RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy11424
(245 letters)
>1gtk_A Porphobilinogen deaminase; lyase, biosynthesis of linear
tetrapyrrole, all alpha/beta; HET: DPM; 1.66A
{Escherichia coli} SCOP: c.94.1.1 d.50.2.1 PDB: 1ah5_A*
2ypn_A* 1ypn_A* 1pda_A*
Length = 313
Score = 325 bits (836), Expect = e-113
Identities = 112/239 (46%), Positives = 153/239 (64%), Gaps = 3/239 (1%)
Query: 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTN 61
A+++ +AD+AVHS+KD+P+ P G L I +REDPRDAF+SN+Y SL LP ++VGT+
Sbjct: 69 ALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTS 128
Query: 62 SLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRIRMLFS 121
SLRR+ + P LII+SLRGN+ TRL+KLD GEY AIILA AGLKRL L+ RIR
Sbjct: 129 SLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALP 188
Query: 122 PNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAA 181
P LPA GQGA+ IE + E+L LNH+ + V AERA++ G C++ + +
Sbjct: 189 PEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIGS 248
Query: 182 FAMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAIEIIK 240
+A + + EI LRA++ P+G +II E G E +G+ AE L GA EI+
Sbjct: 249 YAELID---GEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILA 304
>3ecr_A Porphobilinogen deaminase; heme biosynthesis, porphobilinogen
hinge, alternative splicing, cytoplasm, disease
mutation, porphyrin biosynthesis; HET: DPM; 2.18A {Homo
sapiens} PDB: 3eq1_A*
Length = 364
Score = 296 bits (760), Expect = e-101
Identities = 88/272 (32%), Positives = 141/272 (51%), Gaps = 36/272 (13%)
Query: 2 AIIKGKADLAVHSLKDIPMNLPSGFILCAILKREDPRDAFISND---YISLSTLPKNAVV 58
A+ K + DL VHSLKD+P LP GF + AI KRE+P DA + + +L TLP+ +VV
Sbjct: 87 ALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVV 146
Query: 59 GTNSLRRKVLIKSFFPSLIIKSLRGNIDTRLNKLD-KGEYAAIILAAAGLKRLNLQKRIR 117
GT+SLRR ++ FP L +S+RGN++TRL KLD + E++AIILA AGL+R+ R+
Sbjct: 147 GTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVG 206
Query: 118 MLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKI 177
+ P + + A GQGA+ +E+ +++++++ L+ + AERA R+ G C +
Sbjct: 207 QILHPEECMYAVGQGALGVEVRAKDQDILDLVGVLHDPETLLRCIAERAFLRHLEGGCSV 266
Query: 178 SLAAFAMVNNFNESEINLRAIITNPNGLKIITAEV------------------------- 212
+A + + ++ L + + +G I +
Sbjct: 267 PVAVHTAMKD---GQLYLTGGVWSLDGSDSIQETMQATIHVPAQHEDGPEDDPQLVGITA 323
Query: 213 ----NGPIDTPETVGLYAAELLKKKGAIEIIK 240
GP + +G+ A LL KGA I+
Sbjct: 324 RNIPRGPQLAAQNLGISLANLLLSKGAKNILD 355
>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 = 56.8 bits (136), Expect = 2e-09
Identities = 45/302 (14%), Positives = 84/302 (27%), Gaps = 102/302 (33%)
Query: 25 GFILCAILKREDPRD-AFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSL-IIKSLR 82
F++ I + + R + ++ YI ++ + N V K L LR
Sbjct: 92 KFLMSPI--KTEQRQPSMMTRMYIE----QRDRLYNDNQ----VFAKYNVSRLQPYLKLR 141
