RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 027752
(219 letters)
>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 = 44.5 bits (104), Expect = 1e-05
Identities = 39/194 (20%), Positives = 55/194 (28%), Gaps = 64/194 (32%)
Query: 19 SYEACVESLNK------PNLISLDDYYRKELPSLIHQRNPNPHINT--TELSKLVRWKLT 70
S E +E L K PN S D H N I++ EL +L++ K
Sbjct: 194 SPETVLEMLQKLLYQIDPNWTSRSD----------HSSNIKLRIHSIQAELRRLLKSKP- 242
Query: 71 RGKWRPR-LLVFVSSLDDSSVKSASE-KAF----KSLPDLTKAVSELTVLKGVGPATASA 124
LLV L + V++A AF K L T+ L S
Sbjct: 243 ----YENCLLV----LLN--VQNAKAWNAFNLSCKILL-TTRFKQVTDFLSAATTTHISL 291
Query: 125 VLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKLQAKAKELVSEENCFT-PFDV 183
DE L L + ++L E T P +
Sbjct: 292 D-----HHSMTLTPDEVKS---------------LLLKYLDCRPQDL-PREVLTTNPRRL 330
Query: 184 ERALWSSAIGLKLK 197
S I ++
Sbjct: 331 ------SIIAESIR 338
Score = 33.7 bits (76), Expect = 0.044
Identities = 18/144 (12%), Positives = 50/144 (34%), Gaps = 26/144 (18%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVR-WKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFK 99
++LP + NP ++ +++ +R T W+ ++ + + E +
Sbjct: 316 QDLPREVLTTNP-RRLSI--IAESIRDGLATWDNWK--------HVNCDKLTTIIESSLN 364
Query: 100 SL-PDLTKAV-SELTVL-KGVG-PATASAVLAAYAPDLAPFMSDEAM------GAALGHS 149
L P + + L+V P + +L+ D+ +
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIP---TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 150 KDYSLKQYLLFADKLQAKAKELVS 173
K+ ++ ++ + L+ K + +
Sbjct: 422 KESTISIPSIYLE-LKVKLENEYA 444
Score = 27.9 bits (61), Expect = 3.2
Identities = 25/154 (16%), Positives = 44/154 (28%), Gaps = 46/154 (29%)
Query: 4 EFECSNVNKWKEALASYEACVESLNKPNLIS------------------------LDDYY 39
F+C +V +++ S E + + +S L Y
Sbjct: 32 NFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY 91
Query: 40 RKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFK 99
K L S I P + T + R RL +V +
Sbjct: 92 -KFLMSPIKTEQRQPSMMTRMYI----------EQRDRLYNDNQVFAKYNVSRL-----Q 135
Query: 100 SLPDLTKAVSELT-----VLKGVGPATASAVLAA 128
L +A+ EL ++ GV + + +A
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKT-WVAL 168
>4f9i_A Proline dehydrogenase/delta-1-pyrroline-5-carboxy dehydrogenase;
proline utilization A, PUTA, flavoenzyme, structural
genomic biology; HET: FAD MES; 2.20A {Geobacter
sulfurreducens}
Length = 1026
Score = 40.8 bits (96), Expect = 2e-04
Identities = 15/128 (11%), Positives = 38/128 (29%), Gaps = 9/128 (7%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL----DDSSVKSASEK 96
KE I P+ + K + W + +++ ++ FV + +
Sbjct: 37 KEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIRE 96
Query: 97 AFKSLPDLTKAVSELTVLKGVG-----PATASAVLAAYAPDLAPFMSDEAMGAALGHSKD 151
F + D+ +S + G+ + + F+ E A+ + +
Sbjct: 97 YFGNEQDMPAFMSTGAKVAGMLGSFGGAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEK 156
Query: 152 YSLKQYLL 159
+
Sbjct: 157 LRKDGFAA 164
>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 = 40.0 bits (93), Expect = 4e-04
Identities = 54/304 (17%), Positives = 96/304 (31%), Gaps = 103/304 (33%)
Query: 12 KWKEALASY-EACVESLNKP------------------NLISL-------DDYYRKELPS 45
K KE + +Y A + + +P L+++ DDY+ +EL
Sbjct: 118 KTKELIKNYITARIMA-KRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF-EELRD 175
Query: 46 L--IHQRNPNPHINTTE--LSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASE---KAF 98
L + I + LS+L+R L K + L + L++ S +
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIP 235
