RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 016934
(380 letters)
>3op1_A Macrolide-efflux protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural genomics,
MCSG; HET: PEG; 2.49A {Streptococcus pneumoniae}
Length = 308
Score = 111 bits (279), Expect = 4e-28
Identities = 50/204 (24%), Positives = 81/204 (39%), Gaps = 40/204 (19%)
Query: 100 FSPVAGGIVALGKFDALHIGHRELAIQASKIGAPYLLSFIGM------AEVFGWEPRAPI 153
+ +V LG FD +H GH+EL A+K LL + M P P
Sbjct: 16 IGTPSDSVVVLGYFDGIHKGHQELFRVANKAARKDLLPIVVMTFNESPKIALE--PYHPD 73
Query: 154 VAKC-----DRKRVLSSWAPYCG--NVAPVEFQIQFSSVRHLSPQQFVEKLSRELGVRGV 206
+ +R+R L G + ++F QF+S L+ Q+F + + + +
Sbjct: 74 LFLHILNPAERERKLKR----EGVEELYLLDFSSQFAS---LTAQEFFATYIKAMNAKII 126
Query: 207 VAGENYRFGYKAAGDASELVRLCEEYGMDACIINSVMDKHQDSRDIDCNDSKERGQVSST 266
VAG +Y FG L + + I+ V D+ ++SST
Sbjct: 127 VAGFDYTFGSDKKT----AEDLKNYFDGEVIIVPPVEDEKG--------------KISST 168
Query: 267 RVRQALAMGDMKYVSELLGRQHRL 290
R+RQA+ G++K +LLG
Sbjct: 169 RIRQAILDGNVKEAGKLLGAPLPS 192
>2x0k_A Riboflavin biosynthesis protein RIBF; riboflavin kinase,
nucleotide-binding, transferase, ATP-BIND
multifunctional enzyme; 1.95A {Corynebacterium
ammoniagenes}
Length = 338
Score = 109 bits (274), Expect = 4e-27
Identities = 47/196 (23%), Positives = 78/196 (39%), Gaps = 32/196 (16%)
Query: 105 GGIVALGKFDALHIGHRELAIQASKIGAPYLLSFIGM------AEVFGWEPRAPIVAKCD 158
V +G FD +H GH++L + I + VF +
Sbjct: 16 NSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRRAPLGITTLA 75
Query: 159 RK-RVLSSWAPYCG--NVAPVEFQIQFSSVRHLSPQQFVEK-LSRELGVRGVVAGENYRF 214
+ + S G V ++F + S SP+++VE L L VV G N+ F
Sbjct: 76 ERFALAES----FGIDGVLVIDFTRELSG---TSPEKYVEFLLEDTLHASHVVVGANFTF 128
Query: 215 GYKAAGDASELVRLCEEYGMDACIINSVMDKHQDSRDIDCNDSKERGQVSSTRVRQALAM 274
G AAG A L ++C + + +I+ + D+ ++SST VR+ L+
Sbjct: 129 GENAAGTADSLRQIC-QSRLTVDVIDLLDDEGV--------------RISSTTVREFLSE 173
Query: 275 GDMKYVSELLGRQHRL 290
GD+ + LGR +
Sbjct: 174 GDVARANWALGRHFYV 189
>1mrz_A Riboflavin kinase/FMN adenylyltransferase; rossmann fold, flavin
binding domain, 6-stranded beta barrel nucleotide
binding domain; HET: CIT; 1.90A {Thermotoga maritima}
SCOP: b.43.5.1 c.26.1.3 PDB: 1s4m_A* 1t6x_A* 1t6y_A*
1t6z_A* 2i1l_A
Length = 293
Score = 104 bits (262), Expect = 7e-26
Identities = 44/189 (23%), Positives = 82/189 (43%), Gaps = 33/189 (17%)
Query: 107 IVALGKFDALHIGHREL---AIQ-ASKIGAP-YLLSFIGMAEVFGWEPRAPIVAKCDRKR 161
+V++G FD +HIGH+++ + A + + E F + ++ R
Sbjct: 2 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVE 61
Query: 162 VLSSWAPYCGNVAPVEFQIQFSSVRHLSPQQFVEKLSRELGVRGVVAGENYRFGYKAAGD 221
+LS + F ++ L+P+ FVE+ GV VV G ++RFG A+G+
