RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026500
(237 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 = 303 bits (779), Expect = e-104
Identities = 95/190 (50%), Positives = 123/190 (64%), Gaps = 5/190 (2%)
Query: 1 MALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMK 60
MA HP L +++V + T GD IL PLA +GGKGLF KE++ AL+ ++ DIAVHSMK
Sbjct: 28 MASHPGLV----VELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMK 83
Query: 61 DVPTYLPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSL 120
DVP P+ L +RED RDAF+S + SL LPAGSIVGT+SLRR+ Q+ R P L
Sbjct: 84 DVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDL 143
Query: 121 KVMENFRGNVQTRLRKLNERVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGAIG 180
+ + RGNV TRL KL+ A +LA+AGLKRL + + L + LPAV QGA+G
Sbjct: 144 II-RSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVG 202
Query: 181 IACRSNDEKM 190
I CR +D +
Sbjct: 203 IECRLDDSRT 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 = 294 bits (754), Expect = e-100
Identities = 78/194 (40%), Positives = 118/194 (60%), Gaps = 9/194 (4%)
Query: 1 MALHPELAQEGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMK 60
A +P L +I+ + TTGDKIL L+ IG K LFTKE++ AL +++D+ VHS+K
Sbjct: 46 KASYPGLQ----FEIIAMSTTGDKILDTALSKIGEKSLFTKELEHALEKNEVDLVVHSLK 101
Query: 61 DVPTYLPEKTILPCNLQREDVRDAFIS---LSAASLAELPAGSIVGTASLRRKSQILHRY 117
D+PT LP + +RE+ DA + +L LP S+VGT+SLRR +Q+ ++
Sbjct: 102 DLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEKSVVGTSSLRRAAQLQRKF 161
Query: 118 PSLKVMENFRGNVQTRLRKLNERV-VQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQ 176
P L+ + RGN+ TRLRKL+E+ A +LA AGL+R+ V IL ++ + AV Q
Sbjct: 162 PHLEF-RSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEECMYAVGQ 220
Query: 177 GAIGIACRSNDEKM 190
GA+G+ R+ D+ +
Sbjct: 221 GALGVEVRAKDQDI 234
>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 = 41.8 bits (97), Expect = 1e-04
Identities = 42/264 (15%), Positives = 80/264 (30%), Gaps = 93/264 (35%)
Query: 10 EGAIQIVIIKTTGDKILSQPLADIGGKGLFTKEIDEALINSQIDIAVHSMKDV--PTY-- 65
+ + ++ K D I+ A G LF L++ Q ++ +++V Y
Sbjct: 39 QDMPKSILSKEEIDHIIMSKDAVSGTLRLFWT-----LLSKQEEMVQKFVEEVLRINYKF 93
Query: 66 LPEKTILPCNLQREDVRDAFISLSAASLAELPAGSIVGTASLRRKSQILHRYPSLKVMEN 125
L Q + +I L +Q+ +Y
Sbjct: 94 LMSPIKTEQR-QPSMMTRMYIEQ---------------RDRLYNDNQVFAKY-------- 129
Query: 126 FRGNVQTRLRKLNE-RVVQATLLALAGLKRLSMTENVTNILSVDDMLPAVAQGA-----I 179
NV +RL+ + R L L +NV +D +L G+
Sbjct: 130 ---NV-SRLQPYLKLR---------QALLELRPAKNVL----IDGVL-----GSGKTWVA 167
Query: 180 GIACRSND-EKMVPF--------TTHSQASILNTFNCSGKLCYKLHFGFLNLVE------ 224
C S + + F +S ++L KL Y++ + + +
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ---KLLYQIDPNWTSRSDHSSNIK 224
Query: 225 ---------LRRIIAA-----CLM 234
LRR++ + CL+
Sbjct: 225 LRIHSIQAELRRLLKSKPYENCLL 248
Score = 35.6 bits (81), Expect = 0.014
Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 17/85 (20%)
Query: 53 DIAVHSMKDVPTYLPEKT--ILPCNLQREDVRDAFISLSAASLAEL-PAGSIVGTASL-- 107
++V +P ++ ++ + DV L SL E P S + S+
Sbjct: 377 RLSVF-PPSAH--IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYL 433
Query: 108 -----RRKSQILHRYPSLKVMENFR 127
LHR +++++
Sbjct: 434 ELKVKLENEYALHR----SIVDHYN 454
>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 = 41.2 bits (96), Expect = 2e-04
Identities = 41/252 (16%), Positives = 76/252 (30%), Gaps = 104/252 (41%)
Query: 64 TYLPEKTILPCNLQ------REDVRDAFISLSAASLAELPAGSIVGTAS----------L 107
Y E L+ V D I SA +L+EL ++ L
Sbjct: 168 DYFEE-------LRDLYQTYHVLVGD-LIKFSAETLSELIRTTLDAEKVFTQGLNILEWL 219
Query: 108 RRKS---------------------QILHRYPSLKVMENFRGNVQTRLRKL---NERVVQ 143
S Q+ H + K++ G +++ L+ ++ +V
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT 279
Query: 144 ATLLALA--------------------GLK------RLSMT-----ENVTN-------IL 165
A +A G++ S+ +++ N +L
Sbjct: 280 AVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML 339
Query: 166 SVDDMLPAVAQGAIGIACRSNDEKMVPFTTHSQASILNT---FNCSG---KLCYKLHFGF 219
S+ ++ Q + ++N +P + S++N SG L G
Sbjct: 340 SISNLTQEQVQDYVN---KTNSH--LPAGKQVEISLVNGAKNLVVSGPPQSLY-----G- 388
Query: 220 LNLVELRRIIAA 231
LNL LR+ A
Sbjct: 389 LNL-TLRKAKAP 399
Score = 28.1 bits (62), Expect = 3.7
Identities = 24/112 (21%), Positives = 41/112 (36%), Gaps = 35/112 (31%)
Query: 46 ALINSQIDIAVHSMKDVPTY------LP----EKTILPCNLQREDVRDAFISL--SAASL 93
+L S ++ ++ + + VP+ L + + N + ISL A +L
Sbjct: 318 SLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNL 377
Query: 94 AELPAGSIV-G-TASLRRKSQILHRY--PSLKVMENFRGNVQTRL----RKL 137
+V G SL + L + PS G Q+R+ RKL
Sbjct: 378 -------VVSGPPQSLYGLNLTLRKAKAPS--------GLDQSRIPFSERKL 414
>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 = 30.1 bits (68), Expect = 0.37
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 112 QILHRYPSL--KVMENFRGNVQTRLRKLNERVVQATLL 147
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 = 28.8 bits (63), Expect = 1.1
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 8/29 (27%)
Query: 152 LKRL--SMTENVTNILSVDDMLPAVAQGA 178
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 = 28.0 bits (63), Expect = 2.3
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 133 RLRKLNERVVQATLLALAGLKRLS--MTENVTNILSVDDMLPAVAQGA 178
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 = 2.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 6 ELAQEGAIQIVIIKTTGDKIL 26
+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 = 3.1
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 6 ELAQEGAIQIVIIKTTGDKIL 26
+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
0.321 0.135 0.380
Gapped
Lambda K H
0.267 0.0688 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,485,162
Number of extensions: 205218
Number of successful extensions: 428
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 14
Length of query: 237
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 146
Effective length of database: 4,160,982
Effective search space: 607503372
Effective search space used: 607503372
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 (21.9 bits)
S2: 56 (25.4 bits)