RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein
[Candidatus Liberibacter asiaticus str. psy62]
(190 letters)
>2f1l_A 16S rRNA processing protein; 9949912, structural genomics,
PSI, protein structure initiative, joint center for
structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas
aeruginosa} (A:1-111)
Length = 111
Score = 71.4 bits (175), Expect = 8e-14
Identities = 20/99 (20%), Positives = 40/99 (40%), Gaps = 6/99 (6%)
Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRK 56
D LV++ I + +G+ GEV + S+ + +L + + R+ +++
Sbjct: 14 PTPADDLVVIGKIVSVYGIRGEVKVYSFTDPLDNLLDYRRWTLRRDGEIRQAELVRGRLH 73
Query: 57 NKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEE 95
K A G+D+ A ++ R + LEE
Sbjct: 74 GKVLAAKLKGLDDREEARTFTGYEICIPRSEL--PSLEE 110
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73,
structural genomics, PSI-2, protein structure
initiative; 2.40A {Acinetobacter calcoaceticus}
(A:1-102)
Length = 102
Score = 71.3 bits (175), Expect = 9e-14
Identities = 11/100 (11%), Positives = 35/100 (35%), Gaps = 6/100 (6%)
Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRK 56
+ + + + + +GLNG +++ S + Y+ + + + +
Sbjct: 5 QNVPEDRIQIGQLRSAYGLNGWLWVYSNTEPXSNXFDYLPWYIETKAGWQTVDVKRWKPH 64
Query: 57 NKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEED 96
K + + G+ + A L ++ + + + D
Sbjct: 65 GKGLVVSLKGVSDRTGAESLVASNIWIAKSQL--PKADVD 102
>3h9n_A Ribosome maturation factor RIMM; structural genomics,
PSI-2, protein structure initiative, northeast
structural genomics consortium, NESG; 2.70A
{Haemophilus influenzae} (A:1-93)
Length = 93
Score = 66.7 bits (163), Expect = 2e-12
Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 6/93 (6%)
Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRKNKRFIA 62
+ ++ +G+T+G+ G + I S + ++ + + + + N I
Sbjct: 2 IEVVGKLGSTYGIRGWLRIYSSTEQAESIFDYQPWFLKIKGEWQSIELENWRYHNHEIIV 61
Query: 63 TFSGIDNIHSASELRDLKLYAKRQDFKDEELEE 95
G+D+ +A L ++++ F ELEE
Sbjct: 62 KLKGVDDREAAQILANVEIGVDLSVF--PELEE 92
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal
protein S19, PRC-barrel, structural genomics, NPPSFA;
2.00A {Thermus thermophilus HB8} PDB: 2dog_A (A:1-87)
Length = 87
Score = 66.3 bits (162), Expect = 2e-12
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 5/90 (5%)
Query: 6 KLVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFS 65
+LV + G + L G + L R +Y + I +YR + + +
Sbjct: 2 RLVEIGRFGAPYALKGGLRFRGEPVVL-HLER--VYVEGHGWRAIEDLYRVGEELVVHLA 58
Query: 66 GIDNIHSASELRDLKLYAKRQDFKDEELEE 95
G+ + A L L++YA+ D LEE
Sbjct: 59 GVTDRTLAEALVGLRVYAEVADL--PPLEE 86
>2f1l_A 16S rRNA processing protein; 9949912, structural genomics,
PSI, protein structure initiative, joint center for
structural genomics, JCSG; HET: UNL; 2.46A {Pseudomonas
aeruginosa} (A:112-187)
Length = 76
Score = 66.2 bits (162), Expect = 3e-12
Identities = 16/74 (21%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 97 EFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIK----NTMEKTFLIPFTKFAVLE 152
E++ LE ++ D+ + G + + GA + +K + ++ L+P+T VL
Sbjct: 1 EYYWHQLEGLKVIDQGRQLLGVIDHLLETGANDVXVVKPCAGSLDDRERLLPYTGQCVLS 60
Query: 153 VNLQENKILIDPIA 166
++L + +D A
Sbjct: 61 IDLAAGEXRVDWDA 74
>3h9n_A Ribosome maturation factor RIMM; structural genomics, PSI-2,
protein structure initiative, northeast structural
genomics consortium, NESG; 2.70A {Haemophilus
influenzae} (A:94-177)
Length = 84
Score = 62.7 bits (153), Expect = 3e-11
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 6/76 (7%)
Query: 97 EFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTM-----EKTFLIPFTKFA-V 150
+++ DL + +G G V G+ +L +K ++ LIPF V
Sbjct: 1 DYYWHDLIGCTVVNLEGYTXGTVTEXXETGSNDVLVVKANTKDAFGKQERLIPFLYEQVV 60
Query: 151 LEVNLQENKILIDPIA 166
V+L I +D A
Sbjct: 61 KRVDLTTKTIEVDWDA 76
>2qgg_A 16S rRNA-processing protein RIMM; X-RAY, NESG, ASR73,
structural genomics, PSI-2, protein structure
initiative; 2.40A {Acinetobacter calcoaceticus}
(A:103-182)
Length = 80
