RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13355
(314 letters)
>3d1g_A DNA polymerase III subunit beta; chemical probe, DNA sliding clamp,
DNA replication, rational drug design, antibiotic
target, transferase; HET: DNA 322; 1.64A {Escherichia
coli} SCOP: d.131.1.1 d.131.1.1 d.131.1.1 PDB: 1mmi_A*
1unn_A* 2pol_A* 3bep_A* 3d1e_A* 3d1f_A* 1ok7_A* 3q4j_A*
3q4k_A* 3qsb_A* 3q4l_A* 2xur_A* 1jql_A* 1jqj_A* 3f1v_A*
3pwe_A*
Length = 366
Score = 315 bits (809), Expect = e-107
Identities = 108/307 (35%), Positives = 178/307 (57%), Gaps = 4/307 (1%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+ V + +L PLQ V + + LPIL N+L+ +S TD E+++ A
Sbjct: 1 MKFTVE--REHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVA 58
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ + V ARKF DI R LPE ++ + +E + M ++SG+S+F+L TL A ++P
Sbjct: 59 LVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPN 118
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + + + EFTL Q T+K ++ FS+A QD+RYYLNG+L + + + V++DGHRL
Sbjct: 119 LD-DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRL 177
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
+ I + S S +I+PRK V L R+L+ +NP+ ++I +N I+ + SKL
Sbjct: 178 AVCSMPIGQSLPSHS-VIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKL 236
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSS 300
+DG+F DY+ V+ +K + L ++ R +I+SN+K +GVRL + N LKIT ++
Sbjct: 237 VDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANN 296
Query: 301 SNREKAS 307
+E+A
Sbjct: 297 PEQEEAE 303
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural genomic center
for structural genomics, JCSG, protein structure INI
PSI, transferase; HET: DNA; 2.00A {Thermotoga maritima}
SCOP: d.131.1.1 d.131.1.1 d.131.1.1
Length = 378
Score = 296 bits (760), Expect = 2e-99
Identities = 64/308 (20%), Positives = 142/308 (46%), Gaps = 7/308 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M++ V + + + + KK++ PIL+ L +TD E +
Sbjct: 13 MKVTVT--TLELKDKITIASKALAKKSVKPILAGFLFEVKDGNFYICATDLETGVKATVN 70
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
+ +V +++ LP+ + +E + I SG + F + T+ A E+P
Sbjct: 71 AAEISGEARFVVPGDVIQKMVKVLPDEI-TELSLEGDALVISSGSTVFRITTMPADEFPE 129
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+T F + L+ ++ V F+ A+ + LNG+ K + V+SDG RL
Sbjct: 130 ITPAES-GITFEVDTSLLEEMVEKVIFAAAKDEFMRNLNGVFWELHKNLLRLVASDGFRL 188
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLEN-KENPVELKISNNQIKIIFSNIEIISK 239
+ I+ + + ++ K++ +Q +L+N E + ++ ++ + +++E + +
Sbjct: 189 ALAEEQIENEEEA--SFLLSLKSMKEVQNVLDNTTEPTITVRYDGRRVSLSTNDVETVMR 246
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVS 299
++D +F DYK VI ++ +V+R +L SL+R+ +I++ + V+ I+ N +++
Sbjct: 247 VVDAEFPDYKRVIPETFKTKVVVSRKELRESLKRVMVIASKGSESVKFEIEENVMRLVSK 306
Query: 300 SSNREKAS 307
S + +
Sbjct: 307 SPDYGEVV 314
>2avt_A DNA polymerase III beta subunit; beta clamp, sliding clamp,
replication, transferase; HET: DNA; 2.00A {Streptococcus
pyogenes} PDB: 2awa_A*
Length = 378
Score = 287 bits (737), Expect = 5e-96