Query: 99 KSLP--DLTKAVSELTVLK-----------------GVGPATASAVLAAYAPDLAPFM-- 137
S P + + + K G +AV A F
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 138 SDEAMGAA--LG-HSKDY--------SLKQY------------LLFADKLQAKAKELVSE 174
+A+ +G + S+ + L ++ Q + ++ V++
Sbjct: 296 VRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNK 355
Query: 175 ENCFTPFD--VE----------------RALWSSAIGL-KLKA-SKSNQDSEIKTTKNSK 214
N P VE ++L+ + L K KA S +Q S I S+
Sbjct: 356 TNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQ-SRI---PFSE 411
Query: 215 RKRK 218
RK K
Sbjct: 412 RKLK 415
Score = 33.5 bits (76), Expect = 0.054
Identities = 30/171 (17%), Positives = 47/171 (27%), Gaps = 61/171 (35%)
Query: 15 EALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKW 74
E + S + +L + + + LP + E+S L G
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLP-------AGKQV---EIS------LVNG-- 373
Query: 75 RPRLLVFVS----SLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYA 130
+ LV VS SL + KA KA S L + +
Sbjct: 374 -AKNLV-VSGPPQSLY--GLNLTLRKA--------KAPSGLDQSRIPFSERKLKFSNRFL 421
Query: 131 PDLAPFMSDEAMGAALGHSKDYSLKQYL----------LFADKLQAKAKEL 171
P +PF HS L L + + AK++
Sbjct: 422 PVASPF-----------HSH------LLVPASDLINKDLVKNNVSFNAKDI 455
Score = 28.9 bits (64), Expect = 1.5
Identities = 30/226 (13%), Positives = 55/226 (24%), Gaps = 97/226 (42%)
Query: 69 LTRGKWRPRLLV--------------FVSSLDDSSVKSASEKAFKSLPDL---------- 104
L+ G LLV F L + + A++ + +L
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSS 70
Query: 105 ----TKAVSELTVLKGV---------------------------GPATASAVLAAY---- 129
+K VL ++ Y
Sbjct: 71 LVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITAR 130
Query: 130 ---------APDLAPFMSDEAMGAAL-------GHSKDY------------SLKQYLLF- 160
+ A F + A L G++ DY L L+
Sbjct: 131 IMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKF 190
Query: 161 -ADKLQAKAKELVSEENCFT-PFDVERALWSSAIGLKLKASKSNQD 204
A+ L + + E FT ++ W L+ ++ ++D
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILE--W-----LENPSNTPDKD 229
>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 = 35.3 bits (80), Expect = 0.005
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 23/52 (44%)
Query: 95 EKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAAL 146
EK +A+ +L AS L YA D AP + A+ A +
Sbjct: 18 EK---------QALKKLQ---------AS--LKLYADDSAPAL---AIKATM 46
Score = 29.9 bits (66), Expect = 0.33
Identities = 14/45 (31%), Positives = 17/45 (37%), Gaps = 18/45 (40%)
Query: 155 KQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKAS 199
KQ L KLQA K + D SA L +KA+
Sbjct: 19 KQAL---KKLQASLK-------LYAD-D-------SAPALAIKAT 45
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus}
Length = 207
Score = 33.0 bits (75), Expect = 0.041
Identities = 19/102 (18%), Positives = 34/102 (33%), Gaps = 12/102 (11%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAA--LG-----HSKDYSLK 155
D A L +KG+G AS L + + +G + K S
Sbjct: 111 DQQLARERLLNIKGIGMQEASHFLRNVGYFDLAIIDRHIIDFMRRIGAIGETNVKQLSKS 170
Query: 156 QYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLK 197
Y+ F + L++ A L + ++ +W +K
Sbjct: 171 LYISFENILKSIASNL-----NMSVGILDLFIWYKETNTIVK 207
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair,
DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A
{Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A*
Length = 377
Score = 32.5 bits (74), Expect = 0.091
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 77 RLLVFVSSLDDSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
