RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8083
(303 letters)
>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 = 48.1 bits (114), Expect = 2e-06
Identities = 51/246 (20%), Positives = 83/246 (33%), Gaps = 85/246 (34%)
Query: 19 PGLSVLLCSPRQ-GTNVDE-NSAFIGDLPLLKRVSAPSDVFCSVPGRLSLLSSTSKYKVT 76
P LS+ + Q V++ NS LP K+V +SL++ V+
Sbjct: 337 PMLSISNLTQEQVQDYVNKTNS----HLPAGKQVE------------ISLVNGAKNLVVS 380
Query: 77 VGEVQRRLSPPECLNASLLGGVLRRAKSKNG---GRL-LREKLEKIGLN-LPAGRRKAAN 131
G PP+ L L LR+AK+ +G R+ E+ K LP
Sbjct: 381 -G-------PPQSLYG--LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLP-------- 422
Query: 132 VT------LLTSLVEGEAIHLARDFGYVCETEFPARQVAE--YLSRQHTSDPTESYRRKE 183
V LL + L ++ F A+ + Y T D +
Sbjct: 423 VASPFHSHLLVPASDLINKDLVKN-----NVSFNAKDIQIPVY----DTFDG------SD 467
Query: 184 LIHATKQVTKELMDLLNQDRSPL-----CNTRPQHILDPSIQRHLTHFSLISHGFGSPAI 238
L + +++ ++D + R P+ + HILD F G G +
Sbjct: 468 LRVLSGSISERIVDCII--RLPVKWETTTQFKATHILD---------F-----GPGGASG 511
Query: 239 VAALTA 244
+ LT
Sbjct: 512 LGVLTH 517
Score = 33.1 bits (75), Expect = 0.14
Identities = 23/146 (15%), Positives = 48/146 (32%), Gaps = 28/146 (19%)
Query: 145 HLARDFGYV---CETEFPARQVAEYLSRQHTSDPTESYRR--KELIHATKQVTKELMDLL 199
H +G+ P + + + E+Y E I K T+++ +
Sbjct: 1652 HFKDTYGFSILDIVINNP-VNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFKEI 1710
Query: 200 NQDRSPLCNTRPQHILDPSIQRHLTHFSLISHGFGSPAIVAALTAIQNFL-TESLKHLDK 258
N+ + + +L T F+ PA+ A L ++ L D
Sbjct: 1711 NEHSTSYTFRSEKGLLS------ATQFT-------QPALTLMEKAAFEDLKSKGLIPADA 1757
Query: 259 MYPSGNSL-------SVSSSQGLQDT 277
+ +G+SL S++ ++
Sbjct: 1758 TF-AGHSLGEYAALASLADVMSIESL 1782
Score = 31.9 bits (72), Expect = 0.29
Identities = 36/221 (16%), Positives = 56/221 (25%), Gaps = 75/221 (33%)
Query: 111 LREKLEKIGLNLPAGRRKAANVTLLTSLVEGEAIHLARDF-GYVCETEFPARQVA----- 164
L+E+ KI LP A T+ E L F GYV P++
Sbjct: 33 LQEQFNKI---LPEPTEGFAADDEPTTPAE-----LVGKFLGYVSSLVEPSKVGQFDQVL 84
Query: 165 ---------EYLSRQ--HT-------SDPTESYRRKELIHATKQVTKELMDLLNQDRSPL 206
YL H + T + KELI K + + P
Sbjct: 85 NLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI-------KNYITARIMAKRPF 137
Query: 207 CNTRPQHILDPSIQRHLTHFSLISHGFG------------------SPAIVAALTAIQNF 248
+ + L ++ I FG +V
Sbjct: 138 -DKKSNSALFRAVGEGNAQLVAI---FGGQGNTDDYFEELRDLYQTYHVLVGD------L 187
Query: 249 LTESLKHLDKMYPSGNSLSVSSSQGLQ--------DTKPKD 281
+ S + L ++ + +QGL P
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDK 228
>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 = 44.8 bits (105), Expect = 3e-05
Identities = 54/328 (16%), Positives = 93/328 (28%), Gaps = 110/328 (33%)
Query: 4 KHLARQKKCKIEARRPGLSVLLCSPRQGTNVDENSAFIGDL----------PLLKRVSAP 53
H+ K R L L S + + + F+ ++ P+ P
Sbjct: 52 DHIIMSKDAVSGTLR--LFWTLLS--KQEEMVQ--KFVEEVLRINYKFLMSPIKTEQRQP 105
Query: 54 S---DVFCSVPGRL-SLLSSTSKYKVTVGEVQRRLSPPECLNASLLGGVLRRAKSKNGGR 109
S ++ RL + +KY V+ R +
Sbjct: 106 SMMTRMYIEQRDRLYNDNQVFAKYNVS------R---LQPYLK----------------- 139
