RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2494
(166 letters)
>2d30_A Cytidine deaminase; purines, pyrimidines, nucleosides, nucleotides,
salvage of nucleosides and nucleotides, structural
genomics; 2.40A {Bacillus anthracis} SCOP: c.97.1.1
Length = 141
Score = 154 bits (392), Expect = 3e-49
Identities = 55/112 (49%), Positives = 72/112 (64%), Gaps = 5/112 (4%)
Query: 16 EQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKA 75
+ L +I+AR AY PYSK QVGAALL QD ++ GCNVENASYG+ CAE+TA+ KA
Sbjct: 12 SKQLIQEAIEARKQAYVPYSKFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKA 71
Query: 76 ISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSD 127
+SEG +F IA+ A D+ + V PCG+CRQV+ E D +V +
Sbjct: 72 VSEGDKEFVAIAIVA---DTKRPVPPCGACRQVMVELCKQ--DTKVYLSNLH 118
>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 = 149 bits (378), Expect = 3e-47
Identities = 44/132 (33%), Positives = 74/132 (56%), Gaps = 4/132 (3%)
Query: 7 MEFSALDPIE-QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTI 65
M+ ++ + + L +++A + +Y PYS +VG ++L +D IFTG NVENASY I
Sbjct: 1 MKVGGIEDRQLEALKRAALKACELSYSPYSHFRVGCSILTNNDVIFTGANVENASYSNCI 60
Query: 66 CAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVK 125
CAE++A+ + + G + V ++ VSPCG CRQ I EF D ++++
Sbjct: 61 CAERSAMIQVLMAGHRSGWKCMV-ICGDSEDQCVSPCGVCRQFINEFVVK--DFPIVMLN 117
Query: 126 SDRSQVGLITID 137
S S+ ++T+
Sbjct: 118 STGSRSKVMTMG 129
>1uwz_A Cytidine deaminase; CDD, tetramer, zinc binding, pyrimidine
metabolism, salvage, hydrolase; HET: THU; 1.99A
{Bacillus subtilis} SCOP: c.97.1.1 PDB: 1ux0_A* 1jtk_A*
1ux1_A*
Length = 136
Score = 143 bits (362), Expect = 7e-45
Identities = 56/112 (50%), Positives = 77/112 (68%), Gaps = 5/112 (4%)
Query: 16 EQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKA 75
Q L +++ARD AY PYSK QVGAALL +D ++ GCN+ENA+Y M CAE TA+ KA
Sbjct: 3 RQELITEALKARDMAYAPYSKFQVGAALLTKDGKVYRGCNIENAAYSMCNCAEATALFKA 62
Query: 76 ISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSD 127
+SEG T+F+ +AV+A D+ VSPCG+CRQVI+E + D+ V++
Sbjct: 63 VSEGDTEFQMLAVAA---DTPGPVSPCGACRQVISELCTK--DVIVVLTNLQ 109
>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 = 141 bits (358), Expect = 4e-44
Identities = 60/125 (48%), Positives = 82/125 (65%), Gaps = 6/125 (4%)
Query: 8 EFSALDPIE-QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTIC 66
A++P Q L S +A+ +AYCPYS+ VGAALL D IF+GCN+ENA Y + +C
Sbjct: 6 PSCAVEPEHVQRLLLSSREAKKSAYCPYSRFPVGAALLTGDGRIFSGCNIENACYPLGVC 65
Query: 67 AEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKS 126
AE+TAI KAISEG F+ IA+S+ L + +F+SPCG+CRQV+ EF + V + K
Sbjct: 66 AERTAIQKAISEGYKDFRAIAISSDLQE--EFISPCGACRQVMREFGTD---WAVYMTKP 120
Query: 127 DRSQV 131
D + V
Sbjct: 121 DGTFV 125
>3r2n_A Cytidine deaminase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid,
tuberculosis; 2.30A {Mycobacterium leprae}
Length = 138
Score = 141 bits (357), Expect = 5e-44
Identities = 37/121 (30%), Positives = 61/121 (50%), Gaps = 6/121 (4%)