Identities = 78/315 (24%), Positives = 148/315 (46%), Gaps = 12/315 (3%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+Q +N + +H L + KN +PILS+I + S ++ ++ ++ I
Sbjct: 2 IQFSIN--RTLFIHALNTTKRAISTKNAIPILSSIKIEVTSTGVTLTGSNGQISIENTIP 59
Query: 61 VGYGNSSINII------VAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLD 114
V N+ + I + A FI+I+ SLP+ IE + + SGKS+ TL+ D
Sbjct: 60 VSNENAGLLITSPGAILLEASFFINIISSLPDISINVKEIEQHQVVLTSGKSEITLKGKD 119
Query: 115 AKEYPIMTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQ-KKNIIAV 173
+YP + S + L K LK I+ F+ + Q+ R L G+ + K+ AV
Sbjct: 120 VDQYPRLQEVST-ENPLILKTKLLKSIIAETAFAASLQESRPILTGVHIVLSNHKDFKAV 178
Query: 174 SSDGHRLTYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSN 233
++D HR++ + +D + +++P K++ + + VE+ S +QI +
Sbjct: 179 ATDSHRMSQRLITLDNTSAD-FMVVLPSKSLREFSAVFTDDIETVEVFFSPSQILFRSEH 237
Query: 234 IEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKG-VRLVIKPN 292
I ++L++G + D ++ ++E + N L +++R +ISN G V+L I N
Sbjct: 238 ISFYTRLLEGNYPDTDRLLMTEFETEVVFNTQSLRHAMERAFLISNATQNGTVKLEITQN 297
Query: 293 YLKITVSSSNREKAS 307
++ V+S K +
Sbjct: 298 HISAHVNSPEVGKVN 312
>3t0p_A DNA polymerase III, beta subunit; DNA clamp, structural genomics,
joint center for structural JCSG, protein structure
initiative; HET: DNA MSE; 2.26A {Eubacterium rectale}
Length = 371
Score = 281 bits (721), Expect = 1e-93
Identities = 69/302 (22%), Positives = 145/302 (48%), Gaps = 7/302 (2%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
M+L+ + K +L + +V V + + IL IL+ ++ +I ++ D E+ I T
Sbjct: 2 MKLICS--KANLLKGVNIVSKAVPTRTTMAILECILIDASANEIKLMANDMELGIETIID 59
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
I + A+ F +I+R LP+ + + I K+KF + ++
Sbjct: 60 GT-IEERGIIALDAKIFSEIVRKLPDNDVTIETDASFKTVISCEKAKFNIIGKSGDDFSY 118
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + + LSQ TLK ++ FSIA D + G L ++ + VS DGHR+
Sbjct: 119 IPYVER-NESIVLSQFTLKEVIRQTIFSIADNDNNKLMTGELFEIEENKLRVVSLDGHRI 177
Query: 181 TYYQVNIDKKFSSCSDIIIPRKTVFTLQRLLEN-KENPVELKISNNQIKIIFSNIEIISK 239
+ + + + S +++P KT+ + +++ + V + I+NN I F N ++S+
Sbjct: 178 SIRYIEMKNHYDS-KKVVVPGKTLQEISKIIPGSADEDVVIYITNNHIVFEFENTTVVSR 236
Query: 240 LIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISND-KLKGVRLVIKPNYLKITV 298
LI+G++ ++S+ Y+ +N+ +LL + R +++ + K + + I +++ +
Sbjct: 237 LIEGEYFKIDQMLSSDYDTKVRINKRELLDCIDRATLLVKEGDKKPIIMNITDGNMELRI 296
Query: 299 SS 300
+S
Sbjct: 297 NS 298
>3p16_A DNA polymerase III subunit beta; DNA polymerase III sliding clamp,
transferase; HET: DNA; 2.89A {Mycobacterium
tuberculosis} PDB: 3rb9_A*
Length = 408
Score = 272 bits (697), Expect = 2e-89
Identities = 45/315 (14%), Positives = 132/315 (41%), Gaps = 16/315 (5%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+ + + + + V + + +P+LS +L+ + ++ D EV
Sbjct: 19 LTFRLL--RESFADAVSWVAKNLPARPAVPVLSGVLLTGSDNGLTISGFDYEVSAEAQVG 76
Query: 61 VGYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPI 120
S +++V+ R DI R+LP V +++E + + G ++F+L T+ ++YP
Sbjct: 77 AE-IVSPGSVLVSGRLLSDITRALPNKP-VDVHVEGNRVALTCGNARFSLPTMPVEDYPT 134
Query: 121 MTLNSKYDFEFTLSQKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRL 180
+ + L + ++ V + + D L G+ + + ++ ++D RL
