RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 020472
(326 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 = 347 bits (893), Expect = e-120
Identities = 109/213 (51%), Positives = 141/213 (66%), Gaps = 5/213 (2%)
Query: 67 IIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKG 126
++RI TR SPLAL QAH ++KLMA HP L +++V + T GD IL PLA +GGKG
Sbjct: 5 VLRIATRQSPLALWQAHYVKDKLMASHPGLV----VELVPMVTRGDVILDTPLAKVGGKG 60
Query: 127 LFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELP 186
LF KE++ AL+ ++ DIAVHSMKDVP P+ L +RED RDAF+S + SL LP
Sbjct: 61 LFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALP 120
Query: 187 AGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSM 246
AGSIVGT+SLRR+ Q+ R P L + + RGNV TRL KL+ A +LA+AGLKRL +
Sbjct: 121 AGSIVGTSSLRRQCQLAERRPDLII-RSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGL 179
Query: 247 TENVTNILSVDDMLPAVAQGAIGIACRSNDEKM 279
+ L + LPAV QGA+GI CR +D +
Sbjct: 180 ESRIRAALPPEISLPAVGQGAVGIECRLDDSRT 212
>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 = 338 bits (868), Expect = e-116
Identities = 89/227 (39%), Positives = 133/227 (58%), Gaps = 9/227 (3%)
Query: 57 ASAAVETKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILS 116
+ K+ +IR+GTR S LA Q L A +P L +I+ + TTGDKIL
Sbjct: 13 TAEENSPKMRVIRVGTRKSQLARIQTDSVVATLKASYPGLQ----FEIIAMSTTGDKILD 68
Query: 117 QPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTILPCNLQREDVRDAFIS 176
L+ IG K LFTKE++ AL +++D+ VHS+KD+PT LP + +RE+ DA +
Sbjct: 69 TALSKIGEKSLFTKELEHALEKNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVF 128
Query: 177 ---LSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNERV-VQ 232
+L LP S+VGT+SLRR +Q+ ++P L+ + RGN+ TRLRKL+E+
Sbjct: 129 HPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKFPHLEF-RSIRGNLNTRLRKLDEQQEFS 187
Query: 233 ATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIGIACRSNDEKM 279
A +LA AGL+R+ V IL ++ + AV QGA+G+ R+ D+ +
Sbjct: 188 AIILATAGLQRMGWHNRVGQILHPEECMYAVGQGALGVEVRAKDQDI 234
>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 = 46.6 bits (110), Expect = 8e-06
Identities = 58/364 (15%), Positives = 104/364 (28%), Gaps = 158/364 (43%)
Query: 41 PSFPKSLKKRSFGLVRASAAVETKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEG 100
+L K L++ + ++ R + S AL +A EG
Sbjct: 110 QENDTTLVKTKE-LIKN--YITARIMAKRPFDKKSNSALFRA--------------VGEG 152
Query: 101 AIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDVPTYLPEKTI 160
Q+V I GG+G N+ Y E
Sbjct: 153 NAQLVAI--------------FGGQG-----------NTD------------DYFEE--- 172
Query: 161 LPCNLQ------REDVRDAFISLSAASLAELPAGSIVGTAS----------LRRKS---- 200
L+ V D I SA +L+EL ++ L S
Sbjct: 173 ----LRDLYQTYHVLVGD-LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPD 227
Query: 201 -----------------QILHRYPSLKVMENFRGNVQTRLRKL---NERVVQATLLALA- 239
Q+ H + K++ G +++ L+ ++ +V A +A
Sbjct: 228 KDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETD 287
Query: 240 -------------------GLK------RLSMT-----ENVTN-------ILSVDDMLPA 262
G++ S+ +++ N +LS+ ++
Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQE 347
Query: 263 VAQGAIGIACRSNDEKMVPFTTHSQASILNT---FNCSG---KLCYKLHFGFLNLVELRR 316
Q + ++N +P + S++N SG L G LNL LR+
Sbjct: 348 QVQDYVN---KTNSH--LPAGKQVEISLVNGAKNLVVSGPPQSLY-----G-LNL-TLRK 395
Query: 317 IIAA 320
A
Sbjct: 396 AKAP 399
Score = 33.9 bits (77), Expect = 0.078
Identities = 39/213 (18%), Positives = 63/213 (29%), Gaps = 88/213 (41%)
Query: 44 PKSLKKRSFGLVRASAAVETKVAI----------------IR----IGTRGSPLALAQAH 83
P L+ G S + T VAI I IG R +
Sbjct: 260 PGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVR--------CY 311
Query: 84 ETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDI 143
E +L P + ++ + + S P+ I L +++ + +
Sbjct: 312 EAYPNT-SLPPSILED-------SLENNEGVPS-PMLSI--SNLTQEQVQDYV------- 353
Query: 144 AVHSMKDVPTYLPEKTILPCNLQREDVRDAFISL--SAASLAELPAGSIV-G-TASLRRK 199
++LP + ISL A +L +V G SL
Sbjct: 354 -----NKTNSHLPAG------------KQVEISLVNGAKNL-------VVSGPPQSLYGL 389
Query: 200 SQILHRY--PSLKVMENFRGNVQTRL----RKL 226
+ L + PS G Q+R+ RKL
Sbjct: 390 NLTLRKAKAPS--------GLDQSRIPFSERKL 414