RLL V+ + S + FK+L ++KA V +L ++G+G A A+
Sbjct: 315 RLLKTVARIPLSIGYNVVRM-FKTLDQISKASVEDLKKVEGIGEKRARAI 363
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase,
DNA mismatch, methylation; 2.00A {Methanothermobacter
thermautotrophicusorganism_taxid} SCOP: a.96.1.2
Length = 221
Score = 29.8 bits (68), Expect = 0.50
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 110 ELTVLKGVGPATASAVLA 127
+ L GVG T +AV+
Sbjct: 116 AILDLPGVGKYTCAAVMC 133
>3e2q_A Proline oxidase, proline dehydrogenase; proline utilization A,
PUTA, flavoenzyme, DNA-binding, FAD, flavoprotein,
multifunctional enzyme, NAD; HET: FAD 1PE; 1.75A
{Escherichia coli} PDB: 3e2r_A* 3e2s_A* 1tj2_A* 1tiw_A*
1tj0_A* 1tj1_A* 2fzm_A* 2fzn_A* 3itg_A*
Length = 551
Score = 30.4 bits (68), Expect = 0.53
Identities = 19/105 (18%), Positives = 36/105 (34%), Gaps = 3/105 (2%)
Query: 63 KLVRWKLTRGKWRPRLLVFVSSLDDSSVKS-ASEKAFKSLPDLTKAVSELTVLKGVG--P 119
L+R K++ G W+ + S +++ S + L + G P
Sbjct: 98 ALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEP 157
Query: 120 ATASAVLAAYAPDLAPFMSDEAMGAALGHSKDYSLKQYLLFADKL 164
V A F++ E + AL +++ K + D L
Sbjct: 158 LIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDML 202
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A
{Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A
1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A*
1wef_A* 1kg7_A 1kqj_A
Length = 225
Score = 29.8 bits (68), Expect = 0.59
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 110 ELTVLKGVGPATASAVLA 127
E+ L GVG +TA A+L+
Sbjct: 110 EVAALPGVGRSTAGAILS 127
>1gm5_A RECG; helicase, replication restart; HET: DNA ADP; 3.24A
{Thermotoga maritima} SCOP: a.24.21.1 b.40.4.9 c.37.1.19
c.37.1.19
Length = 780
Score = 29.9 bits (68), Expect = 0.61
Identities = 17/119 (14%), Positives = 41/119 (34%), Gaps = 16/119 (13%)
Query: 6 ECSNVNKWKEALASYEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLV 65
E + K + ++ L+ P L + ++L + + P++ +
Sbjct: 28 EVEKMLKNQVNTRRIHQLLKELDDPLL--ENKDLEEKLQAFLDYVKEIPNLPEARKRYRI 85
Query: 66 RWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASA 124
+ + L + L + E + + + DL+ +++ KGVGP
Sbjct: 86 Q----------KSLEMIEKLRSWFLIDYLECSGEEV-DLS---TDIQYAKGVGPNRKKK 130
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA
glycosylase, transition state analog, DNA repair; HET:
NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A*
1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A*
Length = 369
Score = 29.6 bits (67), Expect = 0.71
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 110 ELTVLKGVGPATASAVLA 127
E + LKGVGP T AVL+
Sbjct: 119 EFSRLKGVGPYTVGAVLS 136
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision
repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori}
SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A*
Length = 218
Score = 29.3 bits (66), Expect = 0.83
Identities = 9/21 (42%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 110 ELTVLKGVGPATASAVLAAYA 130
L KG+G +A A+L YA
Sbjct: 122 WLLDQKGIGKESADAIL-CYA 141
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base
excision, methylation, ALK hydrolase; 1.80A {Escherichia
coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A*
3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A*
3d4v_A* 3ogd_A* 3oh9_A* 3oh6_A*
Length = 282
Score = 29.4 bits (66), Expect = 0.93
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 98 FKSLPDLTKAVSELTVLKGVGPATASAVL--AAYAPDLAP 135
