RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780856|ref|YP_003065269.1| NADH-quinone oxidoreductase, E
subunit [Candidatus Liberibacter asiaticus str. psy62]
(218 letters)
>gnl|CDD|183479 PRK12373, PRK12373, NADH dehydrogenase subunit E; Provisional.
Length = 400
Score = 372 bits (956), Expect = e-104
Identities = 147/214 (68%), Positives = 170/214 (79%), Gaps = 2/214 (0%)
Query: 2 SVRRLAEEEFQPSSFSFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAI 61
+RRL E+ QP SF+F+ E+A W + I++YP R SAVIPLLMRAQEQEGWV+RAAI
Sbjct: 1 MLRRLHED--QPDSFAFTPENAAWAEKQITKYPEGRQASAVIPLLMRAQEQEGWVTRAAI 58
Query: 62 EVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIH 121
E VA++LDMAYIRVLE+ATFYTQFQL PVGTRAH+QVCGTTPCMLRG E L+ VC++KIH
Sbjct: 59 EKVADMLDMAYIRVLEVATFYTQFQLQPVGTRAHIQVCGTTPCMLRGSEALMAVCKSKIH 118
Query: 122 QKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFSTGQGDTIR 181
P N+DGTLSWEEVEC GACVNAPMV IGKD YEDLTPERLEEIIDAF+ G+G ++
Sbjct: 119 AHPHELNADGTLSWEEVECLGACVNAPMVQIGKDYYEDLTPERLEEIIDAFAAGKGPVVK 178
Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDD 215
PGPQI R +S PAGGLTSL + K R K
Sbjct: 179 PGPQIGRYASEPAGGLTSLTEEAGKARYNASKAL 212
>gnl|CDD|181024 PRK07539, PRK07539, NADH dehydrogenase subunit E; Validated.
Length = 154
Score = 237 bits (608), Expect = 1e-63
Identities = 75/157 (47%), Positives = 95/157 (60%), Gaps = 3/157 (1%)
Query: 17 SFSEESAIWVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVL 76
S E + I++YP R SAVIP L QEQ GWV AIE VA+ L M I V
Sbjct: 1 MLSAEELAAIEREIAKYPRPR--SAVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58
Query: 77 EIATFYTQFQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWE 136
E+ATFY+ PVG R +QVC +TPC LRG E ++ + K+ KP +DG +
Sbjct: 59 EVATFYSMIFRQPVG-RHVIQVCTSTPCWLRGGEAILAALKKKLGIKPGETTADGRFTLL 117
Query: 137 EVECQGACVNAPMVMIGKDTYEDLTPERLEEIIDAFS 173
EVEC GAC NAP+VMI DTYEDLTPE+++E++D
Sbjct: 118 EVECLGACDNAPVVMINDDTYEDLTPEKIDELLDELK 154
>gnl|CDD|131013 TIGR01958, nuoE_fam, NADH-quinone oxidoreductase, E subunit. This
model describes the E chain of complexes that resemble
NADH-quinone oxidoreductases. The electron acceptor is a
quinone, ubiquinone, in mitochondria and most bacteria,
including Escherichia coli, where the recommended gene
symbol is nuoB. This model does not identify proteins
from chloroplast and cyanobacteria.
Length = 148
Score = 209 bits (533), Expect = 5e-55
Identities = 70/148 (47%), Positives = 98/148 (66%), Gaps = 1/148 (0%)
Query: 25 WVNEVISRYPPSRCQSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQ 84
+ E+I++YP + +SA++P LM AQEQ+GWV+ AI VA +L + + V E+ATFY+
Sbjct: 1 LIEEIIAKYPDDQKRSAIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSM 60
Query: 85 FQLSPVGTRAHVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGAC 144
F PVG R H+QVC PC LRG E L++ NK+ KP DG + EVEC GAC
Sbjct: 61 FDTEPVG-RYHLQVCTNVPCALRGSEALLKYLENKLGIKPGETTPDGRFTLVEVECLGAC 119
Query: 145 VNAPMVMIGKDTYEDLTPERLEEIIDAF 172
NAP++MI D YE LTPE+L+E+++ +
Sbjct: 120 GNAPVMMINDDYYEFLTPEKLDELLERY 147
>gnl|CDD|136420 PRK07571, PRK07571, bidirectional hydrogenase complex protein HoxE;
Reviewed.
