RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780471|ref|YP_003064884.1| cytochrome o ubiquinol oxidase
subunit IV [Candidatus Liberibacter asiaticus str. psy62]
(119 letters)
>gnl|CDD|182568 PRK10582, PRK10582, cytochrome o ubiquinol oxidase subunit IV;
Provisional.
Length = 109
Score = 99.4 bits (248), Expect = 2e-22
Identities = 49/98 (50%), Positives = 74/98 (75%), Gaps = 1/98 (1%)
Query: 13 SYGTKKQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMS 72
S+G+ K + GFILS+ILT+IPF +VM G ++ TI+ A+ QI+VHLV FLHM+
Sbjct: 11 SHGSVKTYMTGFILSIILTVIPFWMVMTGAA-SPAVILGTILAMAVVQILVHLVCFLHMN 69
Query: 73 TKVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLNNNMM 110
TK ++GW++ A +FT++++AI VGS+W+M++LN NMM
Sbjct: 70 TKSDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNMM 107
>gnl|CDD|131894 TIGR02847, CyoD, cytochrome o ubiquinol oxidase subunit IV.
Cytochrome o terminal oxidase complex is the component
of the aerobic respiratory chain which reacts with
oxygen, reducing it to water with the concomitant
transport of 4 protons across the membrane. Also known
as the cytochrome bo complex, cytochrome o ubiquinol
oxidase contains four subunits, two heme b cofactors and
a copper atom which is believed to be the oxygen active
site. This complex is structurally related to the
cytochrome caa3 oxidases which utilize cytochrome c as
the reductant and contain heme a cofactors, as well as
the intermediate form aa3 oxidases which also react
directly with quinones as the reductant.
Length = 96
Score = 98.1 bits (245), Expect = 5e-22
Identities = 46/97 (47%), Positives = 74/97 (76%), Gaps = 1/97 (1%)
Query: 14 YGTKKQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMST 73
+G+ K L+GF+LS+ILT IPFG+VM G K + + I++ A+ QI+VHLVFFLH++T
Sbjct: 1 HGSLKSYLIGFVLSVILTAIPFGLVMSGTL-SKGLTLVIIIVLAVVQILVHLVFFLHLNT 59
Query: 74 KVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLNNNMM 110
E W++++++FTI+++ I GS+W+M++LN+NMM
Sbjct: 60 SSEQRWNLISLLFTILIIFILIGGSIWIMHNLNHNMM 96
>gnl|CDD|131947 TIGR02901, QoxD, cytochrome aa3 quinol oxidase, subunit IV. This
family (QoxD) encodes subunit IV of the aa3-type quinone
oxidase, one of several bacterial terminal oxidases.
This complex couples oxidation of reduced quinones with
the reduction of molecular oxygen to water and the
pumping of protons to form a proton gradient utilized
for ATP production. aa3-type oxidases contain two heme a
cofactors as well as copper atoms in the active site.
Length = 94
Score = 37.1 bits (86), Expect = 0.001
Identities = 21/82 (25%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 21 LVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWS 80
+ GFILSL+LT + + + L + I++ A Q + L+ F+H +
Sbjct: 10 VNGFILSLLLTFLALWVALYSD-LPLAMGLTIIIIFAFIQAGLQLIMFMHAGESEDGKVQ 68
Query: 81 IMAMIFTIIMVAICFVGSMWVM 102
I + ++ + + GS+WVM
Sbjct: 69 IYNIYYSAFIALVTVFGSLWVM 90
>gnl|CDD|131954 TIGR02908, CoxD_Bacillus, cytochrome c oxidase, subunit IVB. This
model represents a small clade of cytochrome oxidase
subunit IV's found in the Bacilli.
Length = 110
Score = 30.6 bits (69), Expect = 0.086
Identities = 26/85 (30%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 18 KQCLVGFILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVED 77
K+ +V F L + LT+I F VM DK + I+L A Q+ L +F+HM K +
Sbjct: 26 KKQIVTFALMIFLTLIAFFAVMLDEI-DKWFVIPFILLLAAVQVAFQLYYFMHMKDKGHE 84
Query: 78 GWS--IMAMIFTIIMVAICFVGSMW 100
+ I +F ++V + F W
Sbjct: 85 VPAQFIYGGVFVTMLVVLAFTTITW 109
>gnl|CDD|132323 TIGR03280, methan_mark_11, putative methanogenesis marker protein
11. Members of this protein family, to date, are found
in a completed prokaryotic genome if and only if the
species is one of the archaeal methanogens. The exact
function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
Length = 292
Score = 27.4 bits (61), Expect = 0.86
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 94 CFVGSMWVMYH 104
C GS WV+Y
Sbjct: 24 CPSGSEWVIYQ 34
>gnl|CDD|149146 pfam07907, YibE_F, YibE/F-like protein. The sequences featured in
this family are similar to two proteins expressed by
Lactococcus lactis, YibE and YibF. Most of the members
of this family are annotated as being putative membrane
proteins, and in fact the sequences contain a high
proportion of hydrophobic residues.
