RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 028836
(203 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 = 41.2 bits (96), Expect = 1e-04
Identities = 31/179 (17%), Positives = 55/179 (30%), Gaps = 75/179 (41%)
Query: 1 MELEFECSNVNK--WKEALASYEARVESLNKPNLISLDDYYRKELP-SL--IHQRNPNPH 55
M+L ++ S + W A D++++ S+ I NP
Sbjct: 1633 MDL-YKTSKAAQDVWNRA-------------------DNHFKDTYGFSILDIVINNPV-- 1670
Query: 56 INTTELSKLVRWKLTRGKW-RPRLLDFV-SSLDDSSVKSASEKAFKSL-----------P 102
+ + + +GK R + ++ D +K+ EK FK +
Sbjct: 1671 ------NLTIHFGGEKGKRIRENYSAMIFETIVDGKLKT--EKIFKEINEHSTSYTFRSE 1722
Query: 103 ----DLTK---------AVSELTVLK--GVGPATA----------SAVLAAYAPGVAPF 136
T+ + LK G+ PA A +A LA+ A V
Sbjct: 1723 KGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA-LASLA-DVMSI 1779
Score = 40.4 bits (94), Expect = 2e-04
Identities = 38/179 (21%), Positives = 63/179 (35%), Gaps = 59/179 (32%)
Query: 12 KWKEALASY-EARVESLNKP------------------NLISL-------DDYYRKELPS 45
K KE + +Y AR+ + +P L+++ DDY+ +EL
Sbjct: 118 KTKELIKNYITARIMA-KRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYF-EELRD 175
Query: 46 L--IHQRNPNPHINTTE--LSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSL 101
L + I + LS+L+R L K + L+ + L++ S +
Sbjct: 176 LYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPS----------NT 225
Query: 102 PD----LTKAVSELTVLKGVGPATASAVLAAYA-----PGVAPFMSDEAMGAALGHSKD 151
PD L+ +S +G LA Y G P + A GHS+
Sbjct: 226 PDKDYLLSIPIS----CPLIG-VIQ---LAHYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Score = 34.6 bits (79), Expect = 0.021
Identities = 25/145 (17%), Positives = 49/145 (33%), Gaps = 35/145 (24%)
Query: 77 RLLDFVSSL-DDSSVKSASE------KAFKS--LP--DLTKAVSELTVLKGVGPATASAV 125
+ L +VSSL + S V + F++ L D+ ++L +
Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKEL 122
Query: 126 LAAY--APGVAPFMSDEAMGAAL-GHSKDYSLRQYLLFA---------DKLQAKAKVSDI 173
+ Y A +A D+ +AL + + + +F ++L+ D+
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELR------DL 176
Query: 174 FFFKCLCTFQ-FVVCLIVLHHLLLQ 197
+ T+ V LI L
Sbjct: 177 Y-----QTYHVLVGDLIKFSAETLS 196
Score = 30.0 bits (67), Expect = 0.65
Identities = 30/176 (17%), Positives = 49/176 (27%), Gaps = 72/176 (40%)
Query: 15 EALASYEARVESLNKPNLISLDDYYRKELP-------SLIHQRN-PNPHI---NTTELSK 63
E + S + +L + + + LP SL+ N + L
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV---NGAKNLVVSGPPQSLYG 388
Query: 64 LVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEK-AFKS--LPDLTKAVSELTVLKGVGPA 120
L L + K P S LD S + + K F + LP V+
Sbjct: 389 LNLT-LRKAK-AP------SGLDQSRIPFSERKLKFSNRFLP-----VA----------- 424
Query: 121 TASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFA-DKLQAKAKVSDIFF 175
+PF HS L+ A D + +++ F
Sbjct: 425 -------------SPF-----------HSH------LLVPASDLINKDLVKNNVSF 450
>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 = 36.9 bits (86), Expect = 0.003
Identities = 15/128 (11%), Positives = 38/128 (29%), Gaps = 9/128 (7%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSL----DDSSVKSASEK 96
KE I P+ + K + W + +++ ++ FV + +
Sbjct: 37 KEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIRE 96
Query: 97 AFKSLPDLTKAVSELTVLKGVG-----PATASAVLAAYAPGVAPFMSDEAMGAALGHSKD 151
F + D+ +S + G+ + + F+ E A+ + +
Sbjct: 97 YFGNEQDMPAFMSTGAKVAGMLGSFGGAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEK 156
Query: 152 YSLRQYLL 159
+
Sbjct: 157 LRKDGFAA 164
>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 = 35.2 bits (80), Expect = 0.011
Identities = 32/201 (15%), Positives = 58/201 (28%), Gaps = 58/201 (28%)
Query: 20 YEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLL 79
+ VE + + N Y K L S I P + T + R RL
Sbjct: 79 VQKFVEEVLRIN-------Y-KFLMSPIKTEQRQPSMMTRMYIE----------QRDRLY 120
Query: 80 DFVSSLDDSSVKSASEKAFKSLPDLTKAVSELT-----VLKGVGPATASAVLAAYA---P 131
+ +V + L +A+ EL ++ GV + + +A
Sbjct: 121 NDNQVFAKYNVSRL-----QPYLKLRQALLELRPAKNVLIDGVLGSGKT-WVALDVCLSY 174