>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 = 43.7 bits (102), Expect = 6e-05
Identities = 43/289 (14%), Positives = 85/289 (29%), Gaps = 100/289 (34%)
Query: 81 QAHETRNKLMALHPELAQ-------EGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEID 133
++ ++ L + + ++ K D I+ A G LF
Sbjct: 14 HQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT--- 70
Query: 134 EALINSQIDIAVHSMKDV--PTY--LPEKTILPCNLQREDVRDAFISLSAASLAELPAGS 189
L++ Q ++ +++V Y L Q + +I
Sbjct: 71 --LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR-QPSMMTRMYIEQ------------ 115
Query: 190 IVGTASLRRKSQILHRYPSLKVMENFRGNVQTRLRKLNE-RVVQATLLALAGLKRLSMTE 248
L +Q+ +Y NV +RL+ + R L L +
Sbjct: 116 ---RDRLYNDNQVFAKY-----------NV-SRLQPYLKLR---------QALLELRPAK 151
Query: 249 NVTNILSVDDMLPAVAQGA-----IGIACRSND-EKMVPF--------TTHSQASILNTF 294
NV +D +L G+ C S + + F +S ++L
Sbjct: 152 NVL----IDGVL-----GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML 202
Query: 295 NCSGKLCYKLHFGFLNLVE---------------LRRIIAA-----CLM 323
KL Y++ + + + LRR++ + CL+
Sbjct: 203 Q---KLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248
Score = 41.0 bits (95), Expect = 5e-04
Identities = 35/229 (15%), Positives = 65/229 (28%), Gaps = 66/229 (28%)
Query: 11 LCTSR--------GGPMERHCYPGSVSLV----GFSSPRLKTPSFPKSLKKRSFGLVRAS 58
L T+R H +SL + +K+ K L R L R
Sbjct: 269 LLTTRFKQVTDFLSAATTTH-----ISLDHHSMTLTPDEVKS-LLLKYLDCRPQDLPR-- 320
Query: 59 AAVETKVAIIRIGTRGSPLALAQAHETRNKLMALHPELAQEGAIQIVIIKTTGDKILSQP 118
E +P L+ ++A E ++G K L+
Sbjct: 321 ---EVL--------TTNPRRLS--------IIA---ESIRDGLATWDNWKHVNCDKLTTI 358
Query: 119 LADIGGKGLFTKEIDEALINSQ-IDIAVHSMKDVPTYLPEKT--ILPCNLQREDVRDAFI 175
+ ++ A ++V +P ++ ++ + DV
Sbjct: 359 IE------SSLNVLEPAEYRKMFDRLSVF-PPSAH--IPTILLSLIWFDVIKSDVMVVVN 409
Query: 176 SLSAASLAEL-PAGSIVGTASL-------RRKSQILHRYPSLKVMENFR 216
L SL E P S + S+ LHR +++++
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR----SIVDHYN 454
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 30.5 bits (69), Expect = 0.50
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 201 QILHRYPSL--KVMENFRGNVQTRLRKLNERVVQATLL 236
Q+L P L KV+ + R R+ +R++ TL
Sbjct: 147 QLLANMPKLGNKVLIRLLQLLTARFRESYDRILPKTLG 184
>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 = 28.4 bits (62), Expect = 2.2
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 241 LKRL--SMTENVTNILSVDDMLPAVAQGA 267
LK+L S+ L DD PA+A A
Sbjct: 22 LKKLQASLK------LYADDSAPALAIKA 44
>3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer,
structural genomics, PSI-2, protein structure
initiative; 1.71A {Bifidobacterium adolescentis
ATCC15703}
Length = 282
Score = 28.4 bits (64), Expect = 3.1
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 222 RLRKLNERVVQATLLALAGLKRLS--MTENVTNILSVDDMLPAVAQGA 267
LRK + ++ + + LS MT DM A+A+G+
Sbjct: 220 HLRKTRDLILASGEPGTDRCRELSMGMT---------GDMELAIAEGS 258
>3tr5_A RF-3, peptide chain release factor 3; protein synthesis,
translation; HET: GDP; 2.11A {Coxiella burnetii}
Length = 528
Score = 28.5 bits (64), Expect = 3.5
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 95 ELAQEGAIQIVIIKTTGDKIL 115
+L++EGA Q+ + + IL
Sbjct: 417 QLSEEGATQLFRPLDSNELIL 437
>2h5e_A Peptide chain release factor RF-3; beta barrel, translation; HET:
GDP; 2.80A {Escherichia coli} PDB: 2o0f_A 3sfs_W*
3zvo_Y* 3uoq_W*
Length = 529
Score = 28.1 bits (63), Expect = 4.6
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 95 ELAQEGAIQIVIIKTTGDKIL 115
+L++EGA+Q+ + D I+
Sbjct: 418 QLSEEGAVQVFRPISNNDLIV 438
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 0.133 0.376
Gapped
Lambda K H
0.267 0.0815 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,696,935
Number of extensions: 282120
Number of successful extensions: 533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 525
Number of HSP's successfully gapped: 18
Length of query: 326
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 232
Effective length of database: 4,077,219
Effective search space: 945914808
Effective search space used: 945914808
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: 57 (25.6 bits)