D+ +A+ L G+G TA+ A D+
Sbjct: 196 MTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFL 235
>2duy_A Competence protein comea-related protein; helix-hairpin-helix,
structural genomics, NPPSFA; 1.75A {Thermus
thermophilus} SCOP: a.60.2.7
Length = 75
Score = 27.3 bits (61), Expect = 1.0
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 108 VSELTVLKGVGPATASAVLA 127
+ EL L G+GP A ++
Sbjct: 26 LEELMALPGIGPVLARRIVE 45
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 29.5 bits (66), Expect = 1.1
Identities = 20/116 (17%), Positives = 30/116 (25%), Gaps = 18/116 (15%)
Query: 42 ELPSLIHQRNPNPHINTTELS--KLVRWKLTRGKWRPRLLVFVSSLDDSS------VKSA 93
+H PNP I + ++V L R V ++S ++
Sbjct: 352 VWAPNLHYHTPNPEIPALQDGRLQVVDRPLP---IRGG-NVGINSFGFGGSNVHVILQPN 407
Query: 94 SEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGHS 149
S A A+ L G T A + D A L
Sbjct: 408 SRPAPPPAQH--AALPRLLQASG---RTLEA-VQTLLEQGLRHSRDLAFVGMLNEI 457
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices,
helix-hairpin-helix motif, iron-sulfur cluste hydrolase;
2.30A {Homo sapiens}
Length = 287
Score = 28.8 bits (65), Expect = 1.2
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 111 LTVLKGVGPATASAVLA 127
+L GVG TA A+ +
Sbjct: 131 QQLLPGVGRYTAGAIAS 147
>2edu_A Kinesin-like protein KIF22; kinesin-like DNA binding domain, helix
turn helix motif, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.60.2.7
Length = 98
Score = 27.5 bits (61), Expect = 1.3
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 105 TKAVSELTVLKGVGPATASAVLA 127
+ +L L+ +GP A ++
Sbjct: 36 EGSARDLRSLQRIGPKKAQLIVG 58
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 29.0 bits (66), Expect = 1.3
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLA 127
F +L L A + EL + VG AS V
Sbjct: 530 AYFGTLEALEAASIEELQKVPDVGIVVASHVHN 562
>3hhd_A Fatty acid synthase; transferase, multienzyme, megasynthase, fatty
acid synthesis, acetylation, cytoplasm, fatty acid
biosynthesis, hydrolase; 2.15A {Homo sapiens} PDB:
2jfk_A* 2jfd_A
Length = 965
Score = 28.7 bits (65), Expect = 1.6
Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 6/45 (13%)
Query: 42 ELPSLIHQRNPNPHINT-TELS-KLVRWKLTRGKWRPRLLVFVSS 84
+H +PNP I + ++V L R V ++S
Sbjct: 354 LWAPNLHFHSPNPEIPALLDGRLQVVDQPLP---VRGG-NVGINS 394
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair,
N1-methyladenine, N3-methylcytosine, hyperthermophiles,
hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus}
PDB: 2jhj_A
Length = 295
Score = 28.6 bits (64), Expect = 1.6
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 8/78 (10%)
Query: 93 ASEKAFKSLPDLT--KAVSELTVLKGVGPATASAVLA-AYAPDLAPFMSD----EAMGAA 145
A E+ + L + +A LT KG+G TA VL+ A ++ P D A+
Sbjct: 192 AKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALGKNVFP-ADDLGVRRAVSRL 250
Query: 146 LGHSKDYSLKQYLLFADK 163
+ + S ++ A +
Sbjct: 251 YFNGEIQSAEKVREIARE 268
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 26.5 bits (59), Expect = 2.1
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAYAPD 132
K F S+ + A V+EL ++G+G A +
Sbjct: 32 KHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAP 69
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A
{Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2
PDB: 1v9p_A*
Length = 667
Score = 28.2 bits (64), Expect = 2.3
Identities = 11/33 (33%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLA 127
+ F ++ L +A + EL ++ VG TA A+L