Query: 132 GVAPFMSDE----------------AMGAALGHSKDYSLRQYLLFADKL-----QAKAKV 170
V M + M L + D + + + +A++
Sbjct: 175 KVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL 234
Query: 171 SDIFFFKCLCTFQFVVCLIVL 191
+ K + CL+VL
Sbjct: 235 RRLLKSK-----PYENCLLVL 250
Score = 33.7 bits (76), Expect = 0.038
Identities = 24/187 (12%), Positives = 60/187 (32%), Gaps = 54/187 (28%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKS 100
++LP + NP ++ +++ +R L W D ++ + + E +
Sbjct: 316 QDLPREVLTTNP-RRLSI--IAESIRDGLAT--W-----DNWKHVNCDKLTTIIESSLNV 365
Query: 101 L-PDLTKAV-SELTVL-KGVG-PATASAVLAAY----APGVAPFMSDEAMGAAL--GHSK 150
L P + + L+V P + +L+ + ++ +L K
Sbjct: 366 LEPAEYRKMFDRLSVFPPSAHIP---TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422
Query: 151 DYSLRQYLLFADKLQAKAKVSDIF-----------FFKCLCT------------FQFVVC 187
+ ++ ++ L+ K K+ + + K + + +
Sbjct: 423 ESTISIPSIY---LELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIG- 478
Query: 188 LIVLHHL 194
HHL
Sbjct: 479 ----HHL 481
>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 = 33.4 bits (75), Expect = 0.019
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 23/52 (44%)
Query: 95 EKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAAL 146
EK +A+ +L AS L YA AP + A+ A +
Sbjct: 18 EK---------QALKKLQ---------AS--LKLYADDSAPAL---AIKATM 46
>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 = 33.3 bits (76), Expect = 0.041
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 77 RLLDFVSSLDDSSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
RLL V+ + S + FK+L ++KA V +L ++G+G A A+
Sbjct: 315 RLLKTVARIPLSIGYNVVRM-FKTLDQISKASVEDLKKVEGIGEKRARAI 363
>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 = 33.5 bits (76), Expect = 0.046
Identities = 18/105 (17%), Positives = 36/105 (34%), Gaps = 3/105 (2%)
Query: 63 KLVRWKLTRGKWRPRLLDFVSSLDDSSVKS-ASEKAFKSLPDLTKAVSELTVLKGVG--P 119
L+R K++ G W+ + S +++ S + L + G P
Sbjct: 98 ALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEP 157
Query: 120 ATASAVLAAYAPGVAPFMSDEAMGAALGHSKDYSLRQYLLFADKL 164
V A F++ E + AL +++ + + D L
Sbjct: 158 LIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDML 202
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 31.3 bits (70), Expect = 0.13
Identities = 13/103 (12%), Positives = 32/103 (31%), Gaps = 41/103 (39%)
Query: 1 MELEFECSNVNKWKEALASYEARVESLN------KPNLIS-----LDDYYRKELPSLIHQ 49
+ E E + KW+E R++ L+ + L+++ + +
Sbjct: 80 LTQEPES--IRKWRE---EQRKRLQELDAASKVMEQEWREKAKKDLEEWNQ--------R 126
Query: 50 RNPNPHINTTELSKLVRWKLTRGKWRPRLLD--FVSSLDDSSV 90
++ ++ + K R+ D F D +
Sbjct: 127 QSE---------------QVEKNKINNRIADKAFYQQPDADII 154
>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 = 30.7 bits (70), Expect = 0.31
Identities = 17/119 (14%), Positives = 42/119 (35%), Gaps = 16/119 (13%)
Query: 6 ECSNVNKWKEALASYEARVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLV 65
E + K + ++ L+ P L + ++L + + P++ +
Sbjct: 28 EVEKMLKNQVNTRRIHQLLKELDDPLL--ENKDLEEKLQAFLDYVKEIPNLPEARKRYRI 85
Query: 66 RWKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASA 124
+ + L+ + L + E + + + DL+ +++ KGVGP
Sbjct: 86 Q----------KSLEMIEKLRSWFLIDYLECSGEEV-DLS---TDIQYAKGVGPNRKKK 130
>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 = 29.0 bits (65), Expect = 0.40
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 105 TKAVSELTVLKGVGPATASAVLA 127
+ +L L+ +GP A ++
Sbjct: 36 EGSARDLRSLQRIGPKKAQLIVG 58
>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 = 29.7 bits (67), Expect = 0.43
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 110 ELTVLKGVGPATASAVLAAYAPGVAPFMSD 139
L KG+G +A A+L YA + D
Sbjct: 122 WLLDQKGIGKESADAIL-CYACAKEVMVVD 150
>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 = 0.48
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 110 ELTVLKGVGPATASAVLA 127
+ L GVG T +AV+
Sbjct: 116 AILDLPGVGKYTCAAVMC 133