Length = 169
Score = 82.9 bits (205), Expect = 5e-17
Identities = 46/135 (34%), Positives = 65/135 (48%), Gaps = 1/135 (0%)
Query: 39 QSAVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHVQV 98
Q A+I +L +AQE G++ R + VA L + RV +ATFY F L P G V V
Sbjct: 35 QDALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVYGVATFYHLFSLKPSGEHTCV-V 93
Query: 99 CGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKDTYE 158
C T C ++G ++E N++ K +DG LS C GAC AP V+
Sbjct: 94 CTGTACYVKGSAAILEDLENELGIKAGETTADGKLSLLTARCLGACGIAPAVVFDGKVAG 153
Query: 159 DLTPERLEEIIDAFS 173
TPE + E + +
Sbjct: 154 KQTPESVLEKVQGWL 168
>gnl|CDD|180339 PRK05988, PRK05988, formate dehydrogenase subunit gamma; Validated.
Length = 156
Score = 66.9 bits (164), Expect = 4e-12
Identities = 38/135 (28%), Positives = 68/135 (50%), Gaps = 11/135 (8%)
Query: 41 AVIPLLMRAQEQEGWVSRAAIEVVANILDMAYIRVLEIATFYTQFQLSPVGTRAHV-QVC 99
A++P+L Q++ G+V A+ V+A L+++ V + TFY F+ P G HV ++C
Sbjct: 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVHGVITFYHDFRTHPPG--RHVLKLC 81
Query: 100 GTTPCMLRGCEKLIEVCRNKI----HQKPLHRNSDGTLSWEEVECQGACVNAPMVMIGKD 155
C G + L + ++ HQ +DG ++ E V C G C +P M+ +
Sbjct: 82 RAEACQAMGGDALAAHAKARLGIDFHQ----TTADGAVTLEPVYCLGLCACSPAAMLDGE 137
Query: 156 TYEDLTPERLEEIID 170
+ L P+RL+ ++
Sbjct: 138 VHGRLDPQRLDALLA 152
>gnl|CDD|185473 PTZ00139, PTZ00139, Succinate dehydrogenase [ubiquinone]
flavoprotein subunit; Provisional.
Length = 617
Score = 30.1 bits (68), Expect = 0.44
Identities = 13/64 (20%), Positives = 22/64 (34%), Gaps = 9/64 (14%)
Query: 95 HVQVCGTTPCMLRGCEKLIEVCRNKIHQKPLHRNSDGTLSW-----EEVECQGACVNAPM 149
H V + G EK+ E+ + K D +L W E +E + A
Sbjct: 492 HAAVFRIGESLQEGVEKIKEIYSDFKDVKI----KDKSLVWNTDLIETLELENLLTQAKQ 547
Query: 150 VMIG 153
++
Sbjct: 548 TILS 551
>gnl|CDD|161886 TIGR00456, argS, arginyl-tRNA synthetase. This model recognizes
arginyl-tRNA synthetase in every completed genome to
date. An interesting feature of the alignment of all
arginyl-tRNA synthetases is a fairly deep split between
two families. One family includes archaeal, eukaryotic
and organellar, spirochete, E. coli, and Synechocystis
sp. The second, sharing a deletion of about 25 residues
in the central region relative to the first, includes
Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas
and Mycobacteria, and the Gram-negative bacterium
Helicobacter pylori.
