RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy17885
(95 letters)
>2l0w_A Potassium voltage-gated channel, subfamily H (EAG member 2,
isoform CRA_B; HERG, PAS domain, voltage-gated
potassium channel, membrane; NMR {Homo sapiens} PDB:
2l1m_A 2l4r_A
Length = 138
Score = 62.3 bits (152), Expect = 3e-14
Identities = 15/34 (44%), Positives = 26/34 (76%)
Query: 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
F++ANA++ + ++YCN+ FC++ GY+RAEV
Sbjct: 29 SRKFIIANARVENCAVIYCNDGFCELCGYSRAEV 62
>1byw_A Protein (human ERG potassium channel); PAS domain, potassium
channel domain, membrane protein; 2.60A {Homo sapiens}
SCOP: d.110.3.6
Length = 110
Score = 61.0 bits (149), Expect = 6e-14
Identities = 15/32 (46%), Positives = 26/32 (81%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
F++ANA++ + ++YCN+ FC++ GY+RAEV
Sbjct: 3 KFIIANARVENCAVIYCNDGFCELCGYSRAEV 34
>4eet_B Phototropin-2; LOV, blue light photoreceptor, signaling protein,
flavoprote; HET: FMN; 1.20A {Arabidopsis thaliana} PDB:
4ees_A* 4eer_A* 4eep_A* 4eeu_A* 1jnu_A* 1g28_A*
Length = 115
Score = 56.0 bits (136), Expect = 5e-12
Identities = 8/34 (23%), Positives = 24/34 (70%)
Query: 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+ +F++ + ++ D PI++ ++ F +++ Y+R E+
Sbjct: 7 EKNFVITDPRLPDNPIIFASDGFLELTEYSREEI 40
>1n9l_A PHOT-LOV1, putative blue light receptor; phototropin, flavin,
electron transport; HET: FMN; 1.90A {Chlamydomonas
reinhardtii} SCOP: d.110.3.6 PDB: 1n9n_A* 1n9o_A*
Length = 109
Score = 55.2 bits (134), Expect = 9e-12
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+F++A+A + D P+VY +E F ++GY EV
Sbjct: 5 TFVVADATLPDCPLVYASEGFYAMTGYGPDEV 36
>2v0u_A NPH1-1, LOV2; kinase, transferase, ATP-binding,
serine/threonine-protein kinase, light-induced signal
trans phototropin1, nucleotide-binding; HET: FMN; 1.40A
{Avena sativa} PDB: 2v0w_A* 2v1b_A* 2v1a_A* 1jnu_A*
1g28_A*
Length = 146
Score = 54.9 bits (133), Expect = 3e-11
Identities = 9/34 (26%), Positives = 25/34 (73%)
Query: 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+ +F++ + ++ D PI++ ++SF +++ Y+R E+
Sbjct: 12 EKNFVITDPRLPDNPIIFASDSFLQLTEYSREEI 45
>2z6d_A Phototropin-2; PAS-fold, LOV-fold, alternative splicing,
ATP-binding, chromophore, flavoprotein, FMN, kinase,
membrane, nucleotide-binding; HET: FMN; 2.00A
{Arabidopsis thaliana} PDB: 2z6c_A*
Length = 130
Score = 54.1 bits (131), Expect = 4e-11
Identities = 10/34 (29%), Positives = 20/34 (58%)
Query: 37 DSSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+F++++A PIVY + F ++GY+ E+
Sbjct: 16 QQTFVVSDATQPHCPIVYASSGFFTMTGYSSKEI 49
>3d72_A Vivid PAS protein VVD; circadian, photoreceptor, blue-light, LOV,
signaling protein; HET: FAD; 1.65A {Neurospora crassa}
PDB: 3is2_A* 2pd8_A* 3hjk_A* 2pdr_A* 2pd7_A* 2pdt_A*
3hji_A* 3rh8_B*
Length = 149
Score = 54.3 bits (131), Expect = 6e-11
