RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus
Liberibacter asiaticus str. psy62]
(209 letters)
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC
3.1.26.4) (RNAse HII), structural genomics, joint center
for structural genomics; 1.74A {Thermotoga maritima}
(A:1-171)
Length = 171
Score = 180 bits (459), Expect = 1e-46
Identities = 73/166 (43%), Positives = 95/166 (57%), Gaps = 4/166 (2%)
Query: 9 RPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKR 68
H + +K VAG+DE GRG LAGPVV AA++L+ GINDSK++S KR
Sbjct: 9 HHHHXGIDELYKKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKE--IEGINDSKQLSPAKR 66
Query: 69 EELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED 128
E L ++I A + I AS + ID +NI AT A A+ENL V P L+DG+ I
Sbjct: 67 ERLLDEIXEKAAVGIGIASPEEIDLYNIFNATKLAXNRALENLSVKPSFVLVDGKGIELS 126
Query: 129 LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFD 174
+P ++KGD S I AASI+AKV RDRL H+ YP + F
Sbjct: 127 VPGT--CLVKGDQKSKLIGAASIVAKVFRDRLXSEFHRXYPQFSFH 170
>1i39_A Ribonuclease HII, RNAse HII; mixed beta sheet,
helix-loop-helix, hydrolase; 1.95A {Archaeoglobus
fulgidus} (A:1-182)
Length = 182
Score = 175 bits (444), Expect = 5e-45
Identities = 49/177 (27%), Positives = 79/177 (44%), Gaps = 13/177 (7%)
Query: 9 RPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNI--PFGINDSKKISHK 66
H + + + AGIDE G+G + GP+VVA + + G+ DSKK+S
Sbjct: 5 HHHHHHSSGLVPRGSHMKAGIDEAGKGCVIGPLVVAGVACSDEDRLRKLGVKDSKKLSQG 64
Query: 67 KREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVEN--LQVIPRSALIDGRS 124
+REEL E+I + S + +D+ K + + L++ P A +D
Sbjct: 65 RREELAEEIRKICRTEVLKVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPD 124
Query: 125 IPED---------LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYG 172
+ + + A K D +AAASIIAKV R+R + +K+ D+G
Sbjct: 125 VIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERLKEKFGDFG 181
>1io2_A Ribonuclease HII; endonuclease, hydrolase; 2.00A
{Thermococcus kodakarensis KOD1} (A:1-168)
Length = 168
Score = 164 bits (415), Expect = 1e-41
Identities = 50/167 (29%), Positives = 85/167 (50%), Gaps = 18/167 (10%)
Query: 24 WPVAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSA 79
+AGIDE GRG + GP+V+AA+++D N++P + DSKK++ K+RE+L+ +I
Sbjct: 1 MKIAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVL 60
Query: 80 I-ISISSASHQYID--KHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPE--------- 127
I I + +++ ++ A+ +L+V P D + E
Sbjct: 61 DDYVILELPPDVIGSREGTLNEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGE 120
Query: 128 --DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYG 172
+ + A K D I ++AASI+AKVTRDR + ++Y + G
Sbjct: 121 RLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLKEEYGEIG 167
>3kio_A Ribonuclease H2 subunit A; aicardi-goutieres syndrome, RNAse
H2, protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} (A:1-208)
Length = 208
Score = 160 bits (405), Expect = 2e-40
Identities = 43/201 (21%), Positives = 70/201 (34%), Gaps = 28/201 (13%)
Query: 4 NSIPERPHFELEAMVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPF----GIND 59
N+ R + A+ V G+DE GRG + GP V A + + + D
Sbjct: 10 NTGRCRLSSPVPAVC--LKEPCVLGVDEAGRGPVLGPXVYAICYCPLSRLADLEALKVAD 67
Query: 60 SKKISHKKREELYEKITSSA---IISISSASHQYIDK----------HNIHKATLDAIYH 106
SK ++ +RE L+ K ++ S I +++ T +
Sbjct: 68 SKTLTENERERLFAKXEEDGDFVGWALDVLSPNLISTSXLGRVKYNLNSLSHDTAAGLIQ 127
Query: 107 AVENLQVIPRSALIDGRSIPED---------LPCQAFAVIKGDSISLSIAAASIIAKVTR 157
+ V +D PE + K DS+ ++AASI AKV R
Sbjct: 128 YALDQNVNVTQVFVDTVGXPETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVAR 187
Query: 158 DRLMRIAHKKYPDYGFDSHVG 178
D+ ++ DS G
Sbjct: 188 DKAVKNWQFVENLQDLDSDYG 208
>1uax_A Ribonuclease HII, ribonuclease H2; RNA*DNA hybrid
ribonucleotidohydrolase; 2.00A {Pyrococcus horikoshii
OT3} (A:1-168)
Length = 168
Score = 159 bits (404), Expect = 2e-40
Identities = 48/167 (28%), Positives = 82/167 (49%), Gaps = 18/167 (10%)
Query: 24 WPVAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSA 79
VAG+DE GRG + GP+V+ ++D NI G+ DSK+++ +RE+L+ K+
Sbjct: 1 MKVAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLIDIL 60
Query: 80 I-ISISSASHQYIDKHNIHKATLDAIYH--AVENLQVIPRSALIDGRSIPE--------- 127
+ + + ID+ + L+A A+ +L++ P+ +D +
