RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6804
(207 letters)
>2w4l_A DCMP deaminse, deoxycytidylate deaminase; pyrimidine metabolism,
nucleotide biosynthesis, zinc, hexamer, hydrolase,
metal-binding, phosphoprotein; 2.10A {Homo sapiens}
Length = 178
Score = 189 bits (483), Expect = 5e-62
Identities = 83/128 (64%), Positives = 98/128 (76%), Gaps = 6/128 (4%)
Query: 80 SPHKRVDDVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDD 139
S KR DD LEW EYFMA AFL A+RSKDP ++VGA IVN +NKIVG GYNGMP GCSDD
Sbjct: 2 SCKKR-DDYLEWPEYFMAVAFLSAQRSKDPNSQVGACIVNSENKIVGIGYNGMPNGCSDD 60
Query: 140 EFPWDKNTHDELD-----MCHAEMNAILNKNSADTKRCKLYTSLFPCNECAKVIIQSGIK 194
PW + ++LD +CHAE+NAI+NKN D K C +Y +LFPCNECAK+IIQ+GIK
Sbjct: 61 VLPWRRTAENKLDTKYPYVCHAELNAIMNKNLTDVKGCSMYVALFPCNECAKLIIQAGIK 120
Query: 195 EVIYMCDK 202
EVI+M DK
Sbjct: 121 EVIFMSDK 128
Score = 95.6 bits (238), Expect = 4e-25
Identities = 35/66 (53%), Positives = 48/66 (72%)
Query: 1 MNAILNKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPATIASKRMFD 60
+NAI+NKN D K C +Y +LFPCNECAK+IIQ+GIKEVI+M DK+ A++ +F+
Sbjct: 84 LNAIMNKNLTDVKGCSMYVALFPCNECAKLIIQAGIKEVIFMSDKYHDSDEATAARLLFN 143
Query: 61 AAKVHY 66
A V +
Sbjct: 144 MAGVTF 149
>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 = 166 bits (422), Expect = 1e-52
Identities = 46/141 (32%), Positives = 72/141 (51%), Gaps = 5/141 (3%)
Query: 68 SEMDKMNGVQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGT 127
S M M G Q + L W +YFMA+A L++KRS VGAV+V +N+I+ T
Sbjct: 19 SHMASMTGGQQMGRGSM-TNRLSWQDYFMANAELISKRSTCNRAYVGAVLVK-NNRIIAT 76
Query: 128 GYNGMPIGCSD-DEFPWDKNTHDELDMCHAEMNAILN--KNSADTKRCKLYTSLFPCNEC 184
GYNG + D+ + + HAEMNA++ K ++Y + FPC C
Sbjct: 77 GYNGGVADTDNCDDVGHEMEDGHCIRTVHAEMNALIQCAKEGISANNTEIYVTHFPCINC 136
Query: 185 AKVIIQSGIKEVIYMCDKQMS 205
K ++Q+G+K++ Y ++
Sbjct: 137 TKALLQAGVKKITYNTAYRIH 157
Score = 80.5 bits (199), Expect = 2e-19
Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 1 MNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPATIASKRM 58
MNA++ K ++Y + FPC C K ++Q+G+K++ Y + +
Sbjct: 108 MNALIQCAKEGISANNTEIYVTHFPCINCTKALLQAGVKKITYNTAYRIHP----FAIEL 163
Query: 59 FDAAKVHY 66
+V Y
Sbjct: 164 MTQKEVEY 171
>1vq2_A DCMP deaminase, deoxycytidylate deaminase; hydrolase; HET: DDN;
2.20A {Enterobacteria phage T4} SCOP: c.97.1.2
Length = 193
Score = 137 bits (346), Expect = 3e-41
Identities = 45/155 (29%), Positives = 64/155 (41%), Gaps = 42/155 (27%)
Query: 92 HEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIG---CSD---------- 138
+ A+LV++ SK +VGAVI + +I+ TGYNG P G C D
Sbjct: 3 ASTVLQIAYLVSQESKCCSWKVGAVIEK-NGRIISTGYNGSPAGGVNCCDYAAEQGWLLN 61
Query: 139 --------------------DEFPWDKNTHDELD------MCHAEMNAILN--KNSADTK 170
D F K HAE+NAIL +N + +
Sbjct: 62 KPKHAIIQGHKPECVSFGSTDRFVLAKEHRSAHSEWSSKNEIHAELNAILFAAENGSSIE 121
Query: 171 RCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKQMS 205
+Y +L PC +CAK I QSGIK+++Y +
Sbjct: 122 GATMYVTLSPCPDCAKAIAQSGIKKLVYCETYDKN 156
Score = 78.1 bits (192), Expect = 2e-18
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 5/68 (7%)