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 38 SSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+ +L + + D PIVY +E+F ++GY+ AEV
Sbjct: 36 VALILCDLKQKDTPIVYASEAFLYMTGYSNAEV 68
>3ue6_A Aureochrome1; PAS/LOV domain, FMN-binding blue-light
photoreceptor, signal protein; HET: FMN; 2.75A
{Vaucheria frigida} PDB: 3ulf_A*
Length = 166
Score = 51.2 bits (123), Expect = 1e-09
Identities = 10/33 (30%), Positives = 21/33 (63%)
Query: 38 SSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+F++ +A + D PIVY + F ++GY+ ++
Sbjct: 46 QNFVITDASLPDNPIVYASRGFLTLTGYSLDQI 78
>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription
factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter
litoralis}
Length = 258
Score = 51.5 bits (123), Expect = 2e-09
Identities = 7/32 (21%), Positives = 21/32 (65%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+ ++++ ++ D P++ N++F ++GY+ E
Sbjct: 75 ASVVSDPRLADNPLIAINQAFTDLTGYSEEEC 106
>2pr5_A Blue-light photoreceptor; light-oxygen-voltage, LOV,
PER-ARNT-SIM, PAS, flavoprotein, protein; HET: FMN;
1.45A {Bacillus subtilis} PDB: 2pr6_A*
Length = 132
Score = 48.3 bits (116), Expect = 7e-09
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
++ + + D PIVY N+ F +++GY E+
Sbjct: 11 GVVITDPALEDNPIVYVNQGFVQMTGYETEEI 42
>3t50_A Blue-light-activated histidine kinase; PAS superfamily,
blue-light photoreceptor, FMN binding, TRAN; HET: FMN;
1.64A {Brucella melitensis}
Length = 128
Score = 47.9 bits (115), Expect = 9e-09
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
L+ N + D PIV+ N +F K++GY EV
Sbjct: 9 PMLITNPHLPDNPIVFANPAFLKLTGYEADEV 40
>3sw1_A Sensory box protein; light-oxygen-voltage, LOV, PAS, signaling
protein; HET: FMN; 2.63A {Pseudomonas putida}
Length = 162
Score = 47.2 bits (113), Expect = 3e-08
Identities = 9/33 (27%), Positives = 19/33 (57%)
Query: 38 SSFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
++A + D ++Y N +F ++GY+R E+
Sbjct: 36 DGIVVAEKEGDDTILIYVNAAFEYLTGYSRDEI 68
>3ewk_A Sensor protein; PAS domain, alpha/beta fold, kinase,
phosphoprotein, transfe flavoprotein; HET: FAD; 2.34A
{Methylococcus capsulatus}
Length = 227
Score = 37.0 bits (86), Expect = 2e-04
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+Y N++FC +S Y R E+
Sbjct: 11 ILYANDNFCAVSRYGREEL 29
Score = 35.1 bits (81), Expect = 0.001
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 49 DFPIVYCNESFCKISGYNRAEV 70
I+Y N + C+ SG E+
Sbjct: 130 AGRIIYANPALCRFSGMAEGEL 151
>2gj3_A Nitrogen fixation regulatory protein; PAS domain, FAD, redox
sensor, atomic resolution, transferase; HET: FAD; 1.04A
{Azotobacter vinelandii}
Length = 120
Score = 35.9 bits (84), Expect = 3e-04
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+Y N +F I+GY EV
Sbjct: 27 ILYANRAFRTITGYGSEEV 45
>2wkq_A NPH1-1, RAS-related C3 botulinum toxin substrate 1; transferase,
