RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780474|ref|YP_003064887.1| ubiquinol oxidase, subunit II
[Candidatus Liberibacter asiaticus str. psy62]
(332 letters)
>gnl|CDD|182518 PRK10525, PRK10525, cytochrome o ubiquinol oxidase subunit II;
Provisional.
Length = 315
Score = 315 bits (808), Expect = 1e-86
Identities = 133/315 (42%), Positives = 189/315 (60%), Gaps = 14/315 (4%)
Query: 14 KSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAW 73
KSL + LF +V+LSG ++DP G I L+Q SLI A LML++V+P + FAW
Sbjct: 8 KSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAW 67
Query: 74 KYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESK 133
KYR++NK A+Y P W HS +E VW VP++I+ FLAV+TW TH ++P PL
Sbjct: 68 KYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPL------- 120
Query: 134 SIAKNSKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPG 193
A + KP+ +EVV++DWKW F+ PEQ +A +NE+ P + P+ F++T++SVMNSF+IP
Sbjct: 121 --AHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANVPVYFKVTSNSVMNSFFIPR 178
Query: 194 LAGQIYAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGK-SEKGFEDWISKV 252
L QIYAMAGM+T+LH + N+ G Y G SA+YSG GFS M+FK F+ W++K
Sbjct: 179 LGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAEFDQWVAKA 238
Query: 253 KRQGTFLNR-QEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGK---ICMDEMMRI 308
K+ +N + L PSE + V YFS ++ L+ ++N + GK + E
Sbjct: 239 KQSPNTMNDMAAFEKLAAPSEYNPVEYFSSVKPDLFKDVINKFMGHGKSMDMTQPEGEHS 298
Query: 309 DALGGGGMRGIDRHS 323
G GM S
Sbjct: 299 AHEGMEGMDMSHAES 313
>gnl|CDD|130500 TIGR01433, CyoA, cytochrome o ubiquinol oxidase subunit II. This
enzyme catalyzes the oxidation of ubiquinol with the
concomitant reduction of molecular oxygen to water. This
acts as the terminal electron acceptor in the
respiratory chain. Subunit II is responsible for binding
and oxidation of the ubiquinone substrate. This sequence
is closely related to QoxA, which oxidizes quinol in
gram positive bacteria but which is in complex with
subunits which utilize cytochromes a in the reduction of
molecular oxygen. Slightly more distantly related is
subunit II of cytochrome c oxidase which uses cyt. c as
the oxidant.
Length = 226
Score = 314 bits (805), Expect = 3e-86
Identities = 124/235 (52%), Positives = 162/235 (68%), Gaps = 9/235 (3%)
Query: 19 FFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRST 78
LF SV+LSG ++DP G I L++ SLI A LMLL+V+PV LFFAWKYR+T
Sbjct: 1 LSLFAGSVLLSGCNSALLDPKGQIGLEERSLILTAFGLMLLVVIPVILMTLFFAWKYRAT 60
Query: 79 NKKARYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKN 138
NK A Y P W HST +E+ VW +P++I+ FL V+TW TH++DPY PL +
Sbjct: 61 NKDADYSPNWHHSTKIEIVVWTIPILIIIFLGVLTWITTHKLDPYRPLA---------SD 111
Query: 139 SKPLVVEVVALDWKWLFLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQI 198
KP+ +EVVALDWKWLF+ PEQ +A +NE+ P++ P+ F+IT++SVMNSF+IP L QI
Sbjct: 112 VKPITIEVVALDWKWLFIYPEQGIATVNEIAFPVNTPINFKITSNSVMNSFFIPQLGSQI 171
Query: 199 YAMAGMETKLHAVMNKKGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVK 253
YAMAGM+TKLH + N+ G Y G SANYSG GFS M+FK F+ W++KVK
Sbjct: 172 YAMAGMQTKLHLIANEPGVYDGISANYSGPGFSGMKFKAIATDRAAFDQWVAKVK 226
>gnl|CDD|130499 TIGR01432, QOXA, cytochrome aa3 quinol oxidase, subunit II. This
enzyme catalyzes the oxidation of quinol with the
concomitant reduction of molecular oxygen to water. This
acts as the terminal electron acceptor in the
respiratory chain. This subunit contains two
transmembrane helices and a large external domain
responsible for the binding and oxidation of quinol.