Sbjct: 525 RRFGTMDRLLEASLEELIEVEEVGELTARAILE 557
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 27.9 bits (63), Expect = 2.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAAYAPD 132
F SL + A +L ++GVGP A+AV +A D
Sbjct: 547 TEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTEWFAVD 584
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 27.8 bits (61), Expect = 2.7
Identities = 6/45 (13%), Positives = 15/45 (33%), Gaps = 8/45 (17%)
Query: 120 ATASAVLAAYAPDLAP---FMSDEAMGAALGHSKDYSLKQYLLFA 161
++V + + P +S + K++L+ A
Sbjct: 128 VKENSVDSDDKAKVPPLIRIVSGLEL-----SDTKQKGKKFLVIA 167
>3n0u_A Probable N-glycosylase/DNA lyase; structural genomics, ISFI, DNA
repair, 8-oxoguanine, base EX repair, PSI-2, protein
structure initiative; 1.50A {Thermotoga maritima}
Length = 219
Score = 27.7 bits (61), Expect = 2.8
Identities = 20/94 (21%), Positives = 31/94 (32%), Gaps = 13/94 (13%)
Query: 111 LTVLKGVGPATASAVLAAYAPDLAPFMSD-------EAMGAALGHSKDYSLKQYLLFADK 163
+ KG+G AS L + D + G K +S K+YL +
Sbjct: 132 VRNAKGIGWKEASHFL-RNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEI 190
Query: 164 LQAKAKELVSEENCFTPFDVERALWSSAIGLKLK 197
L+ A+ +P + LW G K
Sbjct: 191 LRKVAEAF-----GESPGKFDLYLWYLVKGKVDK 219
>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A;
translation, ribosome, ribosomal, ribosomal R ribosomal
protein, eukaryotic ribosome, RNA-protein C; 3.00A
{Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L
3u5g_S 1s1h_M 3jyv_M* 2zkq_m
Length = 146
Score = 26.9 bits (60), Expect = 3.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K V LT +KGVG ++ V
Sbjct: 22 VDGNIKIVYALTTIKGVGRRYSNLVCKK 49
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain,
DNA-binding domain, DNA binding protein; NMR
{Escherichia coli} SCOP: a.60.2.3
Length = 78
Score = 26.0 bits (58), Expect = 3.6
Identities = 8/34 (23%), Positives = 13/34 (38%), Gaps = 1/34 (2%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLAA 128
K L L A V E+ + G+ A + +
Sbjct: 42 KYMGGLQGLRNASVEEIAKVPGISQGLAEKIFWS 75
>3iko_C Nucleoporin NUP84; NPC, transport, WD repeat, autocatalytic
cleavage, mRNA transport, nuclear pore complex, nucleus,
phosphoprotein; 3.20A {Saccharomyces cerevisiae} PDB:
3jro_C
Length = 460
Score = 27.4 bits (60), Expect = 3.7
Identities = 18/64 (28%), Positives = 34/64 (53%)
Query: 149 SKDYSLKQYLLFADKLQAKAKELVSEENCFTPFDVERALWSSAIGLKLKASKSNQDSEIK 208
S Y +++ F+D L+ E +E+N PF++ R S+A L L + S +S +
Sbjct: 4 SPTYQTERFTKFSDTLKEFKIEQNNEQNPIDPFNIIREFRSAAGQLALDLANSGDESNVI 63
Query: 209 TTKN 212
++K+
Sbjct: 64 SSKD 67
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 152
Score = 26.9 bits (60), Expect = 4.1
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K + LT +KGVG ++ V
Sbjct: 20 VDGKQKIMFALTSIKGVGRRFSNIVCKK 47
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-(apurinic; helix-hairpin-helix,
8-oxoguanine, 8-OXOG, DNA damage, DNA repair,
glycosidase; 2.00A {Methanocaldococcus jannaschii} PDB:
3knt_A*
Length = 214
Score = 27.0 bits (59), Expect = 4.2
Identities = 17/84 (20%), Positives = 29/84 (34%), Gaps = 7/84 (8%)
Query: 95 EKAFKSLPDLTKAVSEL-TVLKGVGPATASAVLA-AYAPDLAPFMSD-----EAMGAALG 147
+ +S + A L +KG+G AS L D+A
Sbjct: 110 KDIVESFENEKVAREFLVRNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDE 169
Query: 148 HSKDYSLKQYLLFADKLQAKAKEL 171
K S ++YL + L+ +E+
Sbjct: 170 IPKTLSRRKYLEIENILRDIGEEV 193
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 26.5 bits (59), Expect = 5.8
