RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C
[Candidatus Liberibacter asiaticus str. psy62]
(202 letters)
>3mcr_A NADH dehydrogenase, subunit C; structural genomics, joint center
for structural genomics, J protein structure initiative,
PSI-2; 2.65A {Thermobifida fusca}
Length = 213
Score = 145 bits (367), Expect = 6e-36
Identities = 42/130 (32%), Positives = 65/130 (50%), Gaps = 2/130 (1%)
Query: 5 IEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVD 64
+E I + ++ V GE++ V L+ + + LRDDP F + + GV
Sbjct: 84 LERSLKEIGTPYDTAISRVVVDRGEITFHVQREHLLDVATRLRDDPALRFELCLGVTGVH 143
Query: 65 FLSR-SNRFDVVYHFLSPKYNRRLRVKIAVAEGK-SVPSIVGIYPGADWFEREVWDMYGI 122
+ N VY S +N +R++++ + +PSIV +YP DW ERE WD +GI
Sbjct: 144 YPEDEGNELHAVYALRSITHNYEIRLEVSCPDSDPHIPSIVSVYPTNDWHEREAWDFFGI 203
Query: 123 FFEGHPDLRR 132
F+GHP L R
Sbjct: 204 IFDGHPALTR 213
>3i9v_5 NADH-quinone oxidoreductase subunit 5; electron transport,
respiratory chain, 4Fe- 4S, cell membrane, flavoprotein,
FMN, iron; HET: FMN; 3.10A {Thermus thermophilus HB8}
PDB: 2fug_5* 3iam_5* 3ias_5*
Length = 207
Score = 134 bits (337), Expect = 2e-32
Identities = 56/188 (29%), Positives = 87/188 (46%), Gaps = 32/188 (17%)
Query: 25 NSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLS----RSNRFDVVYHFLS 80
N +G L + + + + F + D+ G+D+L+ R RF VVY +S
Sbjct: 20 NGLGNLWVVLPRERFKEEMAHYKA---MGFNFLADIVGLDYLTYPDPRPERFAVVYELVS 76
Query: 81 PKY-----NRRLRVKIAV-AEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRIL 134
R V++ V E +P++ ++ A++ EREV+D++GI FEGHPDLR+IL
Sbjct: 77 LPGWKDGDGSRFFVRVYVPEEDPRLPTVTDLWGSANFLEREVYDLFGIVFEGHPDLRKIL 136
Query: 135 TDYGFEGHPLRKDFPV----TGFVELHY----------DDKVKKVVYRPVELMQEHRDYD 180
T EGHPLRKD+P+ T F E Y K + + + +R
Sbjct: 137 TPEDLEGHPLRKDYPLGETPTLFREGRYIIPAEFRAALTGKDPGLTFYKGGSRKGYR--- 193
Query: 181 FLSPWEGV 188
S W +
Sbjct: 194 --SLWADL 199
>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 = 38.4 bits (89), Expect = 0.001
Identities = 26/165 (15%), Positives = 52/165 (31%), Gaps = 57/165 (34%)
Query: 43 CSFLR-DDPHCCFVNIIDLCGVDFLSRSNRFDVV------YHFLSPKYNRR-----LRVK 90
+L +D H L + + +++ ++++ R
Sbjct: 93 NCYLEGNDIHAL---AAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR-- 147
Query: 91 IAVAEGKSVPSIVGIYPGA----DWFE--REVWDMYGIFFE-----GHPDLRRILTD--- 136
AV EG + +V I+ G D+FE R+++ Y + L ++
Sbjct: 148 -AVGEGNA--QLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 137 ----Y--GFE-----GHP-LRKD----------FPVTGFVEL-HY 158
+ G +P D P+ G ++L HY
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHY 249
Score = 25.7 bits (56), Expect = 7.0
Identities = 21/99 (21%), Positives = 39/99 (39%), Gaps = 38/99 (38%)
Query: 22 FAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSP 81
FA +S+GE + D++S+ S + +VV++
Sbjct: 1759 FAGHSLGEYAALASLADVMSIESLV--------------------------EVVFY---- 1788
Query: 82 KYNRRLRVKIAVAE---GKSVPSIVGIYPG--ADWFERE 115
R + +++AV G+S ++ I PG A F +E
Sbjct: 1789 ---RGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQE 1824
Score = 25.7 bits (56), Expect = 8.2
Identities = 23/106 (21%), Positives = 27/106 (25%), Gaps = 52/106 (49%)
Query: 39 LVSLCSFLRD---DPHCCFVNIIDLCGVD-----FLSR----SNRFDVV---YH--FLSP 81
L L LR G+D F R SNRF V +H L P
Sbjct: 386 LYGLNLTLRKAKAPS-----------GLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVP 434
Query: 82 ----------KYNRRLR---VKIAV-----------AEGKSVPSIV 103
K N ++I V G IV
Sbjct: 435 ASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIV 480
>2b3w_A Hypothetical protein YBIA; structure, NESG, structural genomics,
COG 3236, PSI, protein structure initiative; NMR
