RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030389
(178 letters)
>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 = 0.002
Identities = 12/97 (12%), Positives = 30/97 (30%), Gaps = 9/97 (9%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVRWKLTRGKWRPRLLVFVSSL----DDSSVKSASEK 96
KE I P+ + K + W + +++ ++ FV + +
Sbjct: 37 KEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIRE 96
Query: 97 AFKSLPDLTKAVSELTVLKGVG-----PATASAVLAA 128
F + D+ +S + G+ + +
Sbjct: 97 YFGNEQDMPAFMSTGAKVAGMLGSFGGAVLNKVLTSN 133
>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 = 34.5 bits (78), Expect = 0.007
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 20/44 (45%)
Query: 95 EKAFKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPDLAPFMS 138
EK +A+ +L AS L YA D AP ++
Sbjct: 18 EK---------QALKKLQ---------AS--LKLYADDSAPALA 41
>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 = 35.0 bits (80), Expect = 0.010
Identities = 29/175 (16%), Positives = 53/175 (30%), Gaps = 76/175 (43%)
Query: 1 MQLEF-ECSNVNK--WKEALASYEACVESLNKPNLISLDDYYRKELP-SL--IHQRNPNP 54
M ++ + S + W A D++++ S+ I NP
Sbjct: 1631 MGMDLYKTSKAAQDVWNRA-------------------DNHFKDTYGFSILDIVINNPV- 1670
Query: 55 HINTTELSKLVRWKLTRGKW-RPRL--LVFVSSLDDSSVKSASEKAFKSL---------- 101
+ + + +GK R ++F + +D +EK FK +
Sbjct: 1671 -------NLTIHFGGEKGKRIRENYSAMIFETIVDGKLK---TEKIFKEINEHSTSYTFR 1720
Query: 102 -P----DLTK---------AVSELTVLK--GVGPATA----------SAVLAAYA 130
T+ + LK G+ PA A +A LA+ A
Sbjct: 1721 SEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAA-LASLA 1774
Score = 33.5 bits (76), Expect = 0.030
Identities = 23/161 (14%), Positives = 47/161 (29%), Gaps = 41/161 (25%)
Query: 15 EALASYEACVESLNKPNLISLDDYYRKELP-------SLIHQRN-PNPHI---NTTELSK 63
E + S + +L + + + LP SL+ N + L
Sbjct: 332 EGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV---NGAKNLVVSGPPQSLYG 388
Query: 64 LVRW--KL--------TRGKWRPRLLVFVSSLDDSSV-------KSASEKAFKSLP--DL 104
L K +R + R L F + + AS+ K L ++
Sbjct: 389 LNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV 448
Query: 105 TKAVSELTVLKGVGP--ATASAV-LAAYAPDLAPFMSDEVC 142
+ ++ + P T L + ++ + D +
Sbjct: 449 SFNAKDIQI-----PVYDTFDGSDLRVLSGSISERIVDCII 484
Score = 31.9 bits (72), Expect = 0.095
Identities = 32/189 (16%), Positives = 56/189 (29%), Gaps = 54/189 (28%)
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-----------------GVGPATASAVLAAYAPDLAPFMSD 139
S P + + + K G +AV A F
Sbjct: 236 ISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVS 295
Query: 140 EVCFCSFSF 148
+ F
Sbjct: 296 VRKAITVLF 304
Score = 27.7 bits (61), Expect = 2.6
Identities = 15/113 (13%), Positives = 29/113 (25%), Gaps = 39/113 (34%)
Query: 69 LTRGKWRPRLLV--------------FVSSLDDSSVKSASEKAFKSLPDLTKAVSELTVL 114
L+ G LLV F L + + A++ + +L
Sbjct: 11 LSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL---------- 60
Query: 115 KGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLYSLFIYFYLTFVNG 167
+ + L ++S V +L F ++ G
Sbjct: 61 -----------VGKF---LG-YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG 98
>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 = 34.1 bits (78), Expect = 0.016
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
>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 = 32.5 bits (73), Expect = 0.079
Identities = 30/190 (15%), Positives = 50/190 (26%), Gaps = 61/190 (32%)
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-----VLKGVGPATASAVLAAYAPDLAPFMSDEVCFCSFSFKFTLLY 154
L +A+ EL ++ GV + + +A C FK