QuoX is (presently) only found in gram positive bacteria
of the Bacillus/Staphylococcus group. Like CyoA, the
ubiquinol oxidase found in proteobacteria, the residues
responsible for the ligation of Cu(a) and cytochrome c
(found in the related cyt. c oxidases) are absent.
Unlike CyoA, QoxA is in complex with a subunit I which
contains cytochromes a similar to the cyt. c oxidases
(as opposed to cytochromes b).
Length = 217
Score = 163 bits (413), Expect = 7e-41
Identities = 73/219 (33%), Positives = 114/219 (52%), Gaps = 9/219 (4%)
Query: 35 VMDPYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLL 94
V++P G +A Q+ LI ++ ML+IV VF F KYR Y PK + +L
Sbjct: 8 VLNPKGPVASSQSDLILYSIVFMLVIVFVVFVLFTIFLVKYRYRKDNGAYSPKMHGNAIL 67
Query: 95 ELFVWLVPLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWL 154
E ++P++IV LA+ T + + ++ K P+VV + DWKW
Sbjct: 68 ETIWTVIPIIIVIALAIPTVKTIYDYE---------KAPKSTKEKDPMVVYATSADWKWF 118
Query: 155 FLLPEQQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNK 214
F P++ + +N L +P DRP+ F++ ++ M SF+IP L GQ YAM GM + ++
Sbjct: 119 FSYPDEHIETVNYLNIPKDRPVLFKLQSADTMTSFWIPQLGGQKYAMTGMTMNWYLQADQ 178
Query: 215 KGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWISKVK 253
G Y G +AN++G GF+ F SEK F+ W+ + K
Sbjct: 179 VGTYRGRNANFNGEGFADQTFDVNAVSEKDFDKWVKETK 217
>gnl|CDD|163049 TIGR02866, CoxB, cytochrome c oxidase, subunit II. Cytochrome c
oxidase is the terminal electron acceptor of
mitochondria (and one of several possible acceptors in
prokaryotes) in the electron transport chain of aerobic
respiration. The enzyme couples the oxidation of reduced
cytochrome c with the reduction of molecular oxygen to
water. This process results in the pumping of four
protons across the membrane which are used in the proton
gradient powered synthesis of ATP. The oxidase contains
two heme a cofactors and three copper atoms as well as
other bound ions.
Length = 201
Score = 110 bits (276), Expect = 7e-25
Identities = 63/216 (29%), Positives = 100/216 (46%), Gaps = 18/216 (8%)
Query: 38 PYGDIALQQASLIRIAVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELF 97
P G+IA Q A+L +A+ I + V + + WK+R + + K + LE +
Sbjct: 1 PAGEIAEQIATLWLFLLAVATTISLLVAALLAYVVWKFRRKGDEEK-PSKIHGNRALE-Y 58
Query: 98 VWLV-PLVIVGFLAVITWDATHRMDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFL 156
W V PL+IV L T T ++ + ++ L V+V W W F
Sbjct: 59 TWTVIPLIIVVGLIAATVLGTLYLE-----------RPPPED--ALKVKVEGHQWYWSFD 105
Query: 157 LPEQQVAI--INELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNK 214
PE + +NELVVP P+ ++T+ V++SF++P L G+I A+ G L ++
Sbjct: 106 YPESRRGFTTVNELVVPAGTPVRLQVTSKDVIHSFWVPELGGKIDAIPGQYNALWFNADE 165
Query: 215 KGAYSGFSANYSGRGFSHMRFKFYGKSEKGFEDWIS 250
G Y G+ A G G S M FK + F+ +I
Sbjct: 166 PGVYYGYCAELCGAGHSLMLFKVVVVEREEFDAYIE 201
>gnl|CDD|148220 pfam06481, COX_ARM, COX Aromatic Rich Motif. COX2 (Cytochrome O
ubiquinol OXidase 2) is a major component of the
respiratory complex during vegetative growth. It
transfers electrons from a quinol to the binuclear
centre of the catalytic subunit 1. The function of this
region is not known.
