RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780852|ref|YP_003065265.1| NADH dehydrogenase subunit A [Candidatus Liberibacter asiaticus str. psy62] (121 letters) >gnl|CDD|31180 COG0838, NuoA, NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Energy production and conversion]. Length = 123 Score = 121 bits (306), Expect = 3e-29 Identities = 58/121 (47%), Positives = 88/121 (72%) Query: 1 MSDLLTSYAPILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFD 60 M +LL Y P+L+F+ +A + ++++ ++ + P+PEKLS YECG PF AR++F Sbjct: 1 MMELLDEYLPVLIFLVVALLLGVLMLFLSKLLGPRRPNPEKLSPYECGNPPFGGARLRFS 60 Query: 61 IRFCLVSVLFVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 +++ LV++LFV+FD+E+ FLFPWAV FK++ GF M+VF+ +L VGF+Y WKKGALEW Sbjct: 61 VQYYLVAILFVVFDVEVVFLFPWAVSFKELGLFGFLEMLVFIFVLLVGFVYAWKKGALEW 120 Query: 121 D 121 Sbjct: 121 Q 121 >gnl|CDD|177128 MTH00055, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 118 Score = 119 bits (301), Expect = 2e-28 Identities = 60/111 (54%), Positives = 79/111 (71%), Gaps = 2/111 (1%) Query: 13 VFMAIASAIVIVLMIS--PFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLF 70 +F+ + +I + +IS +IV K PD EK+S YECGFDPF+ +R+ F +RF LV +LF Sbjct: 8 IFILLLFSIGLSTVISGASYIVGVKQPDSEKVSVYECGFDPFESSRIPFSVRFFLVGILF 67 Query: 71 VIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEWD 121 +IFDLEI+FLFPW V + QI GF M +FL ILT+G IYEW KG LEW+ Sbjct: 68 LIFDLEISFLFPWCVVYNQIGLFGFWVMYLFLIILTIGLIYEWVKGGLEWE 118 >gnl|CDD|164592 MTH00018, ND3, NADH dehydrogenase subunit 3; Validated. Length = 113 Score = 113 bits (284), Expect = 2e-26 Identities = 53/111 (47%), Positives = 72/111 (64%) Query: 11 ILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLF 70 + + + + + + + + + K PD EK+S YECGFDPF F IRF L+ +LF Sbjct: 3 LFILLIFSVVLSALFSGASYFLGVKQPDREKVSAYECGFDPFGFPGRPFSIRFFLIGILF 62 Query: 71 VIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEWD 121 +IFDLEI+FLFPW V + QI GF +M+ FL ILT+G IYEW KG LEW+ Sbjct: 63 LIFDLEISFLFPWCVLYNQIAPFGFWTMVGFLFILTLGLIYEWIKGGLEWE 113 >gnl|CDD|109558 pfam00507, Oxidored_q4, NADH-ubiquinone/plastoquinone oxidoreductase, chain 3. Length = 102 Score = 109 bits (276), Expect = 2e-25 Identities = 51/101 (50%), Positives = 72/101 (71%), Gaps = 1/101 (0%) Query: 21 IVIVLMISPFIVAFKSPDP-EKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIFDLEIAF 79 + ++L++ F+++ K P EKLS YECGFDP AR+ F +RF L+++LF+IFD+EI Sbjct: 2 LSLILLLLSFLLSPKKPSDREKLSPYECGFDPLGKARLPFSLRFFLIAILFLIFDVEIIL 61 Query: 80 LFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 L PWAV F + +L F M +FL IL +G +YEWKKGAL+W Sbjct: 62 LLPWAVVFNGLGFLSFVEMFLFLLILLLGLLYEWKKGALDW 102 >gnl|CDD|177141 MTH00069, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 114 Score = 104 bits (261), Expect = 6e-24 Identities = 51/112 (45%), Positives = 73/112 (65%), Gaps = 3/112 (2%) Query: 11 ILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLF 70 I++ + I++ + ++L+ F + +PD EKLS YECGFDP AR+ F IRF LV++LF Sbjct: 2 IMLMLLISTILSLILITISFWLPLNNPDSEKLSPYECGFDPLGSARLPFSIRFFLVAILF 61 Query: 71 VIFDLEIAFLF--PWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 ++FDLEIA L PWA T F S ++ + +LT+G IYEW +G LEW Sbjct: 62 LLFDLEIALLLPTPWASQLNTPTNTLFWSTLILI-LLTLGLIYEWIQGGLEW 112 >gnl|CDD|177194 MTH00136, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 116 Score = 101 bits (255), Expect = 3e-23 Identities = 51/113 (45%), Positives = 67/113 (59%), Gaps = 3/113 (2%) Query: 10 PILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVL 69 I + I A+ ++L I F + +PD EKLS YECGFDP AR+ F +RF LV++L Sbjct: 3 LITTILTITIALSLILAIVSFWLPQMTPDHEKLSPYECGFDPLGSARLPFSLRFFLVAIL 62 Query: 70 FVIFDLEIAFLF--PWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 F++FDLEIA L PW F + V L +LT+G IYEW +G LEW Sbjct: 63 FLLFDLEIALLLPLPWGDQLPSPLLTFFWATAV-LILLTLGLIYEWLQGGLEW 114 >gnl|CDD|177175 MTH00113, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 114 Score = 102 bits (256), Expect = 3e-23 Identities = 51/112 (45%), Positives = 67/112 (59%), Gaps = 11/112 (9%) Query: 15 MAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIFD 74 + I+ A+ +L F + PD EKLS YECGFDP AR+ F IRF LV++LF++FD Sbjct: 7 LTISLALSTILTTLNFWLTQTKPDNEKLSPYECGFDPLGSARLPFSIRFFLVAILFLLFD 66 Query: 75 LEIAFLFP--WAVYF----KQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 LEIA L P WA+ +TW + L +LT+G IYEW +G LEW Sbjct: 67 LEIALLLPLPWAINLTTPTTTLTW-----ATIILTLLTLGLIYEWLQGGLEW 113 >gnl|CDD|176964 CHL00022, ndhC, NADH dehydrogenase subunit 3. Length = 120 Score = 97.0 bits (242), Expect = 1e-21 Identities = 49/117 (41%), Positives = 74/117 (63%) Query: 4 LLTSYAPILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRF 63 LL Y F+ I+S I I+ + ++A S PEKLS+YE G +P DA ++F IR+ Sbjct: 3 LLYEYDIFWAFLIISSLIPILAFLISGLLAPISKGPEKLSSYESGIEPMGDAWLQFRIRY 62 Query: 64 CLVSVLFVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 + +++FV+FD+E FL+PWA+ F + F ++F+ IL VG +Y W+KGALEW Sbjct: 63 YMFALVFVVFDVETVFLYPWAMSFDVLGVSAFIEALIFVLILIVGLVYAWRKGALEW 119 >gnl|CDD|164603 MTH00030, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 123 Score = 94.2 bits (234), Expect = 8e-21 Identities = 50/114 (43%), Positives = 67/114 (58%) Query: 8 YAPILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVS 67 ++ +L I + I + + PD EK S YECGFDPF R F I+F LV Sbjct: 10 FSTLLGVGIILLLVSISFTLGNSRIGLTKPDSEKSSIYECGFDPFGKIRTPFTIKFVLVG 69 Query: 68 VLFVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEWD 121 +LF+IFD+EI+FLFPW++ F Q+ F + FL +L +G YEW KG LEWD Sbjct: 70 ILFMIFDIEISFLFPWSIVFNQLNLFSFWIVYTFLIVLAIGLAYEWIKGGLEWD 123 >gnl|CDD|177117 MTH00042, ND3, NADH dehydrogenase subunit 3; Validated. Length = 116 Score = 93.9 bits (234), Expect = 1e-20 Identities = 50/113 (44%), Positives = 71/113 (62%), Gaps = 3/113 (2%) Query: 10 PILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVL 69 ++ F+ I + +L+++ + +SPD EK S YECGFDP + AR+ F RF LV++L Sbjct: 3 NLIFFLLIILILTSLLLLAGHFLPSRSPDLEKSSPYECGFDPLNSARLPFSFRFFLVAIL 62 Query: 70 FVIFDLEIAFLFP--WAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 F++FDLEIA LFP A + L S ++FL ILT+G +YEW G LEW Sbjct: 63 FLLFDLEIALLFPLPPATLITNPSTLLPIS-LIFLIILTIGLVYEWVNGGLEW 114 >gnl|CDD|39861 KOG4662, KOG4662, KOG4662, NADH dehydrogenase subunit 3 and related proteins [Energy production and conversion]. Length = 122 Score = 85.8 bits (212), Expect = 3e-18 Identities = 51/121 (42%), Positives = 67/121 (55%), Gaps = 2/121 (1%) Query: 1 MSDLLTSYAPILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFD 60 M + L+ + SAI + +IS + S EK S YECGFDP DAR+ F Sbjct: 1 MMLAFAIISIFLLILLQVSAIYLAFLISILLSTS-SVGKEKSSPYECGFDPLGDARLPFS 59 Query: 61 IRFCLVSVLFVIFDLEIAFLFPWAVYFKQITWLGFGSMM-VFLGILTVGFIYEWKKGALE 119 IRF LV++ F+IFDLEI L P A+ FG M +F+ IL +G YEW +GAL+ Sbjct: 60 IRFFLVAITFLIFDLEIVLLLPGALPQDMSGLHPFGIMAFIFILILKIGLYYEWSEGALD 