cell adhesion, nucleotide-binding, protein engineering,
RAS superfamily LOV2; HET: GTP FMN; 1.60A {Avena
sativa} PDB: 2wkr_A* 2wkp_A*
Length = 332
Score = 36.5 bits (84), Expect = 4e-04
Identities = 9/32 (28%), Positives = 24/32 (75%)
Query: 39 SFLLANAQIVDFPIVYCNESFCKISGYNRAEV 70
+F++ + ++ D PI++ ++SF +++ Y+R E+
Sbjct: 23 NFVITDPRLPDNPIIFASDSFLQLTEYSREEI 54
>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 = 35.4 bits (81), Expect = 0.001
Identities = 9/42 (21%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 36 PDSSFLLANAQIVDFPIV-------YCNESFCKISGYNRAEV 70
PD +LL+ + P++ Y K+ G+ E+
Sbjct: 226 PDKDYLLSIP--ISCPLIGVIQLAHYVV--TAKLLGFTPGEL 263
Score = 27.3 bits (60), Expect = 0.74
Identities = 23/91 (25%), Positives = 32/91 (35%), Gaps = 24/91 (26%)
Query: 11 RKNTAPEVELVRRTYMYDERQKNGHPDSSFL----------LANA-QIVDFPIVYCNESF 59
RK AP R + ER+ + FL L A +++ +V N SF
Sbjct: 394 RKAKAPSGLDQSRI-PFSERKLKFS--NRFLPVASPFHSHLLVPASDLINKDLVKNNVSF 450
Query: 60 CKISGYNRAEVPSDYDIPTYNLLVGSYLQSL 90
D IP Y+ GS L+ L
Sbjct: 451 N----------AKDIQIPVYDTFDGSDLRVL 471
>3bwl_A Sensor protein; structural genomics, APC87707.1, PAS domain,
HTR-like protei protein structure initiative; HET: MSE
I3A; 1.73A {Haloarcula marismortui atcc 43049}
Length = 126
Score = 34.1 bits (79), Expect = 0.002
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 52 IVYCNESFCKISGYNRAEV----PSDYDIPTYNLLVGSYLQSL 90
I N+ FC GY+ +EV ++D+ V + L
Sbjct: 39 ICEVNQRFCAELGYDESEVLGRSIWEFDLMFDAEDVQTQLSGF 81
>3mqq_A Transcriptional regulator, LUXR family; PAS domain, PSI, MCSG,
structural genomics, center for structural genomics;
1.65A {Burkholderia thailandensis} PDB: 3mqo_A
Length = 120
Score = 32.9 bits (76), Expect = 0.004
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 45 AQIVDFPIVYCNESFCKISGYNRAEV 70
D I CN+ I RA++
Sbjct: 17 VLSRDRVIEDCNDELAAIFRCARADL 42
>3lyx_A Sensory BOX/ggdef domain protein; structural genomics, PSI- 2,
protein structure initiative, northeast structural
genomics consortium; 2.00A {Colwellia psychrerythraea}
Length = 124
Score = 32.5 bits (75), Expect = 0.006
Identities = 4/19 (21%), Positives = 10/19 (52%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+ N+ + GY++ +
Sbjct: 29 IIDWNKGSETLYGYSKEQA 47
>3olo_A Two-component sensor histidine kinase; structural genomics,
PSI-2, protein structure initiative, MI center for
structural genomics, MCSG, TRA; 2.09A {Nostoc SP}
Length = 118
Score = 32.2 bits (74), Expect = 0.008
Identities = 5/18 (27%), Positives = 13/18 (72%)
Query: 52 IVYCNESFCKISGYNRAE 69
+Y N++ C+++ Y+R +
Sbjct: 35 FLYVNDATCRMTEYSREQ 52
>3mjq_A Uncharacterized protein; NESG, structural genomics, PSI-2,
protein structure initiati northeast structural
genomics consortium; 2.60A {Desulfitobacterium
hafniense}
Length = 126
Score = 31.4 bits (72), Expect = 0.015