Length = 244
Score = 27.4 bits (62), Expect = 1.0
Identities = 18/92 (19%), Positives = 41/92 (44%), Gaps = 7/92 (7%)
Query: 25 ILSLILT-IIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMA 83
+LSL+L ++ F +++ N + +TI+L I V L + K ++ A
Sbjct: 26 LLSLVLNFVLLFLVLIPIILAGFNPILVTIILAIII-TAVTLFLVNGFNKK-----TLAA 79
Query: 84 MIFTIIMVAICFVGSMWVMYHLNNNMMSMEGM 115
+ T++ V + + ++ V+ + + E
Sbjct: 80 FLGTLLGVLLAGILALLVIKLTHLQGLGYEEA 111
>gnl|CDD|163109 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. Colanic acid biosynthesis utilizes
a glucose-undecaprenyl carrier, knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 27.2 bits (61), Expect = 1.1
Identities = 6/46 (13%), Positives = 18/46 (39%)
Query: 61 IIVHLVFFLHMSTKVEDGWSIMAMIFTIIMVAICFVGSMWVMYHLN 106
I+ L F L + W ++ + + ++ + + ++ L
Sbjct: 77 ILALLAFLLKTGGEFSRLWLLLWFLLALALLLLGRLILRLLLRRLR 122
>gnl|CDD|152872 pfam12438, DUF3679, Protein of unknown function (DUF3679). This
domain family is found in bacteria, and is approximately
60 amino acids in length.
Length = 56
Score = 26.1 bits (58), Expect = 2.2
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 87 TIIMVAICFVGSMWVMYHLNNNMMSMEGMR 116
I+ V I G + M N+ M SM+G
Sbjct: 2 CILAVIILLFGVLLGMQQANHGMKSMKGYD 31
>gnl|CDD|162944 TIGR02600, TIGR02600, Verrucomicrobium spinosum paralogous
protein TIGR02600. In Verrucomicrobium spinosum, a
five-gene operon that includes proteins with an
N-terminal signal sequence for cleavage and methylation
recurs over twenty times. Each operon is likely to
encode a membrane complex, the function of which is
unknown. This model represents a long paralogous
protein from this putative membrame complex, with
members averaging about 1300 amino acids. The
N-terminal region includes an apparent signal sequence.
The function is unknown.
Length = 1265
Score = 26.0 bits (57), Expect = 2.4
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 49 MCLTIVLCAIAQIIVHLVFFLHMST 73
M L +VL +A I + ++ FL M
Sbjct: 1 MALIMVLIILALITILVLGFLSMVR 25
>gnl|CDD|177754 PLN00151, PLN00151, potassium transporter; Provisional.
Length = 852
Score = 25.9 bits (57), Expect = 2.8
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 51 LTIVLC-AIAQIIVHLVFFLHMSTKVEDG-WSIMAMIFTIIMVAICFV 96
+ +VLC + + V LVFF + + V DG W ++F + + I ++
Sbjct: 526 IFLVLCFPVVFLSVELVFFSSVLSSVGDGGWIP--LVFASVFLCIMYI 571
>gnl|CDD|162339 TIGR01399, hrcV, type III secretion protein, HrcV family. Members
of this family are closely homologous to the flagellar
biosynthesis protein FlhA (TIGR01398) and should all
participate in type III secretion systems. Examples
include InvA (Salmonella enterica), LcrD (Yersinia
enterocolitica), HrcV (Xanthomonas), etc. Type III
secretion systems resemble flagellar biogenesis systems,
and may share the property of translocating special
classes of peptides through the membrane.
Length = 677
Score = 25.4 bits (56), Expect = 3.3
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 22 VGFILSLILTIIPFGIVMKG 41
VG ++ LI+TI+ F ++ KG
Sbjct: 103 VGLVIFLIITIVQFIVITKG 122
>gnl|CDD|178625 PLN03076, PLN03076, ARF guanine nucleotide exchange factor (ARF-GEF);
Provisional.
Length = 1780
Score = 25.2 bits (55), Expect = 4.4
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 75 VEDGWSIMAMIFT 87
V+ GW M M+FT
Sbjct: 1218 VKSGWKSMFMVFT 1230
>gnl|CDD|180350 PRK06012, flhA, flagellar biosynthesis protein FlhA; Validated.
Length = 697
Score = 25.1 bits (56), Expect = 4.5
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 21 LVGFILSLILTIIPFGIVMKG 41
+VG ++ +IL II F ++ KG
Sbjct: 123 VVGIVVFIILVIINFVVITKG 143
>gnl|CDD|130267 TIGR01200, TIGR01200, Porphyromonas gingivalis paralogous family
TIGR01200. No identifiable homologs outside
Porphyromonas gingivalis.
