RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780470|ref|YP_003064883.1| translation initiation factor
IF-1 [Candidatus Liberibacter asiaticus str. psy62]
(110 letters)
>3i4o_A Translation initiation factor IF-1; cytoplasm, protein
biosynthesis; 1.47A {Mycobacterium tuberculosis}
Length = 79
Score = 85.1 bits (211), Expect = 3e-18
Identities = 34/111 (30%), Positives = 51/111 (45%), Gaps = 39/111 (35%)
Query: 1 MPKEE-TLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGV 59
M K++ +E G V E LPNA FR++L
Sbjct: 7 MAKKDGAIEVEGRVVEPLPNAMFRIEL--------------------------------- 33
Query: 60 DPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
+ V+A+ +G+MR+H IRI D+V V ++PYD++R RI YR+K
Sbjct: 34 -----ENGHKVLAHISGKMRQHYIRILPEDRVVVELSPYDLSRGRIVYRYK 79
>1hr0_W Translation initiation factor; ribosomal subunit, ribosome, IF1;
3.20A {Escherichia coli} SCOP: b.40.4.5 PDB: 1zo1_W
Length = 71
Score = 79.7 bits (197), Expect = 2e-16
Identities = 35/106 (33%), Positives = 47/106 (44%), Gaps = 38/106 (35%)
Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62
+++T+ G+V+E LPNA FRVKL
Sbjct: 3 EKDTIRTEGVVTEALPNATFRVKL------------------------------------ 26
Query: 63 SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYR 108
++AY +G+MR H IRI GD+V V + PYD TR RI YR
Sbjct: 27 --DSGPEILAYISGKMRMHYIRILPGDRVVVEITPYDPTRGRIVYR 70
>1ah9_A IF1, initiation factor 1; ribosome binding, protein-RNA
interaction, OB fold; NMR {Escherichia coli} SCOP:
b.40.4.5
Length = 71
Score = 79.0 bits (195), Expect = 2e-16
Identities = 34/108 (31%), Positives = 48/108 (44%), Gaps = 38/108 (35%)
Query: 3 KEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVDPI 62
KE+ +E G V E LPN FRV+L
Sbjct: 2 KEDNIEMQGTVLETLPNTMFRVELE----------------------------------- 26
Query: 63 SYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
+ VV A+ +G+MRK+ IRI GDKV V + PYD+++ RI +R +
Sbjct: 27 ---NGHVVTAHISGKMRKNYIRILTGDKVTVELTPYDLSKGRIVFRSR 71
>1jt8_A EIF-1A, probable translation initiation factor 1A; beta barrel,
translation factor; NMR {Methanocaldococcus jannaschii}
SCOP: b.40.4.5
Length = 102
Score = 55.8 bits (135), Expect = 2e-09
Identities = 19/110 (17%), Positives = 35/110 (31%), Gaps = 40/110 (36%)
Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
+P++E E GI+ ++L + RV+ +
Sbjct: 14 IPRKEENEILGIIEQMLGASRVRVRCL--------------------------------- 40
Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDM-TRARITYRF 109
D + GR++ RI + GD V V + I +R+
Sbjct: 41 -----DGKTRLGRIPGRLKN-RIWVREGDVVIVKPWEVQGDQKCDIIWRY 84
>2oqk_A Putative translation initiation factor EIF-1A; malaria, eukaryotic
initiation factor (EIF), SGC, structural genomics; 1.80A
{Cryptosporidium parvum iowa II}
Length = 117
Score = 48.6 bits (116), Expect = 3e-07
Identities = 14/110 (12%), Positives = 32/110 (29%), Gaps = 39/110 (35%)
Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
+ +E + G V +L N
Sbjct: 26 LVFKEEGQEYGQVQRMLGNGRLDAYCFDGQ------------------------------ 55
Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRFK 110
+ + G+MRK ++ ++ GD V V++ + ++ I ++
Sbjct: 56 --------KRLCHIRGKMRK-KVWVNPGDIVLVSLRDFQDSKGDIILKYT 96
>1d7q_A Translation initiation factor 1A; OB-fold, beta-barrel, RNA-binding
protein; NMR {Homo sapiens} SCOP: b.40.4.5
Length = 143
Score = 48.0 bits (114), Expect = 6e-07
Identities = 13/109 (11%), Positives = 31/109 (28%), Gaps = 39/109 (35%)
Query: 1 MPKEETLEFSGIVSELLPNANFRVKLITNDDDSSADCKLDSKVKSNFSESGSESGNDGVD 60
+ +E + V ++L N
Sbjct: 25 LVFKEDGQEYAQVIKMLGNGRLEAMCF--------------------------------- 51
Query: 61 PISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109
D + + G++RK ++ I+ D + V + Y +A + ++
Sbjct: 52 -----DGVKRLCHIRGKLRK-KVWINTSDIILVGLRDYQDNKADVILKY 94
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 31.8 bits (72), Expect = 0.039
Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 20/55 (36%)
Query: 66 DNAVVIAYTAG----------RMRKHRIRISLG-DKVKVAMNPYDMTRARITYRF 109
N VV +G +RK + G D+ ++ P+ + + + RF
Sbjct: 375 KNLVV----SGPPQSLYGLNLTLRK--AKAPSGLDQSRI---PFSERKLKFSNRF 420
>2ivn_A O-sialoglycoprotein endopeptidase; UP1 keops complex, Fe/Zn
dependent nucleotide phosphatase, metalloprotease,
