RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032641
(136 letters)
>2xzm_L 40S ribosomal protein S12; ribosome, translation; 3.93A
{Tetrahymena thermophila} PDB: 2xzn_L 3j0o_L 3j0l_L
3j0p_L 3j0q_L 3iz6_L 3jyv_L* 1s1h_L*
Length = 142
Score = 145 bits (368), Expect = 2e-46
Identities = 96/133 (72%), Positives = 110/133 (82%)
Query: 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIR 60
+ AGRKL HR+ QRWAD + K LG+ W+ PF G+SHAKG+V EKIGIE+KQPNSA+R
Sbjct: 9 IRAGRKLARHRKDQRWADNDFNKRLLGSRWRNPFMGASHAKGLVTEKIGIESKQPNSAVR 68
Query: 61 KCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSG 120
KC RV L KN KKIAAFVP DGCLN++ ENDEVL+AG GR+GHAVGDIPGVRFKVV V G
Sbjct: 69 KCVRVLLRKNSKKIAAFVPMDGCLNFLAENDEVLVAGLGRQGHAVGDIPGVRFKVVCVKG 128
Query: 121 VSLLALFKEKKEK 133
+SLLALFK KKEK
Sbjct: 129 ISLLALFKGKKEK 141
>3u5c_X RP37, S28, YS14, 40S ribosomal protein S23-A; translation,
ribosome, ribosomal, ribosomal R ribosomal protein,
eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces
cerevisiae} PDB: 3izb_L 3o30_P 3o2z_P 3u5g_X 3jyv_L*
1s1h_L* 2zkq_l 3iz6_L
Length = 145
Score = 140 bits (354), Expect = 3e-44
Identities = 105/137 (76%), Positives = 119/137 (86%), Gaps = 1/137 (0%)
Query: 1 MGAGRKLKSHRRRQRWADKSYKKSHLGNEWKKP-FAGSSHAKGIVLEKIGIEAKQPNSAI 59
+ + RKL+ HRR RWA+ +YKK LG +K F GSSHAKGIVLEK+GIE+KQPNSAI
Sbjct: 9 LNSARKLRVHRRNNRWAENNYKKRLLGTAFKSSPFGGSSHAKGIVLEKLGIESKQPNSAI 68
Query: 60 RKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVS 119
RKC RVQLIKNGKK+ AFVPNDGCLN+++ENDEVL+AGFGRKG A GDIPGVRFKVVKVS
Sbjct: 69 RKCVRVQLIKNGKKVTAFVPNDGCLNFVDENDEVLLAGFGRKGKAKGDIPGVRFKVVKVS 128
Query: 120 GVSLLALFKEKKEKPRS 136
GVSLLAL+KEKKEKPRS
Sbjct: 129 GVSLLALWKEKKEKPRS 145
>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1
PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L*
1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O*
1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ...
