RPS-BLAST 2.2.22 [Sep-27-2009]
Database: scop70_1_75
13,730 sequences; 2,407,596 total letters
Searching..................................................done
Query= gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus
Liberibacter asiaticus str. psy62]
(209 letters)
>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII)
{Thermotoga maritima [TaxId: 2336]}
Length = 221
Score = 180 bits (458), Expect = 7e-47
Identities = 87/188 (46%), Positives = 114/188 (60%), Gaps = 4/188 (2%)
Query: 20 EKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA 79
+K VAG+DE GRG LAGPVV AA++L+ GINDSK++S KRE L ++I A
Sbjct: 8 KKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIE--GINDSKQLSPAKRERLLDEIMEKA 65
Query: 80 IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKG 139
+ I AS + ID +NI AT A+ A+ENL V P L+DG+ I +P ++KG
Sbjct: 66 AVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTC--LVKG 123
Query: 140 DSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRL 199
D S I AASI+AKV RDRLM H+ YP + F H GY T +H I++ G IHRL
Sbjct: 124 DQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRL 183
Query: 200 TFRPLRNL 207
+F P+ L
Sbjct: 184 SFEPVLEL 191
>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Thermococcus kodakaraensis [TaxId: 311400]}
Length = 213
Score = 146 bits (370), Expect = 1e-36
Identities = 55/206 (26%), Positives = 97/206 (47%), Gaps = 28/206 (13%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSAII 81
+AGIDE GRG + GP+V+AA+++D N++P + DSKK++ K+RE+L+ +I
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVLDD 62
Query: 82 SI---SSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED---------- 128
+ + +++ ++ A+ +L+V P D + E+
Sbjct: 63 YVILELPPDVIGSREGTLNEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGERL 122
Query: 129 -LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQV 187
+ A K D I ++AASI+AKVTRDR + ++Y + G GYP+ +
Sbjct: 123 NFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLKEEYGEIGS----GYPSDPRTRA 178
Query: 188 IKEK------GPSCIHRLTFRPLRNL 207
E I R ++ L+ +
Sbjct: 179 FLENYYREHGEFPPIVRKGWKTLKKI 204
>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Pyrococcus horikoshii [TaxId: 53953]}
Length = 211
Score = 133 bits (335), Expect = 1e-32
Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 20/202 (9%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSA-- 79
VAG+DE GRG + GP+V+ ++D NI G+ DSK+++ +RE+L+ K+
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLIDILDD 62
Query: 80 -IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED---------- 128
+ + + H++++ + A+ +L++ P+ +D +
Sbjct: 63 YYVLLVTPKEIDERHHSMNELEAEKFVVALNSLRIKPQKIYVDSADVDPKRFASLIKAGL 122
Query: 129 -LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKH-QQ 186
A K D+ ++AASIIAKVTRDR + +KY ++G T + ++
Sbjct: 123 KYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKLKQKYGEFGSGYPSDPRTKEWLEE 182
Query: 187 VIKEKGPSC-IHRLTFRPLRNL 207
K+ G I R T+ R +
Sbjct: 183 YYKQYGDFPPIVRRTWETARKI 204
>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Archaeoglobus fulgidus [TaxId: 2234]}
Length = 200
Score = 121 bits (304), Expect = 4e-29
Identities = 49/195 (25%), Positives = 80/195 (41%), Gaps = 14/195 (7%)
Query: 27 AGIDEVGRGALAGPVVVAAIILDPNNI--PFGINDSKKISHKKREELYE----------- 73
AGIDE G+G + GP+VVA + + G+ DSKK+S +REEL E
Sbjct: 3 AGIDEAGKGCVIGPLVVAGVACSDEDRLRKLGVKDSKKLSQGRREELAEEIRKICRTEVL 62
Query: 74 KITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQA 133
K++ + +A + + + + + R + E +
Sbjct: 63 KVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEEITGLRV 122
Query: 134 FAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGP 193
A K D +AAASIIAKV R+R + +K+ D+G T + + G
Sbjct: 123 VAEHKADEKYPLVAAASIIAKVEREREIERLKEKFGDFGSGYASDPRTREVLKEWIASGR 182
Query: 194 SC-IHRLTFRPLRNL 207
R+ ++ + NL
Sbjct: 183 IPSCVRMRWKTVSNL 197
