RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 020983
(319 letters)
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding
motif, platform for RNA polymer assembly, transferase;
1.76A {Sulfolobus solfataricus} PDB: 2pmz_D 3hkz_D
2waq_D 2wb1_D 2y0s_D
Length = 265
Score = 205 bits (522), Expect = 3e-65
Identities = 79/288 (27%), Positives = 133/288 (46%), Gaps = 33/288 (11%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
+ + D NA+RR + VP +A+D V N+S L DE +AHR
Sbjct: 2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 71 LGLIPLTSERAM-SMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
L LIP SE A+ + R+ +C C + CE C + ++ A+ ++ + SKD+ S D
Sbjct: 62 LALIPFMSEEALDTYRWPEECIECTEN--CEKCYTKIYIEAEA-PNEPRMIYSKDIKSED 118
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
SVVP+ I IV L Q++ L A R G GK+HAK+ P +
Sbjct: 119 PSVVPIS-------------GDIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVSLSVVR 165
Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
Y P++ I + + V P VF++ G++ V + + T +E ++
Sbjct: 166 YYPKVEILAN---------CEKAVNVCPEGVFELKD--GKLSVKNELSCTLCEECLRYCN 214
Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
G + I ED +I +ES G++K +++L A + + +K++ +
Sbjct: 215 -----GSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELE 257
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide;
transcription, mRNA, multiprotein complex; HET: UTP;
2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1
d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C
1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C*
1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C
1y77_C* ...
Length = 318
Score = 198 bits (504), Expect = 7e-62
Identities = 112/313 (35%), Positives = 161/313 (51%), Gaps = 34/313 (10%)
Query: 7 QRFPKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEF 66
+ P+VKIRE D F L + D +MAN+LRRVMIAE+PT+AID VE+E N++VL DEF
Sbjct: 3 EEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEF 62
Query: 67 IAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLY 126
IAHRLGLIPL S + +SRDC D C+ CSV L+A S+ T +V SKDL
Sbjct: 63 IAHRLGLIPLQSMDIEQLEYSRDCFCEDH---CDKCSVVLTLQAFGESESTTNVYSKDLV 119
Query: 127 SSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATV 186
+ + + P D G++I KLR+GQEL+L +A+KGI K+HAKW PAA +
Sbjct: 120 IVSNLMGR-NIGHPIIQDKEGN--GVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAI 176
Query: 187 TFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIK 246
F Y+P + E+ S E +K + + + D
Sbjct: 177 EFEYDPWNKLKHTDYW----YEQDSAKEWPQSKNCEYEDPPNEGDPFD------------ 220
Query: 247 KAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
A+ D+F VES G+I Q+V+ I+ L++K+ ++ L+ ++ D
Sbjct: 221 ------------YKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 268
Query: 307 DQFGELGAHMRGG 319
G +
Sbjct: 269 KVNFASGDNNTAS 281
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 297
Score = 195 bits (497), Expect = 5e-61
Identities = 96/309 (31%), Positives = 148/309 (47%), Gaps = 37/309 (11%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
+ IR + + F L +T ++AN+LRRV++AE+PT+AIDLVEI VN+SV+ DEF+AH
Sbjct: 5 THITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAH 64
Query: 70 RLGLIPLTSERA--MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYS 127
RLG+IPL S CD D C CSVE L AKC + T+++ ++DL
Sbjct: 65 RLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVV 124
Query: 128 SDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVT 187
S +S + + G +I KLR+ QE+ LR IA+KGI K+HAKWSP + V
Sbjct: 125 SSNSSLGHPILADPKSR------GPLICKLRKEQEISLRCIAKKGIAKEHAKWSPTSAVA 178
Query: 188 FMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
F Y+P + E + E +K D + + +
Sbjct: 179 FEYDPWNKLQHTDYW----FENDADAEWPKSKNADWEEPPREGEPFN------------- 221
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEADD 307
+ F VES G+I +++++ + +L++KL + + + E
Sbjct: 222 -----------FQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVL-VRDLDEEQPT 269
Query: 308 QFGELGAHM 316
Q +M
Sbjct: 270 QLSANELNM 278