Sbjct: 135 LPTLP--EETGLLPAELFAEAISQVAIAAGRDDTLPMLTGIRVEILGETVVLAATDRFRL 192
Query: 181 TYYQVNIDKKFSSCS-DIIIPRKTVFTLQRLLENKENPVELKIS-------NNQIKIIFS 232
++ +++P KT+ + + V L + + + I +
Sbjct: 193 AVRELKWSASSPDIEAAVLVPAKTLAEAAKAGIG-GSDVRLSLGTGPGVGKDGLLGISGN 251
Query: 233 NIEIISKLIDGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPN 292
++L+D +F ++ ++ ++ ++ +L+ +++ ++++++ VR+
Sbjct: 252 GKRSTTRLLDAEFPKFRQLLPTEHTAVATMDVAELIEAIKLVALVADRG-AQVRMEFADG 310
Query: 293 YLKITVSSSNREKAS 307
++++ + + +A
Sbjct: 311 SVRLSAGADDVGRAE 325
>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 = 51.8 bits (123), Expect = 2e-07
Identities = 70/382 (18%), Positives = 133/382 (34%), Gaps = 116/382 (30%)
Query: 8 EKNAILHPLQMVISIVEKKNILPILSNI----------LVCK------NSEKISFLSTDT 51
++I L+ ++ +N L +L N+ L CK + FLS T
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285
Query: 52 EVQITT-YTAVGYGNSSINIIVAARKFIDI-LRSLPETEKVTIY---------------- 93
I+ + ++ + ++ K++D + LP E +T
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPR-EVLTTNPRRLSIIAESIRDGLA 342
Query: 94 -IEN-KHMFIKSGKS--KFTLQTLDAKEY----------------PIMTL-----NSKYD 128
+N KH+ + + +L L+ EY P + L +
Sbjct: 343 TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 129 FEFTLSQKTLKCILNMVYFSIAQQD---IRYYLNGLLLSFQKK--NIIAVSSDGHR--LT 181
+ K + +S+ ++ + + L + K N A+ HR +
Sbjct: 403 DVMVVVNK-------LHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL----HRSIVD 451
Query: 182 YYQVNIDKKFSSCSDIIIPRKTVFTLQRL---LENKENPVELKISNNQIKIIFSNIEIIS 238
+Y NI K F S D+I P + + L+N E+P + +F +
Sbjct: 452 HY--NIPKTFDS-DDLIPPYLDQYFYSHIGHHLKNIEHPERMT--------LFRMV---- 496
Query: 239 KLIDGKFLDYKYVISNK--YEKSFLVNRNKLLRSLQRISI----ISNDKLKGVRLV--IK 290
FLD+++ + K ++ + +L +LQ++ I ++ K RLV I
Sbjct: 497 ------FLDFRF-LEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAIL 549
Query: 291 PNYLKITVSSSNREKASSTDLI 312
KI N + TDL+
Sbjct: 550 DFLPKI---EENLICSKYTDLL 568
Score = 37.5 bits (86), Expect = 0.006
Identities = 48/288 (16%), Positives = 91/288 (31%), Gaps = 63/288 (21%)
Query: 26 KNILPILSNILV----CKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDIL 81
K+IL + + V CK+ + D I + + + S + + + L
Sbjct: 19 KDILSVFEDAFVDNFDCKDVQ-------DMPKSILSKEEIDHIIMSKDAVSGTLRLFWTL 71
Query: 82 RSLPETEKVTIYIENKHM----FIKSGKSKFTLQ-TLDAKEYPIMTLNSKYDFEFTLSQK 136
S E E V ++E F+ S Q ++ + Y + D + +Q
Sbjct: 72 LSKQE-EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMY-----IEQRDRLYNDNQV 125
Query: 137 TLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDG------HRLTYYQVNIDKK 190
K +++++ L LL + + + DG + V + K
Sbjct: 126 FAK-------YNVSRLQPYLKLRQALLELRPAKNVLI--DGVLGSGKTWVAL-DVCLSYK 175
Query: 191 FSSCSDIII----------PRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL 240
D I P + LQ+LL +I N + I ++
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKLL--------YQIDPNWTSRSDHSSNIKLRI 227
Query: 241 IDGKFLDYKYVISNKYEKSFLVNRN----KLLRSLQ---RISIISNDK 281
+ + + S YE LV N K + +I + + K
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK 275
>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 = 40.4 bits (94), Expect = 6e-04