Sbjct: 62 MLSR----YA----RTVVLDFFRIKDLTPEGFVERYL--SGVSAVVVGRDFRFGKNASGN 111
Query: 222 ASELVRLCEEYGMDACIINSVMDKHQDSRDIDCNDSKERGQVSSTRVRQALAMGDMKYVS 281
AS L + G++ I V+ + + +VSS+ +R + G ++ +
Sbjct: 112 ASFL----RKKGVEVYEIEDVVVQGK--------------RVSSSLIRNLVQEGRVEEIP 153
Query: 282 ELLGRQHRL 290
LGR +
Sbjct: 154 AYLGRYFEI 162
>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 = 8e-06
Identities = 50/251 (19%), Positives = 80/251 (31%), Gaps = 78/251 (31%)
Query: 1 MLG--GSSRISHHLRIRECNYHHYHQNQNLGLG-FCSSRIFQLSSFMVRPLS-AAIIGEN 56
ML ++ + + N H + + + ++ +S P S +
Sbjct: 338 MLSISNLTQEQVQDYVNKTN-SHLPAGKQVEISLVNGAKNLVVSGP---PQSLYGLNLTL 393
Query: 57 RKQRLQQRLVSSSSLQSKSPGEMPTLPSCFSERE---DDRELP-AEGF-SPVAGGIVALG 111
RK + S QS+ P FSER+ +R LP A F S + L
Sbjct: 394 RKAK-----APSGLDQSRIP---------FSERKLKFSNRFLPVASPFHSHLLVPASDLI 439
Query: 112 KFDALHIGHRELAIQASKIGAPYLLSFIGMAEVF----GWEPR---APIVAK-CD---RK 160
D + ++ A I P V+ G + R I + D R
Sbjct: 440 NKDLVK---NNVSFNAKDIQIP----------VYDTFDGSDLRVLSGSISERIVDCIIRL 486
Query: 161 RVLSSWAPYCGNVAPVEFQIQFSSVRHL---SP--QQFVEKLSREL----GVRGVVAGE- 210
V W E QF + H+ P + L+ GVR +VAG
Sbjct: 487 PVK--W----------ETTTQFKA-THILDFGPGGASGLGVLTHRNKDGTGVRVIVAGTL 533
Query: 211 ----NYRFGYK 217
+ +G+K
Sbjct: 534 DINPDDDYGFK 544
Score = 33.5 bits (76), Expect = 0.16
Identities = 32/251 (12%), Positives = 63/251 (25%), Gaps = 108/251 (43%)
Query: 46 RPLSAAIIGENRKQRLQQRLVSSSSLQSKSPGEMPTLPSCFS-----EREDDRELPAEGF 100
L +I + + L + + E + P + +
Sbjct: 181 HVLVGDLI-----KFSAETLSELIRTTLDAE---KVFTQGLNILEWLENPSNT--PDKDY 230
Query: 101 ---SPVAGGIVALGKFDALHIGHRELAIQASKIGAPYLLSFIGMAEVFGWEPR------- 150
P++ ++ + IQ L ++ A++ G+ P
Sbjct: 231 LLSIPISCPLIGV--------------IQ--------LAHYVVTAKLLGFTPGELRSYLK 268
Query: 151 -----------APIVAKCDRKRVLSSWAPYCGNVAP---------VEFQIQFS------- 183
A +A+ D SW + +V V +
Sbjct: 269 GATGHSQGLVTAVAIAETD------SWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPS 322
Query: 184 -----------------SVRHLSPQQ---FVEKLSRELGVRGVV--AGENYRFGYKA--- 218
S+ +L+ +Q +V K + L V + N G K
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVN---GAKNLVV 379
Query: 219 AGDASELVRLC 229
+G L L
Sbjct: 380 SGPPQSLYGLN 390
Score = 27.7 bits (61), Expect = 8.5
Identities = 18/84 (21%), Positives = 29/84 (34%), Gaps = 20/84 (23%)
Query: 202 GVRGVVAGENYRFGYKAAGDASELVRLCEEYGMDACIINSVMDKHQDSRDIDCNDSKERG 261
G +G ENY + E +D + + K + E+G
Sbjct: 1678 GEKGKRIRENYS-------------AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG 1724
Query: 262 QVSSTRVRQ-AL------AMGDMK 278
+S+T+ Q AL A D+K
Sbjct: 1725 LLSATQFTQPALTLMEKAAFEDLK 1748
>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 = 37.9 bits (87), Expect = 0.005