119 Query: 120 W 120 W Sbjct: 120 W 120 >gnl|CDD|177205 MTH00148, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 117 Score = 85.7 bits (213), Expect = 3e-18 Identities = 42/112 (37%), Positives = 67/112 (59%), Gaps = 2/112 (1%) Query: 11 ILVFMAIASAIVIVLMISPFIVAFKSP-DPEKLSTYECGFDPFDDARVKFDIRFCLVSVL 69 IL+ + A + VL++ +++ +S D EK S +ECGFDP AR F +RF L+++L Sbjct: 4 ILLSLLFALILSPVLLLLGLVLSKRSYSDREKSSPFECGFDPISSARSPFSLRFFLLAIL 63 Query: 70 FVIFDLEIAFLFP-WAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 F++FD+EI LFP + S+ +FL IL +G +EW +G+L+W Sbjct: 64 FLVFDVEIVLLFPVLQSLGSSFSVWSLTSLFIFLLILILGLFHEWNEGSLDW 115 >gnl|CDD|177217 MTH00161, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 113 Score = 85.2 bits (212), Expect = 4e-18 Identities = 49/112 (43%), Positives = 69/112 (61%), Gaps = 2/112 (1%) Query: 11 ILVFMAIASAIVIVLMISPFIVAFKSP-DPEKLSTYECGFDPFDDARVKFDIRFCLVSVL 69 IL+ + I I I+LMI +++ KS D EK S +ECGFDP AR+ F +RF L++++ Sbjct: 2 ILIILLIILLISIILMILASLLSKKSIMDREKSSPFECGFDPKSSARLPFSLRFFLIAII 61 Query: 70 FVIFDLEIAFLFPWAVYFKQITWLGFGSMM-VFLGILTVGFIYEWKKGALEW 120 F+IFD+EIA L P FK + + F+ IL +G YEW +GALEW Sbjct: 62 FLIFDVEIALLLPMIFIFKTSNMMSWLITSSFFILILLLGLYYEWNQGALEW 113 >gnl|CDD|177248 MTH00203, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 112 Score = 84.6 bits (210), Expect = 7e-18 Identities = 49/110 (44%), Positives = 71/110 (64%), Gaps = 1/110 (0%) Query: 11 ILVFMAIASAIVIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLF 70 I++F IA + ++L+ F + +PD EKLS YECGFDP AR+ F ++F LV++ F Sbjct: 4 IMLFFLIALLLSLILLFIAFWLPKVNPDGEKLSPYECGFDPLGSARLPFSLQFFLVALSF 63 Query: 71 VIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 ++FDLEIA L P + Q++ L +FL +LT+G IYEW +G LEW Sbjct: 64 LLFDLEIALLLPL-PWSNQLSSLSLLLAFLFLILLTLGLIYEWLQGGLEW 112 >gnl|CDD|164588 MTH00012, ND3, NADH dehydrogenase subunit 3; Validated. Length = 117 Score = 73.7 bits (181), Expect = 1e-14 Identities = 38/108 (35%), Positives = 69/108 (63%), Gaps = 2/108 (1%) Query: 15 MAIASAIVIVLMISPFIVAFKSP-DPEKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIF 73 M I+ + +++ + +++A +S D EK S +ECGFDP AR+ F +RF L++++F++F Sbjct: 8 MMISLILPPLVLGAAWVLAARSTADREKTSPFECGFDPHKTARIPFSLRFFLLAIIFIVF 67 Query: 74 DLEIAFLFPW-AVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 D+EI L P + + + ++FL IL +G I+EW++G+L+W Sbjct: 68 DIEIVLLMPVPTILMTSTSKTVVYTSILFLLILVIGLIHEWREGSLDW 115 >gnl|CDD|177168 MTH00106, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 115 Score = 73.4 bits (181), Expect = 1e-14 Identities = 34/83 (40%), Positives = 48/83 (57%), Gaps = 3/83 (3%) Query: 40 EKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIFDLEIAFLF--PWAVYFKQITWLGFGS 97 EK S YECGFDP AR+ F ++F LV++ F++FDLEIA L PWA + Sbjct: 32 EKASPYECGFDPMGSARLPFSMKFFLVAITFLLFDLEIALLLPLPWASQTNNLN-TMLTM 90 Query: 98 MMVFLGILTVGFIYEWKKGALEW 120 ++ + +L + YEW + LEW Sbjct: 91 ALLLISLLALSLAYEWTQKGLEW 113 >gnl|CDD|177247 MTH00202, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 117 Score = 71.6 bits (176), Expect = 5e-14 Identities = 39/100 (39%), Positives = 61/100 (61%), Gaps = 1/100 (1%) Query: 22 VIVLMISPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVLFVIFDLEIAFLF 81 ++ ++S + D EK S +ECGFDP + AR+ F +RF L++V+F++FD+EIA L Sbjct: 16 SLLFLVSWMLSFRSLMDREKSSPFECGFDPKESARLPFSMRFFLLAVIFLVFDIEIALLL 75 Query: 82 PWAVY-FKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 