Sbjct: 136 PYLKLRQALLELRPAKNVLIDGVLGSGKT-WVALDV------CLSYKVQCKMDFKI---- 184
Query: 155 SLFIYFYLTF 164
F+L
Sbjct: 185 -----FWLNL 189
Score = 27.5 bits (60), Expect = 2.6
Identities = 19/132 (14%), Positives = 48/132 (36%), Gaps = 28/132 (21%)
Query: 41 KELPSLIHQRNPNPHINTTELSKLVR-WKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFK 99
++LP + NP ++ +++ +R T W+ ++ + + E +
Sbjct: 316 QDLPREVLTTNP-RRLSI--IAESIRDGLATWDNWK--------HVNCDKLTTIIESSLN 364
Query: 100 SL-PDLTKAV-SELTVL-KGVG-PATASAVLAAYAPDLAPFMSDEVC--FCSFS------ 147
L P + + L+V P + +L+ D+ V +S
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIP---TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQP 421
Query: 148 FKFTL-LYSLFI 158
+ T+ + S+++
Sbjct: 422 KESTISIPSIYL 433
>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 = 29.4 bits (66), Expect = 0.19
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 105 TKAVSELTVLKGVGPATASAVLA 127
+ +L L+ +GP A ++
Sbjct: 36 EGSARDLRSLQRIGPKKAQLIVG 58
>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 = 31.1 bits (71), Expect = 0.20
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
>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 = 28.8 bits (65), Expect = 0.21
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
>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 = 28.8 bits (65), Expect = 0.25
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 103 DLTKA-VSELTVLKGVGPATASAVLA 127
L +A + EL L G+GP A ++
Sbjct: 20 SLNEASLEELMALPGIGPVLARRIVE 45
>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 = 0.39
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
>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 = 0.39
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 110 ELTVLKGVGPATASAVLA 127
+ L GVG T +AV+
Sbjct: 116 AILDLPGVGKYTCAAVMC 133
>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 = 28.3 bits (64), Expect = 0.41
Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 11/64 (17%)
Query: 71 RGKWRPRLLVFVSSLDD-----SSVKSASEKAFKSLPDLTKA-VSELTVLKGVGPATASA 124
RG SSL+ + K L L A V E+ + G+ A
Sbjct: 17 RGSHM-----NTSSLETIEGVGPKRRQMLLKYMGGLQGLRNASVEEIAKVPGISQGLAEK 71
Query: 125 VLAA 128
+ +
Sbjct: 72 IFWS 75
>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 = 0.43
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 = 0.47
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 110 ELTVLKGVGPATASAVLA 127
E + LKGVGP T AVL+
Sbjct: 119 EFSRLKGVGPYTVGAVLS 136
>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 = 0.50
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAAYA 130
D A L +KG+G AS L
Sbjct: 111 DQQLARERLLNIKGIGMQEASHFLRNVG 138
>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 = 0.59
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
>2owo_A DNA ligase; protein-DNA complex, ligase-DNA complex; HET: DNA OMC
AMP; 2.30A {Escherichia coli}
Length = 671
Score = 29.4 bits (67), Expect = 0.63
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
>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 = 0.82
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 111 LTVLKGVGPATASAVLA 127
+L GVG TA A+ +
Sbjct: 131 QQLLPGVGRYTAGAIAS 147
>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 = 1.1
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
>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 = 28.0 bits (63), Expect = 1.1
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K V LT +KGVG ++ V
Sbjct: 22 VDGNIKIVYALTTIKGVGRRYSNLVCKK 49
