiative;
2.20A {Bacteroides fragilis}
Length = 304
Score = 25.8 bits (57), Expect = 8.9
Identities = 8/37 (21%), Positives = 12/37 (32%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
+A+I+ V+ A P L GI
Sbjct: 63 QAVIEEQPDGVMFAPTVPQYTK--GFTDALNELGIPY 97
>3rot_A ABC sugar transporter, periplasmic sugar binding; nysgrc,
PSI-biology, structural genomics; 1.91A {Legionella
pneumophila subsp}
Length = 297
Score = 25.8 bits (57), Expect = 9.2
Identities = 4/37 (10%), Positives = 10/37 (27%), Gaps = 2/37 (5%)
Query: 82 EALIKSGIKKVIIAINDPNPLVSGKGVAQLISAGISV 118
E+ + + + I + + I V
Sbjct: 55 ESALATYPSGIATTIPSDTAFSK--SLQRANKLNIPV 89
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
0.317 0.132 0.389
Gapped
Lambda K H
0.267 0.0662 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,880,665
Number of extensions: 166050
Number of successful extensions: 530
Number of sequences better than 10.0: 1
Number of HSP's gapped: 494
Number of HSP's successfully gapped: 49
Length of query: 192
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 104
Effective length of database: 4,244,745
Effective search space: 441453480
Effective search space used: 441453480
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 (21.6 bits)
S2: 54 (24.7 bits)