Identities = 54/321 (16%), Positives = 106/321 (33%), Gaps = 112/321 (34%)
Query: 29 LPI-----LSNILV-CKNSEKISFLSTDTEVQITTYTAVGYGNSSINIIVAARKFIDILR 82
P+ L++ +V K T E++ A G+ ++ A I
Sbjct: 238 CPLIGVIQLAHYVVTAKLLGF-----TPGELRSYLKGATGHSQG---LVTAV--AI---- 283
Query: 83 SLPETEKVTIYIENKHMFIK----SGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLSQKTL 138
+ ++ + + + I G ++ +A YP +L ++ + +L
Sbjct: 284 AETDSWES--FFVSVRKAITVLFFIG-----VRCYEA--YPNTSLPP------SILEDSL 328
Query: 139 KCILN-------MVYFSIA-------QQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQ 184
+ N M SI+ Q + N L + ++ + +S L
Sbjct: 329 E---NNEGVPSPM--LSISNLTQEQVQDYVNK-TNSHLPAGKQ---VEIS-----L---- 370
Query: 185 VNIDKKFSSCSDIII--PRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKL-I 241
VN K ++ P ++++ L L + P L +Q +I FS KL
Sbjct: 371 VNGAKNL------VVSGPPQSLYGLNLTLRKAKAPSGL----DQSRIPFSE----RKLKF 416
Query: 242 DGKFLDYKYVISNKYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYLKITVSSS 301
+FL +++ + LV + L I+ D L + ++I V +
Sbjct: 417 SNRFL----PVASPFHSHLLVPASDL---------INKD-LVKNNVSFNAKDIQIPVYDT 462
Query: 302 N-----REKASS-----TDLI 312
R + S D I
Sbjct: 463 FDGSDLRVLSGSISERIVDCI 483
Score = 37.0 bits (85), Expect = 0.008
Identities = 33/147 (22%), Positives = 53/147 (36%), Gaps = 27/147 (18%)
Query: 76 KFIDILR-SLPETEKVTIYIENKH-MFIKSGKSKFTLQTLDA---KEYPIMTLN-SKYDF 129
+++ LP ++V I + N + SG + +L L+ K L+ S+ F
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQ-SLYGLNLTLRKAKAPSGLDQSRIPF 409
Query: 130 EFTLSQKTLKCILNMV---------YFSIAQQDIRYYLNGLLLSFQKKNI-IAV--SSDG 177
S++ LK + A I L +SF K+I I V + DG
Sbjct: 410 ----SERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDG 465
Query: 178 HRLTYYQVNIDKKFSSCSDIIIPRKTV 204
L +I + II R V
Sbjct: 466 SDLRVLSGSISE--RIVDCII--RLPV 488
Score = 31.6 bits (71), Expect = 0.43
Identities = 25/163 (15%), Positives = 60/163 (36%), Gaps = 40/163 (24%)
Query: 131 FTLSQKTLKCILNM---VYFSIAQ-QDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVN 186
TLS +L+ +L + +F +Q Q+ F K I+ ++G
Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQE----------QFNK--ILPEPTEGFAA------ 50
Query: 187 IDKKFSSCSDIIIPRKTVFTLQRLLENKENPVE--LKISNNQIKIIF-SNIEI---ISKL 240
D + ++ ++++ + + + +K + L + + + + +I +KL
Sbjct: 51 -DDEPTTPAELVG-KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKL 108
Query: 241 I---DGKFLDYKYVISNKYEKSFLVNR-------NKLLRSLQR 273
+ D + K +I N + R + L R++
Sbjct: 109 LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGE 151
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 32.5 bits (74), Expect = 0.18
Identities = 9/37 (24%), Positives = 18/37 (48%)
Query: 201 RKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEII 237
K TL + ++ P++ + ++ IF NIE +
Sbjct: 38 EKYTDTLGSIQQHFMKPLQRFLKPQDMETIFVNIEEL 74
>1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase
homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP:
c.66.1.26
Length = 343
Score = 32.1 bits (73), Expect = 0.21
Identities = 34/233 (14%), Positives = 72/233 (30%), Gaps = 32/233 (13%)
Query: 77 FIDILRSLPETEKV--TIYIENKHMFIKSGKSKFTLQTLDAKEYPIMTLNSKYDFEFTLS 134
F+ IL LP +K+ I +EN F S +QT++ N + ++
