RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033652
(114 letters)
>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U*
1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0
2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 3pio_T* 3pip_T*
1pnu_U 1pny_U 1vor_X 1vou_X ...
Length = 91
Score = 139 bits (352), Expect = 9e-45
Identities = 51/88 (57%), Positives = 63/88 (71%), Gaps = 1/88 (1%)
Query: 6 ATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYA 65
A KK GS+KNGRDS PK LGVKKFGGE V GNI+VRQRGT+F G VGMG+DHTL+A
Sbjct: 2 AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFA 61
Query: 66 LKEGRVKFEKHKLSGRKWVHVEPKEGHV 93
L +G+V F K G +++ +E + V
Sbjct: 62 LSDGKVVFIN-KGKGARFISIEAAQTEV 88
>3bbo_X Ribosomal protein L27; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
Length = 198
Score = 142 bits (360), Expect = 9e-45
Identities = 52/101 (51%), Positives = 65/101 (64%), Gaps = 1/101 (0%)
Query: 1 MFRRWATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKD 60
+ A KK AGSTKNGRDS + LGVK +G + PG IIVRQRGT+FH G VG+GKD
Sbjct: 54 LTIESAHKKGAGSTKNGRDSPGQRLGVKIYGDQVAKPGAIIVRQRGTKFHAGKNVGIGKD 113
Query: 61 HTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHVLHPLYANA 101
HT+++L +G VKFEK RK + V P+E +P A
Sbjct: 114 HTIFSLIDGLVKFEK-FGPDRKKISVYPREIVPENPNSYRA 153
>3v2d_0 50S ribosomal protein L27; ribosome associated inhibitor A, RAIA,
protein Y, stress RES stationary phase, ribosome
hibernation, ribosome; 2.70A {Thermus thermophilus}
PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0
2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0
2wro_0 2wrr_0 2x9s_0 2x9u_0 2xg0_0 ...
Length = 85
Score = 134 bits (339), Expect = 7e-43
Identities = 47/83 (56%), Positives = 61/83 (73%), Gaps = 1/83 (1%)
Query: 6 ATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYA 65
A KK GST+NGRDS+ K LGVK++ G+ V GNI+VRQRGTRF PG VGMG+D TL+A
Sbjct: 2 AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFA 61
Query: 66 LKEGRVKFEKHKLSGRKWVHVEP 88
L +G V+F+ + ++VHV P
Sbjct: 62 LVDGVVEFQD-RGRLGRYVHVRP 83
>3r8s_W 50S ribosomal protein L27; protein biosynthesis, RNA, tRNA,
transfer RNA, 23S ribosomal subunit, ribosome recycling
factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
2qam_W* 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W
2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W
2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W 2qoz_W* ...
Length = 76
Score = 132 bits (334), Expect = 3e-42
Identities = 44/76 (57%), Positives = 58/76 (76%)
Query: 14 TKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKF 73
T+NGRDS+ K LGVK+FGGE V+ G+IIVRQRGT+FH G VG G+DHTL+A +G+VKF
Sbjct: 1 TRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKF 60
Query: 74 EKHKLSGRKWVHVEPK 89
E RK++ +E +
Sbjct: 61 EVKGPKNRKFISIEAE 76
>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27;
mitochondrial ribosome, large ribosomal subunit,
ribosomal R ribosome; 12.10A {Bos taurus} PDB: 3iy9_O
Length = 69
Score = 121 bits (305), Expect = 7e-38
Identities = 35/69 (50%), Positives = 47/69 (68%), Gaps = 1/69 (1%)
Query: 6 ATKKTAGSTKN-GRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLY 64
A+KK+ GS+KN G S + G+KK G V GNII QR R+HPG +VG+GK+ LY
Sbjct: 1 ASKKSGGSSKNLGGKSSGRRQGIKKMEGHYVHAGNIIATQRHFRWHPGAHVGVGKNKCLY 60
Query: 65 ALKEGRVKF 73
AL+EG V++
Sbjct: 61 ALEEGIVRY 69
>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 = 0.002
Identities = 20/89 (22%), Positives = 33/89 (37%), Gaps = 22/89 (24%)
Query: 41 IVRQRGTRFH---PGDYVGMGKDHTLYALKEGRV--KFEKHKLSGRKWV-HVEPKEGHVL 94