>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 = 47.0 bits (111), Expect = 6e-06
Identities = 62/355 (17%), Positives = 100/355 (28%), Gaps = 144/355 (40%)
Query: 1 MDGASYQRFPKVK-IRELKDDYAK----FELRDTDASMANALRRVMIAEVPTIAIDLVEI 55
MD Y+ + + D++ K F + D ++ P
Sbjct: 1633 MD--LYKTSKAAQDVWNRADNHFKDTYGFSILD------------IVINNPV-------- 1670
Query: 56 EVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCE--FCSVEFHLRAKC- 112
N ++ R+ E +M F DG + E F + H +
Sbjct: 1671 --NLTIHFGGEKGKRI------RENYSAMIFE---TIVDGKLKTEKIFKEINEHSTSYTF 1719
Query: 113 -HSDQTLDVT-------------------SKDLYSSD-----HSV------VPVDFVDPA 141
L T SK L +D HS+ + A
Sbjct: 1720 RSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASL-----A 1774
Query: 142 GYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDLM 201
S + + +V R G ++ A+ R +G+ + M I IN +
Sbjct: 1775 DVMSIES--LVEVVFYR-GMTMQ-VAVPRDELGRSNYG---------M----IAINPGRV 1817
Query: 202 -ESLSLEEKQSWVE--SSPTKVFDIDP---NT-GQVYVVDAEAYTYDDEVIKKAEAMGKP 254
S S E Q VE T ++ N Q YV A
Sbjct: 1818 AASFSQEALQYVVERVGKRTGWL-VEIVNYNVENQQYVA----------------A---- 1856
Query: 255 GLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE----DTVEA 305
G + A+ VLN I++ QK+D + L + + VE
Sbjct: 1857 GDLR----------------ALDTVTNVLNFIKL--QKIDIIELQKSLSLEEVEG 1893
Score = 39.6 bits (92), Expect = 0.001
Identities = 37/180 (20%), Positives = 55/180 (30%), Gaps = 48/180 (26%)
Query: 170 RKGIGKDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPT-KVFDIDPNTG 228
+G+G D K S AA + + H + S+ V ++P G
Sbjct: 1628 EQGMGMDLYKTSKAAQDVWN-RADNHFKDTYGFSI-----LDIVINNPVNLTIHFGGEKG 1681
Query: 229 QVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQ-----LVL 283
+ + A + E I + + EI S+ F G + A+Q L L
Sbjct: 1682 KRIRENYSAMIF--ETIVDGKLKTEKIFKEINEHSTSYTFR-SEKGLLSATQFTQPALTL 1738
Query: 284 --NAI-EVLKQKLDAVRLSEDTVEADDQF-----GELGA-----------------HMRG 318
A E LK S+ + AD F GE A RG
Sbjct: 1739 MEKAAFEDLK--------SKGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRG 1790
Score = 38.1 bits (88), Expect = 0.004
Identities = 45/311 (14%), Positives = 79/311 (25%), Gaps = 135/311 (43%)
Query: 34 ANALRRVMIA--------EVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMS-- 83
A + R + ++ VPT +S L ++F L T A
Sbjct: 3 AYSTRPLTLSHGSLEHVLLVPT------ASFFIASQLQEQFNKI---LPEPTEGFAADDE 53
Query: 84 --------MRF----SRDCDACDGDGQCEFCSV------EFH---LRAKCHSDQTLDVTS 122
+F S + +F V EF L D+
Sbjct: 54 PTTPAELVGKFLGYVSSLVEP---SKVGQFDQVLNLCLTEFENCYLEGN-------DI-- 101
Query: 123 KDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRA--IARKGIGKDHAKW 180
H++ A + L + +EL ++ AR + K
Sbjct: 102 -------HALA-------AKLLQENDT------TLVKTKEL-IKNYITARIMAKRPFDKK 140
Query: 181 SPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTY 240
S +A L + V ++ I GQ Y
Sbjct: 141 SNSA---------------LFRA---------VGEGNAQLVAIFG--GQ-----GNTDDY 169
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSE 300
+E L ++Y + L+ + E L + L
Sbjct: 170 FEE------------LRDLYQTYHVLV-----------GDLIKFSAETLSE------LIR 200
Query: 301 DTVEADDQFGE 311
T++A+ F +
Sbjct: 201 TTLDAEKVFTQ 211
>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 = 36.5 bits (83), Expect = 0.004
Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 19/48 (39%)
Query: 241 DDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNA-IE 287
+ + +KK +A +++YA +DS A L + A +E
Sbjct: 18 EKQALKKLQAS-----LKLYA-DDS------------APALAIKATME 47
>1ncg_A N-cadherin; cell adhesion protein; 2.10A {Mus musculus} SCOP:
b.1.6.1 PDB: 1nch_A 1nci_A
Length = 110
Score = 30.3 bits (69), Expect = 0.26
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ PT +F I+P +GQ+ V
Sbjct: 45 ADQPPTGIFIINPISGQLSV 64
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase
holoenzyme, streptolydigin, antibiotic, transcription
regulation; HET: STD; 2.40A {Thermus thermophilus}
SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A*
2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A*
2ppb_A* 3aoh_A* 3aoi_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A*
1l9z_A 1l9u_A* 1ynn_A* ...