Query: 10 SALDPIE-QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAE 68
++ + L ++ AR N+Y PYS VG A D + TG NVENASYG+ +CAE
Sbjct: 3 GSMGDVNWDTLQKAAVAARANSYAPYSNFPVGVAGFVNDGRLITGVNVENASYGLALCAE 62
Query: 69 KTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSDR 128
+ IS + G + + + + PCG CRQ++ E P +++++ K +
Sbjct: 63 CSMISALYATGGGRLVAVYCVD---GNGDSLMPCGRCRQLLYEHGGP--ELKIMTPKGVQ 117
Query: 129 S 129
+
Sbjct: 118 T 118
>3mpz_A Cytidine deaminase; ssgcid, structu genomics, seattle structural
genomics center for infectious hydrolase; 1.70A
{Mycobacterium smegmatis} PDB: 3ijf_X
Length = 150
Score = 136 bits (344), Expect = 5e-42
Identities = 41/137 (29%), Positives = 57/137 (41%), Gaps = 16/137 (11%)
Query: 1 MVGHDIMEFSALDPIE---------QNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIF 51
M H L+ L + +I+ +AY PYS VGAA L D
Sbjct: 1 MAHHHHHHMGTLEAQTQGPGSMVNWNALRSKAIEVSRHAYAPYSGFPVGAAALVDDGRTV 60
Query: 52 TGCNVENASYGMTICAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAE 111
TGCNVEN SYG+ +CAE + S G + ++ + PCG CRQV+ E
Sbjct: 61 TGCNVENVSYGLGLCAECAVVCALHSGGGGRLVALSCVG---PDGGVLMPCGRCRQVLLE 117
Query: 112 FSSPACDIQVLIVKSDR 128
++LI +
Sbjct: 118 H----GGPELLIDHAHG 130
>3dmo_A Cytidine deaminase; structural genomics, seattle structural
genomics center for infectious disease, ssgcid,
hydrolase; 1.60A {Burkholderia pseudomallei}
Length = 138
Score = 134 bits (338), Expect = 3e-41
Identities = 44/112 (39%), Positives = 69/112 (61%), Gaps = 3/112 (2%)
Query: 16 EQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISKA 75
L + AR+ AY PYS +VGAAL+ D +F GCNVENASYG+ CAE+TA+ A
Sbjct: 11 HHALIEAAKAAREKAYAPYSNFKVGAALVTNDGKVFHGCNVENASYGLCNCAERTALFSA 70
Query: 76 ISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSD 127
++ G + A+ A++ +++ ++PCG+CRQV+ E P ++V++
Sbjct: 71 LAAGYRPGEFAAI-AVVGETHGPIAPCGACRQVMIELGKP--TLEVVLTNMQ 119
>1ctt_A Cytidine deaminase; hydrolase; HET: DHZ; 2.20A {Escherichia coli}
SCOP: c.97.1.1 c.97.1.1 PDB: 1aln_A* 1af2_A* 1ctu_A*
Length = 294
Score = 131 bits (330), Expect = 3e-38
Identities = 24/111 (21%), Positives = 47/111 (42%), Gaps = 1/111 (0%)
Query: 12 LDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTA 71
L+ +I A + ++ PYSK G AL C+D IF+G ENA++ T+ + A
Sbjct: 184 YALTGDALSQAAIAAANRSHMPYSKSPSGVALECKDGRIFSGSYAENAAFNPTLPPLQGA 243
Query: 72 ISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVL 122
+ +G + I + + ++ + + + + D +L
Sbjct: 244 LILLNLKGY-DYPDIQRAVLAEKADAPLIQWDATSATLKALGCHSIDRVLL 293
Score = 116 bits (291), Expect = 2e-32
Identities = 34/129 (26%), Positives = 53/129 (41%), Gaps = 13/129 (10%)
Query: 6 IMEFSALDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVE--NASYGM 63
+ + LD L A A P S VGA T + G N+E A+
Sbjct: 41 LKSATGLDEDAL-AFALLPLAAACARTPLSNFNVGAIARGVSGTWYFGANMEFIGATMQQ 99
Query: 64 TICAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLI 123
T+ AE++AIS A G+ I V+ +PCG CRQ + E +S D+++ +
Sbjct: 100 TVHAEQSAISHAWLSGEKALAAITVN---------YTPCGHCRQFMNELNSGL-DLRIHL 149
Query: 124 VKSDRSQVG 132
+ +