+V RG P D +G ++ + A+ GRV F + L + V V + G ++
Sbjct: 1785 VVFYRGMTMQVAVPRDELGRS-NYGMIAINPGRVAASFSQEAL--QYVVERVGKRTGWLV 1841
Query: 95 HPLYANATANASSPQ---------LETAA 114
N N + Q L+T
Sbjct: 1842 EI--VN--YNVENQQYVAAGDLRALDTVT 1866
Score = 29.2 bits (65), Expect = 0.27
Identities = 6/12 (50%), Positives = 6/12 (50%), Gaps = 2/12 (16%)
Query: 54 YVGMGKDHTLYA 65
GMG D LY
Sbjct: 1628 EQGMGMD--LYK 1637
Score = 26.6 bits (58), Expect = 2.2
Identities = 16/74 (21%), Positives = 23/74 (31%), Gaps = 27/74 (36%)
Query: 13 STKNGRDSKPKNLGVKKFGGERVIPGNI---IVRQR----------GTR---FHPGDYVG 56
T +G D ++ G I I I+R T F PG G
Sbjct: 461 DTFDGSD-------LRVLSGS--ISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASG 511
Query: 57 MGKDHTLYALKEGR 70
+G + K+G
Sbjct: 512 LGV--LTHRNKDGT 523
>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity,
CRP, CLP, C-DI-GMP receptor, quorum SENS binding,
transcription; 2.30A {Xanthomonas campestris PV}
Length = 230
Score = 30.0 bits (68), Expect = 0.13
Identities = 11/39 (28%), Positives = 13/39 (33%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
T F PGD TLY + G V + R
Sbjct: 40 PTRTDVFRPGD-----PAGTLYYVISGSVSIIAEEDDDR 73
>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary
phase, DNA-binding, transcription regulation; 1.50A
{Thermus thermophilus}
Length = 202
Score = 29.9 bits (68), Expect = 0.13
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 4/39 (10%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+ G +PG G Y + EG V+ E G
Sbjct: 11 KAGDVILYPGVP---GPRDRAYRVLEGLVRLEAVDEEGN 46
>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE
JCSG, PSI, protein structure initiative, joint center
for S genomics; 2.30A {Thermotoga maritima} SCOP:
b.82.3.2
Length = 213
Score = 29.5 bits (67), Expect = 0.18
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
H D + + L EG +K E +G+
Sbjct: 34 KHQDDPI-----EDVLILLEGTLKTEHVSENGK 61
>4ev0_A Transcription regulator, CRP family; CAMP binding, winged
helix-turn-helix motif, DNA binding, transcription
activator; HET: CMP; 2.40A {Thermus thermophilus}
Length = 216
Score = 29.1 bits (66), Expect = 0.20
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+G F+ GD LY + G+V+ + L G+
Sbjct: 28 PQGKPIFYQGD-----LGQALYLVASGKVRLFRTHLGGQ 61
>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription,
transcription regulation; HET: BOG; 1.90A {Anabaena}
PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*
Length = 243
Score = 29.2 bits (66), Expect = 0.22
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+R F PGD +Y L +G VK + +G
Sbjct: 49 ERNKTIFFPGD-----PAERVYFLLKGAVKLSRVYEAGE 82
>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics,
porphyromona gingivalis, PSI, protein structure
initiative; 1.90A {Porphyromonas gingivalis} SCOP:
a.4.5.4 b.82.3.2
Length = 232
Score = 29.1 bits (66), Expect = 0.24
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
++ + F GD + L+ L EG++K + + GR
Sbjct: 39 KKASTVFSEGD-----IPNNLFYLYEGKIKILREGVYGR 72
>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP),
dimer, inactive(APO, unliganded allostery, DNA binding,
cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB:
3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*
Length = 227
Score = 28.7 bits (65), Expect = 0.28
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
RG F G+ LY + G+VK + GR
Sbjct: 35 PRGHTVFAEGE-----PGDRLYIIISGKVKIGRRAPDGR 68
>3b02_A Transcriptional regulator, CRP family; structural genomics, riken
structural genomics/proteomics in RSGI; 1.92A {Thermus
thermophilus} PDB: 2zdb_A