Identities = 8/43 (18%), Positives = 12/43 (27%), Gaps = 4/43 (9%)
Query: 52 IVYCNESFCKISGYNRAEV----PSDYDIPTYNLLVGSYLQSL 90
++Y N + K GY E+ L L
Sbjct: 21 LLYANTAVPKKLGYTHEELMSMHILTITSAGKMAEGEKILAEL 63
>2r78_A Sensor protein; sensory box sensor histidine kinase/response
regulator, structural genomics, PSI, MCSG; 1.60A
{Geobacter sulfurreducens pca}
Length = 117
Score = 30.2 bits (69), Expect = 0.038
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 52 IVYCNESFCKISGYNRAE 69
+ N + C GY R E
Sbjct: 33 YLDVNPAICSAIGYTRDE 50
>3fc7_A HTR-like protein, sensor protein; APC87712.1, HTR-like
protein,haloarcula marismortui ATCC 430 structural
genomics, PSI-2; 2.65A {Haloarcula marismortui}
Length = 125
Score = 29.2 bits (66), Expect = 0.10
Identities = 4/19 (21%), Positives = 7/19 (36%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+ N S G + +
Sbjct: 41 ILSVNPSMAGRLGADPDTL 59
>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 = 28.4 bits (62), Expect = 0.25
Identities = 7/37 (18%), Positives = 13/37 (35%), Gaps = 10/37 (27%)
Query: 12 KNTAPEVELVRRTYMYDERQKNGHPDSSFLLA-NAQI 47
K +++ + Y DS+ LA A +
Sbjct: 19 KQALKKLQASLKLYA---------DDSAPALAIKATM 46
>3eeh_A Putative light and redox sensing histidine kinase; structural
genomic MCSG, protein structure initiative, midwest
center for STRU genomics; HET: PG5; 1.95A {Haloarcula
marismortui}
Length = 125
Score = 27.9 bits (63), Expect = 0.32
Identities = 4/24 (16%), Positives = 12/24 (50%)
Query: 52 IVYCNESFCKISGYNRAEVPSDYD 75
++ N ++ I G + A++ +
Sbjct: 34 VLVINSAYEDIWGRSVAKLRENPH 57
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transfe two-component regulatory
system; 3.80A {Thermotoga maritima}
Length = 349
Score = 28.0 bits (63), Expect = 0.35
Identities = 4/19 (21%), Positives = 8/19 (42%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I N+ ++ G + V
Sbjct: 30 ITEWNKKAEQLFGLKKENV 48
>1ll8_A PAS kinase; PAS domain, ligand binding, ligand screening, kinase
regulation, transferase; NMR {Homo sapiens} SCOP:
d.110.3.5
Length = 114
Score = 27.4 bits (61), Expect = 0.50
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I+ N+ C + GY+ ++
Sbjct: 21 ILVANDKACGLLGYSSQDL 39
>3vol_A Aerotaxis transducer AER2; heme, oxygen sensor protein, PAS,
HAMP, cyanoMet, CN-bound, protein; HET: HEM; 2.40A
{Pseudomonas aeruginosa}
Length = 233
Score = 27.2 bits (59), Expect = 0.72
Identities = 8/43 (18%), Positives = 18/43 (41%)
Query: 49 DFPIVYCNESFCKISGYNRAEVPSDYDIPTYNLLVGSYLQSLY 91
D I+Y N + ++ G A++ L+G+ + +
Sbjct: 41 DLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRLMGANIDVFH 83
>3luq_A Sensor protein; PAS, histidine, kinase, PSI, MCSG, structural
genomics, midwest center for structural genomics; HET:
PGE; 2.49A {Geobacter sulfurreducens}
Length = 114
Score = 26.4 bits (59), Expect = 0.83