Query: 1 MNAILN--KNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPATIASKRM 58
+NAIL +N + + +Y +L PC +CAK I QSGIK+++Y K KP +
Sbjct: 107 LNAILFAAENGSSIEGATMYVTLSPCPDCAKAIAQSGIKKLVYCETYDKNKP---GWDDI 163
Query: 59 FDAAKVHY 66
A +
Sbjct: 164 LRNAGIEV 171
>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 = 74.2 bits (183), Expect = 4e-17
Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 25/117 (21%)
Query: 90 EWHEYFMASAFLVAKRSKD----PVTRVGAVIV-NEDNKIVGTGYNGMPIGCSDDEFPWD 144
+W + M A+ A P+ G ++ N+D ++G G+N M
Sbjct: 12 KWDQKGMDIAYEEAALGYKEGGVPI---GGCLINNKDGSVLGRGHN-MRFQKGS---A-- 62
Query: 145 KNTHDELDMCHAEMNAILNKNSADTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
T H E++ + N + K LYT+L PC+ C II GI +
Sbjct: 63 --TL------HGEISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVV 111
Score = 38.4 bits (90), Expect = 4e-04
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 1 MNAILNKNSADTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 41
++ + N + K LYT+L PC+ C II GI +
Sbjct: 68 ISTLENCGRLEGKVYKDTTLYTTLSPCDMCTGAIIMYGIPRCVV 111
>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 = 67.4 bits (165), Expect = 2e-14
Identities = 33/121 (27%), Positives = 43/121 (35%), Gaps = 27/121 (22%)
Query: 92 HEYFMASAFLVAKRSKD-----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKN 146
HE F+ A +A + P GAVIV D I+ G N
Sbjct: 11 HETFLKRAVTLACEGVNAGIGGPF---GAVIVK-DGAIIAEGQN-NVTT----------- 54
Query: 147 THDELDMCHAEMNAI----LNKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYMCDK 202
++D HAE+ AI + C LYTS PC C I + K V Y +
Sbjct: 55 SNDPT--AHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEH 112
Query: 203 Q 203
Sbjct: 113 T 113
Score = 40.0 bits (94), Expect = 1e-04
Identities = 13/37 (35%), Positives = 15/37 (40%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHKQKPA 51
C LYTS PC C I + K V Y + A
Sbjct: 82 CILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEA 118
>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 = 66.5 bits (163), Expect = 4e-14
Identities = 30/121 (24%), Positives = 47/121 (38%), Gaps = 32/121 (26%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
E +M A +AK + + PV G ++V +N++VG G N T
Sbjct: 26 TEKWMEEAMHMAKEALENTEVPV---GCLMV-YNNEVVGKGRN-EVNQ-----------T 69
Query: 148 HDELDMCHAEMNAI-------LNKNSADTKR---CKLYTSLFPCNECAKVIIQSGIKEVI 197
+ HAEM AI + ++ LY ++ PC CA + I V+
Sbjct: 70 KNAT--RHAEMVAIDQVLDWCRQSGKSPSEVFEHTVLYVTVEPCIMCAAALRLMKIPLVV 127
Query: 198 Y 198
Y
Sbjct: 128 Y 128
Score = 33.0 bits (76), Expect = 0.032
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
LY ++ PC CA + I V+Y
Sbjct: 102 TVLYVTVEPCIMCAAALRLMKIPLVVY 128
>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 = 66.7 bits (163), Expect = 5e-14
Identities = 22/133 (16%), Positives = 41/133 (30%), Gaps = 31/133 (23%)
Query: 80 SPHKRVDDVLEWHEYFMASAFLVAKRSKD----PVTRVGAVIV-NEDNKIVGTGYNGMPI 134
VL E M + + + P A + + ++ G N +
Sbjct: 16 VQANNEPRVLAAPEARMGYVLELVRANIAADGGPF---AAAVFERDSGLLIAAGTN-RVV 71