Identities = 47/358 (13%), Positives = 95/358 (26%), Gaps = 128/358 (35%)
Query: 22 YHQNQNLGL--GFCSSRIFQLSSFMVR--PLSAAIIGE------NRKQRLQQ----RL-- 65
++ L + R L ++ P +II E + +L
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 66 VSSSSLQSKSPGEMPTLPSCFSEREDDRELPAEGFSPVAGGIVALGKFDALHIGHRELAI 125
+ SSL P E R++ FD L++
Sbjct: 358 IIESSLNVLEPAEY-------------RKM-----------------FD-------RLSV 380
Query: 126 --QASKIGAPY-LLSFIGMAEVFGW------EPRAPIVAKCDRKRVLSSWAPYCGNVAPV 176
++ I P LLS I W + +V K + ++ P
Sbjct: 381 FPPSAHI--PTILLSLI-------WFDVIKSDVMV-VVNKLHKYSLVEKQ--------PK 422
Query: 177 EFQ-----IQFSSVRHLSP-----QQFVEK----LSRELGVRGVVAGENYRF---GY--K 217
E I L + V+ + + + Y + G+ K
Sbjct: 423 ESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLK 482
Query: 218 AAGDASELVRLCEEYGMDACIINSVMDKHQDSRDIDCNDSKERGQVSSTRVRQALA--MG 275
+ + D R + + K R ++ ++ +
Sbjct: 483 NIEHPERMTLFRMVF--------------LDFRFL---EQKIRHDSTAWNASGSILNTLQ 525
Query: 276 DMK----YVSELLGRQHRLILTVNDHDELISTSNKHRVSVPKSCLLNL---PPKEGFY 326
+K Y+ + + RL VN + + ++ + + LL + E +
Sbjct: 526 QLKFYKPYICDNDPKYERL---VNAILDFLPKIEENLICSKYTDLLRIALMAEDEAIF 580
Score = 37.5 bits (86), Expect = 0.008
Identities = 59/428 (13%), Positives = 131/428 (30%), Gaps = 117/428 (27%)
Query: 18 NYHHYHQNQNLG-LGFCSSRIFQ--LSSF-----------MVRP-LSAA----IIGE-NR 57
++HH+H + G + I +F M + LS II +
Sbjct: 1 HHHHHHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDA 60
Query: 58 KQRLQQRLVSSSSLQSKSPGEM----------PTLPSCFSEREDDRELPAEGF----SPV 103
RL + + + + L S + + + +
Sbjct: 61 VSGT-LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRL 119
Query: 104 AGGIVALGKFDA----LHIGHRELAIQASKIGAPYLLSFIGMAEVFGWEPRAPIVAKCDR 159
K++ ++ R+ ++ A +L G+ G
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELRP--AKNVLID-GVLG-SG------------- 162
Query: 160 KRVLSSWAPYCGNVAPV---EFQIQFSSVRHL-SPQQFVE---KLSRELGVRGVVAGE-- 210
K ++ C + +F+I + ++++ SP+ +E KL ++ +
Sbjct: 163 KTWVALDV--CLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS 220
Query: 211 -NYRFGYKAAGDASELVRLCEEYGMDACIINSVMDKHQDSR-----DIDCNDSKERGQV- 263
N + + EL RL + + C++ V+ Q+++ ++ C ++
Sbjct: 221 SNIKLRIHSIQA--ELRRLLKSKPYENCLL--VLLNVQNAKAWNAFNLSC-------KIL 269
Query: 264 SSTRVRQALAMGDMKYVSELLGRQHRLILTVNDHDELISTSNKHRVSVPKSCLLNLPPKE 323
+TR +Q + + H + LT ++ L+ + L P+E
Sbjct: 270 LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKY----LDCRPQDL----PRE 321
Query: 324 GFYGNSVL--LFGE---ENPV-----------KCRICIDASHIHLEMDKVGFCNFDHSQD 367
N + E + K I++S LE ++ +
Sbjct: 322 VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA-------EYRKM 374
Query: 368 FKLLGIEF 375
F L + F
Sbjct: 375 FDRLSV-F 381
Score = 30.2 bits (67), Expect = 1.5