Length = 315
Score = 31.3 bits (72), Expect = 0.41
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 10 PKVKIRELKDDYAKFELR-------DTDASMANALRRVMIAEVPTIAIDLVEIE 56
P +R +Y +F L T + N LRR++++ +P A+ V IE
Sbjct: 9 PVFTVRTQGREYGEFVLEPLERGFGVT---LGNPLRRILLSSIPGTAVTSVYIE 59
>2lli_A Protein AIR2; RNA surveillance, RNA degradation, RNA binding,
exosome, RNA protein; NMR {Saccharomyces cerevisiae}
Length = 124
Score = 30.1 bits (67), Expect = 0.41
Identities = 7/29 (24%), Positives = 11/29 (37%)
Query: 86 FSRDCDACDGDGQCEFCSVEFHLRAKCHS 114
+ C QC C + H + +C S
Sbjct: 54 YRSQCPHKWKKVQCTLCKSKKHSKERCPS 82
>2ygk_A NURA; hydrolase, DNA repair, replication; HET: MSE; 2.50A
{Sulfolobus solfataricus}
Length = 339
Score = 31.0 bits (69), Expect = 0.52
Identities = 15/108 (13%), Positives = 32/108 (29%), Gaps = 14/108 (12%)
Query: 196 INEDLMESLSLEEKQSWVESSPTKVFDIDPNT--------------GQVYVVDAEAYTYD 241
I L + + + + W E G VY V AE+ D
Sbjct: 23 IANYLKQEIQDKVNEYWNEYVINHEQSETCKFVAIDGGSFGRPMRIGIVYAVGAESVIGD 82
Query: 242 DEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVL 289
++ +K G+ G+ + I + + + + + +
Sbjct: 83 NKGVKTLSEDGQIGIFKPGNDAQERISLLMEALELSLALRDGSKGDYI 130
>2omz_B Epithelial-cadherin; leucine-rich-repeat, nvasion protein, IG-like
domain, adhesi protein, cell invasion-cell adhesion
complex; 1.60A {Homo sapiens} SCOP: b.1.6.1 PDB: 2omt_B
2omu_B 2omv_B 1o6s_B 2omy_B 2omx_B 3ff8_A 3ff7_A 2omw_B
Length = 105
Score = 28.9 bits (65), Expect = 0.66
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
++ P VF I+ TG + V
Sbjct: 47 ADTPPVGVFIIERETGWLKV 66
>2yqg_A Desmoglein-2, HDGC; cadherin, structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 123
Score = 29.2 bits (66), Expect = 0.71
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ P +F + +TG++ V
Sbjct: 55 ITEPPFGIFVFNKDTGELNV 74
>3k6d_A T-cadherin; cell adhesion; 1.80A {Xenopus laevis} PDB: 2v37_A
Length = 99
Score = 28.9 bits (65), Expect = 0.73
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
V+ P +F I+ N+G+V V
Sbjct: 42 VDQEPKGIFKINENSGEVSV 61
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA
polymerase, nucleotidyltransferase, transcription,
transferase; 11.20A {Escherichia coli} PDB: 3iyd_A
Length = 329
Score = 30.1 bits (69), Expect = 0.95
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 10/53 (18%)
Query: 11 KVKIRELKDDYAKFELR-------DTDASMANALRRVMIAEVPTIAIDLVEIE 56
V I ++ +AK L T + NALRR++++ +P A+ VEI+
Sbjct: 13 LVDIEQVSSTHAKVTLEPLERGFGHT---LGNALRRILLSSMPGCAVTEVEID 62
>3k6f_A T-cadherin; cell adhesion, calcium, cell membrane, cleavage on PAIR
of basic residues, glycoprotein, GPI-anchor,
lipoprotein, membrane; 1.81A {Mus musculus}
Length = 100
Score = 28.5 bits (64), Expect = 1.1
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
V+ P F I+ NTG V V
Sbjct: 43 VDQDPKGTFRINENTGSVSV 62
>3dsm_A Uncharacterized protein bacuni_02894; seven_blated beta propeller,
structural genomics, PSI-2, Pro structure initiative;
1.90A {Bacteroides uniformis}
Length = 328
Score = 30.0 bits (67), Expect = 1.1
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 14/54 (25%)
Query: 223 IDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAI 276
++PN G+VYV DA Y + G+V Y+ + I G I
Sbjct: 274 VNPNNGEVYVADAIDYQ-------------QQGIVYRYSPQGKLIDEFY-VGII 313
>2d8v_A Zinc finger FYVE domain-containing protein 19; zfyve19, ZF- B_BOX,
structural genomics, NPPSFA; NMR {Mus musculus} SCOP:
g.43.1.1
Length = 67
Score = 27.3 bits (60), Expect = 1.4
Identities = 11/35 (31%), Positives = 12/35 (34%)