Sbjct: 61 DDYYVLLVTPKEIDERHHSMNELEAEKFVVALNSLRIKPQKIYVDSADVDPKRFASLIKA 120
Query: 128 --DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYG 172
A K D+ ++AASIIAKVTRDR + +KY ++G
Sbjct: 121 GLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKLKQKYGEFG 167
>1eke_A Ribonuclease HII; endonuclease, structural genomics, BSGC
structure funded by NIH, protein structure initiative,
PSI; HET: MES; 2.00A {Methanocaldococcus jannaschii}
(A:1-180)
Length = 180
Score = 153 bits (388), Expect = 1e-38
Identities = 43/178 (24%), Positives = 69/178 (38%), Gaps = 32/178 (17%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSAII 81
+ GIDE GRG + GP VV A ++ G+ DSK+++ KR L + + + +
Sbjct: 3 IIGIDEAGRGPVLGPXVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYV 62
Query: 82 SISSASHQYID----KHNIHKATLDAIYHAVENLQ------VIPRSALIDGRSIPE---- 127
+ I+ N++ ++A +NL ID S
Sbjct: 63 EKRILEAEEINQLXNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFE 122
Query: 128 --------------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDY 171
+L + A K D+ ++AASIIAK RD ++ K Y D
Sbjct: 123 DSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDI 180
>2d0b_A RNAse HIII, ribonuclease HIII; RNA/DNA hybrid, hydrolase;
2.10A {Geobacillus stearothermophilus} PDB: 2d0a_A
2d0c_A (A:83-265)
Length = 183
Score = 151 bits (383), Expect = 5e-38
Identities = 35/180 (19%), Positives = 65/180 (36%), Gaps = 26/180 (14%)
Query: 19 REKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEK 74
+ G DEVG G GP+VVAA +D +I G+ DSK+++ + + +
Sbjct: 4 HQLGSLSAIGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAPA 63
Query: 75 ITSSAIISISSASHQYID-----KHNIHKATLDAIYHAVENLQ-----VIPRSALIDGRS 124
I + +++ + + K + L P + +ID
Sbjct: 64 IMETVPHAVTVLDNPQYNRWQRSGMPQTKMKALLHNRTLVKLVDAIAPAEPEAIIIDEFL 123
Query: 125 IPE-----------DLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF 173
+ + + + K +S+ +S+AAASIIA+ M +
Sbjct: 124 KRDSYFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIARYVFLEEMEQLSRAVG-LLL 182
>2etj_A Ribonuclease HII, RNAse HII; TM0915, ribonuclease HII (EC
3.1.26.4) (RNAse HII), structural genomics, joint center
for structural genomics; 1.74A {Thermotoga maritima}
(A:172-250)
Length = 79
Score = 51.0 bits (122), Expect = 1e-07
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 176 HVGYPTAKHQQVIKEKGPSCIHRLTFRPLRNL 207
H GY T +H I++ G IHRL+F P+ L
Sbjct: 1 HKGYATKEHLNEIRKNGVLPIHRLSFEPVLEL 32
>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:389-434,A:733-794)
Length = 108
Score = 30.5 bits (69), Expect = 0.15
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 57 INDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPR 116
+ + K+ + K R+EL E +SI +A ++ ++ + DA Y VE + PR
Sbjct: 48 VPELKEFTAKLRKELVETSEVRKAVSIETA----LEHKVVNGNSADAAYAQVE---IQPR 100
Query: 117 S 117
+
Sbjct: 101 A 101
>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 = 26.8 bits (59), Expect = 2.2
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 16/40 (40%)
Query: 11 HFELEAMVREK---NMW--------P-VAGIDEVGRGALA 38
EA + + W P +A + RGALA
Sbjct: 73 EIHNEAESQLRAAQQQWGNDFYKRDPRIAPL----RGALA 108
>2o4w_A Lysozyme; protein folding, protein stability, protein
engineering, hydrolase; 1.90A {Enterobacteria phage T4}
(A:)
Length = 171
Score = 25.5 bits (55), Expect = 5.2
Identities = 16/95 (16%), Positives = 33/95 (34%)
Query: 17 MVREKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKIT 76
M+R K G +G G L + G N + I+ + E+L+ +
Sbjct: 1 MLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDV 60
Query: 77 SSAIISISSASHQYIDKHNIHKATLDAIYHAVENL 111
+A+ I + ++ A+ + V +
Sbjct: 61 DAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQM 95
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
0.320 0.135 0.397
Gapped
Lambda K H
0.267 0.0518 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,598,530
Number of extensions: 68749
Number of successful extensions: 209
Number of sequences better than 10.0: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 21
Length of query: 209
Length of database: 4,956,049
Length adjustment: 85
Effective length of query: 124
Effective length of database: 2,082,624
Effective search space: 258245376
Effective search space used: 258245376
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.3 bits)