Length = 195
Score = 28.7 bits (65), Expect = 0.29
Identities = 10/33 (30%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+ G+ + TLY L+EG V+ + GR
Sbjct: 11 YLRGE-----EARTLYRLEEGLVRVVELLPDGR 38
>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration;
HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense}
SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A
3e5x_A* 3e5q_A 2h6b_A* 2h6c_A
Length = 250
Score = 28.8 bits (65), Expect = 0.30
Identities = 7/33 (21%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
PG+ + ++ L EG++K + G
Sbjct: 44 IMPGE-----EITSMIFLVEGKIKLDIIFEDGS 71
>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional
regulat transcription; HET: PR3; 2.3A {Listeria
monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A*
1omi_A
Length = 238
Score = 28.9 bits (65), Expect = 0.31
Identities = 6/33 (18%), Positives = 9/33 (27%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
F+ D L +G K +G
Sbjct: 30 FNQWD-----PQEYCIFLYDGITKLTSISENGT 57
>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural
genomics, joint center for structura genomics, JCSG;
2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4
b.82.3.2
Length = 232
Score = 28.8 bits (65), Expect = 0.31
Identities = 4/33 (12%), Positives = 8/33 (24%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
G+ L L +G + +
Sbjct: 55 IKSGNPC-----TQLCFLLKGEISIVTNAKENI 82
>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix,
homodimer, transcription regulator; 3.60A {Pseudomonas
aeruginosa}
Length = 227
Score = 28.8 bits (65), Expect = 0.32
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+G F G+ H Y L G VK + G+
Sbjct: 38 DKGAYVFRQGE-----PAHAFYYLISGCVKIYRLTPEGQ 71
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 28.7 bits (65), Expect = 0.33
Identities = 8/39 (20%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
+ + GD + TL+ + +G V GR
Sbjct: 19 TAKSTIIYAGD-----RCETLFFIIKGSVTILIEDDDGR 52
>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP),
allostery, DNA binding cyclic A transcription
regulator; HET: CMP; 1.60A {Escherichia coli} PDB:
2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A*
1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A
3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...
Length = 210
Score = 28.4 bits (64), Expect = 0.37
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
H G+ K TLY + +G V G+
Sbjct: 31 IHQGE-----KAETLYYIVKGSVAVLIKDEEGK 58
>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1,
structural genomics, joint center for structural
genomics, JCSG; HET: MSE; 1.86A {Deinococcus
geothermalis dsm 11300}
Length = 231
Score = 28.4 bits (64), Expect = 0.43
Identities = 7/39 (17%), Positives = 12/39 (30%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
Q + L+ + G V+ + L GR
Sbjct: 35 QPDELVVEQDA-----EGEALHLVTTGVVRVSRVSLGGR 68
>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding,
DNA-binding nucleotide-binding, transcription,
transcription regulation; HET: CMP; 1.66A {Escherichia
coli}
Length = 260
Score = 27.7 bits (62), Expect = 0.66
Identities = 9/33 (27%), Positives = 13/33 (39%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
H G+ K TLY + +G V G+
Sbjct: 81 IHQGE-----KAETLYYIVKGSVAVLIKDEEGK 108
>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP
regulatory protein, structural genomi 2, protein
structure initiative; 2.20A {Ruegeria pomeroyi} PDB:
3h3z_A*
Length = 237
Score = 28.0 bits (63), Expect = 0.67
Identities = 8/39 (20%), Positives = 15/39 (38%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
