RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780472|ref|YP_003064885.1| cytochrome o ubiquinol oxidase
subunit III [Candidatus Liberibacter asiaticus str. psy62]
(210 letters)
>1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane
protein, oxidoreductase; HET: HEM HEO; 3.50A
{Escherichia coli} SCOP: f.25.1.1
Length = 204
Score = 125 bits (315), Expect = 7e-30
Identities = 96/184 (52%), Positives = 125/184 (67%), Gaps = 1/184 (0%)
Query: 27 HDGTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSL 86
GFWIYLMSDC++F++ F TYAVL A GP D+F++ + V T +LL SS+
Sbjct: 22 GGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSI 81
Query: 87 SCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFF 146
+ A +A + +SWL +T FG FI MEIYEF HLI P RS FLS+FF
Sbjct: 82 TYGMAAIAMYKNN-KSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFF 140
Query: 147 ALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYL 206
ALVG HGLHV GLIW+ VL++QI ++GL S N+ R++CLS+FWHFLD++WICVF+ VYL
Sbjct: 141 ALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYL 200
Query: 207 MGVV 210
MG +
Sbjct: 201 MGAM 204
>1qle_C Cytochrome C oxidase polypeptide III; oxidoreductase/immune system,
complex (oxidoreductase/antibody), electron transport;
HET: HEA PC1; 3.0A {Paracoccus denitrificans} SCOP:
f.25.1.1
Length = 273
Score = 97.4 bits (242), Expect = 2e-21
Identities = 47/188 (25%), Positives = 90/188 (47%), Gaps = 14/188 (7%)
Query: 32 LGFWIYLMSDCLMFAVFFVTYAVLGKNYAAG----------PAPIDVFDISGI-FVSTIV 80
GF +++MS+ + F +F + P I FD + ++T++
Sbjct: 88 YGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLI 147
Query: 81 LLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSA 140
LLLS ++ ++A A + T++ L+V G+ F ++ YE++H +
Sbjct: 148 LLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFG---LADTV 204
Query: 141 FLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICV 200
+ +F+ G HG HV G I+LFV +I++LK + + +WHF+D++W+ +
Sbjct: 205 YAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFL 264
Query: 201 FSFVYLMG 208
F +Y+ G
Sbjct: 265 FVVIYIWG 272
>1m56_C Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA
PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.25.1.1 PDB:
1m57_C*
Length = 266
Score = 95.1 bits (236), Expect = 9e-21
Identities = 43/191 (22%), Positives = 86/191 (45%), Gaps = 14/191 (7%)
Query: 29 GTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAP----------IDVFDISGI-FVS 77
G GF +++MS+ + F+ +F ++ +P I FD + ++
Sbjct: 78 GLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLIN 137
Query: 78 TIVLLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQ 137
T++LL S + ++A A + L + G +F + + YE++H
Sbjct: 138 TLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSH---AAFGFA 194
Query: 138 RSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIW 197
+ + ++FF G HG HV G I+L V +I++ + +WHF+D++W
Sbjct: 195 GNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVW 254
Query: 198 ICVFSFVYLMG 208
+ +F+ +Y+ G
Sbjct: 255 LFLFASIYIWG 265
>1v54_C Cytochrome C oxidase polypeptide III; oxidoreductase; HET: FME TPO
HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: f.25.1.1 PDB: 1v55_C* 2dyr_C* 2eij_C* 2eik_C*
2eil_C* 2eim_C* 2ein_C* 2zxw_C* 2occ_C* 1oco_C* 1occ_C*
1ocz_C* 1ocr_C* 2dys_C*
Length = 261
Score = 84.3 bits (208), Expect = 2e-17
Identities = 40/186 (21%), Positives = 72/186 (38%), Gaps = 9/186 (4%)
Query: 29 GTYLGFWIYLMSDCLMFAVFF------VTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLL 82
G G ++++S+ L F FF P I + + + +L
Sbjct: 78 GLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVL 137
Query: 83 LSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFL 142
L+S S + + L +T G+ F +++ E+ +
Sbjct: 138 LASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYE---APFTISDGVYG 194
Query: 143 SSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFS 202
S+FF G HGLHV G +L V + LK S + + +WHF+D++W+ ++
Sbjct: 195 STFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYV 254
Query: 203 FVYLMG 208
+Y G
Sbjct: 255 SIYWWG 260
>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 = 29.5 bits (66), Expect = 0.55
Identities = 20/136 (14%), Positives = 42/136 (30%), Gaps = 51/136 (37%)