Sbjct: 98 FLHILDILPRLQKLPKYILLENVKGFEVSSTRDLLIQTIE---------NCGFQYQEF-- 146
Query: 135 QKTLKCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDGHRLTYYQVNIDKKFSSC 194
+L+ I +RY+L + + + G L K
Sbjct: 147 ------LLSPTSLGIPNSRLRYFLIA----KLQSEPLPFQAPGQVLM----EFPKIEIHR 192
Query: 195 SDIIIPRKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISN 254
+ +V L+ LE+ + + + + ++I+ K S
Sbjct: 193 KNQQDSDLSVKMLKDFLEDDTDVNQYLLPPKSLLRYALLLDIVQPTCRRSVCFTKGYGSY 252
Query: 255 KYEKSFLVNRNKLLRSLQRISIISNDKLKGVRLVIKPNYL-KITVSSSNREKA 306
++ + ++ ++N + + L T +E A
Sbjct: 253 IEGTGSVLQTAEDVQVENIYKSLTNLSQEEQITKLLILKLRYFTP----KEIA 301
>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
pleckst homology domain, C1 domain, guanine-nucleotide
releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
2d86_A
Length = 587
Score = 30.8 bits (69), Expect = 0.63
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 201 RKTVFTLQRLLENKENPVELKISNNQIKIIFSNIEII 237
K TL + ++ P++ + I+IIF NIE +
Sbjct: 210 EKYTDTLGSIQQHFLKPLQRFLKPQDIEIIFINIEDL 246
>3qq5_A Small GTP-binding protein; hydrogenase, H-cluster, HYDA maturation,
GTP-binding domain, maturation enzyme, oxidoreductase;
2.99A {Thermotoga neapolitana}
Length = 423
Score = 30.0 bits (68), Expect = 1.1
Identities = 10/86 (11%), Positives = 25/86 (29%), Gaps = 13/86 (15%)
Query: 1 MQLVVNTEKNAILHPLQMVISIVEKKNILPILSNILVCKNSEKISFLSTDTEVQITTYTA 60
+ ++V ++ + + L + LV K E +
Sbjct: 212 LVILVVPIDLGAPKGRLIMPQVHAIREALDREAIALVVKERELRYVMENI---------- 261
Query: 61 VGYGNSSINIIVAARKFIDILRSLPE 86
G +I ++ + + +PE
Sbjct: 262 ---GMKPKLVITDSQVAMKVASDVPE 284
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 29.2 bits (65), Expect = 1.9
Identities = 4/31 (12%), Positives = 15/31 (48%)
Query: 207 LQRLLENKENPVELKISNNQIKIIFSNIEII 237
+ R L++ ++ ++ +++ S + I
Sbjct: 52 VMRALDDMDHEGRDTLAREELRQGLSELPAI 82
>1by1_A Protein (PIX); RHO-GTPase exchange factor, transport protein; NMR
{Homo sapiens} SCOP: a.87.1.1
Length = 209
Score = 28.4 bits (64), Expect = 2.4
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 2/39 (5%)
Query: 201 RKTVFTLQRLLENKENPVELK--ISNNQIKIIFSNIEII 237
+ LQ +L P++ +S+ I + N+E I
Sbjct: 26 NEYSKELQTVLSTYLRPLQTSEKLSSANISYLMGNLEEI 64
>3ka7_A Oxidoreductase; structural genomics, PSI-2, protein structure
initiative, northeast structural genomics consortium,
NESG; HET: FAD; 1.80A {Methanosarcina mazei}
Length = 425
Score = 28.5 bits (64), Expect = 2.9
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 207 LQRLLENKENPVELKISNNQIKIIFSNIEIISKLIDGKFLDYKYVISN 254
L+ ++ N ++ KI+ N + + D + D VISN
Sbjct: 202 LETVIS--ANGGKIHTGQEVSKILIENGKAAGIIADDRIHDADLVISN 247
>2dlh_A Receptor-type tyrosine-protein phosphatase delta; protein-tyrosine
phosphatase delta, R-PTP-delta, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 121
Score = 27.4 bits (61), Expect = 3.3
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 39 KNSEKISFLSTDTE--VQITTYTAVGYGNSSINIIV 72
I L V++ +T++G G S +I V
Sbjct: 75 SQITTIGNLVPQKTYSVKVLAFTSIGDGPLSSDIQV 110
>1uen_A KIAA0343 protein; immunoglobulin-like beta-sandwich fold,