RG F + K ++ + +G VK + +G
Sbjct: 40 DRGETLFLQEE-----KAQAIHVVIDGWVKLFRMTPTGS 73
>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 = 27.6 bits (60), Expect = 0.76
Identities = 12/45 (26%), Positives = 14/45 (31%), Gaps = 22/45 (48%)
Query: 74 EKH---KLSGR-KWVHVEPKEGHVLHPLYANATANASSPQLETAA 114
EK KL K LYA+ +A P L A
Sbjct: 18 EKQALKKLQASLK--------------LYADDSA----PALAIKA 44
>2yyo_A SPRY domain-containing protein 3; NPPSFA, national project on
protein structural and functional analyses; 2.00A {Homo
sapiens}
Length = 171
Score = 27.6 bits (61), Expect = 0.80
Identities = 13/71 (18%), Positives = 30/71 (42%), Gaps = 3/71 (4%)
Query: 5 WATKKTAGSTKNGRDSKPKNLGVKKFGGERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLY 64
+ + + G P ++ G ++ G RQ G++ + GD +G G + +
Sbjct: 60 LVPQYYSLDHQPGWL--PDSVAYHADDG-KLYNGRAKGRQFGSKCNSGDRIGCGIEPVSF 116
Query: 65 ALKEGRVKFEK 75
++ ++ F K
Sbjct: 117 DVQTAQIFFTK 127
>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic
nucleotide-binding domain, structural genomics, joint
for structural genomics; 2.55A {Eubacterium rectale
atcc 33656}
Length = 220
Score = 27.2 bits (61), Expect = 0.92
Identities = 7/39 (17%), Positives = 14/39 (35%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
++GT + L +K G+++ GR
Sbjct: 32 KKGTIIHNGNM-----DCTGLLLVKSGQLRTYILSDEGR 65
>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1;
DNA transcription regulator, DNA binding protein; HET:
HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB:
2hkx_A*
Length = 220
Score = 27.2 bits (61), Expect = 1.1
Identities = 5/30 (16%), Positives = 13/30 (43%), Gaps = 6/30 (20%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVK 72
+ + P + + ++ +K GRV+
Sbjct: 33 SKKAILYTPNT-----ERNLVFLVKSGRVR 57
>2z69_A DNR protein; beta barrel, dimerization helix, transcription
regulator; 2.10A {Pseudomonas aeruginosa}
Length = 154
Score = 26.9 bits (60), Expect = 1.3
Identities = 9/33 (27%), Positives = 12/33 (36%), Gaps = 5/33 (15%)
Query: 49 FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
F G+ H Y L G VK + G+
Sbjct: 47 FRQGE-----PAHAFYYLISGCVKIYRLTPEGQ 74
>2pqq_A Putative transcriptional regulator; APC7345, streptomyces
coelicolor structural genomics, PSI-2, protein
structure initiative; 2.00A {Streptomyces coelicolor
A3}
Length = 149
Score = 26.5 bits (59), Expect = 1.5
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
RG FH GD LY + EG+VK + GR
Sbjct: 34 ARGDTLFHEGD-----PGDRLYVVTEGKVKLHRTSPDGR 67
>1q5x_A Regulator of RNAse E activity A; 3-layer sandwich, alpha-beta
structure, parallel beta sheet, antiparallel beta sheet,
hydrolase inhibitor; 2.00A {Escherichia coli} SCOP:
c.8.7.1
Length = 161
Score = 26.5 bits (59), Expect = 1.7
Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
+ GE ++ V G F GD++
Sbjct: 119 AAGEGIGES----DVRVNFGGVTFFSGDHL 144
>2pcn_A S-adenosylmethionine:2-demethylmenaquinone methyltransferase; beta,
beta alpha domain; 1.90A {Geobacillus kaustophilus}
Length = 161
Score = 25.6 bits (57), Expect = 3.0
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
K+ G R ++++ G R+ PG YV
Sbjct: 117 SKKEGKGAR----DVVLEFGGVRWEPGAYV 142
>1nxj_A Probable S-adenosylmethionine:2- demethylmenaquinone
methyltransferase; beta/BETA/alpha domain, structural
genomics, PSI; HET: TLA; 1.90A {Mycobacterium
tuberculosis} SCOP: c.8.7.1
Length = 183
Score = 25.7 bits (57), Expect = 3.8
Identities = 9/30 (30%), Positives = 12/30 (40%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
K GER ++ + G F PGD
Sbjct: 148 STKTGAGER----DVEITLGGVTFVPGDIA 173