Identities = 26/137 (18%), Positives = 45/137 (32%), Gaps = 41/137 (29%)
Query: 8 ISHHLRIRECNYHHYHQNQNLGLGFCSSRIFQLSSFMVRPLSAAIIGENRKQRLQQRLVS 67
I HHL+ E + + L F +F F L+Q++
Sbjct: 477 IGHHLKNIE-------HPERMTL-F--RMVFLDFRF-----------------LEQKIRH 509
Query: 68 SSSLQSKSPGEMPTLPS--------CFSEREDDRELPA-EGFSPVAGGIVALGKF-DALH 117
S+ + S + TL C ++ + +R + A F P + K+ D L
Sbjct: 510 DSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLR 569
Query: 118 IG----HRELAIQASKI 130
I + +A K
Sbjct: 570 IALMAEDEAIFEEAHKQ 586
>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 = 36.1 bits (82), Expect = 0.007
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 58 KQRLQQRLVSSSSLQSKSPGEMPTL 82
KQ L+ +L +SL+ + P L
Sbjct: 19 KQALK-KL--QASLKLYADDSAPAL 40
Score = 28.4 bits (62), Expect = 2.4
Identities = 5/25 (20%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 160 KRVLSSWAPYCGNVAP---VEFQIQ 181
K++ +S Y + AP ++ ++
Sbjct: 23 KKLQASLKLYADDSAPALAIKATME 47
>1ej2_A Nicotinamide mononucleotide adenylyltransferase; dinucleotide
binding fold, structural genomics, PSI; HET: NAD; 1.90A
{Methanothermobacter thermautotrophicusorganism_taxid}
SCOP: c.26.1.3 PDB: 1m8g_A* 1hyb_A* 1m8j_A* 1m8f_A*
1m8k_A*
Length = 181
Score = 35.0 bits (80), Expect = 0.016
Identities = 26/168 (15%), Positives = 49/168 (29%), Gaps = 34/168 (20%)
Query: 110 LGKFDALHIGHRELAIQASKIGAPYLLSFIGMAEVFGWEPRAPIVAKCDRKRVLSSWAPY 169
+G+ H GH ++ + L+ IG A++ R P A +R +L+
Sbjct: 9 VGRMQPFHRGHLQVIKSILEE-VDELIICIGSAQL-SHSIRDPFTAG-ERVMMLTKALSE 65
Query: 170 CGNVAPVEFQIQFSSVRHLSP-QQFVEKLSRELGVRGVVAGENYRFGYKAAGDASELVRL 228
G A + I + + ++ L+ + RL
Sbjct: 66 NGIPASRYYIIPVQDIECNALWVGHIKMLTPPFDR--------------VYSGNPLVQRL 111
Query: 229 CEEYGMDACIINSVMDKHQDSRDIDCNDSKERGQVSSTRVRQALAMGD 276
E G + + R + S T VR+ +
Sbjct: 112 FSEDGYE----------------VTAPPLFYRDRYSGTEVRRRMLDDG 143
>3do8_A Phosphopantetheine adenylyltransferase; protein with unknown
function, structural genomics, MCSG, PSI-2, protein
structure initiative; 1.60A {Archaeoglobus fulgidus}
Length = 148
Score = 31.9 bits (72), Expect = 0.13
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 107 IVAL-GKFDALHIGHRELAIQASKIGAPYLLSFI 139
VAL G F+ LH GH++L A K+G + +
Sbjct: 2 KVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGV 35
>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase,
disease mutation, DNA replication, DNA-binding,
DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo
sapiens}
Length = 1172
Score = 32.2 bits (72), Expect = 0.30
Identities = 8/30 (26%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 272 LAMGDMKYVSELLGRQHRLILTVNDHDELI 301
L + MK++ E R +++ HDE+
Sbjct: 1044 LMLVAMKWLFEEFAIDGRFCISI--HDEVR 1071