Query: 135 GCSDDEFPWDKNTHDELDMCHAEMNAI---------LNKNSADTKRCKLYTSLFPCNECA 185
HAE+ A+ + ++ C+L TS PC C
Sbjct: 72 PGRC---S----------AAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCF 118
Query: 186 KVIIQSGIKEVIY 198
+I SG++ ++
Sbjct: 119 GAVIWSGVRSLVC 131
Score = 38.2 bits (89), Expect = 6e-04
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIYMCDKHK 47
C+L TS PC C +I SG++ ++
Sbjct: 105 CELVTSAEPCVMCFGAVIWSGVRSLVCAARSDD 137
>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 = 65.7 bits (161), Expect = 7e-14
Identities = 35/115 (30%), Positives = 53/115 (46%), Gaps = 26/115 (22%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
EYF+ A AKR+ + PV GA+IV ++ +I+ +N
Sbjct: 23 KEYFLKVALREAKRAFEKGEVPV---GAIIV-KEGEIISKAHN-SVEE-----------L 66
Query: 148 HDELDMCHAEMNAILNKNSA-DTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
D HAEM AI +TK C+LY +L PC C+ ++ S I++VI+
Sbjct: 67 KDPT--AHAEMLAIKEACRRLNTKYLEGCELYVTLEPCIMCSYALVLSRIEKVIF 119
Score = 32.5 bits (75), Expect = 0.051
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
C+LY +L PC C+ ++ S I++VI+
Sbjct: 93 CELYVTLEPCIMCSYALVLSRIEKVIF 119
>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 = 67.6 bits (166), Expect = 1e-13
Identities = 37/125 (29%), Positives = 50/125 (40%), Gaps = 37/125 (29%)
Query: 92 HEYFMASAFLVAKRSKDPVT---RVGAVIVNEDNKIVGTGY---NGMPIGCSDDEFPWDK 145
+E FM A +AK+ V VGAV+V D +I+ G+ G P
Sbjct: 14 YETFMKRAIELAKKGLGRVNPNPPVGAVVVK-DGRIIAEGFHPYFGGP------------ 60
Query: 146 NTHDELDMCHAEMNAI--LNKNSADTKRCKLYTSLFPCNE------CAKVIIQSGIKEVI 197
HAE AI K D + L +L PC+ C +II+SGIK V+
Sbjct: 61 ---------HAERMAIESARKKGEDLRGATLIVTLEPCDHHGKTPPCTDLIIESGIKTVV 111
Query: 198 Y-MCD 201
D
Sbjct: 112 IGTRD 116
Score = 31.4 bits (72), Expect = 0.17
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 9/52 (17%)
Query: 2 NAI--LNKNSADTKRCKLYTSLFPCNE------CAKVIIQSGIKEVIY-MCD 44
AI K D + L +L PC+ C +II+SGIK V+ D
Sbjct: 65 MAIESARKKGEDLRGATLIVTLEPCDHHGKTPPCTDLIIESGIKTVVIGTRD 116
>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 = 63.3 bits (155), Expect = 4e-13
Identities = 31/115 (26%), Positives = 46/115 (40%), Gaps = 26/115 (22%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
YFM A AK++ P+ GA+I +D++++ +N +
Sbjct: 7 DIYFMTLAIEEAKKAAQLGEVPI---GAIIT-KDDEVIARAHN-LRET-----------L 50
Query: 148 HDELDMCHAEMNAILNKNSA-DTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
HAE AI + R C LY +L PC CA I+ S I V+Y
Sbjct: 51 QQPT--AHAEHIAIERAAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVY 103
Score = 30.5 bits (70), Expect = 0.20
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
C LY +L PC CA I+ S I V+Y
Sbjct: 77 CTLYVTLEPCVMCAGTIVMSRIPRVVY 103
>2nx8_A TRNA-specific adenosine deaminase; TAD, hydrolase; 2.00A
{Streptococcus pyogenes serotype M6}
Length = 179
Score = 63.8 bits (156), Expect = 4e-13
Identities = 32/115 (27%), Positives = 48/115 (41%), Gaps = 26/115 (22%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
YFM A +++S P+ G VIV D +I+G G+N +
Sbjct: 16 QTYFMQEALKESEKSLQKAEIPI---GCVIVK-DGEIIGRGHN-AREE-----------S 59