Length = 135
Score = 48.1 bits (114), Expect = 3e-08
Identities = 38/130 (29%), Positives = 67/130 (51%), Gaps = 22/130 (16%)
Query: 7 LKSHRRRQRWADKSYKKSHLGNEWKKPFAGSSHAKGIVLEKIGIEAKQPNSAIRKCARVQ 66
++ R + R K G+ +G+ + K+PNSA+RK A+V+
Sbjct: 11 VRKGREKVRKKSKVP-----------ALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVR 59
Query: 67 LIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKGHAVGDIPGVRFKVVKVSGVSLLAL 126
L +G ++ A++P +G + ++E+ VLI +G V D+PGVR+ +V+ GV A
Sbjct: 60 L-TSGYEVTAYIPGEG--HNLQEHSVVLI-----RGGRVKDLPGVRYHIVR--GVYDAAG 109
Query: 127 FKEKKEKPRS 136
K++K+ RS
Sbjct: 110 VKDRKKS-RS 118
>3l9w_A Glutathione-regulated potassium-efflux system Pro linker, ancillary
protein KEFF; potassium channel regulation, domains,
antiport; HET: FMN AMP GSH; 1.75A {Escherichia coli}
PDB: 3eyw_A* 3l9x_A*
Length = 413
Score = 31.3 bits (71), Expect = 0.075
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 88 EENDEVLIAGFGRKGHAVGDI 108
V+IAGFGR G G +
Sbjct: 2 SHGMRVIIAGFGRFGQITGRL 22
>1k4m_A NAMN adenylyltransferase; nucleotidyltransferase; HET: NAD CIT;
1.90A {Escherichia coli} SCOP: c.26.1.3 PDB: 1k4k_A*
Length = 213
Score = 30.7 bits (70), Expect = 0.11
Identities = 8/34 (23%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
+ IR + ++NG+ +P + L YI +
Sbjct: 182 TIIR-----ERLQNGESCEDLLP-EPVLTYINQQ 209
>1yum_A 'probable nicotinate-nucleotide adenylyltransferase; alpha/beta
domain; HET: CIT NCN; 1.70A {Pseudomonas aeruginosa}
PDB: 1yul_A* 1yun_A*
Length = 242
Score = 30.4 bits (69), Expect = 0.13
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
+ IR L+ G+ + VP D LNYIE +
Sbjct: 200 TQIR-----ALLGAGRSVRFLVP-DAVLNYIEAH 227
>2qtr_A Nicotinate (nicotinamide) nucleotide adenylyltran; NAD,
nucleotidyltransferase, pyridine nucleotide biosynthesi
transferase; HET: NXX; 1.70A {Bacillus anthracis} PDB:
3dv2_A 3mla_A* 3hfj_A* 3mlb_A* 3mmx_A* 3e27_A* 2qtn_A*
2qtm_A*
Length = 189
Score = 30.2 bits (69), Expect = 0.16
Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
S +R + K K +P + YIE N
Sbjct: 157 SLLR-----ERYKEKKTCKYLLP-EKVQVYIERN 184
>1kam_A Deamido-NAD(+), nicotinate-nucleotide adenylyltransferase; rossman
fold; 2.10A {Bacillus subtilis} SCOP: c.26.1.3 PDB:
1kaq_A*
Length = 194
Score = 29.8 bits (68), Expect = 0.17
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
+ IR + K+ K +P D Y+EEN
Sbjct: 162 TMIR-----ERFKSKKPTDYLIP-DKVKKYVEEN 189
>2h29_A Probable nicotinate-nucleotide adenylyltransferase; NADD, namnat,
nmnat; HET: DND; 2.00A {Staphylococcus aureus} PDB:
2h2a_A*
Length = 189
Score = 29.8 bits (68), Expect = 0.18
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
+ IR Q + GK I VP NYI+
Sbjct: 157 TMIR-----QRVSEGKSIQVLVP-KSVENYIKGE 184
>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 = 30.4 bits (68), Expect = 0.19
Identities = 29/176 (16%), Positives = 48/176 (27%), Gaps = 91/176 (51%)
Query: 29 EWKKPFAGSS-HAKGIV------------------------LEKIGIEAKQ--PNS---- 57
E + G++ H++G+V L IG+ + PN+
Sbjct: 262 ELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321
Query: 58 ------------------AIRKCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGF- 98