>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 = 29.6 bits (66), Expect = 0.51
Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 7/78 (8%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAA--LG-----HSKDYSLR 155
D A L +KG+G AS L + + +G + K S
Sbjct: 111 DQQLARERLLNIKGIGMQEASHFLRNVGYFDLAIIDRHIIDFMRRIGAIGETNVKQLSKS 170
Query: 156 QYLLFADKLQAKAKVSDI 173
Y+ F + L++ A ++
Sbjct: 171 LYISFENILKSIASNLNM 188
>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 = 28.1 bits (63), Expect = 0.54
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 108 VSELTVLKGVGPATASAVLA 127
+ EL L G+GP A ++
Sbjct: 26 LEELMALPGIGPVLARRIVE 45
>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 = 29.4 bits (67), Expect = 0.56
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 110 ELTVLKGVGPATASAVLA 127
E+ L GVG +TA A+L+
Sbjct: 110 EVAALPGVGRSTAGAILS 127
>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 = 0.66
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 110 ELTVLKGVGPATASAVLA 127
E + LKGVGP T AVL+
Sbjct: 119 EFSRLKGVGPYTVGAVLS 136
>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 = 1.1
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 111 LTVLKGVGPATASAVLA 127
+L GVG TA A+ +
Sbjct: 131 QQLLPGVGRYTAGAIAS 147
>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 = 27.3 bits (61), Expect = 1.1
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAV 125
K F S+ + A V+EL ++G+G A +
Sbjct: 32 KHFGSVERVFTASVAELMKVEGIGEKIAKEI 62
>4dgw_C PRE-mRNA-splicing factor PRP11; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 231
Score = 28.5 bits (63), Expect = 1.2
Identities = 6/45 (13%), Positives = 15/45 (33%), Gaps = 8/45 (17%)
Query: 120 ATASAVLAAYAPGVAP---FMSDEAMGAALGHSKDYSLRQYLLFA 161
++V + V P +S + +++L+ A
Sbjct: 128 VKENSVDSDDKAKVPPLIRIVSGLEL-----SDTKQKGKKFLVIA 167
>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
>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 = 2.1
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
>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 = 27.8 bits (62), Expect = 2.3
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 98 FKSLPDLTKAVSELTVLKGVGPATASAVL 126
D+ +A+ L G+G TA+
Sbjct: 196 MTIPGDVEQAMKTLQTFPGIGRWTANYFA 224
>3i8b_A Xylulose kinase; strain ATCC 15703 / DSM 20083, 11200J,,
transferase, structural genomics, PSI-2; 2.00A
{Bifidobacterium adolescentis ATCC15703}
Length = 515
Score = 28.1 bits (63), Expect = 2.4
Identities = 11/82 (13%), Positives = 25/82 (30%), Gaps = 13/82 (15%)
Query: 67 WKLTRGKWRPRLLDFVSSLDDSSVKSASEKAFKSLPDL----------TKAVSELTVLKG 116
+ ++R L+ V + + + S LP + ++G
Sbjct: 205 YDAASNEYRRDLIAMVLEAAEGAKAAQSHAEAIVLPTVLGPRDAAPVKADPAIAGKNVEG 264
Query: 117 ---VGPATASAVLAAYAPGVAP 135
+ P +A+ G+A
Sbjct: 265 GCLLAPGGGDNAMASLGLGMAV 286
>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 = 27.2 bits (61), Expect = 2.6
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K V LT +KGVG ++ V
Sbjct: 22 VDGNIKIVYALTTIKGVGRRYSNLVCKK 49
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 27.9 bits (63), Expect = 2.7
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 96 KAFKSLPDLTKA-VSELTVLKGVGPATASAVLA 127
F SL + A +L ++GVGP A+AV
Sbjct: 547 TEFGSLDAIAAASTDQLAAVEGVGPTIAAAVTE 579
>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 = 27.2 bits (61), Expect = 2.8
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K + LT +KGVG ++ V
Sbjct: 20 VDGKQKIMFALTSIKGVGRRFSNIVCKK 47
>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 = 27.7 bits (62), Expect = 2.9
Identities = 20/89 (22%), Positives = 28/89 (31%), Gaps = 2/89 (2%)
Query: 89 SVKSASEKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPGVAPFMSDEAMGAALGH 148
+ A +KA V + GV A S + Y G D A+
Sbjct: 455 CTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFE 514
Query: 149 SKDYSLRQYLL--FADKLQAKAKVSDIFF 175
L + + KL A + SD FF