Query: 148 HDELDMCHAEMNAILNKNSA-DTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
+ + HAEM AI N+ R L+ ++ PC C+ I + I VIY
Sbjct: 60 NQAI--MHAEMMAINEANAHEGNWRLLDTTLFVTIEPCVMCSGAIGLARIPHVIY 112
Score = 31.0 bits (71), Expect = 0.14
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
L+ ++ PC C+ I + I VIY
Sbjct: 86 TTLFVTIEPCVMCSGAIGLARIPHVIY 112
>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 = 65.6 bits (161), Expect = 5e-13
Identities = 40/142 (28%), Positives = 59/142 (41%), Gaps = 42/142 (29%)
Query: 73 MNGVQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDPVT---RVGAVIVNEDNKIVGTGY 129
M G + H ++ EY+M A +AK+ + VGAV+V D +IVG G
Sbjct: 1 MRGSHHHHHHGSME------EYYMKLALDLAKQGEGQTESNPLVGAVVVK-DGQIVGMGA 53
Query: 130 ---NGMPIGCSDDEFPWDKNTHDELDMCHAEMNAILNKNSADTKRCKLYTSLFPCNE--- 183
G HAE++A ++ A + +Y +L PC+
Sbjct: 54 HLKYGEA---------------------HAEVHA-IHMAGAHAEGADIYVTLEPCSHYGK 91
Query: 184 ---CAKVIIQSGIKEVIY-MCD 201
CA++II SGIK V M D
Sbjct: 92 TPPCAELIINSGIKRVFVAMRD 113
Score = 31.3 bits (72), Expect = 0.17
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 7/35 (20%)
Query: 17 LYTSLFPCNE------CAKVIIQSGIKEVIY-MCD 44
+Y +L PC+ CA++II SGIK V M D
Sbjct: 79 IYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRD 113
>2a8n_A Cytidine and deoxycytidylate deaminase; RNA editing, RNA binding
protein; 1.60A {Agrobacterium tumefaciens} SCOP:
c.97.1.2
Length = 144
Score = 62.5 bits (153), Expect = 7e-13
Identities = 28/115 (24%), Positives = 45/115 (39%), Gaps = 26/115 (22%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
+FM A + A+ + + P+ GAV+V D +++ N
Sbjct: 4 RTHFMELALVEARSAGERDEVPI---GAVLV-LDGRVIARSGN-RTRE-----------L 47
Query: 148 HDELDMCHAEMNAILNKNSA-DTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
+D HAE+ I A +R LY +L PC CA I + I+ + Y
Sbjct: 48 NDVT--AHAEIAVIRMACEALGQERLPGADLYVTLEPCTMCAAAISFARIRRLYY 100
Score = 30.9 bits (71), Expect = 0.13
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
LY +L PC CA I + I+ + Y
Sbjct: 74 ADLYVTLEPCTMCAAAISFARIRRLYY 100
>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 = 62.6 bits (153), Expect = 9e-13
Identities = 40/115 (34%), Positives = 56/115 (48%), Gaps = 26/115 (22%)
Query: 92 HEYFMASAFLVAKRSKD----PVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNT 147
HEY+M A +AKR+ D PV GAV+V+ +N+++G G+N PIG
Sbjct: 9 HEYWMRHALTLAKRAWDEREVPV---GAVLVH-NNRVIGEGWN-RPIG-----------R 52
Query: 148 HDELDMCHAEMNAILNKNSA-DTKR---CKLYTSLFPCNECAKVIIQSGIKEVIY 198
HD HAE+ A+ R LY +L PC CA +I S I V++
Sbjct: 53 HDPT--AHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVF 105
Score = 31.4 bits (72), Expect = 0.12
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 15 CKLYTSLFPCNECAKVIIQSGIKEVIY 41
LY +L PC CA +I S I V++
Sbjct: 79 ATLYVTLEPCVMCAGAMIHSRIGRVVF 105
>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 = 63.0 bits (154), Expect = 4e-12
Identities = 40/147 (27%), Positives = 54/147 (36%), Gaps = 39/147 (26%)
Query: 71 DKMNGVQNGSPHKRVDDVLEW---HEYFMASAFLVAKRSKDPVT---RVGAVIVNEDNKI 124
D G K + L EY+MA A +A+R + VG VIV D +I