+I + Q+ K + +P +V I+
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLP---------AGKQVEISLVN 372
Query: 99 GRKGHAVGDIPGVRFKVVKVSG--VSL----LALFKEK-------------KEKPR 135
G K + V VSG SL L L K K + K +
Sbjct: 373 GAK-NLV------------VSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLK 415
Score = 28.5 bits (63), Expect = 0.72
Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 16/94 (17%)
Query: 49 GIEAKQPNSAIRKCARVQLIKNGKKIAAFVPNDGCL----NYIEENDEVLIAGFGRKGHA 104
G+ A P ++ L +++ G L NY EN + + AG A
Sbjct: 1808 GMIAINPGRVAASFSQEALQYVVERVGK---RTGWLVEIVNYNVENQQYVAAG---DLRA 1861
Query: 105 VGDIPGVRFKVVKVSGVSLLAL-----FKEKKEK 133
+ D +K+ + ++ L +E +
Sbjct: 1862 L-DTVTNVLNFIKLQKIDIIELQKSLSLEEVEGH 1894
>3fwz_A Inner membrane protein YBAL; TRKA-N domain, E.coli, structural
genomics, PSI-2, Pro structure initiative; HET: MSE AMP;
1.79A {Escherichia coli k-12}
Length = 140
Score = 29.0 bits (66), Expect = 0.25
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 85 NYIEENDEVLIAGFGRKGHAVGDI 108
N ++ + L+ G+GR G +G+
Sbjct: 2 NAVDICNHALLVGYGRVGSLLGEK 25
>3h05_A Uncharacterized protein VPA0413; nucleotidylyl, transferase, MCSG,
midwest center for structu genomics, PSI; 1.65A {Vibrio
parahaemolyticus}
Length = 177
Score = 29.1 bits (66), Expect = 0.36
Identities = 5/34 (14%), Positives = 10/34 (29%), Gaps = 6/34 (17%)
Query: 57 SAIRKCARVQLIKNGKKIAAFVPNDGCLNYIEEN 90
+ IR + GK I+ + +
Sbjct: 140 TDIR-----NALIEGKDISTYTT-PTVSELLLNE 167
>1r9d_A Glycerol dehydratase; radical SAM, lyase; 1.80A {Clostridium
butyricum} SCOP: c.7.1.1 PDB: 1r8w_A 1r9e_A
Length = 787
Score = 28.4 bits (63), Expect = 0.88
Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 24/65 (36%)
Query: 54 QPNSAIR-----------KCARVQLIKNGKKIAAFVPNDGCLNYIEENDEVLIAGFGRKG 102
QP+ ++R + A + + G + A+ NDEV+I +G
Sbjct: 373 QPSLSVRIWNKTPDEFLLRAAEL--TREGLGLPAY-----------YNDEVIIPALVSRG 419
Query: 103 HAVGD 107
+ D
Sbjct: 420 LTLED 424
>3c85_A Putative glutathione-regulated potassium-efflux S protein KEFB;
TRKA domain; HET: AMP; 1.90A {Vibrio parahaemolyticus
rimd 2210633}
Length = 183
Score = 27.8 bits (62), Expect = 1.1
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 88 EENDEVLIAGFGRKGHAVGD 107
+ +VLI G GR G D
Sbjct: 37 PGHAQVLILGMGRIGTGAYD 56
>3og2_A Beta-galactosidase; TIM barrel domain, glycoside hydrolase, family
35, glycoprot hydrolase; HET: NAG BMA MAN GLC; 1.20A
{Trichoderma reesei} PDB: 3ogr_A* 3ogs_A* 3ogv_A*
Length = 1003
Score = 26.3 bits (57), Expect = 4.8
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 10/53 (18%)
Query: 48 IGIEAKQPNSAIRKCARVQLIKNGKKIAAFVPN----------DGCLNYIEEN 90
I + N+ R L NG + +V N +G L+Y +N
Sbjct: 902 IPLSFVFDNATAAAPYRALLYVNGFQYGKYVSNIGPQTEFPVPEGILDYNGDN 954
>3a8u_X Omega-amino acid--pyruvate aminotransferase; large pleated sheet,
transaminase, pyridox phosphate; HET: PLP; 1.40A
{Pseudomonas putida}
Length = 449
Score = 26.0 bits (58), Expect = 5.3
Identities = 18/56 (32%), Positives = 19/56 (33%), Gaps = 23/56 (41%)
Query: 73 KIAAF------------VPNDGCLNYIEE----------NDEVLIAGFGRKGHAVG 106
IAA VP +G L E DEV I GFGR G G
Sbjct: 219 NIAAVFVEPLAGSAGVLVPPEGYLKRNREICNQHNILLVFDEV-ITGFGRTGSMFG 273