Sbjct: 515 EVPAQLTEAEKKQWIAKLTAVSLSSDAFF 543
>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 = 3.1
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
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 26.9 bits (60), Expect = 3.9
Identities = 5/28 (17%), Positives = 10/28 (35%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ LT ++G+G A +
Sbjct: 22 IDGKRITPIALTGIRGIGRRFAYIICKV 49
>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 = 26.9 bits (59), Expect = 4.1
Identities = 14/70 (20%), Positives = 24/70 (34%), Gaps = 8/70 (11%)
Query: 111 LTVLKGVGPATASAVLAAYAPGVAPFMSD-------EAMGAALGHSKDYSLRQYLLFADK 163
+ KG+G AS L + D + G K +S ++YL +
Sbjct: 132 VRNAKGIGWKEASHFL-RNTGVEDLAILDKHVLRLMKRHGLIQEIPKGWSKKRYLYVEEI 190
Query: 164 LQAKAKVSDI 173
L+ A+
Sbjct: 191 LRKVAEAFGE 200
>2kp7_A Crossover junction endonuclease MUS81; helix-hairpin-helix, tumour
suppressor, DNA damage, DNA recombination, DNA repair,
hydrolase, magnesium; NMR {Mus musculus}
Length = 87
Score = 25.7 bits (56), Expect = 4.5
Identities = 11/71 (15%), Positives = 24/71 (33%), Gaps = 9/71 (12%)
Query: 62 SKLVRWKLTRGKWRPRLLDFVSSLDDSSVKSAS------EKAFKSL---PDLTKAVSELT 112
S+ + P + +++ D + +KA +SL P ++ E
Sbjct: 2 SRRASVRPLPVCPNPLFVRWLTEWRDEAASRGRHTRFVFQKALRSLQRYPLPLRSGKEAK 61
Query: 113 VLKGVGPATAS 123
+L+ G
Sbjct: 62 ILQHFGDRLCR 72
>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 = 26.7 bits (58), Expect = 5.1
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
>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 = 26.6 bits (59), Expect = 5.6
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
>1vq8_Y 50S ribosomal protein L32E; 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: c.9.2.1 PDB: 1vq4_Y*
1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y*
1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y*
1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Length = 241
Score = 26.4 bits (57), Expect = 6.1
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAA 128
+ + +ELT + GVGP+ A ++ A
Sbjct: 9 EAEEEYTELTDISGVGPSKAESLREA 34
>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 = 26.8 bits (60), Expect = 6.3
Identities = 8/38 (21%), Positives = 13/38 (34%), Gaps = 5/38 (13%)
Query: 42 ELPSLIHQRNPNPHINT-TELS-KLVRWKLTRGKWRPR 77
+H +PNP I + ++V L R
Sbjct: 354 LWAPNLHFHSPNPEIPALLDGRLQVVDQPLP---VRGG 388
>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 = 6.7
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 102 PDLTKAVSELTVLKGVGPATA 122
P L + EL+ L G+GP +A
Sbjct: 5 PSLVSLIRELSRLPGIGPKSA 25
>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P;
2.25A {Thermus thermophilus} PDB: 3asy_A*
Length = 211
Score = 26.0 bits (58), Expect = 6.7
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
>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 = 26.3 bits (58), Expect = 7.9
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 93 ASEKAFKSLPDLT--KAVSELTVLKGVGPATASAVL 126
A E+ + L + +A LT KG+G TA VL
Sbjct: 192 AKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVL 227
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 26.4 bits (58), Expect = 9.7
Identities = 8/38 (21%), Positives = 12/38 (31%), Gaps = 5/38 (13%)
Query: 42 ELPSLIHQRNPNPHINTTELS--KLVRWKLTRGKWRPR 77
+H PNP I + ++V L R
Sbjct: 352 VWAPNLHYHTPNPEIPALQDGRLQVVDRPLP---IRGG 386
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 0.134 0.393
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: 2,989,729
Number of extensions: 164860
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 482
Number of HSP's successfully gapped: 57
Length of query: 203
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 114
Effective length of database: 4,216,824
Effective search space: 480717936
Effective search space used: 480717936
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: 55 (25.0 bits)