Length = 292
Score = 24.9 bits (54), Expect = 5.0
Identities = 7/34 (20%), Positives = 20/34 (58%)
Query: 83 AMIFTIIMVAICFVGSMWVMYHLNNNMMSMEGMR 116
++ ++ + ICF+ S+ + ++++EGM+
Sbjct: 1 SLFRILLYILICFLLSIVGIQSPVPRIITLEGMK 34
>gnl|CDD|185010 PRK15050, PRK15050, 2-aminoethylphosphonate transport system
permease PhnU; Provisional.
Length = 296
Score = 25.0 bits (55), Expect = 5.1
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 20 CLV-GFILSLILTIIPF-GIVMKGFFLD 45
CLV G +L+L+L +PF G + G F+D
Sbjct: 89 CLVLGVLLALVLAFVPFPGASLVGRFID 116
>gnl|CDD|162106 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the lysosomal
accumulation of unestrified cholesterol. It is an
integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis.
Length = 1204
Score = 24.8 bits (54), Expect = 5.1
Identities = 7/49 (14%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 52 TIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMAMIFTIIMVAICFVGSMW 100
++ I+ + +V + + S + ++ ++ M+ + VG M
Sbjct: 1050 ALINLGISLGAIFIVTLVLLGLNA---LSAVNVVISVGMIVVNLVGIMH 1095
>gnl|CDD|180240 PRK05759, PRK05759, F0F1 ATP synthase subunit B; Validated.
Length = 156
Score = 24.7 bits (55), Expect = 5.1
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 82 MAMIFTIIMVAICFVGSMWV 101
M + T+I I F+ +W
Sbjct: 1 MNLNGTLIGQLIAFLILVWF 20
>gnl|CDD|162292 TIGR01301, GPH_sucrose, GPH family sucrose/H+ symporter. This
model represents sucrose/proton symporters, found in
plants, from the Glycoside-Pentoside-Hexuronide
(GPH)/cation symporter family. These proteins are
predicted to have 12 transmembrane domains. Members may
export sucrose (e.g. SUT1, SUT4) from green parts to the
phloem for long-distance transport or import sucrose
(e.g SUT2) to sucrose sinks such as the tap root of the
carrot.
Length = 477
Score = 24.4 bits (53), Expect = 6.5
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 89 IMVAICFVGSMWVMYHLNN 107
I++AIC ++ V Y N
Sbjct: 344 IILAICLAATVLVTYVAKN 362
>gnl|CDD|162465 TIGR01652, ATPase-Plipid, phospholipid-translocating P-type ATPase,
flippase. This model describes the P-type ATPase
responsible for transporting phospholipids from one
leaflet of bilayer membranes to the other. These ATPases
are found only in eukaryotes.
Length = 1057
Score = 24.6 bits (54), Expect = 6.6
Identities = 9/49 (18%), Positives = 19/49 (38%), Gaps = 3/49 (6%)
Query: 49 MCLTIVLCAIAQIIVHLVFFL---HMSTKVEDGWSIMAMIFTIIMVAIC 94
M I + + L S ++D S+ ++FT ++V +
Sbjct: 920 MLDGIYQSLVIFFFPMFAYILGDFVSSGSLDDFSSVGVIVFTALVVIVN 968
>gnl|CDD|163048 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs.
Length = 764
Score = 24.3 bits (53), Expect = 7.2
Identities = 17/80 (21%), Positives = 31/80 (38%), Gaps = 6/80 (7%)
Query: 24 FILSLILTIIPFGIVMKGFFLDKNIMCLTIVLCAIAQIIVHLVFFLHMSTKVEDGWSIMA 83
L L+ II V+K K + IV+ + V+ +F + V + +
Sbjct: 61 KYLLLVAVIILLSYVLKNLTDKKKTVVPPIVV--FLEAAVYAIFGYLQNKLV----TPLD 114
Query: 84 MIFTIIMVAICFVGSMWVMY 103
I +I+ ++ FV Y
Sbjct: 115 FILSIVEASLSFVLYYIFNY 134
>gnl|CDD|181866 PRK09450, cyaA, adenylate cyclase; Provisional.
Length = 830
Score = 24.1 bits (53), Expect = 8.5
Identities = 6/18 (33%), Positives = 13/18 (72%)
Query: 6 IHNMNMHSYGTKKQCLVG 23
N+++ S+G +++ LVG
Sbjct: 577 FRNLDVFSFGGEQENLVG 594
>gnl|CDD|178466 PLN02878, PLN02878, homogentisate phytyltransferase.
Length = 280
Score = 23.9 bits (52), Expect = 9.2
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 57 AIAQIIVHLVFFLHMSTKV 75
A+ ++V L FFLHM T V
Sbjct: 129 AVRAVVVQLAFFLHMQTHV 147
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
0.336 0.143 0.457
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: 1,852,834
Number of extensions: 105450
Number of successful extensions: 617
Number of sequences better than 10.0: 1
Number of HSP's gapped: 608
Number of HSP's successfully gapped: 121
Length of query: 119
Length of database: 5,994,473
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,244,225
Effective search space: 161280550
Effective search space used: 161280550
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 51 (23.4 bits)