Query: 83 GNIDTRLNKLDKGEYAAI---------ILAAAGLKRLNLQKR------------------ 115
L +L + I +A +Q +
Sbjct: 142 ----QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPET 197
Query: 116 -IRML------FSPNQILPAPGQGAIAIEILDNRKELMEM---------LIPLNHYFSEQ 159
+ ML PN + I + I + EL + L+ L + + +
Sbjct: 198 VLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK 257
Query: 160 TVKAERAVSRNFNGSCKI-------SLAAFAMVNN------------FNESE-------- 192
A FN SCKI + F E
Sbjct: 258 AWNA-------FNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY 310
Query: 193 INLR-------AIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKK--KGAIEIIKSYE 243
++ R + TNP L II + + T + + L + ++ +++ E
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE 370
Query: 244 KK 245
+
Sbjct: 371 YR 372
Score = 34.1 bits (77), Expect = 0.041
Identities = 45/238 (18%), Positives = 81/238 (34%), Gaps = 44/238 (18%)
Query: 27 ILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVL---IKSFFPSLIIKSLRG 83
I+ + L +P + + LS P +A + T L ++ + +++ L
Sbjct: 358 IIESSLNVLEPAE--YRKMFDRLSVFPPSAHIPTILL--SLIWFDVIKSDVMVVVNKLH- 412
Query: 84 NIDTRLNKLDKGEYAAII------LAAAGLKRLNLQKRI------RMLFSPNQILPAPGQ 131
L + E I L L + I F + ++P
Sbjct: 413 --KYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLD 470
Query: 132 GAIAIEI---LDN-----RKELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCKISLAAFA 183
I L N R L M+ L+ F EQ ++ + + + N +GS +L
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVF-LDFRFLEQKIRHD-STAWNASGSILNTLQQLK 528
Query: 184 -----MVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAI 236
+ +N + E + AI+ + E N I + T L A L+ + AI
Sbjct: 529 FYKPYICDNDPKYERLVNAILDF-----LPKIEEN-LICSKYTDLLRIA-LMAEDEAI 579
>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 = 48.5 bits (115), Expect = 1e-06
Identities = 35/189 (18%), Positives = 66/189 (34%), Gaps = 65/189 (34%)
Query: 77 IIKSLRGNIDTRLNKLDK-------GEYAAIILAA-AGLKRLNLQKRIRMLF----SPNQ 124
+KS +G I D GEYAA LA+ A + ++++ + ++F +
Sbjct: 1746 DLKS-KGLIP-----ADATFAGHSLGEYAA--LASLADV--MSIESLVEVVFYRGMTMQV 1795
Query: 125 ILPAPGQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKA--ERAVSRNFNGSCKISLAAF 182
+P G ++ + FS++ ++ ER V + +I
Sbjct: 1796 AVPRDELGRSNYGMIAINPGRVAAS------FSQEALQYVVER-VGKRTGWLVEI----- 1843
Query: 183 AMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLK--KKGAIEIIK 240
V N+N N + ++ +DT +L K I+II+
Sbjct: 1844 --V-NYNV-----------ENQQYVAAGDLRA-LDT-------VTNVLNFIKLQKIDIIE 1881
Query: 241 -----SYEK 244
S E+
Sbjct: 1882 LQKSLSLEE 1890
Score = 45.0 bits (106), Expect = 1e-05
Identities = 52/247 (21%), Positives = 79/247 (31%), Gaps = 95/247 (38%)
Query: 19 PM----NLPSGFILCAILK--REDPRDAFISNDYISLSTLPKNAVV-GTNSLRRKVLIKS 71
PM NL + + K P + ISL KN VV G
Sbjct: 337 PMLSISNLTQEQVQDYVNKTNSHLPAGKQV---EISLVNGAKNLVVSG------------ 381
Query: 72 FFPSLIIKSLRGNIDTRLNKLDKGEYAAIILAAAGLKRLNLQKRI----RML-FSPNQIL 126