Length = 47
Score = 56.0 bits (136), Expect = 1e-08
Identities = 20/47 (42%), Positives = 27/47 (57%)
Query: 253 KRQGTFLNRQEYLLLKKPSERDSVRYFSPIEKGLYYSILNLCVHPGK 299
K L+R YL L KPSE + V YFS ++ GL+ I+N + GK
Sbjct: 1 KASPKTLDRATYLALAKPSENNPVEYFSSVDPGLFDDIVNKYMGGGK 47
>gnl|CDD|147912 pfam06011, TRP, Transient receptor potential (TRP) ion channel.
This family of proteins are transient receptor potential
(TRP) ion channels. They are essential for cellular
viability and are involved in cell growth and cell wall
synthesis. The genes for these proteins are homologous
to polycystic kidney disease related ion channel genes.
Length = 532
Score = 32.2 bits (74), Expect = 0.18
Identities = 17/83 (20%), Positives = 29/83 (34%), Gaps = 12/83 (14%)
Query: 6 NWMGVSVGKSLKFFFLFFSSVM-LSGFEFIVMDPYGDIALQQASLIRIAVALMLLIVVP- 63
W G L+ +FF ++ LS ++F D + L AV + L++
Sbjct: 295 KWWPFLKGTLLRLVLIFFPPIVILSLWQFTQADSAAAVVL--------AVVFLALLLGLL 346
Query: 64 --VFFSILFFAWKYRSTNKKARY 84
F ++ A K Y
Sbjct: 347 GWAAFRVISIARKSVRLYGNPAY 369
>gnl|CDD|185413 PTZ00047, PTZ00047, cytochrome c oxidase subunit II; Provisional.
Length = 162
Score = 32.1 bits (73), Expect = 0.23
Identities = 16/61 (26%), Positives = 34/61 (55%)
Query: 160 QQVAIINELVVPIDRPLEFRITASSVMNSFYIPGLAGQIYAMAGMETKLHAVMNKKGAYS 219
+Q+ + L +P + F ITA+ V++S+ +P L + A+ G K++ + ++G +
Sbjct: 67 RQLEVDKRLTLPTRTHIRFLITATDVIHSWSVPSLGIKADAIPGRLHKINTFILREGVFY 126
Query: 220 G 220
G
Sbjct: 127 G 127
>gnl|CDD|116854 pfam08270, PRD_Mga, M protein trans-acting positive regulator (MGA)
PRD domain. Mga is a DNA-binding protein that activates
the expression of several important virulence genes in
group A streptococcus in response to changing
environmental conditions. This corresponds to the PRD
like region.
Length = 217
Score = 30.3 bits (69), Expect = 0.78
Identities = 14/38 (36%), Positives = 19/38 (50%)
Query: 230 FSHMRFKFYGKSEKGFEDWISKVKRQGTFLNRQEYLLL 267
F FK Y +K EDW++++ G LN YLL
Sbjct: 174 FYQGNFKLYKILKKIVEDWLAEIGGSGMLLNHHLYLLC 211
>gnl|CDD|177630 PHA03394, lef-8, DNA-directed RNA polymerase subunit beta-like
protein; Provisional.
Length = 865
Score = 28.7 bits (65), Expect = 2.2
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 277 RYFSPIEKGLYYSILNLCVHPGKICMDEMMRIDA 310
R SPIE L +IL + H G IC+ + +RID
Sbjct: 427 RNRSPIELKLANNILFVNHHEGMICIKKKLRIDN 460
>gnl|CDD|185245 PRK15347, PRK15347, two component system sensor kinase SsrA;
Provisional.
Length = 921
Score = 28.5 bits (64), Expect = 2.8
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 107 GFLAVITWDATHRMDPYAPLERISESKSIAK 137
F+ +I ++P P R+ E SIAK
Sbjct: 327 RFVDIINKTGPAALEPRLPENRLDELGSIAK 357
>gnl|CDD|179489 PRK02870, PRK02870, heat shock protein HtpX; Provisional.