>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 = 28.6 bits (65), Expect = 1.1
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
>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 = 28.0 bits (63), Expect = 1.1
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ K + LT +KGVG ++ V
Sbjct: 20 VDGKQKIMFALTSIKGVGRRFSNIVCKK 47
>2vz8_A Fatty acid synthase; transferase, phosphopantetheine, multienzyme,
megasynthase, fatty acid synthesis; 3.2A {Sus scrofa}
PDB: 2vz9_A*
Length = 2512
Score = 28.7 bits (64), Expect = 1.2
Identities = 10/45 (22%), Positives = 16/45 (35%), Gaps = 6/45 (13%)
Query: 42 ELPSLIHQRNPNPHINTTELS--KLVRWKLTRGKWRPRLLVFVSS 84
+H PNP I + ++V L R V ++S
Sbjct: 352 VWAPNLHYHTPNPEIPALQDGRLQVVDRPLP---IRGG-NVGINS 392
>3sgi_A DNA ligase; HET: DNA AMP; 3.50A {Mycobacterium tuberculosis}
Length = 615
Score = 28.3 bits (64), Expect = 1.3
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
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 27.6 bits (62), Expect = 1.5
Identities = 5/28 (17%), Positives = 10/28 (35%)
Query: 101 LPDLTKAVSELTVLKGVGPATASAVLAA 128
+ LT ++G+G A +
Sbjct: 22 IDGKRITPIALTGIRGIGRRFAYIICKV 49
>1ovy_A 50S ribosomal protein L18; ribosome; NMR {Geobacillus
stearothermophilus} SCOP: c.55.4.1
Length = 120
Score = 27.2 bits (61), Expect = 1.8
Identities = 20/76 (26%), Positives = 28/76 (36%), Gaps = 17/76 (22%)
Query: 65 VRWKLTRGKWRPRLLVFVSS-------LDDSSVK---SAS--EKAFKSLPDLTKAVSELT 112
+R K+ RPRL VF S+ +DD+ SAS +K F ++
Sbjct: 18 IRKKIFGTTERPRLSVFRSNKHIYAQIIDDTKSATIVSASTLDKEFGLDSTNNIEAAKK- 76
Query: 113 VLKGVGPATASAVLAA 128
VG A L
Sbjct: 77 ----VGELVAKRALEK 88
>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 = 27.8 bits (62), Expect = 2.1
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 93 ASEKAFKSLPDLT--KAVSELTVLKGVGPATASAVLA-AYAPDLAP 135
A E+ + L + +A LT KG+G TA VL+ A ++ P
Sbjct: 192 AKEENLEELKEWGEEEAYEYLTSFKGIGRWTAELVLSIALGKNVFP 237
>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 = 27.5 bits (60), Expect = 2.3
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 103 DLTKAVSELTVLKGVGPATASAVLAA 128
+ + +ELT + GVGP+ A ++ A
Sbjct: 9 EAEEEYTELTDISGVGPSKAESLREA 34
>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 = 27.7 bits (61), Expect = 2.5
Identities = 12/69 (17%), Positives = 22/69 (31%), Gaps = 3/69 (4%)
Query: 63 KLVRWKLTRGKWRPRLLVFVSSLDDSSVKS-ASEKAFKSLPDLTKAVSELTVLKGVG--P 119
L+R K++ G W+ + S +++ S + L + G P
Sbjct: 98 ALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEP 157
Query: 120 ATASAVLAA 128
V A
Sbjct: 158 LIRKGVDMA 166
>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 = 27.1 bits (59), Expect = 2.6
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
>2vq2_A PILW, putative fimbrial biogenesis and twitching motility protein;
secretin, TPR repeat, type IV pilus, bacterail
virulence; 1.54A {Neisseria meningitidis}
Length = 225
Score = 27.2 bits (61), Expect = 2.8
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 7 CSNVNKWKEALASYEACVESLNKPN 31
C +N+ E++A ++ + P
Sbjct: 87 CGRLNRPAESMAYFDKALADPTYPT 111
>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 = 27.0 bits (60), Expect = 3.0
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
>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 = 26.8 bits (60), Expect = 3.0
Identities = 12/42 (28%), Positives = 16/42 (38%), Gaps = 11/42 (26%)
Query: 92 SASEKA-FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132
+ F +L L+V GVGP A A LA +
Sbjct: 80 DGETRDLFLTL---------LSV-SGVGPRLAMAALAVHDAP 111