>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
Methanococcus jannaschii [TaxId: 2190]}
Length = 225
Score = 121 bits (304), Expect = 4e-29
Identities = 48/220 (21%), Positives = 80/220 (36%), Gaps = 42/220 (19%)
Query: 26 VAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSAII 81
+ GIDE GRG + GP+VV A ++ G+ DSK+++ KR L + + + +
Sbjct: 3 IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYV 62
Query: 82 SISSASHQY-------------------------IDKHNIHKATLDAIYHAVENLQVIPR 116
+ I+K NI ++ A
Sbjct: 63 EKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFE 122
Query: 117 SALIDGRSIPEDLPCQAF---AVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF 173
+ D A K D+ ++AASIIAK RD ++ K Y D G
Sbjct: 123 DSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGS 182
Query: 174 DSHVGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL 207
GYP+ K + +++ K I R ++ + +
Sbjct: 183 ----GYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRI 218
>d1oaoa_ e.26.1.2 (A:) Bifunctional carbon monoxide
dehydrogenase/acetyl-CoA synthase (CODH/ACS) beta (CODH)
subunit {Moorella thermoacetica [TaxId: 1525]}
Length = 673
Score = 26.0 bits (57), Expect = 2.6
Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 43 VAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLD 102
+ A+ +D I I+ + H + IT++ I A H ++
Sbjct: 345 IDAMCVDVQCIMPSISAVAECYHTRI------ITTADNAKIPGAYHIDYQTATAIESAKT 398
Query: 103 AIYHAVEN 110
AI A+E
Sbjct: 399 AIRMAIEA 406
>d2dt5a2 c.2.1.12 (A:78-203) Transcriptional repressor Rex,
C-terminal domain {Thermus aquaticus [TaxId: 271]}
Length = 126
Score = 25.9 bits (57), Expect = 2.8
Identities = 4/50 (8%), Positives = 14/50 (28%)
Query: 42 VVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYI 91
+ +DP + + + A++++ + Q
Sbjct: 30 LRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKA 79
>d1su7a_ e.26.1.2 (A:) Ni-containing carbon monoxide dehydrogenase
{Carboxydothermus hydrogenoformans [TaxId: 129958]}
Length = 633
Score = 25.2 bits (55), Expect = 4.0
Identities = 11/69 (15%), Positives = 25/69 (36%), Gaps = 6/69 (8%)
Query: 42 VVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATL 101
+ A+ILD I + + + IT+ + I+ A+H + +
Sbjct: 320 ALDAMILDYQCIQPSVATIAECTGTTV------ITTMEMSKITGATHVNFAEEAAVENAK 373
Query: 102 DAIYHAVEN 110
+ A++
Sbjct: 374 QILRLAIDT 382
>d1t64a_ c.42.1.2 (A:) Histone deacetylase 8, HDAC8 {Human (Homo
sapiens) [TaxId: 9606]}
Length = 364
Score = 24.4 bits (52), Expect = 7.9
Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 5/59 (8%)
Query: 110 NLQVIPRS-----ALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRI 163
NL R +I G+++ ++P F G L I + + R+ +I
Sbjct: 294 NLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQI 352
>d1jqka_ e.26.1.2 (A:) Ni-containing carbon monoxide dehydrogenase
{Rhodospirillum rubrum [TaxId: 1085]}
Length = 610
Score = 24.1 bits (52), Expect = 9.4
Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 6/68 (8%)
Query: 43 VAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLD 102
+ A+++D I + + H + IT+ IS A+H D+H +
Sbjct: 302 LEAMVVDVQCIMPSLPRIAECFHTQI------ITTDKHNKISGATHVPFDEHKAVETAKT 355
Query: 103 AIYHAVEN 110
I A+
Sbjct: 356 IIRMAIAA 363
Database: scop70_1_75
Posted date: Mar 27, 2010 6:21 PM
Number of letters in database: 2,407,596
Number of sequences in database: 13,730
Lambda K H
0.320 0.135 0.397
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 789,679
Number of extensions: 35767
Number of successful extensions: 109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 16
Length of query: 209
Length of database: 2,407,596
Length adjustment: 81
Effective length of query: 128
Effective length of database: 1,295,466
Effective search space: 165819648
Effective search space used: 165819648
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: 51 (23.6 bits)