>3elb_A Ethanolamine-phosphate cytidylyltransferase; kennedy pathway, CMP,
CTP, phosphoethanolamine, cytidylyltra SGC, structural
genomics consortium; HET: C5P; 2.00A {Homo sapiens}
Length = 341
Score = 30.5 bits (69), Expect = 0.82
Identities = 25/117 (21%), Positives = 45/117 (38%), Gaps = 9/117 (7%)
Query: 56 NRKQRLQQRLVSSSSLQSKSPGEMPTLPSCFSEREDDRELPAEGFSPVAGGIVAL--GKF 113
+++ + R + S + T S F + A G P G V G F
Sbjct: 148 SQEMSSEYREYADSFGKCPGGRNPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAF 207
Query: 114 DALHIGHRELAIQASKIG-APYLLSFIGM---AEVFGWE-PRAPIVAKCDRKRVLSS 165
D HIGH + + ++ PY++ G+ EV ++ PI+ +R + +
Sbjct: 208 DLFHIGHVDFLEKVHRLAERPYII--AGLHFDQEVNHYKGKNYPIMNLHERTLSVLA 262
>2q02_A Putative cytoplasmic protein; structural genomics, joint CEN
structural genomics, JCSG, protein structure initiative;
2.40A {Salmonella typhimurium LT2} SCOP: c.1.15.4
Length = 272
Score = 30.3 bits (68), Expect = 0.92
Identities = 16/72 (22%), Positives = 29/72 (40%), Gaps = 2/72 (2%)
Query: 172 NVAPVEFQIQFSSVRHLSPQQFVEKLSRELGVRGV-VAGENYRFGYKAAGDASELVRLCE 230
N+ F I LS + F L + L V + + + +++ L E
Sbjct: 3 NIEKTRFCINRKIAPGLSIEAFFR-LVKRLEFNKVELRNDMPSGSVTDDLNYNQVRNLAE 61
Query: 231 EYGMDACIINSV 242
+YG++ IN+V
Sbjct: 62 KYGLEIVTINAV 73
>3hl4_A Choline-phosphate cytidylyltransferase A; rossmann fold,
phospholipid synthesis, phosphatidylcholine,
phosphocholine, CTP, CDP-choline; HET: CDC; 2.20A
{Rattus norvegicus}
Length = 236
Score = 28.4 bits (63), Expect = 2.9
Identities = 18/101 (17%), Positives = 27/101 (26%)
Query: 31 GFCSSRIFQLSSFMVRPLSAAIIGENRKQRLQQRLVSSSSLQSKSPGEMPTLPSCFSERE 90
S+++ P E+ QR + E+ S R
Sbjct: 3 AQSSAKVNSRKRRKEVPGPNGATEEDGIPSKVQRCAVGLRQPAPFSDEIEVDFSKPYVRV 62
Query: 91 DDRELPAEGFSPVAGGIVALGKFDALHIGHRELAIQASKIG 131
E + A G FD H GH +QA +
Sbjct: 63 TMEEACRGTPCERPVRVYADGIFDLFHSGHARALMQAKNLF 103
>3glv_A Lipopolysaccharide core biosynthesis protein; structural GEN PSI,
MCSG, protein structure initiative; HET: AMP; 1.99A
{Thermoplasma volcanium GSS1}
Length = 143
Score = 27.5 bits (62), Expect = 3.8
Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 15/62 (24%)
Query: 111 GKFDALHIGHRELAIQASKIGAPYLLSF-------IGMAEVFGWEPRAPIVAKCDRKRVL 163
G FD LH+GH ++ K+G ++ + PI + R ++
Sbjct: 9 GVFDILHLGHIHYLKESKKLGDELVVVVARDSTARNN--------GKIPIFDENSRLALI 60
Query: 164 SS 165
S
Sbjct: 61 SE 62
>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase,
ribosylnicotinamide KINA transferase; HET: NAD; 2.90A
{Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1
Length = 365
Score = 28.3 bits (62), Expect = 3.8
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 106 GIVALGKFDALHIGHRELAIQASKI 130