fibronectin type III, NG-CAM related cell adhesion
molecule, structural genomics; NMR {Homo sapiens} SCOP:
b.1.2.1
Length = 125
Score = 27.0 bits (60), Expect = 3.9
Identities = 5/36 (13%), Positives = 12/36 (33%), Gaps = 2/36 (5%)
Query: 39 KNSEKISFLSTDTE--VQITTYTAVGYGNSSINIIV 72
K + L + + + G G +S + +
Sbjct: 79 KTHGMLPGLEPFSHYTLNVRVVNGKGEGPASPDRVF 114
>2edy_A Receptor-type tyrosine-protein phosphatase F; LAR protein,
leukocyte antigen related, structural genomics, NPPSFA;
NMR {Homo sapiens}
Length = 103
Score = 26.5 bits (59), Expect = 4.2
Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 39 KNSEKISFLSTDTE--VQITTYTAVGYGNSSINIIV 72
++ L DT +++ +T+ G G S +I
Sbjct: 63 DTRFTLTGLKPDTTYDIKVRAWTSKGSGPLSPSIQS 98
>3o6x_A Glutamine synthetase; type III, beta barrel,dodecamer, ligas; HET:
P3S ADP; 3.50A {Bacteroides fragilis}
Length = 729
Score = 28.0 bits (62), Expect = 4.6
Identities = 21/141 (14%), Positives = 47/141 (33%), Gaps = 17/141 (12%)
Query: 62 GYGNSSINIIVAARKFIDILRSLPETEKVTIYIENKHMFIKSGKSKFTLQTLDAKEYPIM 121
G G S AAR+ + + +PE + +++ + I + E
Sbjct: 536 GDGYSEEWKQEAARRGLTNICHVPEALMHYMDNQSRAVLIGER-------IFNETE---- 584
Query: 122 TLNSKYDFEFTLSQKTL----KCILNMVYFSIAQQDIRYYLNGLLLSFQKKNIIAVSSDG 177
L + + E + + + ++ I + Y N LL + + I +
Sbjct: 585 -LACRLEVELEKYTMKVQIESRVLGDLAINHIVPIAVS-YQNRLLENLCRMKEIFSEEEY 642
Query: 178 HRLTYYQVNIDKKFSSCSDII 198
++ + + K+ S I
Sbjct: 643 EVMSADRKELIKEISHRVSAI 663
>1x4y_A Biregional cell adhesion molecule-related/DOWN- regulated oncogenes
(CDON)binding...; fibronectin type III, FN3; NMR {Mus
musculus} SCOP: b.1.2.1
Length = 114
Score = 26.7 bits (59), Expect = 5.0
Identities = 7/36 (19%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 39 KNSEKISFLSTDT--EVQITTYTAVGYGNSSINIIV 72
+ IS L +T ++++ + G S +I
Sbjct: 68 RYWHSISHLQPETSYDIKMQCFNEGGESEFSNVMIC 103
>3jv3_A Intersectin-1; SH3 domain, DH domain, guanine nucleotide exchange
factor, autoinhibition, domain-swapped, cell junction,
cell project endocytosis; 2.40A {Mus musculus} PDB:
3gf9_A
Length = 283
Score = 27.4 bits (61), Expect = 6.4
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 204 VFTLQRLLENKENPVELK--ISNNQIKIIFSNIEII 237
V LQ + E + P+ ++ ++ +IF N + +
Sbjct: 98 VNDLQLVTEIFQKPLTESELLTEKEVAMIFVNWKEL 133
>3p4l_A Neogenin; iron homeostasis, hemojuvelin receptor, FNIII domain,
fibron type III, cell adhesion; 1.80A {Homo sapiens}
PDB: 1x5k_A
Length = 211
Score = 26.7 bits (59), Expect = 9.3
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 44 ISFLSTDTE--VQITTYTAVGYGNSSINIIV 72
I L+ DT +I + G G S +
Sbjct: 170 IQELTLDTPYYFKIQARNSKGMGPMSEAVQF 200
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 0.135 0.364
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,397,151
Number of extensions: 254198
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 731
Number of HSP's successfully gapped: 57
Length of query: 314
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 221
Effective length of database: 4,105,140
Effective search space: 907235940
Effective search space used: 907235940
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 (25.8 bits)