>3i5t_A Aminotransferase; pyridoxal 5'-phosphate, PSI-2, NYSGXRC, ST
genomics, protein structure initiative; HET: PLP; 2.00A
{Rhodobacter sphaeroides 2}
Length = 476
Score = 25.7 bits (57), Expect = 5.7
Identities = 8/16 (50%), Positives = 9/16 (56%), Gaps = 1/16 (6%)
Query: 91 DEVLIAGFGRKGHAVG 106
DEV + GFGR G
Sbjct: 261 DEV-VTGFGRCGEWFA 275
>3hmu_A Aminotransferase, class III; structural genomics, pyridoxal
phosphate, PSI-2, protein structure initiative; 2.10A
{Silicibacter pomeroyi}
Length = 472
Score = 25.7 bits (57), Expect = 5.8
Identities = 10/16 (62%), Positives = 11/16 (68%), Gaps = 1/16 (6%)
Query: 91 DEVLIAGFGRKGHAVG 106
DEV I GFGR G+ G
Sbjct: 263 DEV-ICGFGRTGNWFG 277
>4a6r_A Omega transaminase; transferase, PLP-binding enzyme, transaminase
fold type I; HET: TA8; 1.35A {Chromobacterium violaceum}
PDB: 4a6t_A* 4a6u_A 4a72_A* 4ah3_A*
Length = 459
Score = 25.6 bits (57), Expect = 7.1
Identities = 10/16 (62%), Positives = 10/16 (62%), Gaps = 1/16 (6%)
Query: 91 DEVLIAGFGRKGHAVG 106
DEV I GFGR G G
Sbjct: 259 DEV-ICGFGRTGEWFG 273
>3nui_A Pyruvate transaminase; amino transferase, transferase; 2.00A
{Vibrio fluvialis}
Length = 478
Score = 25.2 bits (56), Expect = 7.8
Identities = 15/53 (28%), Positives = 17/53 (32%), Gaps = 23/53 (43%)
Query: 73 KIAAF------------VPNDGCLNYIEE----------NDEVLIAGFGRKGH 103
IA F P G I +DEV I GFGR G+
Sbjct: 230 TIAGFFAEPVMGAGGVIPPAKGYFQAILPILRKYDIPVISDEV-ICGFGRTGN 281
>1e8c_A UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- diaminopimelate
ligase; peptidoglycan biosynthesis; HET: KCX UAG API;
2.00A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1
c.72.2.1
Length = 498
Score = 25.2 bits (56), Expect = 8.9
Identities = 10/16 (62%), Positives = 12/16 (75%), Gaps = 3/16 (18%)
Query: 88 EENDEVLIAGFGRKGH 103
+END VL+AG KGH
Sbjct: 455 KENDVVLVAG---KGH 467
>1wty_A Hypothetical protein TTHA0048; structural genomics, riken
structural genomics/proteomics in RSGI, unknown
function; 2.20A {Thermus thermophilus} SCOP: a.24.16.2
PDB: 2ywa_A
Length = 119
Score = 24.6 bits (53), Expect = 9.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 44 VLEKIGIEAKQPNSAIRKCARVQLIKNG 71
LE G+EA+ P +AIR +V L+
Sbjct: 45 FLELQGLEARSPRAAIRGAFQVGLLPED 72
>3gju_A Putative aminotransferase; pyridoxal phosphate, PLP-dependent
transferase-like fold, ST genomics, joint center for
structural genomics, JCSG; HET: MSE LLP PLP; 1.55A
{Mesorhizobium loti} PDB: 3fcr_A*
Length = 460
Score = 25.3 bits (56), Expect = 9.4
Identities = 9/16 (56%), Positives = 10/16 (62%), Gaps = 1/16 (6%)
Query: 91 DEVLIAGFGRKGHAVG 106
DEV + GFGR G G
Sbjct: 261 DEV-VTGFGRLGTMFG 275
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
0.317 0.135 0.400
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,132,255
Number of extensions: 120244
Number of successful extensions: 274
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 30
Length of query: 136
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 52
Effective length of database: 4,356,429
Effective search space: 226534308
Effective search space used: 226534308
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: 52 (23.7 bits)