G++ GKF +H GH + +A
Sbjct: 5 GVI-FGKFYPVHTGHINMIYEAFSK 28
>3u0h_A Xylose isomerase domain protein; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, TIM barrel;
2.30A {Alicyclobacillus acidocaldarius subsp}
Length = 281
Score = 27.8 bits (62), Expect = 6.2
Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 183 SSVRHLSPQQFVEKLSRELGVRGVVAGENYRFGYKAAGDASELVRLCEEYGM 234
+ V S +++ L+RE G R V ++ + + + + G+
Sbjct: 11 TLVDETSLVLYLD-LARETGYRYVDVPFHWLEAEAERHGDAAVEAMFQRRGL 61
>3ryc_B Tubulin beta chain; alpha-tubulin, beta-tubulin, GTPase,
microtubule, tubulin, cell cycle; HET: GTP GDP; 2.10A
{Ovis aries} PDB: 3ryf_B* 3ryh_B* 3ryi_B* 3hke_B*
3du7_B* 3e22_B* 3hkc_B* 3hkd_B* 3hkb_B* 3n2g_B* 3n2k_B*
1z2b_B* 2xrp_A* 1tvk_B* 1tub_B* 1jff_B* 1ia0_B* 1ffx_B*
1sa0_B* 1sa1_B* ...
Length = 445
Score = 27.8 bits (62), Expect = 6.3
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 155 AKCDRK--RVLSSWAPYCGNVAPVEFQIQFSSVRHLSPQQFVE 195
A CD + R L+ + G ++ E Q ++++ + FVE
Sbjct: 301 AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVE 343
>1jx4_A DNA polymerase IV (family Y); protein-DNA complex, Y-family,
transferase-D complex; HET: DNA MSE ADI; 1.70A
{Sulfolobus solfataricus} SCOP: d.240.1.1 e.8.1.7 PDB:
1jxl_A* 1n48_A* 1n56_A* 1ryr_A* 1rys_A* 1s0m_A* 1s0n_A*
1s0o_A* 1s10_A* 1s97_A* 1s9f_A* 2ia6_A* 2ibk_A* 2r8g_A*
2r8h_A* 2r8i_A* 2rdj_A* 3fds_A* 3m9m_B* 3m9n_B* ...
Length = 352
Score = 27.5 bits (62), Expect = 6.8
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 194 VEKLSRELGVRGVVAGENY---RFGYKAAGDASELVRLC 229
V S G VA NY +FG KA E ++
Sbjct: 30 VCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKIL 68
>1im4_A DBH; DNA polymerase PALM, thumb, fingers, helix-hairpin-helix,
fidelity, processivity, transferase; 2.30A {Sulfolobus
solfataricus} SCOP: e.8.1.7
Length = 221
Score = 27.1 bits (61), Expect = 8.3
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 194 VEKLSRELGVRGVVAGENY---RFGYKAAGDASELVRLC 229
V S G VA NY + G KA + +++
Sbjct: 35 VCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIA 73
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 0.137 0.414
Gapped
Lambda K H
0.267 0.0627 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,822,105
Number of extensions: 345112
Number of successful extensions: 883
Number of sequences better than 10.0: 1
Number of HSP's gapped: 875
Number of HSP's successfully gapped: 34
Length of query: 380
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 285
Effective length of database: 4,049,298
Effective search space: 1154049930
Effective search space used: 1154049930
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: 58 (26.3 bits)