Identities = 5/26 (19%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 53 VYCNESFCKISGYNRAEVP--SDYDI 76
+ + + + G ++ S YDI
Sbjct: 26 LAVSRRWREDYGLGDGDILGMSHYDI 51
>3iuz_A Putative glyoxalase superfamily protein; struct genomics, joint
center for structural genomics, JCSG, prote structure
initiative, PSI-2; HET: MLY P6G PGE; 1.90A {Ralstonia
eutropha}
Length = 340
Score = 27.0 bits (59), Expect = 0.98
Identities = 8/29 (27%), Positives = 10/29 (34%)
Query: 18 VELVRRTYMYDERQKNGHPDSSFLLANAQ 46
E + R D + D F NAQ
Sbjct: 303 YEFITRDRFADAPAASPRVDLGFDAGNAQ 331
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.9 bits (56), Expect = 1.9
Identities = 9/64 (14%), Positives = 17/64 (26%), Gaps = 12/64 (18%)
Query: 8 RGWRKNTAPEVELVRRTYMYDERQKNGHPDSSFLLANAQ--IVDFPIVYCNESFCKISGY 65
R WR+ ++ E A+ + ++ +E K
Sbjct: 88 RKWREEQRKRLQ---------ELDAASKVMEQEWREKAKKDLEEWNQRQ-SEQVEKNKIN 137
Query: 66 NRAE 69
NR
Sbjct: 138 NRIA 141
>3mr0_A Sensory box histidine kinase/response regulator; PAS fold,
structural genomics, PSI-2; HET: PG5; 1.49A
{Burkholderia thailandensis}
Length = 142
Score = 25.6 bits (57), Expect = 2.0
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 53 VYCNESFCKISGYNRAEVPSDYD 75
+Y + F KI GY E+P +
Sbjct: 32 MYLSPHFKKIMGYEDHELPDEIT 54
>3l8d_A Methyltransferase; structural genomics, PSI, nysgrc, protein
structure initiative, NEW YORK SGX research center for
structural genomics; 1.70A {Bacillus thuringiensis}
Length = 242
Score = 25.6 bits (56), Expect = 2.8
Identities = 6/36 (16%), Positives = 13/36 (36%), Gaps = 5/36 (13%)
Query: 30 RQKNGHPDSSFLLANAQIVDFP-----IVYCNESFC 60
+++ PD SF+ + + F + S
Sbjct: 92 KERGEGPDLSFIKGDLSSLPFENEQFEAIMAINSLE 127
>1v9y_A Heme PAS sensor protein; signaling protein; HET: HEM; 1.32A
{Escherichia coli} SCOP: d.110.3.2 PDB: 1v9z_A* 1vb6_A*
1s67_L* 1s66_L*
Length = 167
Score = 25.3 bits (56), Expect = 3.3
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 52 IVYCNESFCKISGYNRAEV 70
+++ N + K+ GY R EV
Sbjct: 62 VMFFNPAAEKLWGYKREEV 80
>1t0b_A THUA-like protein; trehalose metabolism, NCS symmetry, structural
genomics, PSI, protein structure initiative; 1.70A
{Geobacillus stearothermophilus} SCOP: c.23.16.6
Length = 252
Score = 25.5 bits (55), Expect = 3.3
Identities = 7/43 (16%), Positives = 11/43 (25%), Gaps = 1/43 (2%)
Query: 16 PEVELVRRTYMYDERQKNGHPDSS-FLLANAQIVDFPIVYCNE 57
+ + MY E PD + F+ F
Sbjct: 147 GPYIELEQEEMYGEFFDIPEPDETIFISWFEGGEVFRSGCTFT 189
>1d06_A Nitrogen fixation regulatory protein FIXL; oxygen sensor,
histidine kinase, PAS, high-resolution, two-C system,
signaling protein; HET: HEM; 1.40A {Sinorhizobium
meliloti} SCOP: d.110.3.2 PDB: 1ew0_A*
Length = 130
Score = 24.8 bits (55), Expect = 4.0
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 52 IVYCNESFCKISGYNRAEV 70
IV N + + GY EV
Sbjct: 38 IVSFNAAAVRQFGYAEEEV 56