Identities = 5/28 (17%), Positives = 10/28 (35%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ LT ++G+G A +
Sbjct: 22 IDGKRITPIALTGIRGIGRRFAYIICKV 49
>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P;
2.25A {Thermus thermophilus} PDB: 3asy_A*
Length = 211
Score = 26.4 bits (59), Expect = 6.1
Identities = 5/18 (27%), Positives = 10/18 (55%), Gaps = 1/18 (5%)
Query: 24 VESLN-KPNLISLDDYYR 40
+L + L+ +D YY+
Sbjct: 27 ARTLGERVALLPMDHYYK 44
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger,
toprim, walker B ATP binding motif; 2.50A {Deinococcus
radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A
Length = 228
Score = 26.4 bits (59), Expect = 6.5
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 102 PDLTKAVSELTVLKGVGPATA 122
P L + EL+ L G+GP +A
Sbjct: 5 PSLVSLIRELSRLPGIGPKSA 25
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease,
nucleotide excision repair; 2.8A {Aeropyrum pernix}
SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A
Length = 219
Score = 26.4 bits (57), Expect = 6.6
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
+ F SL A +E++ ++G+G A +
Sbjct: 180 ERFGSLERFFTASKAEISKVEGIGEKRAEEI 210
>1g8m_A Aicar transformylase-IMP cyclohydrolase; homodimer, 2 functional
domains, IMPCH domain = alpha/beta/alpha; HET: G; 1.75A
{Gallus gallus} SCOP: c.24.1.3 c.97.1.4 PDB: 1thz_A*
2b1g_A* 2b1i_A* 2iu0_A* 2iu3_A* 1m9n_A* 1oz0_A* 1pkx_A*
1p4r_A* 1pl0_A*
Length = 593
Score = 27.0 bits (60), Expect = 6.8
Identities = 23/126 (18%), Positives = 34/126 (26%), Gaps = 3/126 (2%)
Query: 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMSDEAMGAALGH 148
+ A +KA V + GV A S + Y D A+
Sbjct: 455 CTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFE 514
Query: 149 SKDYSLKQYLLFADKLQAKAKELVSEENCFTPF-DVERALWSSAIGLKLKASKSNQDSEI 207
L + + A L S+ F PF D + + S S D +
Sbjct: 515 EVPAQLTEAEKKQWIAKLTAVSLSSD--AFFPFRDNVDRAKRIGVQFIVAPSGSAADEVV 572
Query: 208 KTTKNS 213
N
Sbjct: 573 IEACNE 578
>3s6i_A DNA-3-methyladenine glycosylase 1; DNA glycosylase, DNA repair,
helix-hairpin-helix (HHH), ABAS tetrahydrofuran (THF);
HET: 3DR; 2.28A {Schizosaccharomyces pombe}
Length = 228
Score = 26.2 bits (58), Expect = 7.4
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 94 SEKAFKSLPDLTKAVSELTVLKGVGPATA 122
+++ + L + + + LT +KG+G T
Sbjct: 125 TKEEAERLSN-EELIERLTQIKGIGRWTV 152
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 26.0 bits (58), Expect = 8.4
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 116 GVGPATASAVLAAYAPD 132
GVGP A A+L+A P
Sbjct: 79 GVGPKVALALLSALPPR 95
>2ztd_A Holliday junction ATP-dependent DNA helicase RUVA; recombination,
branch migration, DNA BIND oligomerization, acidic PIN;
2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A
2h5x_A 1bvs_A
Length = 212
Score = 26.1 bits (58), Expect = 8.8
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 116 GVGPATASAVLAAYAPD 132
GVGP A A LA +
Sbjct: 95 GVGPRLAMAALAVHDAP 111
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
0.313 0.127 0.361
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,070,787
Number of extensions: 169261
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 61
Length of query: 219
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 129
Effective length of database: 4,188,903
Effective search space: 540368487
Effective search space used: 540368487
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.0 bits)