>1ft9_A Carbon monoxide oxidation system transcription regulator; heme
sensor, catabolite gene activator protein; HET: HEM;
2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1
Length = 222
Score = 25.7 bits (57), Expect = 3.9
Identities = 3/30 (10%), Positives = 13/30 (43%), Gaps = 6/30 (20%)
Query: 44 QRGTR-FHPGDYVGMGKDHTLYALKEGRVK 72
+G+ ++ ++ + +GR++
Sbjct: 29 AKGSLVCTGEG-----DENGVFVVVDGRLR 53
>1j3l_A Demethylmenaquinone methyltransferase; vitamine K2, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; 2.30A {Thermus thermophilus} SCOP:
c.8.7.1
Length = 164
Score = 25.2 bits (56), Expect = 4.0
Identities = 6/30 (20%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
K+ GE ++ ++ G PG ++
Sbjct: 118 SAKEGKGEV----DVPLKVLGVEVLPGSFL 143
>1vi4_A Regulator of ribonuclease acivity A protein 1; structural genomics,
unknown function; 1.87A {Vibrio cholerae} SCOP: c.8.7.1
Length = 174
Score = 25.3 bits (56), Expect = 4.1
Identities = 7/30 (23%), Positives = 13/30 (43%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
K+ G+ N+ + + PGDY+
Sbjct: 122 TEKRGAGQV----NVTLTMQNQIVEPGDYL 147
>3qcw_A Neurexin-1-alpha; synaptic adhesion molecule, cell adhesion; HET:
NAG; 2.65A {Bos taurus} PDB: 3r05_A* 3poy_A*
Length = 1245
Score = 26.0 bits (56), Expect = 4.1
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 54 YVGMGKDHTLYALKEGRVKFEKHKLSGRKWVHVEPKEGHV 93
+ G D+ ALK G V + SG VEP G
Sbjct: 273 HTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNGKF 312
>3c8o_A Regulator of ribonuclease activity A; RRAA, PAO1, RNAse E
regulater, hydrolase regulator; HET: PGE PG4; 1.90A
{Pseudomonas aeruginosa}
Length = 162
Score = 25.2 bits (56), Expect = 5.0
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 26 GVKKFGGERVIPGNIIVRQRGTRFHPGDYV 55
K+ G+ N+ V G F PG++V
Sbjct: 119 TDKRGIGDL----NVAVTFGGVTFRPGEFV 144
>3gyd_A CNMP-BD protein, cyclic nucleotide-binding domain; nucleotide
binding protein, structural genomics; HET: MSE CMP;
1.79A {Methylobacillus flagellatus KT}
Length = 187
Score = 24.7 bits (54), Expect = 7.3
Identities = 6/49 (12%), Positives = 11/49 (22%), Gaps = 12/49 (24%)
Query: 33 ERVIPGNIIVRQRGTRFHPGDYVGMGKDHTLYALKEGRVKFEKHKLSGR 81
++ + GD L + G V K +
Sbjct: 65 YAAPRDCQLLTE-------GD-----PGDYLLLILTGEVNVIKDIPNKG 101
>3ezo_A Malonyl COA-acyl carrier protein transacylase; ssgcid,
acyl-carrier-protein S-malonyltransferase,
acyltransferase, transferase; 2.05A {Burkholderia
pseudomallei 1710B}
Length = 318
Score = 24.8 bits (55), Expect = 7.7
Identities = 4/22 (18%), Positives = 7/22 (31%), Gaps = 2/22 (9%)
Query: 54 YVGMGKDHTLYALKEGRVKFEK 75
VGM + R ++
Sbjct: 22 SVGMLNA--FADVAVVRETLDE 41
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xct_B* 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 24.6 bits (54), Expect = 8.9
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 11 AGSTKNGRDSKP--------KNLGVKKFGGERVIPGNIIVRQRGTRFHPG 52
GSTK+GRDS+ K L V+K +R++ N I RQ T F G
Sbjct: 32 GGSTKSGRDSRTQAILPLRGKILNVEKARLDRILNNNEI-RQMITAFGTG 80
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
0.316 0.134 0.408
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,776,585
Number of extensions: 99130
Number of successful extensions: 260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 257
Number of HSP's successfully gapped: 54
Length of query: 114
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 37
Effective length of database: 4,551,876
Effective search space: 168419412
Effective search space used: 168419412
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.3 bits)