Sbjct: 150 PGREAHALR 158
>3oj6_A Blasticidin-S deaminase; ssgcid, seattle structural genomics for
infectious disease, hydrolase; 1.70A {Coccidioides
immitis}
Length = 158
Score = 127 bits (320), Expect = 3e-38
Identities = 34/126 (26%), Positives = 55/126 (43%), Gaps = 10/126 (7%)
Query: 7 MEFSALDPIEQNLANLSIQARDNAYCPYSK-LQVGAALLCQDDTIFTGCNVENASYGMTI 65
M L QNL + + P S V +A + D +F+G NV + + G
Sbjct: 22 MAPEPLSAAGQNLIDTATSVI--NGIPVSDFYSVASAAISDDGRVFSGVNVYHFNGG--P 77
Query: 66 CAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVK 125
CAE + A + G TK I I + +SPCG CRQV+A+ I+ +++
Sbjct: 78 CAELVVLGVAAAAGATKLTHIVA--IANEGRGILSPCGRCRQVLADLHP---GIKAIVIG 132
Query: 126 SDRSQV 131
+ ++
Sbjct: 133 KEGPKM 138
>2z3g_A Blasticidin-S deaminase; hydrolase, cytidine deaminase family,
zinc, tetramer; HET: TRE; 1.50A {Aspergillus terreus}
SCOP: c.97.1.1 PDB: 1wn6_A* 1wn5_A* 2z3h_A* 2z3j_A
2z3i_A*
Length = 130
Score = 124 bits (314), Expect = 1e-37
Identities = 31/116 (26%), Positives = 46/116 (39%), Gaps = 8/116 (6%)
Query: 12 LDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTA 71
L E L + N+ V +A L D IFTG NV + + G CAE
Sbjct: 3 LSQEESTLIERATATI-NSIPISEDYSVASAALSSDGRIFTGVNVYHFTGG--PCAELVV 59
Query: 72 ISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLIVKSD 127
+ A + I ++ +SPCG CRQV+ + I+ ++ SD
Sbjct: 60 LGTAAAAAAGNLTCIVAIG--NENRGILSPCGRCRQVLLDLHP---GIKAIVKDSD 110
>3b8f_A Putative blasticidin S deaminase; cytidine deaminase, structural
genomics, MCSG, protein structure initiative; 1.90A
{Bacillus anthracis}
Length = 142
Score = 125 bits (314), Expect = 1e-37
Identities = 27/114 (23%), Positives = 49/114 (42%), Gaps = 6/114 (5%)
Query: 15 IEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENASYGMTICAEKTAISK 74
IEQ L ++ Q + Y + AA+ +D TI+T + + +C E AI +
Sbjct: 3 IEQQLYDVVKQLIEQRYP--NDWGGAAAIRVEDGTIYTSVAPDVINASTELCMETGAILE 60
Query: 75 AISEGQTKFKRIAVSAILPDSN-KFVSPCGSCRQVIAEFSSPACDIQVLIVKSD 127
A + I ++ S K +SPCG C++ + + ++Q I +
Sbjct: 61 AHKFQKKVTHSICLARENEHSELKVLSPCGVCQERLFYWGP---EVQCAITNAK 111
>4eg2_A Cytidine deaminase; UMP synthesis, Zn binding, hydrolase; HET: URI;
2.20A {Vibrio cholerae}
Length = 298
Score = 123 bits (309), Expect = 4e-35
Identities = 21/124 (16%), Positives = 54/124 (43%), Gaps = 4/124 (3%)
Query: 1 MVGHDIMEFSALDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVENAS 60
+ ++ L +++A + ++ PY++ G AL + I+ G ENA+
Sbjct: 177 SGLMSPVNHGKTSDDDEELIQQALRAMNISHSPYTQNFSGVALKMRSGAIYLGAYAENAA 236
Query: 61 YGMTICAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQ 120
+ ++ + A+++A+ G+ F+ I +A++ + +S + + DI
Sbjct: 237 FNPSLPPLQVALAQAMMMGE-SFEDIEAAALVESATGKISHLADTQATLEVI---NPDIP 292
Query: 121 VLIV 124
+ +
Sbjct: 293 LSYL 296
Score = 115 bits (288), Expect = 6e-32
Identities = 32/120 (26%), Positives = 56/120 (46%), Gaps = 13/120 (10%)
Query: 6 IMEFSALDPIEQNLANLSIQARDNAYCPYSKLQVGAALLCQDDTIFTGCNVE--NASYGM 63
++ S L+ + L A +Y P S+ VGA + ++ G N+E A G
Sbjct: 44 LLTLSGLEDADL-RVALLPIAAAYSYAPISEFYVGAIVRGISGRLYLGANMEFTGAQLGQ 102