Sbjct: 6 DDDKGSSTSLYKKAGSETLYIQGQDEYYMARALKLAQRGRFTTHPNPNVGCVIVK-DGEI 64
Query: 125 VGTGY---NGMPIGCSDDEFPWDKNTHDELDMCHAEMNAILNKNSADTKRCKLYTSLFPC 181
VG GY G P HAE++A L K Y +L PC
Sbjct: 65 VGEGYHQRAGEP---------------------HAEVHA-LRMAGEKAKGATAYVTLEPC 102
Query: 182 NE------CAKVIIQSGIKEVIY-MCD 201
+ C +I +G+ V+ M D
Sbjct: 103 SHHGRTPPCCDALIAAGVARVVASMQD 129
Score = 31.0 bits (71), Expect = 0.28
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 17 LYTSLFPCNE------CAKVIIQSGIKEVIY-MCD 44
Y +L PC+ C +I +G+ V+ M D
Sbjct: 95 AYVTLEPCSHHGRTPPCCDALIAAGVARVVASMQD 129
>3g8q_A Predicted RNA-binding protein, contains thump domain; cytidine
deaminase, ferredoxin-like domain; 2.40A {Methanopyrus
kandleri}
Length = 278
Score = 42.4 bits (99), Expect = 4e-05
Identities = 13/51 (25%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 149 DELDMCHAEMNAILNKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYM 199
+E D HAE ++ ++ + K ++ + PC CA+ + ++G+ V+Y+
Sbjct: 38 EEADDEHAE-RKLVRRHDVEGK--VVFVTARPCLYCARELAEAGVAGVVYL 85
Score = 38.2 bits (88), Expect = 0.001
Identities = 8/39 (20%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 4 ILNKNSADTKRCKLYTSLFPCNECAKVIIQSGIKEVIYM 42
++ ++ + K ++ + PC CA+ + ++G+ V+Y+
Sbjct: 49 LVRRHDVEGK--VVFVTARPCLYCARELAEAGVAGVVYL 85
>2fr5_A Cytidine deaminase; tetrahydrouridine, protein-inhibitor COM
alternate conformation of Arg68, hydrolase; HET: TYU;
1.48A {Mus musculus} SCOP: c.97.1.1 PDB: 1zab_A* 2fr6_A*
1mq0_A*
Length = 146
Score = 32.1 bits (73), Expect = 0.058
Identities = 24/122 (19%), Positives = 40/122 (32%), Gaps = 25/122 (20%)
Query: 96 MASAFLVAKRSKDPVT--RVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELDM 153
+ S+ K + P + VGA ++ D +I +G N E
Sbjct: 19 LLSSREAKKSAYCPYSRFPVGAALLTGDGRIF-SGCN--------IENA------CYPLG 63
Query: 154 CHAEMNAILNKNSADTKRCKLYTS--------LFPCNECAKVIIQSGIKEVIYMCDKQMS 205
AE AI S K + + PC C +V+ + G +YM +
Sbjct: 64 VCAERTAIQKAISEGYKDFRAIAISSDLQEEFISPCGACRQVMREFGTDWAVYMTKPDGT 123
Query: 206 YK 207
+
Sbjct: 124 FV 125
>3b8f_A Putative blasticidin S deaminase; cytidine deaminase, structural
genomics, MCSG, protein structure initiative; 1.90A
{Bacillus anthracis}
Length = 142
Score = 29.5 bits (66), Expect = 0.46
Identities = 17/123 (13%), Positives = 31/123 (25%), Gaps = 26/123 (21%)
Query: 96 MASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIGCSDDEFPWDKNTHDELDMCH 155
+ ++ A I ED I + D + ++C
Sbjct: 8 YDVVKQLIEQRYPNDWGGAAAIRVEDGTIY--------TSVAPD------VINASTELC- 52
Query: 156 AEMNAILNKNSADTKRCKL-----------YTSLFPCNECAKVIIQSGIKEVIYMCDKQM 204
E AIL + K L PC C + + G + + + +
Sbjct: 53 METGAILEAHKFQKKVTHSICLARENEHSELKVLSPCGVCQERLFYWGPEVQCAITNAKQ 112
Query: 205 SYK 207
Sbjct: 113 DII 115
>1ecs_A Bleomycin resistance protein; arm-exchange, antibiotic inhibitor;
HET: PG4; 1.70A {Klebsiella pneumoniae} SCOP: d.32.1.2
PDB: 1ewj_A* 1niq_B* 1mh6_A
Length = 126
Score = 28.3 bits (63), Expect = 0.88
Identities = 5/55 (9%), Positives = 15/55 (27%)
Query: 59 FDAAKVHYWSEMDKMNGVQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDPVTRV 113
