RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy145
(203 letters)
>3flo_A DNA polymerase alpha subunit B; protein-protein complex,
phosphoesterase fold, OB fold, zinc-binding motif, DNA
replication; HET: DNA; 2.50A {Saccharomyces cerevisiae}
Length = 460
Score = 86.0 bits (212), Expect = 5e-20
Identities = 30/95 (31%), Positives = 43/95 (45%), Gaps = 3/95 (3%)
Query: 65 TTEITAIGRIVCD--TSDGKLNAASVLLEGDEVTSGGRSISLKLPE-TGVAVFPGQIVAA 121
+EI A+GRIV D T D LN S+ LE + GR + L L + ++ F GQIVA
Sbjct: 46 QSEIYAVGRIVPDSPTYDKFLNPESLSLETSRMGGVGRRVRLDLSQVNELSFFLGQIVAF 105
Query: 122 RGSNPSRNQFIATKIYSDASLPLSETRPALDQNTE 156
+G N + + F I + Q +
Sbjct: 106 KGKNANGDYFTVNSILPLPYPNSPVSTSQELQEFQ 140
>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 = 37.3 bits (86), Expect = 0.003
Identities = 28/169 (16%), Positives = 50/169 (29%), Gaps = 50/169 (29%)
Query: 37 LSQFNAIIGLGTVTIGDI-TLLVPFLFGDTTEITAIGRIV------CDTSDGKLN--AAS 87
L++F G DI L L + T + ++ + + + S
Sbjct: 88 LTEFENCYLEGN----DIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNS 143
Query: 88 VLLEGDEVTSGGRSISLKLPETGVAVFPGQIVAARGSNPS-----RNQFIATKIYSDASL 142
L V G + VA+F GQ G+ R+ + + Y
Sbjct: 144 ALFRA--VGEGNAQL--------VAIFGGQ-----GNTDDYFEELRDLY---QTYHVLVG 185
Query: 143 PL-SETRPALDQ-NTEMYKLRVSYEKGL------------PLADYLVNV 177
L + L + + +GL P DYL+++
Sbjct: 186 DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSI 234
Score = 34.3 bits (78), Expect = 0.028
Identities = 27/183 (14%), Positives = 52/183 (28%), Gaps = 66/183 (36%)
Query: 22 SNPQP-------SAYRIPWISN-LSQFNAII-G--LG----TVTIGDITLLVPFLFGDTT 66
QP +A+ S L +A G LG ++ D+
Sbjct: 1730 QFTQPALTLMEKAAFED-LKSKGLIPADATFAGHSLGEYAALASLADV-----MSIESLV 1783
Query: 67 EITAIGRIVCDTSDGKLNAASVLLEGDEVTSGGRSISLKLPETGVAVFPGQIVAARGSNP 126
E+ R G +V DE+ + +A+ PG++ A +
Sbjct: 1784 EVVFY-R-------GMTMQVAV--PRDELGRSNYGM--------IAINPGRVAA--SFSQ 1823
Query: 127 SRNQFIATKIYSDASLPL--------------SETRPALD-----------QNTEMYKLR 161
Q++ ++ + + ALD Q ++ +L+
Sbjct: 1824 EALQYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLRALDTVTNVLNFIKLQKIDIIELQ 1883
Query: 162 VSY 164
S
Sbjct: 1884 KSL 1886
Score = 32.3 bits (73), Expect = 0.12
Identities = 28/158 (17%), Positives = 47/158 (29%), Gaps = 56/158 (35%)
Query: 46 LGTVTIGDITLLVP----FLFGDTTEITAIGR--------IVCDTS-DGKLNAASVLLEG 92
G +I DI + P FG G+ ++ +T DGKL + E
Sbjct: 1657 YG-FSILDIVINNPVNLTIHFGGEK-----GKRIRENYSAMIFETIVDGKLKTEKIFKEI 1710
Query: 93 DEVTSG----GRSISLKLPE--------TGVAVFPGQIVAARGSNPSRNQFIATKIYSDA 140
+E ++ L + A F + + ++G P+ F A
Sbjct: 1711 NEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAF--EDLKSKGLIPADATF--------A 1760
Query: 141 SLPLSE-TRPALDQNTEMYKLRVSYEKGLPLAD--YLV 175
L E AL S + + +V
Sbjct: 1761 GHSLGEYA--AL----------ASLADVMSIESLVEVV 1786
>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 = 32.1 bits (72), Expect = 0.14
Identities = 41/251 (16%), Positives = 74/251 (29%), Gaps = 70/251 (27%)
Query: 5 MSNQMKSVL-----DKIRPEWESNPQPSAYRIPWISNLSQFNAI-IGLGTVTIGDITLLV 58
+ + KS+L D I + R+ W Q + + V + L+
Sbjct: 38 VQDMPKSILSKEEIDHIIMS--KDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLM 95
Query: 59 PFLFGDTTEITAIGRIVCDTSDGKLNAASVLLEGDEVTSGGRSISLK--L----PETGVA 112
+ + + + + R+ + D +L + + V+ + L+ L P V
Sbjct: 96 SPIKTEQRQPSMMTRMYIEQRD-RLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVL 154
Query: 113 VF--PG---QIVAARG-SNPSRNQFIATKIY--------------------------SDA 140
+ G VA + + KI+ +
Sbjct: 155 IDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 141 SLPLSETRPALDQNTEMYKLRV-----SYEKGLPLADYLV--NVFEKSYNSAF------- 186
S + L ++ +LR YE L LV NV +AF
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL-----LVLLNVQNAKAWNAFNLSCKIL 269
Query: 187 ITT----VADF 193
+TT V DF
Sbjct: 270 LTTRFKQVTDF 280
Score = 28.7 bits (63), Expect = 1.9
Identities = 20/114 (17%), Positives = 38/114 (33%), Gaps = 24/114 (21%)