Query: 64 TICAEKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLI 123
T+ AE+ AIS A +G+ I ++ SPCG CRQ + E ++ + +++ +
Sbjct: 103 TVHAEQCAISHAWMKGEKGVADITIN---------FSPCGHCRQFMNELTTAS-SLKIQL 152
>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 = 40.0 bits (93), Expect = 2e-04
Identities = 22/126 (17%), Positives = 40/126 (31%), Gaps = 34/126 (26%)
Query: 3 GHDIMEFSAL------DPIEQ---------NLANLSIQARDNAYCPYSKLQVG----AAL 43
GH + E++AL IE +++ + Y + + AA
Sbjct: 1761 GHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAAS 1820
Query: 44 LCQDDTIF--------TGCNVE----NASYGMTICA-EKTAISKAISE-GQTKFKRIAVS 89
Q+ + TG VE N + A + A+ + K ++I +
Sbjct: 1821 FSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDII 1880
Query: 90 AILPDS 95
L S
Sbjct: 1881 E-LQKS 1885
Score = 38.5 bits (89), Expect = 5e-04
Identities = 32/180 (17%), Positives = 56/180 (31%), Gaps = 42/180 (23%)
Query: 3 GHDIMEFSALDPIEQNLANLSIQARDNAY---CPYSKLQVGAALLCQDDTIFTGCNVENA 59
G +I+E+ L N S D Y P S +G L +
Sbjct: 212 GLNILEW---------LENPS-NTPDKDYLLSIPISCPLIGVIQLAH---YVVTAKLLGF 258
Query: 60 SY--------GMTICAEKTAISKAISEGQT--KFKRIAVSAILPDSNKFVSPCGS-CRQV 108
+ G T ++ + AI+E + F AI + G C +
Sbjct: 259 TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI-----TVLFFIGVRCYEA 313
Query: 109 IAEFSSPACDIQVLIVKSDRSQVG----LITIDGMYL-TLHCCWERGNLVLP-DPKLTIS 162
S P ++ S + G +++I + + + N LP ++ IS
Sbjct: 314 YPNTSLPPSILE----DSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEIS 369
>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 = 34.5 bits (78), Expect = 0.006
Identities = 12/56 (21%), Positives = 16/56 (28%), Gaps = 27/56 (48%)
Query: 68 EKTAISKAISEGQTKFKRIAVSAILPDSNKFVSPCGSCRQVIAEFSSPACDIQVLI 123
EK A+ K Q K A DS +PA I+ +
Sbjct: 18 EKQALKKL----QASLKLYA-----DDS------------------APALAIKATM 46
>1sji_A Calsequestrin 2, calsequestrin, cardiac muscle isoform;
glycoprotein, calcium-binding, muscle protein, metal
binding protein; 2.40A {Canis lupus familiaris} PDB:
2vaf_A
Length = 350
Score = 26.6 bits (58), Expect = 4.7
Identities = 4/40 (10%), Positives = 15/40 (37%)
Query: 98 FVSPCGSCRQVIAEFSSPACDIQVLIVKSDRSQVGLITID 137
+ S + +F ++++ + +G + +D
Sbjct: 35 YHESVSSDKVAQKQFQLKEIVLELVAQVLEHKDIGFVMVD 74
>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 = 25.6 bits (56), Expect = 8.9
Identities = 5/13 (38%), Positives = 7/13 (53%)
Query: 100 SPCGSCRQVIAEF 112
SPC +C I +
Sbjct: 92 SPCAACADRIIKT 104
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
0.320 0.135 0.404
Gapped
Lambda K H
0.267 0.0552 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,331,495
Number of extensions: 121150
Number of successful extensions: 240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 23
Length of query: 166
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 79
Effective length of database: 4,272,666
Effective search space: 337540614
Effective search space used: 337540614
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: 53 (24.6 bits)