Query: 90 CDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKD 124
C CDGD C C E H QT +
Sbjct: 22 CAGCDGDLYCARCFREGHDNFDLKEHQTSPYHPRR 56
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble;
2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1
Length = 235
Score = 29.3 bits (67), Expect = 1.4
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 11 KVKIRELKDDYAKFELR-------DTDASMANALRRVMIAEVPTIAIDLVEIE 56
V I ++ +AK L T + NALR ++++ +P A+ VEI+
Sbjct: 13 LVDIEQVSSTHAKVTLEPLERGFGHT---LGNALRAILLSSMPGCAVTEVEID 62
>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural
genomics, protein structure initiative, MCSG; 1.60A
{Thermoplasma acidophilum} SCOP: d.74.3.2
Length = 115
Score = 28.3 bits (63), Expect = 1.5
Identities = 3/28 (10%), Positives = 12/28 (42%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALR 38
+++ + + E+ + D ++ L
Sbjct: 12 SLRVISKEKNSITVEMINYDNTLLRTLV 39
>3k6i_A T-cadherin; cell adhesion, alternative splicing, calcium, cell
membrane, cleavage on PAIR of basic residues,
glycoprotein, GPI-anchor, lipoprotein; 1.13A {Gallus
gallus}
Length = 99
Score = 27.8 bits (62), Expect = 1.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
V+ P +F I+ +G V V
Sbjct: 42 VDQDPKGIFRINEISGDVSV 61
>2zkr_d 60S ribosomal protein L11; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 178
Score = 28.7 bits (65), Expect = 1.9
Identities = 9/37 (24%), Positives = 13/37 (35%), Gaps = 2/37 (5%)
Query: 143 YDSTDQQRG--IIIVKLRRGQELRLRAIARKGIGKDH 177
YD + G +V R G + + IG H
Sbjct: 119 YDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKH 155
>2qvi_A Cadherin-2; beta barrel, strand SWAP, domain SWAP, calcium, cell
adhesion, cleavage on PAIR of basic residues,
glycoprotein, membrane; 3.01A {Mus musculus} SCOP:
b.1.6.1 b.1.6.1 PDB: 1ncj_A
Length = 215
Score = 28.1 bits (63), Expect = 3.0
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ PT +F I+P +GQ+ V
Sbjct: 43 ADQPPTGIFIINPISGQLSV 62
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S
binding motif, platform for RNA polymer assembly,
transferase; 1.76A {Sulfolobus solfataricus} PDB:
2pmz_L 3hkz_L 2waq_L 2wb1_L 2y0s_L
Length = 92
Score = 26.7 bits (59), Expect = 3.4
Identities = 5/31 (16%), Positives = 17/31 (54%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVM 41
+++I + + +Y + E+ D ++ N + +
Sbjct: 2 EIRILKSESNYLELEIEGEDHTLGNLIAGTL 32
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 3.6
Identities = 17/103 (16%), Positives = 32/103 (31%), Gaps = 11/103 (10%)
Query: 32 SMANALRRVMIAEVPTIAIDLVEIEVNSSVLND--EFIAHRLGLIPLTSERAMSMRFSRD 89
R I + ++ +++E D EF+ R I +E +
Sbjct: 1250 KRQLVTREAQIKDWVENELEALKLEAEEIPSEDQNEFLLERTREIHNEAESQL------- 1302
Query: 90 CDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDL-YSSDHS 131
A G + + + + T +T DL +S H
Sbjct: 1303 RAAQQQWGNDFYKR-DPRIAPLRGALATYGLTIDDLGVASFHG 1344
>3k5r_A Cadherin 13; mouse, structural protein; 2.00A {Mus musculus} PDB:
3k5s_A
Length = 218
Score = 27.7 bits (62), Expect = 4.0
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
V+ P F I+ NTG V V
Sbjct: 43 VDQDPKGTFRINENTGSVSV 62
>3qrb_A Cadherin-1; cell adhesion; HET: PGE; 1.80A {Mus musculus} PDB:
1ff5_A 3lng_A 2qvf_B 1edh_A 3lne_A 1q1p_A 3lni_A 3q2l_A*
3q2n_A* 3lnh_A 3lnf_A 2o72_A 1suh_A
Length = 213
Score = 27.7 bits (62), Expect = 4.5
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ P VF I+ TG + V
Sbjct: 43 ADKPPVGVFIIERETGWLKV 62
>3q2w_A Cadherin-2; cell adhesion, calcium binding; HET: MAN NAG; 3.20A