>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P;
2.25A {Thermus thermophilus} PDB: 3asy_A*
Length = 211
Score = 26.8 bits (60), Expect = 3.1
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
>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 = 26.8 bits (60), Expect = 3.4
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 11/42 (26%)
Query: 92 SASEKA-FKSLPDLTKAVSELTVLKGVGPATASAVLAAYAPD 132
A F+ L L+V GVGP A A+L+A P
Sbjct: 64 DEENLALFELL---------LSV-SGVGPKVALALLSALPPR 95
>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 = 26.8 bits (60), Expect = 3.7
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 102 PDLTKAVSELTVLKGVGPATA 122
P L + EL+ L G+GP +A
Sbjct: 5 PSLVSLIRELSRLPGIGPKSA 25
>3bbo_Q Ribosomal protein L18; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 161
Score = 26.6 bits (59), Expect = 3.8
Identities = 25/76 (32%), Positives = 35/76 (46%), Gaps = 13/76 (17%)
Query: 65 VRWKLTRGKWRPRLLVFVSS-------LDDSSVK---SAS--EKAFKSLPDLTKAVSELT 112
+R K+ RPRL VF S+ +DDS + SAS +K+ D + + +
Sbjct: 55 IRKKVEGTPERPRLCVFRSNKHLYVQVIDDSKMHTLASASTMQKSISEELDYSSS-PTIE 113
Query: 113 VLKGVGPATASAVLAA 128
V K VG ASA L
Sbjct: 114 VAKKVGEVIASACLEK 129
>3kha_A Toxin RELE; toxin-antitoxin systems, translational control,
ribosome, RE stress response, transcription,
transcription regula; 2.50A {Escherichia coli} PDB:
2kc8_A 2kc9_A 3kiq_y* 3kis_y* 3kiu_y* 3kix_y*
Length = 95
Score = 26.0 bits (57), Expect = 3.9
Identities = 9/47 (19%), Positives = 17/47 (36%), Gaps = 3/47 (6%)
Query: 32 LISLDDYYRKELPSLIHQRNPNPHINTTELS---KLVRWKLTRGKWR 75
L R++L + + +P I +L + KL +R
Sbjct: 15 WRKLGSTVREQLKKKLVEVLESPRIEANKLRGMPDCYKIKLRSSGYR 61
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 26.8 bits (59), Expect = 4.6
Identities = 6/45 (13%), Positives = 16/45 (35%)
Query: 60 ELSKLVRWKLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLPDL 104
L +++ K + + + + SE+A + P+
Sbjct: 597 RLQEVLHKKQIVDSRGHTIPIIYVEDEVAIRYQNSERAAQEFPNK 641
>2qfy_A Isocitrate dehydrogenase [NADP]; rossmann fold, oxidoreductase;
HET: AKG; 2.10A {Saccharomyces cerevisiae} PDB: 2qfw_A*
2qfx_A* 2qfv_A*
Length = 427
Score = 26.7 bits (58), Expect = 5.1
Identities = 7/52 (13%), Positives = 20/52 (38%), Gaps = 6/52 (11%)
Query: 20 YEACVESLNKPNLISLDDYYRKELPSLIHQRNPNPHINTTELSKLVRWKLTR 71
A + ++ + +++ K+L + ++ T E V +L +
Sbjct: 376 ESATLNTVQQDGIMT------KDLALACGNNERSAYVTTEEFLDAVEKRLQK 421
>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI,
protein structure initiative; 1.90A {Geobacillus
stearothermophilus} SCOP: c.37.1.6
Length = 201
Score = 26.1 bits (58), Expect = 5.5
Identities = 8/60 (13%), Positives = 18/60 (30%), Gaps = 11/60 (18%)
Query: 24 VESLNKPN----LISLDDYYRKELPSLIHQRNPNP------HINTTELSKLVRWKLTRGK 73
++L + + +DD+ E H N + L+ + +L
Sbjct: 43 SQTLREQGISVCVFHMDDHI-VERAKRYHTGNEEWFEYYYLQWDVEWLTHQLFRQLKASH 101
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, struc
genomics, PSI-2, protein structure initiative, joint
center structural genomics; 2.55A {Bacillus halodurans}
Length = 233
Score = 26.2 bits (58), Expect = 5.8
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 91 KSASEKAFKSLPDLTKAVSELTVLKGVGPATA 122
+ T + +LT +KG+G TA
Sbjct: 121 GRLDFTELEGAEA-TTVIEKLTAIKGIGQWTA 151
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 26.8 bits (59), Expect = 5.8
Identities = 10/75 (13%), Positives = 22/75 (29%), Gaps = 10/75 (13%)
Query: 40 RKELPSLIHQRNPNPHINTT----------ELSKLVRWKLTRGKWRPRLLVFVSSLDDSS 89
