RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780786|ref|YP_003065199.1| ribosome-binding factor A
[Candidatus Liberibacter asiaticus str. psy62]
(128 letters)
>2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural
genomics, PSI-2, protein struc initiative; NMR
{Thermotoga maritima}
Length = 106
Score = 87.8 bits (218), Expect = 6e-19
Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 4/102 (3%)
Query: 7 KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPLD 65
+ R + E++ LM + + +D + +D ++ S V +S D R A VY+S L
Sbjct: 3 NPAYRKAMLESEIQKLLMEAL--QQLRDPRLKKDFVTFSRVELSKDKRYADVYVSFLGTP 60
Query: 66 VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSL 107
+ LN F R I ++LR L PE+RF D +
Sbjct: 61 EERKETVEILNRAKGFFRTFIAKNLR-LYVAPEIRFYEDKGI 101
>1jos_A RBFA, ribosome-binding factor A; RNA binding protein, structure 2
function project, S2F, structural genomics; 1.70A
{Haemophilus influenzae} SCOP: d.52.7.1 PDB: 1kkg_A
Length = 128
Score = 81.0 bits (200), Expect = 7e-17
Identities = 34/114 (29%), Positives = 63/114 (55%), Gaps = 7/114 (6%)
Query: 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD 65
+ +R+ RV +E++ + VIL E +D I +++S+V +S DL A ++++ D
Sbjct: 2 AREFKRSDRVAQEIQKEIA-VILQREVKDPRIGM--VTVSDVEVSSDLSYAKIFVTFLFD 58
Query: 66 VSP---DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116
++ + L +IR +G+++R LR VPE+RF YD SL +++ L
Sbjct: 59 HDEMAIEQGMKGLEKASPYIRSLLGKAMR-LRIVPEIRFIYDQSLVEGMRMSNL 111
>1pa4_A Probable ribosome-binding factor A; structural genomics, distant
homology, BSGC structure funded by NIH, protein
structure initiative, PSI; NMR {Mycoplasma pneumoniae}
SCOP: d.52.7.1
Length = 116
Score = 72.9 bits (179), Expect = 2e-14
Identities = 19/110 (17%), Positives = 45/110 (40%), Gaps = 4/110 (3%)
Query: 8 NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS 67
S + R+ ++ + + +E + + ++ V +S DL TVY+
Sbjct: 2 ASYKKERLENDIIRLINR-TVIHEIYNETVKT--GHVTHVKLSDDLLHVTVYLDCYNREQ 58
Query: 68 PDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117
DRV+ A N + +L L ++ F D ++ + ++ +++
Sbjct: 59 IDRVVGAFNQAKGVFSRVLAHNLY-LAKAVQIHFVKDKAIDNAMRIESII 107
>2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.52.7.1
Length = 129
Score = 72.6 bits (178), Expect = 2e-14
Identities = 19/112 (16%), Positives = 40/112 (35%), Gaps = 3/112 (2%)
Query: 7 KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPLD 65
++ R + + AL ++ E L + +S+V ++ D Y
Sbjct: 10 EDHARLRALNGLLYKALTDLLCTPEVSQELYDL-NVELSKVSLTPDFSACRAYWKTTLSA 68
Query: 66 VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117
+ + L + +R + LR VP + F D + +L+ L+
Sbjct: 69 EQNAHMEAVLQRSAAHMRHLLMSQQT-LRNVPPIVFVQDKGNAALAELDQLL 119
>2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain,
structural genomics, NPPSFA; 1.84A {Thermus thermophilus
HB8} SCOP: d.52.7.1 PDB: 2r1c_A
Length = 95
Score = 61.3 bits (149), Expect = 7e-11
Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 7/98 (7%)
Query: 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP 68
+ + +++ AL I +D + +++ V +S D V +VY+
Sbjct: 2 AYGKAHLEAQLKRALAEEI--QALEDPRLFL--LTVEAVRLSKDGSVLSVYVEA--FREE 55
Query: 69 DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTS 106
+ + AL+ + + + R +R +R +P L F +
Sbjct: 56 EGALRALSRAERRLVAALARRVR-MRRLPRLEFLPWRA 92
>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 = 34.5 bits (79), Expect = 0.007
Identities = 26/141 (18%), Positives = 43/141 (30%), Gaps = 59/141 (41%)
Query: 7 KNSRRALRV----GEEVRSALMWVILNNEFQDRLISRDVISISE-------VCM-SV-DL 53
+ R+A+ V G VR + + + ++ S M S+ +L
Sbjct: 294 VSVRKAITVLFFIG--VRC-------YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL 344
Query: 54 RVATV--YI-----SLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYV----PELRFR 102
V Y+ LP + + I + G +NL V P+
Sbjct: 345 TQEQVQDYVNKTNSHLP----AGKQVE-----ISLVNGA-----KNL--VVSGPPQ---- 384
Query: 103 YDTSLQSYWKLNALMCLPKIP 123
SL LN + K P
Sbjct: 385 ---SLYG---LNLTLRKAKAP 399
Score = 34.1 bits (78), Expect = 0.008
Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 28/104 (26%)
Query: 40 DVISISEVCMSVDLRVATVYISLPLD-----------VSPDRVISALNCN-IKFIRGRIG 87
DV+SI + V R T+ +++P D ++P RV ++ + ++++ R+G
Sbjct: 1775 DVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG 1834
Query: 88 R-----------SLRNLRYVP--ELRFRYD--TSLQSYWKLNAL 116
+ ++ N +YV +LR D T++ ++ KL +
Sbjct: 1835 KRTGWLVEIVNYNVENQQYVAAGDLR-ALDTVTNVLNFIKLQKI 1877
Score = 28.0 bits (62), Expect = 0.64
Identities = 19/105 (18%), Positives = 31/105 (29%), Gaps = 27/105 (25%)
Query: 19 VRSALMWVILNNEFQDR-LISRDV-------ISISEVCMSVDLRVATVY---ISLPLDVS 67
+ L EF++ L D+ + ++ + + Y +
Sbjct: 84 LNLCL------TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPF 137
Query: 68 PDRVISAL-------NCNIKFIRGRIGRSLRNLRYVPELRFRYDT 105
+ SAL N + I G G Y ELR Y T
Sbjct: 138 DKKSNSALFRAVGEGNAQLVAIFGGQGN---TDDYFEELRDLYQT 179
>2oem_A 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; rubisco-like
protein, isomerase; HET: KCX 1AE; 1.70A {Geobacillus
kaustophilus} PDB: 2oel_A* 2oek_A* 2oej_A
Length = 413
Score = 24.8 bits (54), Expect = 5.7
Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 10/85 (11%)
Query: 25 WVILNNEFQDRLISRD--VISISEV--------CMSVDLRVATVYISLPLDVSPDRVISA 74
W L Q++L V++I E+ L+ A V I+ P + +
Sbjct: 32 WTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPAL 91
Query: 75 LNCNIKFIRGRIGRSLRNLRYVPEL 99
L + L +L + E
Sbjct: 92 LVTTFGKLSLDGEVRLLDLEFPDEW 116
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
0.325 0.138 0.406
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,072,319
Number of extensions: 43348
Number of successful extensions: 159
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 12
Length of query: 128
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 46
Effective length of database: 3,705,222
Effective search space: 170440212
Effective search space used: 170440212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.7 bits)