Length = 336
Score = 28.1 bits (63), Expect = 3.6
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 8 MGVSVGKSLKFFFLFFSSVMLSGFEFIVMDPYGDIALQQASLIRI 52
M + S+ F F +MLSG E+ + P ++LQ+ L +
Sbjct: 76 MSLVAVISILVTFQNFDKIMLSGTEYKEITPENALSLQERQLYNV 120
>gnl|CDD|163155 TIGR03147, cyt_nit_nrfF, cytochrome c nitrite reductase, accessory
protein NrfF.
Length = 126
Score = 27.8 bits (62), Expect = 3.6
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 83 RYDPKWCHSTLLELFVWLVPLVIVGFLAVITWDATHR 119
Y+P + TLL +WL+P++++ V+ W R
Sbjct: 92 LYNPPFKWQTLL---LWLLPVLLLLLAFVLLWRVRRR 125
>gnl|CDD|162509 TIGR01734, D-ala-DACP-lig, D-alanine--poly(phosphoribitol) ligase,
subunit 1. This model represents the enzyme (also
called D-alanine-D-alanyl carrier protein ligase) which
activates D-alanine as an adenylate via the reaction
D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes
the condensation of the amino acid adenylate with the
D-alanyl carrier protein (D-ala-ACP). The D-alanine is
then further transferred to teichoic acid in the
biosynthesis of lipoteichoic acid (LTA) and wall
teichoic acid (WTA) in gram positive bacteria, both
polysacchatides.
Length = 502
Score = 27.4 bits (61), Expect = 5.8
Identities = 20/91 (21%), Positives = 28/91 (30%), Gaps = 28/91 (30%)
Query: 102 PLVIVGFLAVITWDATHR---MDPYAPLERISESKSIAKNSKPLVVEVVALDWKWLFLLP 158
P ++V FL I + H +D P ERI A LV+ L
Sbjct: 61 PHMLVAFLGSIK--SGHAYIPVDTSIPSERIEMIIEAAG--PELVIHTAEL--------- 107
Query: 159 EQQVAIINELVVPIDRPLEFRITASSVMNSF 189
ID IT S++ +
Sbjct: 108 ------------SIDAVGTQIITLSALEQAE 126
>gnl|CDD|152283 pfam11847, DUF3367, Domain of unknown function (DUF3367). This
domain is functionally uncharacterized. This domain is
found in bacteria and archaea. This presumed domain is
typically between 667 to 694 amino acids in length.
Length = 677
Score = 27.0 bits (60), Expect = 7.3
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 53 AVALMLLIVVPVFFSILFFAWKYRSTNKKARYDPKWCHSTLLELFVWLVPLVIVG----- 107
A A + ++ + + +L A R R W + LL W+VPL+++G
Sbjct: 169 ATATLAALLPALLW-LLCHARGRR----WWRLLAWWLLAVLLASAWWIVPLLVLGRYGPP 223
Query: 108 FLAVI 112
FL I
Sbjct: 224 FLDFI 228
>gnl|CDD|178837 PRK00068, PRK00068, hypothetical protein; Validated.
Length = 970
Score = 26.5 bits (59), Expect = 8.8
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 59 LIVVPVFFSILFFAWKYR--STNKKARYDPKWCHSTLLE----LFVWLVPLVIVGFLAVI 112
L+V + F L+ A++ R K DP + ++E LF+ +P +G LA I
Sbjct: 69 LLVGGIVFISLWLAYRSRPVFVPKADSNDPVARYRAVVEKRLRLFLIGIP-SFIGLLAGI 127
Query: 113 T 113
Sbjct: 128 F 128
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
0.326 0.141 0.437
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,624,289
Number of extensions: 364100
Number of successful extensions: 1086
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1075
Number of HSP's successfully gapped: 55
Length of query: 332
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 238
Effective length of database: 3,963,321
Effective search space: 943270398
Effective search space used: 943270398
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.7 bits)