+ +++ S R+DD+ E++ + +
Sbjct: 40 RGDLMLEFFAHPGLDPLASWFSCCLRLDDLAEFYRQCKSVGIQETSSGYPRIHAP 94
>3b4x_A 367AA long hypothetical cytochrome P450; HEM protein, heme, iron,
metal-binding, monooxygenase, oxidoreductase; HET: HEM;
1.94A {Sulfolobus tokodaii} PDB: 1ue8_A*
Length = 367
Score = 29.1 bits (66), Expect = 0.92
Identities = 8/50 (16%), Positives = 14/50 (28%), Gaps = 3/50 (6%)
Query: 60 DAAKVHYWSEMDKMNGVQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDP 109
D KV WS++ + + LE + + R
Sbjct: 136 DVKKVKDWSDLVALRLGRADEIFSIGRKYLELISFSKK---ELDSRKGKE 182
>3v4k_A DNA DC->DU-editing enzyme apobec-3G; antiviral defense, HOST-virus
interaction, hydrola metal-binding, nucleus; HET: DNA;
1.38A {Homo sapiens} PDB: 3v4j_A* 3ir2_A* 2kem_A*
2jyw_A* 2kbo_A* 3e1u_A* 3iqs_A*
Length = 203
Score = 28.3 bits (63), Expect = 1.4
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 8/61 (13%)
Query: 135 GCSDDEFPWDKNTHDELDMCHAEMNAI-----LNKNSADTKRCKLYTSLFPCNECAKVII 189
G ++ P + H L+ HAE+ + + R +TS PC CA+ +
Sbjct: 63 GFLANQAP---HKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMA 119
Query: 190 Q 190
+
Sbjct: 120 K 120
>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 = 28.7 bits (63), Expect = 1.5
Identities = 23/118 (19%), Positives = 45/118 (38%), Gaps = 30/118 (25%)
Query: 22 FPCNECAKVIIQSGIKEVIYMCD-KH--KQKPATIASKRMFDAAKVHYWSEMDK-MNGVQ 77
F C + +Q K ++ + H K A + R+F W+ + K VQ
Sbjct: 33 FDCKD-----VQDMPKSILSKEEIDHIIMSKDAVSGTLRLF-------WTLLSKQEEMVQ 80
Query: 78 NGSPHKRVDDVLEWHEY-FMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPI 134
K V++VL Y F+ S + P + + + + + +++ YN +
Sbjct: 81 -----KFVEEVLR-INYKFLMSPI--KTEQRQP-SMMTRMYIEQRDRL----YNDNQV 125
>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase,
nucleotide-binding, Pro serine protease, stress
response; HET: ADP; 3.40A {Bacillus subtilis} PDB:
1x37_A
Length = 543
Score = 28.2 bits (64), Expect = 1.9
Identities = 8/26 (30%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 140 EFPWDKNTHDELDMCHAEMNAILNKN 165
PW T D+LD+ A +L++
Sbjct: 59 ALPWTDETDDKLDLKEAG--RLLDEE 82
>2a8j_A Taspase 1, threonine aspartase 1; MLL, glycosylspraginase,
asparaginase, hydrolase; 1.90A {Homo sapiens} PDB:
2a8i_A 2a8m_A 2a8l_A
Length = 420
Score = 28.0 bits (62), Expect = 2.5
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 10/85 (11%)
Query: 76 VQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVNEDNKIVGTGYNGMPIG 135
+Q H+ + + M + F+ + +G VIV + +
Sbjct: 310 LQAEDAHQALLET-------MQNKFISSPFLASEDGVLGGVIVLRSCRCSAEPDSSQNKQ 362
Query: 136 CSDDEFPWDKNTHDELDMCHAEMNA 160
EF W T MC M+A
Sbjct: 363 TLLVEFLWSHTT---ESMCVGYMSA 384
>3tnl_A Shikimate dehydrogenase; structural genomics, center for structural
genomics of infec diseases, csgid; HET: NAD SKM; 1.45A
{Listeria monocytogenes} PDB: 3toz_A*
Length = 315
Score = 27.6 bits (62), Expect = 3.2
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
VGAV +VN+D + G+
Sbjct: 117 LVGAVNTVVNDDGVLT--GHI 135
>1npy_A Hypothetical shikimate 5-dehydrogenase-like protein HI0607;