P +SL G ++ L K A +GL Q RI R L FS N+ L
Sbjct: 382 -PP----QSLYG-LNLTLRKAK---------APSGLD----QSRIPFSERKLKFS-NRFL 421
Query: 127 P--AP-------------GQGAIAIEILDNRKELMEMLIPLNHYFSEQTVKAERAVSRNF 171
P +P + + + N K++ IP+ F + R
Sbjct: 422 PVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQ---IPVYDTFDGSDL-------RVL 471
Query: 172 NGSCKISLAAFAMVNNFN-ESEINLRA--II-------------TNPN----GLKIITAE 211
+GS + + E+ +A I+ T+ N G+++I A
Sbjct: 472 SGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVRVIVA- 530
Query: 212 VNGPIDT 218
G +D
Sbjct: 531 --GTLDI 535
Score = 40.8 bits (95), Expect = 3e-04
Identities = 32/202 (15%), Positives = 69/202 (34%), Gaps = 63/202 (31%)
Query: 27 ILCAILKR-EDPRDAFISNDYI-SL-STLPKNAVVGTNSLRRKVLIKSFFPSLIIKSLRG 83
+L L E+ ++ + I +L + L + T ++ K LIK++ + I+
Sbjct: 83 VLNLCLTEFEN---CYLEGNDIHALAAKLLQEN--DTTLVKTKELIKNYITARIM----- 132
Query: 84 NIDTRLNK-LDKGEYAAIILAA-AGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDN 141
+ DK +A+ A G ++ +F GQG
Sbjct: 133 -----AKRPFDKKSNSALFRAVGEG------NAQLVAIF--------GGQGNT------- 166
Query: 142 RKELMEMLIPLNHYFSE-QTV-KAERAVSRNFNGSCKISLAAFAMVNNFNESEINLRAII 199
+ YF E + + + + + I +A ++ + ++ +
Sbjct: 167 -----------DDYFEELRDLYQTYHVLVGDL-----IKFSA-ETLSELIRTTLDAEKVF 209
Query: 200 TNPNGLKIITAEVNGPIDTPET 221
GL I+ + P +TP+
Sbjct: 210 --TQGLNILEW-LENPSNTPDK 228
Score = 38.9 bits (90), Expect = 0.001
Identities = 23/121 (19%), Positives = 45/121 (37%), Gaps = 26/121 (21%)
Query: 24 SGFILCAILKREDPRDAFISNDYISLSTLPKNAVVGTNSLRRKVLIKSFFPSLIIKSLRG 83
G + + D ++F + +++ L +G +P+ SL
Sbjct: 275 QGLVTAVAIAETDSWESFFVSVRKAITVL---FFIGVRCYEA-------YPNT---SLPP 321
Query: 84 NI--DTRLNKLDKGE-YAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILD 140
+I D+ L+ E + +L+ + L + +Q + N LPA Q I+ L
Sbjct: 322 SILEDS----LENNEGVPSPMLSISNLTQEQVQDYVNKT---NSHLPAGKQVEIS---LV 371
Query: 141 N 141
N
Sbjct: 372 N 372
Score = 30.8 bits (69), Expect = 0.48
Identities = 20/126 (15%), Positives = 37/126 (29%), Gaps = 50/126 (39%)
Query: 148 MLIPLNHYFSEQTVKAE-----RAVSRNFNG----SCKISLAA-F--------------- 182
+L+P +F ++ + + F + L F
Sbjct: 20 LLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQ 79
Query: 183 ------AMVNNFNESEINLRAIITNPNGLKIITAEVNGPIDTPETVGLYAAELLKKKGAI 236
+ F E+ L N + + A++ DT L+K K
Sbjct: 80 FDQVLNLCLTEF-ENCY-LEG-----NDIHALAAKLLQENDTT---------LVKTK--- 120
Query: 237 EIIKSY 242
E+IK+Y
Sbjct: 121 ELIKNY 126
Score = 27.7 bits (61), Expect = 4.9
Identities = 28/147 (19%), Positives = 41/147 (27%), Gaps = 36/147 (24%)
Query: 97 YAAIILAAAGLKRLNLQKRIRMLFSPNQILPAPGQGAIAIEILDNRKELMEMLIPLNHYF 156
Y A R + + FS I +++N L +F
Sbjct: 1636 YKTSKAAQDVWNRADNHFKDTYGFSILDI------------VINNPVNLTI-------HF 1676
Query: 157 SEQTVKAERAVSRNFNGSC--KISLAAFAMVNNFNESEINLRAII-TNPNGLKIITAEVN 213
+ K R N++ I F E + + + GL T