Query: 110 LLREKLEKIGLNLPAGRRKAANVTLL-------TSLVEGEAIHLARDFGYVCETEFP--- 159
LR+ L ++ R A NV + T + A+ + + C+ +F
Sbjct: 140 -LRQALLEL--------RPAKNVLIDGVLGSGKTWV----ALDVCLSYKVQCKMDFKIFW 186
Query: 160 --------ARQVAEYLSR-------QHTSDPTESYRRKELIHATKQVTKELM-------D 197
V E L + TS S K IH+ + + L+
Sbjct: 187 LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC 246
Query: 198 LL---N-QDRSPL------CN----TRPQHILDPSIQRHLTHFSLISH--GFGSPAIVAA 241
LL N Q+ C TR + + D TH SL H
Sbjct: 247 LLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD---EV 303
Query: 242 LTAIQNFLTESLKHLDKMYPSGNSLSVS 269
+ + +L + L + + N +S
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLS 331
>1jqn_A Pepcase, PEPC, phosphoenolpyruvate carboxylase; beta barrel, Mn2+
and DCDP complex, lyase; HET: DCO; 2.35A {Escherichia
coli} SCOP: c.1.12.3 PDB: 1fiy_A* 1qb4_A
Length = 883
Score = 35.1 bits (81), Expect = 0.028
Identities = 30/157 (19%), Positives = 49/157 (31%), Gaps = 49/157 (31%)
Query: 93 SLLGGVLRRAKSKNGGRLLREKLEKIGLNLPAGRRKAAN-----VTLLTSLVEGEAIHLA 147
+LG ++ A G + E++E I + R +T L +L E + +A
Sbjct: 17 KVLGETIKDA----LGEHILERVETIRKLSKSSRAGNDANRQELLTTLQNLSNDELLPVA 72
Query: 148 RDFGY----------------------------------VCETEFPARQVAEYLSRQH-- 171
R F + E + + +
Sbjct: 73 RAFSQFLNLANTAEQYHSISPKGEAASNPEVIARTLRKLKNQPELSEDTIKKAVESLSLE 132
Query: 172 ---TSDPTESYRRKELIHATKQVTKELMDLLNQDRSP 205
T+ PTE RR LIH +V L L N+D +
Sbjct: 133 LVLTAHPTEITRR-TLIHKMVEVNACLKQLDNKDIAD 168
>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain
III (ATPase domain), ATP-binding, cytoplasm, DNA
replication; HET: ADP; 3.00A {Thermotoga maritima} PDB:
2z4r_A*
Length = 440
Score = 31.5 bits (72), Expect = 0.34
Identities = 8/47 (17%), Positives = 20/47 (42%), Gaps = 12/47 (25%)
Query: 160 ARQVAEYLSRQHTSDPTESYRR--KEL-------IHATKQVTKELMD 197
AR++ Y+++ + S R ++ + + K+V L+
Sbjct: 374 ARRIGMYVAKNYLK---SSLRTIAEKFNRSHPVVVDSVKKVKDSLLK 417
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D-
structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB:
1i6v_D* 2gho_D
Length = 1265
Score = 29.6 bits (67), Expect = 1.4
Identities = 6/33 (18%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 176 TESYRRKELI----HATKQVTKELMDLLNQDRS 204
T+ R ++I T++VT+ + + ++
Sbjct: 725 TDRERYDQVIQLWTETTEKVTQAVFNNFEENYP 757
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2
PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D*
2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D*
3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Length = 1524
Score = 29.7 bits (67), Expect = 1.5
Identities = 5/33 (15%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 176 TESYRRKELI----HATKQVTKELMDLLNQDRS 204
T+ R +++ T++VT+ + ++
Sbjct: 984 TDRERYDQILQLWTETTEKVTQAVFKNFEENYP 1016
>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix
motif, interacting with DNAA-BOX, DNAA-box; HET: DNA;
2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*
Length = 101
Score = 27.2 bits (61), Expect = 2.4