{Mus musculus}
Length = 559
Score = 28.1 bits (63), Expect = 5.0
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ PT +F I+P +GQ+ V
Sbjct: 43 ADQPPTGIFIINPISGQLSV 62
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 27.7 bits (62), Expect = 5.5
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 230 VYVVDAEAYTYDDEVIKKAEAMGKP 254
+ V D+ Y+D+V+ + M P
Sbjct: 118 ILVTDSAPTPYEDDVVNLFKEMEIP 142
>3q2v_A Cadherin-1; cell adhesion, calcium binding; HET: MAN; 3.40A {Mus
musculus}
Length = 550
Score = 27.7 bits (62), Expect = 6.0
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
+ P VF I+ TG + V
Sbjct: 43 ADKPPVGVFIIERETGWLKV 62
>1sen_A Thioredoxin-like protein P19; endoplasmic reticulum, RP19,
structural genomics, PSI, protein structure initiative;
1.20A {Homo sapiens} SCOP: c.47.1.1 PDB: 2k8v_A
Length = 164
Score = 26.9 bits (59), Expect = 6.0
Identities = 8/24 (33%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 238 YTYDDEVIKKAEAMGKPGLVEIYA 261
T + + K+A A G P +V I+
Sbjct: 33 RTLE-DGKKEAAASGLPLMVIIHK 55
>1q55_A EP-cadherin, C-cadherin; trans interaction, desmosome, junction,
adhesion, structural protein; HET: NAG NDG; 30.00A {Mus
musculus} SCOP: i.20.1.1 PDB: 1q5a_A* 1q5b_A* 1q5c_A*
Length = 880
Score = 27.9 bits (62), Expect = 6.2
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
++ P VF I+ TG + V
Sbjct: 198 ADNPPQGVFRIEWETGWMLV 217
Score = 27.1 bits (60), Expect = 8.3
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 7/48 (14%)
Query: 214 ESSPTKVFDIDPNTGQVYVV----DAEAY-TYDDEVIKKAEAMGKPGL 256
E +F I+ TG + ++ D E + Y + +A + GL
Sbjct: 311 EEPIPNLFTINRETGVISLIGTGLDREKFPEY--TLTVQATDLEGAGL 356
>1l3w_A EP-cadherin, C-cadherin; cell adhesion, calcium binding,
extracellular, ECT metal binding protein; HET: NAG NDG;
3.08A {Xenopus laevis} SCOP: b.1.6.1 b.1.6.1 b.1.6.1
b.1.6.1 b.1.6.1
Length = 546
Score = 27.7 bits (62), Expect = 6.8
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 213 VESSPTKVFDIDPNTGQVYV 232
++ P VF I+ TG + V
Sbjct: 49 ADNPPQGVFRIEWETGWMLV 68
>1vq8_D 50S ribosomal protein L5P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: d.77.1.1 PDB: 1vq4_D*
1vq5_D* 1vq6_D* 1vq7_D* 1s72_D* 1vq9_D* 1vqk_D* 1vql_D*
1vqm_D* 1vqn_D* 1vqo_D* 1vqp_D* 1yhq_D* 1yi2_D* 1yij_D*
1yit_D* 1yj9_D* 1yjn_D* 1yjw_D* 2otj_D* ...
Length = 177
Score = 26.8 bits (60), Expect = 7.3
Identities = 13/49 (26%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 143 YDSTDQQRG--IIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
YD + G + + +R G + R A + I H + +PA V F+
Sbjct: 120 YDPSIGIYGLDVTVNLVRPGYRVAKRDKASRSIPTKH-RLNPADAVAFI 167
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_e
Length = 244
Score = 26.4 bits (59), Expect = 8.9
Identities = 4/37 (10%), Positives = 10/37 (27%), Gaps = 2/37 (5%)
Query: 143 YDSTDQQRG--IIIVKLRRGQELRLRAIARKGIGKDH 177
+ ++ + V+ R+ I K
Sbjct: 118 FLKVNKATINMLRRVEPYVTYGYPNLKSVRELIYKRG 154
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 0.134 0.379
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,073,289
Number of extensions: 318531
Number of successful extensions: 949
Number of sequences better than 10.0: 1
Number of HSP's gapped: 930
Number of HSP's successfully gapped: 57
Length of query: 319
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 225
Effective length of database: 4,077,219
Effective search space: 917374275
Effective search space used: 917374275
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 (21.7 bits)
S2: 57 (25.6 bits)