Query: 77 DTSDGKLNAAS------VLLEGDEVTSGGRSISLKL--PETGVAVFPGQIVAARGSNPSR 128
D D + S +++ D V+ R L E V F +++
Sbjct: 37 DVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLR-------I 89
Query: 129 N-QFIATKIYSDASLPLSETR-PALDQNTEMYKLRVSYEKGLPLADYLVNVFEK 180
N +F+ + I +E R P++ + + Y A Y V+ +
Sbjct: 90 NYKFLMSPIK-------TEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQP 136
>4fl4_A Glycoside hydrolase family 9; structural genomics,
montreal-kingston bacterial structural initiative,
BSGI, dockerin; 2.80A {Clostridium thermocellum} PDB:
3p0d_A
Length = 88
Score = 28.8 bits (65), Expect = 0.36
Identities = 10/42 (23%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 47 GTVTIGDITLLVPFLFGDTTEI-TAIGRIVCD-TSDGKLNAA 86
G V D+TLL ++ + + ++ D DG++N++
Sbjct: 29 GKVNSTDLTLLKRYVLKAVSTLPSSKAEKNADVNRDGRVNSS 70
>2wd5_B Structural maintenance of chromosomes protein 3; DNA damage, cell
cycle, cell division; 2.70A {Mus musculus}
Length = 213
Score = 30.0 bits (68), Expect = 0.45
Identities = 14/93 (15%), Positives = 31/93 (33%), Gaps = 26/93 (27%)
Query: 13 LDKIRPEWESNPQPSAYRIPWISNLSQFNAIIGLGTVTIGDITLLVPFLFGDTTEITAIG 72
L+K+ + P+ + + + ++N +FG T
Sbjct: 107 LNKLDVRDTAYPETNDAI--PMISKLRYNP----------RFDKAFKHVFGKT------- 147
Query: 73 RIVCDTSD------GKLNAASVLLEGDEVTSGG 99
++C + + + LEGD+V+ G
Sbjct: 148 -LICRSMEVSTQLARAFTMDCITLEGDQVSHRG 179
>2ccl_B Endo-1,4-beta-xylanase Y; cell adhesion, cohesin/dockerin
complex, cellulosome, cohesi dockerin, scaffolding,
cellulose degradation; 2.03A {Clostridium thermocellum}
SCOP: a.139.1.1 PDB: 1ohz_B
Length = 63
Score = 27.1 bits (61), Expect = 0.99
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 47 GTVTIGDITLLVPFLFGDTTEITAIGRIVCD-TSDGKLNAA 86
GT+ D+T+L + +T + D +G +NAA
Sbjct: 11 GTINSTDLTMLKRSVLR-AITLTDDAKARADVDKNGSINAA 50
>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 = 28.0 bits (61), Expect = 1.4
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 6/23 (26%)
Query: 135 KIYSDASLPLSETRPALDQNTEM 157
K+Y+D ++ PAL M
Sbjct: 30 KLYAD------DSAPALAIKATM 46
>4axq_A Archaemetzincin; metalloprotease, protease, hydrolase, metal-bindi;
1.40A {Archaeoglobus fulgidus} PDB: 2xhq_A
Length = 163
Score = 27.6 bits (61), Expect = 1.7
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 110 GVAVFPGQIVAARGSNPSRNQFIATKIYS 138
V V P V+ + N SR Q+ +T I
Sbjct: 32 EVFVLPASDVSLKCYNASRRQYNSTCILR 60
>1ua7_A Alpha-amylase; beta-alpha-barrels, acarbose, greek-KEY motif,
hydrolase; HET: ACI GLD GLC G6D BGC; 2.21A {Bacillus
subtilis} SCOP: b.71.1.1 c.1.8.1 PDB: 1bag_A* 3dc0_A
Length = 422
Score = 27.8 bits (62), Expect = 2.4
Identities = 10/96 (10%), Positives = 27/96 (28%), Gaps = 11/96 (11%)
Query: 28 AYRIPWISNLSQFNAIIGLGTVTI----GDITLLVPFLFGDTTEITAI---GRIVCDTSD 80
+ I+ +++F+ ++ + G+ + + G + V +
Sbjct: 326 LFEDQAITAVNRFHNVMAGQPEELSNPQGNNQIFM-NQRGSHG-VVLANAGSSSVSINTA 383
Query: 81 GKLNAASV--LLEGDEVTSGGRSISLKLPETGVAVF 114
KL ++ + VAV
Sbjct: 384 TKLPDGRYDNKAGAGSFQVNDGKLTGTINARSVAVL 419
>3lmc_A Peptidase, zinc-dependent; structural genomics, PSI-2, protein
structure initiative, no structural genomics consortium,
NESG, MUR16; 2.00A {Methanocorpusculum labreanum}
Length = 210
Score = 27.5 bits (60), Expect = 3.0
Identities = 12/81 (14%), Positives = 22/81 (27%), Gaps = 2/81 (2%)
Query: 108 ETGVAVFPGQIVAARGSNPSRNQFIATKIYSDASLPLSETRPALDQNTEMYKLRVSYEKG 167
E V+ I G +P RNQ+ A K+ + + +
Sbjct: 28 EMPVSRIDDGIFPLEGFDPVRNQYDAVKVLLKLDMFRRRMPQIFKPADMDLEFYNKFNHL 87
Query: 168 LPLADYLVNV--FEKSYNSAF 186
+ +E + F
Sbjct: 88 HEKILLVTPGDLYEPLADFVF 108
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
0.316 0.133 0.380
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,026,296
Number of extensions: 173670
Number of successful extensions: 394
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 19
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.9 bits)