>2vv6_A FIXL, sensor protein FIXL; signaling protein, transferase,
phosphoprotein, nitrogen FIX PER-ARNT-SIM,
metal-binding, PAS, iron, heme; HET: HEM; 1.5A
{Bradyrhizobium japonicum} PDB: 1xj6_A* 1xj4_A* 2vv7_A*
2vv8_A* 1lsw_A* 1dp8_A* 1dp9_A* 1drm_A* 1lsv_A* 1dp6_A*
1lsx_A* 1lt0_A* 1y28_A* 2cmn_A* 1xj3_A* 1xj2_A* 2owh_A*
2owj_A*
Length = 119
Score = 24.8 bits (55), Expect = 4.1
Identities = 3/19 (15%), Positives = 9/19 (47%)
Query: 52 IVYCNESFCKISGYNRAEV 70
I + + ++ G++ E
Sbjct: 15 IQLFSTAAERLFGWSELEA 33
>3fac_A Putative uncharacterized protein; complete proteome, structural
genomics, PSI-2, protein structure initiative; 2.50A
{Rhodobacter sphaeroides 2}
Length = 118
Score = 24.2 bits (52), Expect = 6.8
Identities = 6/29 (20%), Positives = 8/29 (27%)
Query: 51 PIVYCNESFCKISGYNRAEVPSDYDIPTY 79
C+ SFC+ G A
Sbjct: 22 DARRCDCSFCRRRGAIAATARLSDLRVVR 50
>1jfx_A 1,4-beta-N-acetylmuramidase M1; beta-alpha-barrel, cellosyl,
lysozyme, hydrolase; 1.65A {Streptomyces coelicolor}
SCOP: c.1.8.8
Length = 217
Score = 24.3 bits (53), Expect = 7.0
Identities = 2/26 (7%), Positives = 8/26 (30%)
Query: 51 PIVYCNESFCKISGYNRAEVPSDYDI 76
++Y S+ + + +
Sbjct: 135 VVIYTTASWWNTCTGSWNGMAAKSPF 160
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS
finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2
b.113.1.1 g.39.1.8
Length = 364
Score = 24.5 bits (53), Expect = 7.2
Identities = 3/9 (33%), Positives = 5/9 (55%)
Query: 16 PEVELVRRT 24
PE+ L +
Sbjct: 5 PELHLASQF 13
>3u6p_A Formamidopyrimidine-DNA glycosylase; DNA glycosylase, DNA repair,
sequence context; HET: DNA 08Q; 1.60A {Geobacillus
stearothermophilus} PDB: 3u6d_A* 3u6c_A* 3u6l_A*
3u6m_A* 3u6o_A* 3u6e_A* 3u6q_A* 3u6s_A* 3gp1_A* 3sbj_A*
2f5q_A* 2f5s_A* 3gq4_A* 3gpy_A* 2f5n_A 2f5o_A 2f5p_A
3sau_A* 3sar_A* 3sav_A* ...
Length = 273
Score = 24.4 bits (54), Expect = 7.9
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 16 PEVELVRRT 24
PEVE +RRT
Sbjct: 4 PEVETIRRT 12
>2x8r_A Glycosyl hydrolase; peptidoglycan cleavage,
endo-N-acetylmuramidases, motif; 1.70A {Aspergillus
fumigatus}
Length = 210
Score = 24.3 bits (53), Expect = 8.1
Identities = 3/26 (11%), Positives = 7/26 (26%)
Query: 51 PIVYCNESFCKISGYNRAEVPSDYDI 76
P++Y + N +
Sbjct: 134 PMIYTTADWWNRCTGNAKGFGDKCPL 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 0.137 0.420
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,469,266
Number of extensions: 71657
Number of successful extensions: 125
Number of sequences better than 10.0: 1
Number of HSP's gapped: 125
Number of HSP's successfully gapped: 50
Length of query: 95
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 33
Effective length of database: 4,970,691
Effective search space: 164032803
Effective search space used: 164032803
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 (21.7 bits)
S2: 51 (23.2 bits)