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 160 ARQVAEYLSRQHTS 173
+RQ+A YL R+ T
Sbjct: 37 SRQIAMYLCRELTD 50
>1jqo_A Phosphoenolpyruvate carboxylase; beta barrel, carbon dioxide
fixation, lyase; 3.00A {Zea mays} SCOP: c.1.12.3
Length = 970
Score = 28.7 bits (64), Expect = 3.2
Identities = 17/107 (15%), Positives = 30/107 (28%), Gaps = 16/107 (14%)
Query: 94 LLGGVLRRAKSKNGGRLLREKLEKIGLNLPAGRRKAAN------VTLLTSLVEGEAIHLA 147
+L+ G LRE +++ K LT L +AI +A
Sbjct: 44 RFLNILQDL----HGPSLREFVQECYEVSADYEGKGDTTKLGELGAKLTGLAPADAILVA 99
Query: 148 RDFGY------VCETEFPARQVAEYLSRQHTSDPTESYRRKELIHAT 188
+ + E A + ++ S + I T
Sbjct: 100 SSILHMLNLANLAEEVQIAHRRRNSKLKKGGFADEGSATTESDIEET 146
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+,
helix-turn-helix, nucleotide-binding, DNA binding, REP
initiation, DNA binding protein; HET: ADP; 2.70A
{Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A*
2hcb_A*
Length = 324
Score = 28.3 bits (64), Expect = 3.5
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 160 ARQVAEYLSRQHTS 173
AR++A YL R+ S
Sbjct: 260 ARKIAMYLCRKVCS 273
>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA
compl protease/ntpase/helicase, hydrolase; 1.95A
{Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A*
1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A*
3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A
Length = 666
Score = 27.7 bits (61), Expect = 5.8
Identities = 5/31 (16%), Positives = 9/31 (29%)
Query: 159 PARQVAEYLSRQHTSDPTESYRRKELIHATK 189
Y+S+ H DP + +
Sbjct: 269 ATLGFGAYMSKAHGIDPNIRTGVRTITTGAP 299
>4fsd_A Arsenic methyltransferase; rossmann fold; 1.75A {Cyanidioschyzon
SP} PDB: 4fr0_A* 4fs8_A 3p7e_A 3qnh_A 3qhu_A
Length = 383
Score = 27.4 bits (60), Expect = 6.5
Identities = 16/86 (18%), Positives = 24/86 (27%), Gaps = 10/86 (11%)
Query: 1 MLAKHLARQKKCKIEARRPGLSVLLCSPRQGTNVDENSAFIGDLPLLKRVSAPSDVFCSV 60
L AR+ + +NV FI +L + P V
Sbjct: 120 QLEV--ARKYVEYHAEK-------FFGSPSRSNVRFLKGFIENLATAEPEGVPDSSVDIV 170
Query: 61 PGRLSLLSSTSKYKVTVGEVQRRLSP 86
ST+K + E+ R L
Sbjct: 171 ISNCVCNLSTNKLAL-FKEIHRVLRD 195
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_D*
Length = 1407
Score = 27.2 bits (61), Expect = 9.8
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 176 TESYRRKELI----HATKQVTKELMDLLNQDR 203
T R ++I A +V+K +MD L +
Sbjct: 674 TAGERYNKVIDIWAAANDRVSKAMMDNLQTET 705
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
0.317 0.132 0.382
Gapped
Lambda K H
0.267 0.0528 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,343,972
Number of extensions: 251138
Number of successful extensions: 613
Number of sequences better than 10.0: 1
Number of HSP's gapped: 611
Number of HSP's successfully gapped: 17
Length of query: 303
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 210
Effective length of database: 4,105,140
Effective search space: 862079400
Effective search space used: 862079400
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: 57 (26.2 bits)