P + + G +FL IL G I+EWK+G+L+W Sbjct: 76 PLPLVLKSSWSKGGLLGGTIFLLILIGGLIHEWKEGSLDW 115 >gnl|CDD|177155 MTH00092, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 111 Score = 39.5 bits (93), Expect = 2e-04 Identities = 31/111 (27%), Positives = 56/111 (50%), Gaps = 5/111 (4%) Query: 11 ILVFMAIASAIVIVLMI-SPFIVAFKSPDPEKLSTYECGFDPFDDARVKFDIRFCLVSVL 69 +L+F+ + + ++++L+ F ++ K D K+S++ECGF+ + F I F + ++ Sbjct: 3 VLIFVFLFTLLLLMLLYLLNFFLSVKKFDLLKVSSFECGFESVGKIQNSFSIHFFKIMLM 62 Query: 70 FVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFLGILTVGFIYEWKKGALEW 120 FVIFDLEI + + S + + + GF EW G L W Sbjct: 63 FVIFDLEIVMF----LGLLVSDFSSLISFFMLMIFIFFGFYMEWWYGKLIW 109 >gnl|CDD|177132 MTH00060, ND3, NADH dehydrogenase subunit 3; Provisional. Length = 116 Score = 36.0 bits (84), Expect = 0.002 Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 2/78 (2%) Query: 43 STYECGFDPFDDARVKFDIRFCLVSVLFVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFL 102 S++ECGF + F + + V FVIFDLEI+ L + F+ + + F FL Sbjct: 39 SSFECGFFSSGLSENCFSFTYFFLLVFFVIFDLEISLLL--NMPFQGLLFYNFWYYYFFL 96 Query: 103 GILTVGFIYEWKKGALEW 120 +L +GF+ E G + W Sbjct: 97 LLLFLGFVVELFSGYVRW 114 >gnl|CDD|37730 KOG2519, KOG2519, KOG2519, 5'-3' exonuclease [Replication, recombination and repair]. Length = 449 Score = 26.1 bits (57), Expect = 2.3 Identities = 11/28 (39%), Positives = 16/28 (57%) Query: 35 KSPDPEKLSTYECGFDPFDDARVKFDIR 62 K+PD E L + G F++ RV+ IR Sbjct: 297 KTPDTEGLIQFLVGEKQFNEERVRKGIR 324 >gnl|CDD|33787 COG4028, COG4028, Predicted P-loop ATPase/GTPase [General function prediction only]. Length = 271 Score = 25.7 bits (56), Expect = 3.3 Identities = 8/27 (29%), Positives = 15/27 (55%) Query: 17 IASAIVIVLMISPFIVAFKSPDPEKLS 43 +A +I + + +P V PDPE++ Sbjct: 65 VAESIDRIELENPVAVLLVPPDPERIG 91 >gnl|CDD|147601 pfam05505, Ebola_NP, Ebola nucleoprotein. This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus. Length = 717 Score = 25.7 bits (56), Expect = 3.5 Identities = 6/19 (31%), Positives = 9/19 (47%) Query: 92 WLGFGSMMVFLGILTVGFI 110 W G MMV ++ F+ Sbjct: 173 WQSVGHMMVIFRLMRTNFL 191 >gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]. Length = 3738 Score = 25.5 bits (55), Expect = 4.2 Identities = 13/43 (30%), Positives = 17/43 (39%), Gaps = 3/43 (6%) Query: 60 DIRFCLVSVLFVIFDLEIAFLFPWAVYFKQITWLGFGSMMVFL 102 D++F + L V L FL A Q L F M F+ Sbjct: 454 DVKFTIQGDLQVPHQLP-EFLP--ANLHPQTVDLHFTREMAFI 493 >gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29). Length = 404 Score = 24.5 bits (54), Expect = 6.7 Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 4/40 (10%) Query: 33 AFKSPDPEKLSTYE----CGFDPFDDARVKFDIRFCLVSV 68 DPE+++ Y+ P A + + +C+V+ Sbjct: 106 LLADVDPERIAAYQKARGPALKPRRSATMSNKVSWCVVAY 145 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.334 0.147 0.480 Gapped Lambda K H 0.267 0.0572 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,667,165 Number of extensions: 89887 Number of successful extensions: 621 Number of sequences better than 10.0: 1 Number of HSP's gapped: 600 Number of HSP's successfully gapped: 97 Length of query: 121 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 39 Effective length of database: 4,491,799 Effective search space: 175180161 Effective search space used: 175180161 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 39 (21.5 bits) S2: 51 (23.8 bits)