Sbjct: 1677 GGEKGKRIRE---NYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQ--F 1731
Query: 214 GPIDT-P--ETVGLYAA-ELLKKKGAI 236
T P + AA E LK KG I
Sbjct: 1732 ----TQPALTLME-KAAFEDLKSKGLI 1753
>2jzj_A Cyanovirin-N homolog; CVNH, antiviral protein, carbohydrate binding
protein; NMR {Ceratopteris richardii}
Length = 124
Score = 32.2 bits (73), Expect = 0.054
Identities = 13/64 (20%), Positives = 25/64 (39%), Gaps = 10/64 (15%)
Query: 150 IPLNHYFSEQTVKAERAVSRNFNGSCK-ISLAAFAMVN--------NFNESEINLRAIIT 200
I LN+Y + E +F SC +L + +++S ++L ++
Sbjct: 35 INLNYYIGNDNGRLEYP-GESFGSSCVKTALNDGHTLTASCKGADGQYHDSSMDLNYVVG 93
Query: 201 NPNG 204
N G
Sbjct: 94 NSYG 97
>3s3z_A CV-N, tandem cyanovirin-N dimer CVN2L10; sugar-binding, GP120,
engineered dimer, antivi protein; 1.75A {Nostoc
ellipsosporum} PDB: 3s3y_A 1n02_A
Length = 223
Score = 31.1 bits (70), Expect = 0.23
Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 10/64 (15%)
Query: 150 IPLNHYFSEQTVKAERAVSRNFNGSCK-------ISLAAFAMVNN--FNESEINLRAIIT 200
I LN + NF +C+ LAA F ++INL I
Sbjct: 45 IDLNSVIENVDGSLKWQ-PSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIA 103
Query: 201 NPNG 204
N +G
Sbjct: 104 NIDG 107
Score = 26.5 bits (58), Expect = 9.0
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 9/46 (19%)
Query: 168 SRNFNGSCK-ISLAA--------FAMVNNFNESEINLRAIITNPNG 204
NF +C+ LA F ++INL I N +G
Sbjct: 173 PSNFIETCRNTQLAGSSELAAECKTRAQQFVSTKINLDDHIANIDG 218
>2jzk_A Cyanovirin-N homolog; CVNH, antiviral protein, carbohydrate binding
protein; NMR {Tuber borchii}
Length = 106
Score = 29.1 bits (65), Expect = 0.57
Identities = 12/65 (18%), Positives = 18/65 (27%), Gaps = 11/65 (16%)
Query: 150 IPLNHYFSEQTVKAERAVSRNFNGSCK-ISLAAFAMV---------NNFNESEINLRAII 199
+ L+ +NF+ S + I L F E + I
Sbjct: 38 LDLDTCIGNPNGFLGWG-MQNFSHSSEDIKLEEGGRKLTCRPKTVDGGFRERQGIDLNRI 96
Query: 200 TNPNG 204
N NG
Sbjct: 97 QNVNG 101
>3lhc_A Cyanovirin-N, CV-N; sugar binding protein, HIV-inactivating, GP120
antiviral protein, protein synthesis inhibitor, lectin;
1.34A {Nostoc ellipsosporum} PDB: 2rp3_A 3czz_A 1iiy_A*
1j4v_A 1l5b_A* 1l5e_A 1m5j_A* 1m5m_A* 2ezm_A 2ezn_A
3ezm_A 3gxy_A* 3gxz_A* 1lom_A 2rdk_A* 2pys_A* 2z21_A
Length = 100
Score = 27.9 bits (62), Expect = 1.3
Identities = 15/64 (23%), Positives = 24/64 (37%), Gaps = 11/64 (17%)
Query: 150 IPLNHYFSEQTVKAERAVSRNFNGSCK-ISLAAFAMVN--------NFNESEINLRAIIT 200
I LN + + NF +C+ LA + + F ++INL I
Sbjct: 34 IDLNSVIAAVDGSLKW--PSNFIEACRNTQLAGSSELAAECKTAAGQFVSTKINLDDHIA 91
Query: 201 NPNG 204
N +G
Sbjct: 92 NIDG 95
>1lfw_A PEPV; hydrolase, dipeptidase; HET: AEP; 1.80A {Bacteria} SCOP:
c.56.5.4 d.58.19.1
Length = 470
Score = 28.0 bits (62), Expect = 2.8
Identities = 10/41 (24%), Positives = 14/41 (34%), Gaps = 8/41 (19%)
Query: 82 RGNIDTRLNKLDKGEYAAIILAAAGLKRLN--LQKRIRMLF 120
RG+ D DKG LK +K+I +