{Escherichia coli} SCOP: d.336.1.1
Length = 168
Score = 32.2 bits (73), Expect = 0.090
Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 8/98 (8%)
Query: 48 DDPHCCFVNI----IDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKSVPSIV 103
D + F N I + G + + + F FL KY +R + +
Sbjct: 23 SDDYGDFSNFAAWPIKVDGKTWPTSEHYF-QAQKFLDEKYREEIRRVSSPMVAARMGRDR 81
Query: 104 GIYPGADWFEREVWDMYGIF---FEGHPDLRRILTDYG 138
+W + M FE H +LR +L
Sbjct: 82 SKPLRKNWESVKEQVMRKALRAKFEQHAELRALLLATA 119
>3gr7_A NADPH dehydrogenase; flavin, FMN, beta-alpha-barrel,
oxidoreductase, flavoprotein; HET: FMN; 2.30A
{Geobacillus kaustophilus} PDB: 3gr8_A*
Length = 340
Score = 30.7 bits (69), Expect = 0.25
Identities = 15/109 (13%), Positives = 33/109 (30%), Gaps = 16/109 (14%)
Query: 77 HFLSPKYNRRL---------RVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGH 127
FLSP NRR R + +V + P + G+ + +
Sbjct: 173 EFLSPLSNRRQDEYGGSPENRYRFLGEVIDAVREVWD-GPLFVRISASDYHPDGLTAKDY 231
Query: 128 PDLRRILTDYGF------EGHPLRKDFPVTGFVELHYDDKVKKVVYRPV 170
+ + + G G + V ++ + + +++ P
Sbjct: 232 VPYAKRMKEQGVDLVDVSSGAIVPARMNVYPGYQVPFAELIRREADIPT 280
>3hgj_A Chromate reductase; TIM barrel, oxidoreductase; HET: FMN; 2.00A
{Thermus scotoductus} PDB: 3hf3_A*
Length = 349
Score = 29.7 bits (66), Expect = 0.43
Identities = 25/113 (22%), Positives = 38/113 (33%), Gaps = 17/113 (15%)
Query: 75 VYHFLSPKYNRR---------------LRVKIAVAEGKSVPSIVGIYPGADWFEREVWDM 119
+ FLSP N+R L+V AV E + + A + W +
Sbjct: 179 LSSFLSPLSNQRTDAYGGSLENRMRFPLQVAQAVREVVPRELPLFVRVSATDWGEGGWSL 238
Query: 120 --YGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPV 170
F +L L D G LR P+ ++ + D V+K V
Sbjct: 239 EDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPFADAVRKRVGLRT 291
>3khs_A Purine nucleoside phosphorylase; alpha-beta structure, mixed
beta-barrel, hydrolase; 2.38A {Grouper iridovirus}
Length = 285
Score = 28.3 bits (63), Expect = 1.2
Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 14/99 (14%)
Query: 22 FAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSN--RFDVVYHFL 79
N+ G L+ GD + + D +N+ L G + L+ N + +
Sbjct: 109 VLTNAAGGLNPSYRPGDFM-----VVRD----HINLPGLAGANPLTGPNDDTEGERFPSM 159
Query: 80 SPKYNRRLR---VKIAVAEGKSVPSIVGIYPGADWFERE 115
+ Y++ LR + A G S + G+Y + E
Sbjct: 160 TSVYDKTLRKYAISAARELGMSYATHEGVYCCVNGPSFE 198
>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A
2dno_A
Length = 105
Score = 27.3 bits (60), Expect = 2.5
Identities = 17/84 (20%), Positives = 27/84 (32%), Gaps = 9/84 (10%)
Query: 27 VGELSLDVDCGDLVSLCSFLRDDPHCCFV--NIIDLCGVDFLSRSNRFDVVY-------H 77
VG L+ D++ L C + G F+ S+ +
Sbjct: 20 VGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHALHGS 79
Query: 78 FLSPKYNRRLRVKIAVAEGKSVPS 101
P + L VK A + +S PS
Sbjct: 80 QTMPGASSSLVVKFADTDKESGPS 103
>2nl9_A Fusion protein consisting of induced myeloid leukemia cell
differentiation protein...; apoptosis, MCL-1, BIM; HET:
MSE; 1.55A {Rattus norvegicus} PDB: 2nla_A 3d7v_A 3io9_A
2pqk_A 1wsx_A 2jm6_B 2roc_A 2rod_A
Length = 157
Score = 26.8 bits (59), Expect = 3.0
Identities = 12/85 (14%), Positives = 27/85 (31%), Gaps = 18/85 (21%)
Query: 119 MYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRD 178
M +F +G + RI+T F + ++ + ++ + +++
Sbjct: 80 MIHVFSDGVTNWGRIVTLISFGAFVAKH------LKTINQESCIEPLAESITDVLVRT-- 131
Query: 179 YDFLSP-------WEGVNSLFAKED 196
W+G F ED
Sbjct: 132 ---KRDWLVKQRGWDGFVEFFHVED 153
>2e7h_A Ephrin type-B receptor 4; FN3 domain, tyrosine- protein kinase
receptor HTK, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 109
Score = 26.9 bits (58), Expect = 3.4