Score = 62.0 bits (151), Expect = 5e-11
Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 97 EFFNTDLEEMETFD----RQGKYWGQVCGVYNFGAGSILEIKNTM----EKTFLIPFTKF 148
E++ +DL+ + Q GQ+ ++ GA + ++ T + IP+ K
Sbjct: 1 EYYWSDLKGLTVLGLDDEEQEVNLGQIHELFETGANDVXVVRATPDSIDSEERXIPWHKD 60
Query: 149 AVLEVNLQENKILIDPIA 166
V V+L+ +I ++
Sbjct: 61 VVQRVDLEAGRIYVNWGV 78
>2dyi_A Probable 16S rRNA-processing protein RIMM; ribosomal protein
S19, PRC-barrel, structural genomics, NPPSFA; 2.00A
{Thermus thermophilus HB8} PDB: 2dog_A (A:88-162)
Length = 75
Score = 60.8 bits (148), Expect = 1e-10
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 97 EFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTME-----KTFLIPFTKFAVL 151
++ L + + +G+ G+V + + GA +L I+ E L+P
Sbjct: 1 RYYYFALIGLPVYV-EGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQ---AP 56
Query: 152 EVNLQENKILIDPIAAGL 169
V ++E I +DPI GL
Sbjct: 57 YVRVEEGSIHVDPI-PGL 73
>1gkm_A Histidine ammonia-lyase; histidine degradation; 1.0A
{Pseudomonas putida} (A:197-509)
Length = 313
Score = 33.1 bits (75), Expect = 0.026
Identities = 15/114 (13%), Positives = 41/114 (35%), Gaps = 12/114 (10%)
Query: 10 MATIGTTHGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGID- 68
++ + L + + + + + +N +L + ++ G+D
Sbjct: 202 LSHPHSVDSLPTSANQEDHVSMAPAAGKRLWEMAENTR-GVLAIE-----WLGACQGLDL 255
Query: 69 --NIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120
+ ++++L + A R + + D FF D+E+ +G G +
Sbjct: 256 RKGLKTSAKLEKARQ-ALRSEV--AHYDRDRFFAPDIEKAVELLAKGSLTGLLP 306
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae} (A:1221-1330,A:1541-1688)
Length = 258
Score = 28.7 bits (64), Expect = 0.56
Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 11/53 (20%)
Query: 70 IHSA----SELRDLKLYAKRQ-DFKDEELEED-----EFFNTDLEEMETFDRQ 112
HS+ S ++K Y KRQ ++ ++++ E + EE+ + D+
Sbjct: 13 HHSSVKYASPNLNMK-YRKRQLVTREAQIKDWVENELEALKLEAEEIPSEDQN 64
>1zbs_A Hypothetical protein PG1100; alpha-beta protein., structural
genomics, PSI, protein structure initiative; 2.30A
{Porphyromonas gingivalis W83} (A:1-107,A:270-291)
Length = 129
Score = 27.1 bits (60), Expect = 1.8
Identities = 11/63 (17%), Positives = 19/63 (30%), Gaps = 7/63 (11%)
Query: 98 FFNTDLEEMETFDRQG------KYWGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVL 151
F E++T R + + VY +GAG + + +
Sbjct: 34 FQQDR-NEIDTALRSEVLPAIGQKASSIRAVYFYGAGCTPAKAPXLNEALDSXLPHCDRI 92
Query: 152 EVN 154
EV
Sbjct: 93 EVA 95
>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown
function, PSI-2, protein structure initiative; 1.60A
{Pyrococcus horikoshii OT3} (A:)
Length = 260
Score = 25.6 bits (54), Expect = 4.1
Identities = 5/63 (7%), Positives = 15/63 (23%), Gaps = 5/63 (7%)
Query: 17 HGLNGEVYIDSYANNPIDLNRYVLYSNDNRELRILKMY-----RKNKRFIATFSGIDNIH 71
+ + A+ + + + REL ++K + +
Sbjct: 193 KDKRVLLSVYRRADYVLKTRSSLGENGIKRELLVIKTPKPIEELVRFEYEFKGNEPKLRR 252
Query: 72 SAS 74
Sbjct: 253 EGH 255
>1y08_A Hypothetical protein SPY0861; cysteine proteinase,
papain-like fold with major insertions, hydrolase; 1.93A
{Streptococcus pyogenes} (A:1-94,A:150-323)
Length = 268
Score = 24.9 bits (54), Expect = 7.9
Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 1/55 (1%)
Query: 23 VYI-DSYANNPIDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNIHSASEL 76
+Y+ DS +N I + +Y + N ++ I K A G+ + + +
Sbjct: 209 IYVTDSDSNASIGMKKYFVGVNSAGKVAISAKEIKEDNIGAQVLGLFTLSTGQDS 263
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.318 0.137 0.392
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,437,209
Number of extensions: 64467
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 235
Number of HSP's successfully gapped: 23
Length of query: 190
Length of database: 4,956,049
Length adjustment: 84
Effective length of query: 106
Effective length of database: 2,116,429
Effective search space: 224341474
Effective search space used: 224341474
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 (21.7 bits)
S2: 52 (23.8 bits)