Query: 4 QKIGKSP-NFSLFYVK--------DKKESCVDHDGTYLGFWIYLMS---DC-----LMFA 46
++ ++ + + + + + D D YL+S C + A
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD--------YLLSIPISCPLIGVIQLA 247
Query: 47 VFFVTYAVLGKNYAAGPAPIDVFD-IS-------GIFVSTIVLLLSSLSCSFAMLASATK 98
+ VT +LG P ++ + G+ + + S SF +
Sbjct: 248 HYVVTAKLLGFT------PGELRSYLKGATGHSQGLVTAVAIAETDSWE-SFFVSV---- 296
Query: 99 RLIHKTVSWLLVTAFF 114
K ++ L FF
Sbjct: 297 ---RKAITVL----FF 305
Score = 29.1 bits (65), Expect = 0.80
Identities = 31/209 (14%), Positives = 55/209 (26%), Gaps = 96/209 (45%)
Query: 1 MSRQKIGKSPNFSLF-YVKDKKESCVDHDGTYLGFWIYLMSDCLMFAVF----------- 48
M+++ K N +LF V + + A+F
Sbjct: 132 MAKRPFDKKSNSALFRAVGEGNAQ--------------------LVAIFGGQGNTDDYFE 171
Query: 49 -----FVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKRLIHK 103
+ TY VL V D + LS L +++ +
Sbjct: 172 ELRDLYQTYHVL------------VGD----LIKFSAETLSELI----RTTLDAEKVFTQ 211
Query: 104 ---TVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSF---FALVGLHGL-HV 156
+ WL + P + +L S L+G+ L H
Sbjct: 212 GLNILEWL------------------ENP---SNTPDK-DYLLSIPISCPLIGVIQLAH- 248
Query: 157 FFGLIWLFVLVIQILKKGLISGNQRRLIC 185
+V+ ++L G G R +
Sbjct: 249 -------YVVTAKLL--GFTPGELRSYLK 268
Score = 25.7 bits (56), Expect = 8.0
Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 11/33 (33%)
Query: 94 ASATKRLI----HKTVSWLLVTAF-------FG 115
S ++R++ V W T F FG
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFG 505
>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}
Length = 1688
Score = 27.5 bits (60), Expect = 2.4
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 162 WLFVLVIQILKKGLISGNQ 180
W+ +QIL G+I GN+
Sbjct: 1392 WMMNGALQILNSGIIPGNR 1410
>2r9r_B Paddle chimera voltage gated potassium channel KV1.2-KV2.1; voltage
sensor, voltage dependent, ION channel, shaker, membrane
protein; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB:
2a79_B*
Length = 514
Score = 27.1 bits (59), Expect = 3.0
Identities = 19/143 (13%), Positives = 47/143 (32%), Gaps = 10/143 (6%)
Query: 66 IDVFDISGIFVSTIVLLLSSLSC-----SFAMLASATKRLIHKTVSWLLVTAFFGMIFII 120
I + + I +S + L +L T ++ + F F I
Sbjct: 184 IAIVSVMVILISIVSFCLETLPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPFFI 243
Query: 121 ME-----IYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGL 175
+E + F L+ A P ++ F ++ ++ + + ++ I+L +L+
Sbjct: 244 VETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQN 303
Query: 176 ISGNQRRLICLSMFWHFLDLIWI 198
+ + + + F
Sbjct: 304 VRRVVQIFRIMRILRIFKLSRHS 326
>1b22_A DNA repair protein RAD51; DNA binding, riken structural
genomics/proteomics initiative, RSGI, structural
genomics; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1
Length = 114
Score = 26.4 bits (58), Expect = 5.4
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 62 GPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR 99
GP PI + GI + + L + + +A A K+
Sbjct: 21 GPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKK 58
>1mhs_A Proton pump, plasma membrane ATPase; ION transport, membrane
protein, P-type ATPase, active transport, cryo-electron
microscopy; 8.00A {Neurospora crassa} SCOP: i.18.1.1
Length = 920
Score = 25.8 bits (56), Expect = 6.5
Identities = 20/130 (15%), Positives = 40/130 (30%), Gaps = 25/130 (19%)
Query: 43 LMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR-LI 101
++ ++T + YA G V + + ++ L SL+ ++ + +
Sbjct: 765 VLAVGTWITVTTM---YAQGENGGIVQNFGNM--DEVLFLQISLTENWLIFITRANGPFW 819
Query: 102 HKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLI 161
SW L A F + + F S ++V I
Sbjct: 820 SSIPSWQLSGAIFLVDILAT------------CFTIWGWFEHSDTSIVA-------VVRI 860
Query: 162 WLFVLVIQIL 171
W+F I +
Sbjct: 861 WIFSFGIFCI 870
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
0.335 0.146 0.465
Gapped
Lambda K H
0.267 0.0455 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,792,869
Number of extensions: 74598
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 42
Length of query: 210
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 122
Effective length of database: 3,559,758
Effective search space: 434290476
Effective search space used: 434290476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 54 (25.3 bits)