structural genomics, PSI, protein structure initiative;
1.75A {Haemophilus influenzae} SCOP: c.2.1.7 c.58.1.5
Length = 271
Score = 27.5 bits (62), Expect = 3.2
Identities = 6/21 (28%), Positives = 11/21 (52%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
+ +V IVN++ + YN
Sbjct: 83 AIESVNTIVNDNGFLR--AYN 101
>2egg_A AROE, shikimate 5-dehydrogenase; dimer, X-RAY diffraction,
structural genomics, NPPSFA; 2.25A {Geobacillus
kaustophilus}
Length = 297
Score = 27.1 bits (61), Expect = 3.5
Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
R+GAV I+N D ++V GYN
Sbjct: 103 RIGAVNTIINNDGRLV--GYN 121
>3t4e_A Quinate/shikimate dehydrogenase; structural genomics, center for
structural genomics of infec diseases, csgid; HET: NAD;
1.95A {Salmonella enterica subsp} PDB: 1npd_A* 1o9b_A*
1vi2_A*
Length = 312
Score = 27.2 bits (61), Expect = 3.5
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
VGA+ IVN+D + GYN
Sbjct: 111 LVGAINTIVNDDGYLR--GYN 129
>1nvt_A Shikimate 5'-dehydrogenase; structural genomics, PSI, protein
structure initiative; HET: NAP; 2.35A
{Methanocaldococcus jannaschii} SCOP: c.2.1.7 c.58.1.5
Length = 287
Score = 27.1 bits (61), Expect = 3.8
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
+GAV I ED K + GYN
Sbjct: 91 LIGAVNTIKIEDGKAI--GYN 109
>2d5c_A AROE, shikimate 5-dehydrogenase; substrate, dimer, structural
genomics, NPPSFA, Na project on protein structural and
functional analyses; HET: SKM; 1.65A {Thermus
thermophilus} PDB: 1wxd_A* 2cy0_A* 2ev9_A*
Length = 263
Score = 27.1 bits (61), Expect = 4.4
Identities = 6/21 (28%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
R+GAV ++ + ++ G+N
Sbjct: 80 RIGAVNTVLQVEGRLF--GFN 98
>3don_A Shikimate dehydrogenase; alpha-beta structure, rossman fold,
amino-acid biosynthesis, amino acid biosynthesis, NADP,
oxidoreductase; 2.10A {Staphylococcus epidermidis} PDB:
3doo_A*
Length = 277
Score = 27.1 bits (61), Expect = 4.6
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
VGAV ++ +D K + GYN
Sbjct: 80 SVGAVNTVLVKDGKWI--GYN 98
>3fio_A A cystathionine beta-synthase domain protein fused to A
Zn-ribbon-like domain; PF1953,APC40009,cystathionine
beta-synthase domain protein; 1.81A {Pyrococcus
furiosus} PDB: 3ghd_A
Length = 70
Score = 25.2 bits (56), Expect = 4.6
Identities = 5/15 (33%), Positives = 11/15 (73%)
Query: 112 RVGAVIVNEDNKIVG 126
+ G+ +V E ++I+G
Sbjct: 22 KAGSAVVMEGDEILG 36
>3grn_A MUTT related protein; structural genomics, hydrolase, PSI-2,
protein structure INI NEW YORK SGX research center for
structural genomics; 1.70A {Methanosarcina mazei}
Length = 153
Score = 26.2 bits (58), Expect = 5.6
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 105 RSKDPVTRVGAVIVNEDNKI 124
K + V A+I NE +
Sbjct: 3 LEKPYIISVYALIRNEKGEF 22
>1rya_A GDP-mannose mannosyl hydrolase; GDP-glucose, nudix, nudix
Mg-complex; HET: GDP; 1.30A {Escherichia coli} SCOP:
d.113.1.5 PDB: 2gt2_A 2gt4_A* 2i8t_A* 2i8u_A*
Length = 160
Score = 26.0 bits (57), Expect = 6.6
Identities = 3/31 (9%), Positives = 10/31 (32%)