Length = 566
Score = 28.1 bits (63), Expect = 2.0
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 60 AIEVVANILDMAYIRVLEIATFYTQFQLSP 89
A E+V + I +E A + F LSP
Sbjct: 57 AEEIVLKLKTGEIIEKVEAAGPFINFFLSP 86
>gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein;
Provisional.
Length = 267
Score = 27.8 bits (62), Expect = 2.1
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 54 GWVSRAAIEVVANILDMA 71
G V A E V IL+MA
Sbjct: 16 GVVDPAHREEVKRILEMA 33
>gnl|CDD|178672 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 27.3 bits (60), Expect = 3.0
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 182 PGPQIDRISSAPAGGLTSLLDNNSKKRGKKKKDDKI 217
PG I IS + L +L++N + KRG K DKI
Sbjct: 233 PGDDIPIISGSALLALEALMENPNIKRGDNKWVDKI 268
>gnl|CDD|183390 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 27.5 bits (62), Expect = 3.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 16 FSFSEESAIWVNEVISRYPP 35
FS S IWV++ + RYPP
Sbjct: 335 FSKSRGWGIWVDDALERYPP 354
>gnl|CDD|180170 PRK05626, rpsO, 30S ribosomal protein S15; Reviewed.
Length = 89
Score = 27.4 bits (62), Expect = 3.1
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 13/58 (22%)
Query: 160 LTPERLEEIIDAFSTGQGDTIRPGPQI----DRISSAPAGGLTSLLDNNSK----KRG 209
LT E+ EII + +GDT P Q+ +RI+ LT L + K +RG
Sbjct: 3 LTKEKKAEIIKEYGRHEGDTGSPEVQVALLTERINH-----LTEHLKEHKKDHHSRRG 55
>gnl|CDD|162887 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2, ) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 27.3 bits (61), Expect = 3.5
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 7/83 (8%)
Query: 108 GCEKLIEVCRNKIHQKPLHRNSDGTLSWEEV------ECQGACVNAPMVMIGKD-TYEDL 160
GC K +EVC + + + +C AC + + ++G++ T E++
Sbjct: 52 GCGKCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKCTEACPSGALSIVGEEMTVEEV 111
Query: 161 TPERLEEIIDAFSTGQGDTIRPG 183
L + I ++G G T+ G
Sbjct: 112 MRVVLRDSIFYRNSGGGVTLSGG 134
>gnl|CDD|177740 PLN00129, PLN00129, succinate dehydrogenase [ubiquinone]
iron-sulfur subunit.
Length = 276
Score = 27.1 bits (60), Expect = 3.6
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 11/46 (23%)
Query: 155 DTYEDLTPERLEEIIDAFSTGQGDTIR-----------PGPQIDRI 189
D+ ++ T ERLE + D F + TIR P I +I
Sbjct: 224 DSRDEYTKERLEALDDEFKLYRCHTIRNCSNACPKGLNPAKAIAKI 269
>gnl|CDD|177871 PLN02226, PLN02226, 2-oxoglutarate dehydrogenase E2 component.
Length = 463
Score = 26.3 bits (57), Expect = 5.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 168 IIDAFSTGQGDTIRPGPQIDRISSA 192
+I F +GDT+ PG ++ IS +
Sbjct: 144 VIQEFLVKEGDTVEPGTKVAIISKS 168
>gnl|CDD|178776 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 26.0 bits (57), Expect = 8.5
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 11/55 (20%)
Query: 119 KIHQKP----LHRNSDGTLSWEEVE-------CQGACVNAPMVMIGKDTYEDLTP 162
I Q P ++G LS EV+ CQ C+ A + + K Y D+ P
Sbjct: 72 DIRQPPGGGIYGAVTEGPLSVFEVDGKKAKVYCQNLCLLAKLFLDHKTLYYDVDP 126
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.317 0.132 0.393
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,595,000
Number of extensions: 219092
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 484
Number of HSP's successfully gapped: 16
Length of query: 218
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 128
Effective length of database: 4,049,753
Effective search space: 518368384
Effective search space used: 518368384
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.0 bits)