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)