Query: 95 FMASAFLVAKRSKDPVTRVGAVIVNEDNKIV 125
F+ P+ + ++ N + +
Sbjct: 3 FLRQEDFATVVRSTPLVSLDFIVENSRGEFL 33
>3eg7_A Spermidine N1-acetyltransferase; structural genomics, IDP016
transferase, center for structural genomics of
infectious D csgid; HET: MSE; 2.38A {Vibrio cholerae}
Length = 176
Score = 26.0 bits (58), Expect = 6.9
Identities = 7/68 (10%), Positives = 20/68 (29%), Gaps = 11/68 (16%)
Query: 60 DAAKVHYWSEMDKMNGVQNGSPHKRVDDVLEWHEYFMASAFLVAKRSKDPVTRVGAVIVN 119
D +H + + P++ D++ E + + V+ +
Sbjct: 17 DLRFIHNLNNNRNIMSYWFEEPYESFDELEELYNKHIHDN-----------AERRFVVED 65
Query: 120 EDNKIVGT 127
++G
Sbjct: 66 AQKNLIGL 73
>2hk9_A Shikimate dehydrogenase; shikimate pathway, drug design,
oxidoreductase; HET: ATR SKM NAP; 2.20A {Aquifex
aeolicus} PDB: 2hk8_A 2hk7_A
Length = 275
Score = 26.3 bits (59), Expect = 7.1
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
+GAV + E+ K GYN
Sbjct: 92 EIGAVNTVKFENGKAY--GYN 110
>2nyt_A Probable C->U-editing enzyme apobec-2; cytidine deaminase, zinc-ION
binding, hydrolase; 2.50A {Homo sapiens} PDB: 2rpz_A
Length = 190
Score = 25.9 bits (57), Expect = 7.9
Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 5/59 (8%)
Query: 137 SDDEFPWDKNT-HDELDMCHAEMNAI--LNKNSADTKRCKL--YTSLFPCNECAKVIIQ 190
+ + DE HAE + R + Y S PC CA II+
Sbjct: 45 KGGQVQASRGYLEDEHAAAHAEEAFFNTILPAFDPALRYNVTWYVSSSPCAACADRIIK 103
>2rc3_A CBS domain; in SITU proteolysis, BR, structural genomics, PSI-2,
protein structure initiative; HET: NAD; 1.60A
{Nitrosomonas europaea atcc 19718} SCOP: d.37.1.1
Length = 135
Score = 25.6 bits (57), Expect = 8.0
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 112 RVGAVIVNEDNKIVG 126
+GA++V +D K+VG
Sbjct: 39 NIGALLVMKDEKLVG 53
>3fbt_A Chorismate mutase and shikimate 5-dehydrogenase fusion protein;
structural genomics, oxidoreductase, amino-acid
biosynthesis; 2.10A {Clostridium acetobutylicum}
Length = 282
Score = 26.3 bits (59), Expect = 8.2
Identities = 6/21 (28%), Positives = 10/21 (47%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
++GAV + I G+N
Sbjct: 85 KIGAVNTLKFSREGIS--GFN 103
>3phh_A Shikimate dehydrogenase; shikimate pathway, helicobacter PYL
oxidoreductase, alpha/beta domain, rossmann fold; HET:
SKM; 1.42A {Helicobacter pylori} PDB: 3phg_A* 3phi_A*
3phj_A*
Length = 269
Score = 26.0 bits (58), Expect = 9.9
Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 4/21 (19%)
Query: 112 RVGAV--IVNEDNKIVGTGYN 130
GAV +V E++++V GYN
Sbjct: 85 ECGAVNTLVLENDELV--GYN 103
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
0.319 0.132 0.411
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,080,832
Number of extensions: 173936
Number of successful extensions: 716
Number of sequences better than 10.0: 1
Number of HSP's gapped: 665
Number of HSP's successfully gapped: 61
Length of query: 207
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 118
Effective length of database: 4,216,824
Effective search space: 497585232
Effective search space used: 497585232
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 (21.8 bits)
S2: 55 (24.9 bits)