Identities = 7/78 (8%), Positives = 18/78 (23%)
Query: 24 VNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKY 83
V SL + + + D + +++ L
Sbjct: 16 VTRSSPSSLSLAWAVPRAPSGAVLDYEVKYHEKGAEGPSSVRFLKTSENRAELRGLKRGA 75
Query: 84 NRRLRVKIAVAEGKSVPS 101
+ ++V+ G
Sbjct: 76 SYLVQVRARSEAGYGPFG 93
>1u09_A Polyprotein; protein-DNA complex, RNA-dependent RNA polymerase,
transferase; 1.91A {Foot-and-mouth disease virus c-s8c1}
SCOP: e.8.1.4 PDB: 1wne_A 2e9r_X* 2e9t_A* 2e9z_A* 2ec0_A
2f8e_X* 2d7s_A*
Length = 476
Score = 25.7 bits (56), Expect = 7.4
Identities = 10/38 (26%), Positives = 11/38 (28%)
Query: 48 DDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNR 85
D FV + V FL R D F P
Sbjct: 368 DKSDKGFVLGHSITDVTFLKRHFHMDYGTGFYKPVMAS 405
>2nvv_A Acetyl-COA hydrolase/transferase family protein; alpha beta
protein, structural genomics, PSI-2, protein structure
initiative; 2.70A {Porphyromonas gingivalis W83}
Length = 506
Score = 25.8 bits (56), Expect = 7.5
Identities = 9/29 (31%), Positives = 10/29 (34%), Gaps = 6/29 (20%)
Query: 127 HPDLRRILTDY------GFEGHPLRKDFP 149
HPD R +L Y G L F
Sbjct: 449 HPDYRPLLRQYLELGVKGQTPQNLDCCFA 477
>3nzo_A UDP-N-acetylglucosamine 4,6-dehydratase; structural genomics,
PSI-2, protein structure initiative, MI center for
structural genomics, MCSG, NAD; HET: MSE NAD; 2.10A
{Vibrio fischeri}
Length = 399
Score = 25.2 bits (54), Expect = 9.6
Identities = 10/78 (12%), Positives = 27/78 (34%), Gaps = 9/78 (11%)
Query: 1 MVRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDL 60
+ ++I ++ S E ++ D+ S ++ D ++I +
Sbjct: 51 VTKEIFKRNPQKLHVVDIS---------ENNMVELVRDIRSSFGYINGDFQTFALDIGSI 101
Query: 61 CGVDFLSRSNRFDVVYHF 78
F+ ++D V +
Sbjct: 102 EYDAFIKADGQYDYVLNL 119
>1fp2_A Isoflavone O-methytransferase; protein-product complex; HET: SAH
HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12
PDB: 1fpx_A* 2qyo_A*
Length = 352
Score = 25.1 bits (54), Expect = 9.6
Identities = 20/158 (12%), Positives = 38/158 (24%), Gaps = 36/158 (22%)
Query: 32 LDVDCGDLVSLCSFLRDDPHCCFVNI--------------IDLCGVDFLSRSNRFDVVYH 77
+DV G + P + + G D + D V
Sbjct: 193 VDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLL 252
Query: 78 FLSPKYNRRLRVKIAVAE--------GKSVPSIVGIYPGADWFEREVW-------DMYGI 122
+ + GK + + D+
Sbjct: 253 KYILHNWTDKDCLRILKKCKEAVTNDGKRGKVTIIDMVIDKKKDENQVTQIKLLMDVNMA 312
Query: 123 FFEGHP----DLRRILTDYGFEGHPLRKDFPVTGFVEL 156
G + +++ + GF+ K P+TGF+ L
Sbjct: 313 CLNGKERNEEEWKKLFIEAGFQ---HYKISPLTGFLSL 347
>2cqd_A RNA-binding region containing protein 1; RNA recognition motif,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
d.58.7.1
Length = 116
Score = 25.1 bits (54), Expect = 9.9
Identities = 13/88 (14%), Positives = 17/88 (19%), Gaps = 6/88 (6%)
Query: 27 VGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCG------VDFLSRSNRFDVVYHFLS 80
VG L L D + V R+
Sbjct: 22 VGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDPNP 81
Query: 81 PKYNRRLRVKIAVAEGKSVPSIVGIYPG 108
R+ V +A K G G
Sbjct: 82 IIDGRKANVNLAYLGAKPRSLQTGFAIG 109
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 0.144 0.457
Gapped
Lambda K H
0.267 0.0469 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,997,460
Number of extensions: 98307
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 384
Number of HSP's successfully gapped: 30
Length of query: 202
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 114
Effective length of database: 3,559,758
Effective search space: 405812412
Effective search space used: 405812412
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 (21.5 bits)
S2: 54 (25.2 bits)