Sbjct: 115 RGSAD------DKGPSLTAYYGMLLLKEAGFKPKKKIDFVL 149
>2l2f_A Cyanovirin-N homolog; lectin, carbohydrate binding protein, binding
protein; NMR {Gibberella zeae}
Length = 108
Score = 26.8 bits (59), Expect = 3.2
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 15/75 (20%)
Query: 144 ELMEMLIPLNHYFSEQTVKAERAVSRNFNGSCK-ISLAAFAMVNN-------------FN 189
+ +E + L++Y NF+GS I+L N
Sbjct: 29 DYVESTLDLDYYIGNDDGSFSWG-GENFSGSASNITLDIEGDDNIPVLRAELNPMDGDPV 87
Query: 190 ESEINLRAIITNPNG 204
E+ +NL I N G
Sbjct: 88 EANVNLSERIGNDCG 102
>2jzl_A Cyanovirin-N homolog; CVNH, antiviral protein, carbohydrate binding
protein; NMR {Neurospora crassa}
Length = 114
Score = 26.4 bits (58), Expect = 5.2
Identities = 11/70 (15%), Positives = 21/70 (30%), Gaps = 16/70 (22%)
Query: 150 IPLNHYFSEQTVKAERAVSRNFNGSCK-ISLAAFAMVNN--------------FNESEIN 194
L+ + +NF + + I F++ ++N
Sbjct: 40 YELDQIIGNNDGHFQWG-GQNFTETAEDIRFHPKEGAAEQPILRARLRDCNGEFHDRDVN 98
Query: 195 LRAIITNPNG 204
L I+ N NG
Sbjct: 99 LTEIVENVNG 108
>2ji4_A Phosphoribosyl pyrophosphate synthetase-associated protein 2;
phosphorylation, nucleotide biosynthesis, transferase;
2.55A {Homo sapiens} PDB: 2c4k_A*
Length = 379
Score = 26.9 bits (60), Expect = 5.9
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 216 IDTPETVGLYAAELLKKKGAIEII 239
ID ++ L AAE LK++GA +I
Sbjct: 282 IDDVDSF-LAAAETLKERGAYKIF 304
>2i3o_A Gamma-glutamyltransferase related protein; structural genomics,
PSI, protein structure initiative; 2.03A {Thermoplasma
acidophilum} SCOP: d.153.1.6
Length = 516
Score = 27.1 bits (61), Expect = 6.9
Identities = 4/14 (28%), Positives = 5/14 (35%)
Query: 126 LPAPGQGAIAIEIL 139
QG IE +
Sbjct: 251 TSPNSQGITVIEWI 264
>2nlz_A Cephalosporin acylase; structural genomics, protein structure
initiative, PSI, nysgxrc; 2.70A {Bacillus halodurans}
SCOP: d.153.1.6
Length = 547
Score = 26.7 bits (60), Expect = 8.7
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 126 LPAPGQGAIAIEIL 139
+P GQG +A+E L
Sbjct: 267 IPPNGQGLVALEAL 280
>3tsy_A Fusion protein 4-coumarate--COA ligase 1, resvera synthase;
transferase; 3.10A {Arabidospis thaliana}
Length = 979
Score = 26.5 bits (59), Expect = 9.4
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 104 AAGLKRLNLQK--RIRMLFSPNQI 125
AA +L + + + ML PN
Sbjct: 102 AANFHKLGVNQNDVV-MLLLPNCP 124
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 0.137 0.376
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,739,925
Number of extensions: 231274
Number of successful extensions: 602
Number of sequences better than 10.0: 1
Number of HSP's gapped: 592
Number of HSP's successfully gapped: 37
Length of query: 245
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,160,982
Effective search space: 640791228
Effective search space used: 640791228
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: 56 (25.4 bits)