L ++I PN L +++ K + + + +
Sbjct: 564 EDTLDNIIQSCQPNAIGINGPNPKTQKFYKRLQEVLHKKQIVDSRGHTIPIIYVEDEVAI 623
Query: 90 VKSASEKAFKSLPDL 104
SE+A + P+
Sbjct: 624 RYQNSERAAQEFPNK 638
>2kc7_A BFR218_protein; tetratricopeptide repeat, all-alpha,
GFT-structural genomics, PSI-2, protein structure
initiative; NMR {Bacteroides fragilis}
Length = 99
Score = 25.4 bits (56), Expect = 6.1
Identities = 9/41 (21%), Positives = 23/41 (56%), Gaps = 9/41 (21%)
Query: 11 NKWKEALASYEACVESLN--------KPNLISLDDYYRKEL 43
W++AL +Y++ +E LN + ++ + ++Y K++
Sbjct: 49 GDWQKALNNYQSAIE-LNPDSPALQARKMVMDILNFYNKDM 88
>3guw_A Uncharacterized protein AF_1765; alpha-beta protein, structural
genomics, PSI-2, protein structure initiative; 3.20A
{Archaeoglobus fulgidus dsm 4304}
Length = 261
Score = 26.2 bits (58), Expect = 6.6
Identities = 10/60 (16%), Positives = 17/60 (28%), Gaps = 20/60 (33%)
Query: 14 KEALASYEACVESLNKPNL-----ISLDDYYRKE---------------LPSLIHQRNPN 53
+ YE + L + I L+ +E +P +IH N
Sbjct: 75 RCIPPDYEFVLGYLEEGEWVAFGEIGLELVTDEEIEVLKSQLELAKRMDVPCIIHTPRGN 134
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA
recombination; 1.90A {Escherichia coli} SCOP: a.5.1.1
a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A
Length = 203
Score = 25.7 bits (57), Expect = 6.8
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 116 GVGPATASAVLAAYAPD 132
GVGP A A+L+ +
Sbjct: 80 GVGPKLALAILSGMSAQ 96
>2xhi_A N-glycosylase/DNA lyase; lyase-DNA complex, lyase/DNA complex,
separation-OF-function helix-hairpin-helix, DNA repair;
HET: 8OG; 1.55A {Homo sapiens} PDB: 1ko9_A 1lwy_A*
1hu0_A* 1lwv_A* 1lww_A* 2noe_A* 2noh_A* 2nol_A* 1n3c_A*
1fn7_A* 2noz_A* 1yqk_A 1yqr_A* 1yql_A* 1yqm_A* 2noi_A
1ebm_A* 1m3q_A* 1m3h_A* 1n39_A* ...
Length = 360
Score = 26.2 bits (57), Expect = 7.1
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 102 PDLTKAVSELTVLKGVGPATASAVL 126
+A L +L GVG A +
Sbjct: 246 SSYEEAHKALCILPGVGTCVADKIC 270
>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1,
nicotinic acid riboside kinase activity, NAD
biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB:
2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*
Length = 207
Score = 25.6 bits (56), Expect = 8.0
Identities = 5/17 (29%), Positives = 11/17 (64%)
Query: 24 VESLNKPNLISLDDYYR 40
+ L ++IS DD+++
Sbjct: 42 QKHLPNCSVISQDDFFK 58
>1zg2_A Hypothetical UPF0213 protein BH0048; BHR2, structure,
autostructure, northeast structural genomics consortium,
PSI; NMR {Bacillus halodurans}
Length = 107
Score = 24.9 bits (55), Expect = 8.3
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 68 KLTRGKWRPRLLVFVSSLDDSSVKSASEKAFKSLP 102
K TRG+ P LV + E K L
Sbjct: 42 KYTRGR-GPFRLVATWAFPSKEEAMRWEYEVKHLS 75
>2yg9_A DNA-3-methyladenine glycosidase II, putative; hydrolase, DNA
repair; 1.95A {Deinococcus radiodurans} PDB: 2yg8_A
Length = 225
Score = 25.4 bits (56), Expect = 9.6
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 98 FKSLPDLT--KAVSELTVLKGVGPATA 122
F L ++EL L G+G TA
Sbjct: 133 FAHLSGQPDELVIAELVQLPGIGRWTA 159
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
0.319 0.134 0.407
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: 2,597,129
Number of extensions: 136021
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 60
Length of query: 178
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 91
Effective length of database: 4,272,666
Effective search space: 388812606
Effective search space used: 388812606
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: 54 (24.6 bits)