hypothetical protein, zinc; HET: ANP; 1.65A {Pyrococcus
abyssi} PDB: 2ivo_A 2ivp_A*
Length = 330
Score = 26.4 bits (57), Expect = 1.7
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)
Query: 34 SADCKLDSKVKSNFSESGSESGNDGVDPISYL-DNAVVIAYTAGRMRKHRIRISLGD 89
+A+ +L ++ + G + V P DN +IAYT RM K I L +
Sbjct: 255 AANNRLREMLRIMTEDRGIKFF---VPPYDLCRDNGAMIAYTGLRMYKAGISFRLEE 308
>3eno_A Putative O-sialoglycoprotein endopeptidase; hydrolase,
metal-binding, metalloprotease, protease, zinc, keops
complex, ATPase, metal ION binding; 3.02A {Thermoplasma
acidophilum}
Length = 334
Score = 25.2 bits (54), Expect = 3.4
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 66 DNAVVIAYTAGRMRKHRIRISLGD 89
DN ++IA A M K +R+S+ +
Sbjct: 290 DNGIMIAQAALLMYKSGVRMSVEE 313
>3k8u_A Putative ABC transporter, ATP-binding protein COMA; cysteine
protease, quorum-sensing, hydrolase; 1.90A
{Streptococcus mutans}
Length = 156
Score = 25.0 bits (54), Expect = 3.7
Identities = 7/24 (29%), Positives = 12/24 (50%), Gaps = 1/24 (4%)
Query: 1 MPKEETLE-FSGIVSELLPNANFR 23
M KE ++G+ L P N++
Sbjct: 122 MSKERFQSEWTGLAIFLAPQPNYK 145
>2z1d_A Hydrogenase expression/formation protein HYPD; [NIFE] hydrogenase
maturation, [4Fe-4S] cluster, thiol redox; HET: CSW;
2.07A {Thermococcus kodakarensis KOD1}
Length = 372
Score = 25.0 bits (55), Expect = 4.7
Identities = 7/35 (20%), Positives = 14/35 (40%)
Query: 59 VDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKV 93
+ P+ + +I A + I + GD K+
Sbjct: 70 ITPVEDIVAMQLIMRKAREEGEEIILTTFGDMYKI 104
>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA
sliding clamp, AAA+ ATPase, DNA polymerase; HET: ATG
ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1
c.37.1.20
Length = 516
Score = 24.8 bits (53), Expect = 4.9
Identities = 5/10 (50%), Positives = 7/10 (70%)
Query: 38 KLDSKVKSNF 47
K+ + VKS F
Sbjct: 492 KIPATVKSGF 501
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
family, hydrolase; 2.35A {Escherichia coli K12} SCOP:
b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
Length = 644
Score = 24.5 bits (52), Expect = 6.0
Identities = 8/45 (17%), Positives = 13/45 (28%), Gaps = 4/45 (8%)
Query: 53 ESGNDGVDPISYL----DNAVVIAYTAGRMRKHRIRISLGDKVKV 93
++G P +L D V K + D + V
Sbjct: 582 DNGAIAFIPAPFLHAVRDELVCSQENGTVQIKGETVYKVTDVIDV 626
>1giy_D 50S ribosomal protein L2; ribosome assembly, protein synthesis,
LIFE; 5.50A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
1ml5_d* 1yl3_D 2b66_D 2b9n_D 2b9p_D
Length = 178
Score = 24.4 bits (53), Expect = 6.5
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 75 AGRMR-KHRIRISLGDKVK-VAMNPYD 99
AG K + R + V+ VAMN D
Sbjct: 148 AGNKHHKMKARGTKWPNVRGVAMNAVD 174
>2kh2_B SCFV; single chain FV, IL-1B, antibody, cytokine, inflammatory
response, mitogen, pyrogen, secreted, cytokine/immune
system complex; NMR {Mus musculus}
Length = 254
Score = 24.5 bits (53), Expect = 6.6
Identities = 12/30 (40%), Positives = 12/30 (40%), Gaps = 2/30 (6%)
Query: 36 DCKLDSKVKSNFSESGSESGNDGVDPISYL 65
L V S F SGS SG IS L
Sbjct: 51 AKTLADGVPSRF--SGSGSGTQFTLTISSL 78
>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with
oligonucleotide binding fold, central GTP binding
domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5
c.37.1.8
Length = 307
Score = 24.0 bits (51), Expect = 8.7
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 59 VDPISYLDNAVVIAYTAGRMRKHRIRISLGDKVKVAMNPYDMTRARITYRF 109
V S + V+ G RK++I +GD V + +
Sbjct: 25 VLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVY--QAENDKEGYLMEIK 73
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.315 0.132 0.365
Gapped
Lambda K H
0.267 0.0549 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 897,076
Number of extensions: 35756
Number of successful extensions: 126
Number of sequences better than 10.0: 1
Number of HSP's gapped: 123
Number of HSP's successfully gapped: 29
Length of query: 110
Length of database: 5,693,230
Length adjustment: 74
Effective length of query: 36
Effective length of database: 3,899,174
Effective search space: 140370264
Effective search space used: 140370264
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 (21.5 bits)
S2: 50 (23.4 bits)