RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780448|ref|YP_003064861.1| hypothetical protein
CLIBASIA_01665 [Candidatus Liberibacter asiaticus str. psy62]
(311 letters)
>gnl|CDD|119324 cd06582, TM_PBP1_LivH_like, Transmembrane subunit (TM) of
Escherichia coli LivH and related proteins. LivH is one
of two TMs of the E. coli LIV-1/LS transporter, a
Periplasmic Binding Protein (PBP)-dependent ATP-Binding
Cassette (ABC) transporter involved in the uptake of
branched-chain amino acids (AAs). These types of
transporters generally bind type 1 PBPs. PBP-dependent
ABC transporters consist of a PBP, two TMs, and two
cytoplasmic ABCs, and are mainly involved in importing
solutes from the environment. The solute is captured by
the PBP, which delivers it to a gated translocation
pathway formed by the two TMs. The two ABCs bind and
hydrolyze ATP and drive the transport reaction. E. coli
LivH forms a heterodimer with another TM, LivM, to
generate the transmembrane pore. LivM is not included in
this subgroup. The LIV-1/LS transporter is comprised of
two TMs (LivM and LivH), two ABCs (LivG and LivF), and
one of two alternative PBPs, LivJ (LIV-BP) or LivK
(LS-BP). In addition to transporting branched-chain AAs
including leucine, isoleucine and valine, the E. coli
LIV-1/LS transporter is involved in the uptake of the
aromatic AA, phenylalanine..
Length = 272
Score = 30.5 bits (70), Expect = 0.60
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 9/50 (18%)
Query: 29 LLAIPAAYLGKVLFGLV---------RGSSIATKIATTGIATVVQEATVM 69
LA+ A L L G++ RG+ + T + T G ++ + ++
Sbjct: 52 WLALLLALLVAALLGVLLERLVLRPLRGAPLLTLLITFGGLLILLQGLLL 101
>gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 28.8 bits (64), Expect = 1.9
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 14/94 (14%)
Query: 217 EKVQLISSYAHEHIFCKPFTKDLLNLANKNIYQLSNPRYSYQ-FNTLKDKTIS----FVA 271
+ ++LI+++ H HIF P DL + + PR S+ ++ IS V+
Sbjct: 984 KHIRLIAAFDHRHIFIDP-NPDLAVSFAERKRLFALPRSSWSDYDA---SKISKGGGVVS 1039
Query: 272 KEEGLVTYLNGSLHRNYGIKAEGILSRNAPPELH 305
+ +T + GI AP EL
Sbjct: 1040 RSAKAITLSPEVIAAL-GIDKT----ELAPNELI 1068
>gnl|CDD|33905 COG4158, COG4158, Predicted ABC-type sugar transport system,
permease component [General function prediction only].
Length = 329
Score = 27.6 bits (61), Expect = 4.7
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 23 IVSDVALLAIPAAYLGKVLFGLVRGSSIATK-----IATTGIATVVQEA 66
++ A L+IPAA L +L GL G +A I T G T ++ A
Sbjct: 98 LMPGWAALSIPAALLAGLLLGLFNGLLVAYAGLPPFIVTLGTYTALRGA 146
>gnl|CDD|33750 COG3969, COG3969, Predicted phosphoadenosine phosphosulfate
sulfotransferase [General function prediction only].
Length = 407
Score = 27.6 bits (61), Expect = 4.8
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 241 NLANKNIYQLSNPRYSYQFNTLKDKTISFV-AKEEGLVTYLNGSLHRNYGIKAEGIL 296
++N+ + + R + FNT +SF K+ GL+ +L + R G +L
Sbjct: 6 IYLDENVLEAAIERLEWIFNTFPRVCVSFSGGKDSGLMLHLVAEVARENGRDKISVL 62
>gnl|CDD|37214 KOG2003, KOG2003, KOG2003, TPR repeat-containing protein [General
function prediction only].
Length = 840
Score = 27.4 bits (60), Expect = 4.8
Identities = 37/175 (21%), Positives = 73/175 (41%), Gaps = 20/175 (11%)
Query: 68 VMTKTTQEGALLAKEGIEATHIMEGGSTAIKSESVGAKELISASQNSQTVTQTGNIS--- 124
V K + A A + A ++GG ++ L N+ +T GNI+
Sbjct: 444 VFEKKDNKTASAAANNLCALRFLQGGKDFADAQQYADIALNIDRYNAAALTNKGNIAFAN 503
Query: 125 -DATKASSTIKDAQSIDRS--QAIFQ-----------KMPLEEYPRLQKIGINYFRDFKL 170
D KA+ K+A + D S +A+F L+ + +L I +N L
Sbjct: 504 GDLDKAAEFYKEALNNDASCTEALFNIGLTAEALGNLDEALDCFLKLHAILLNNAE--VL 561
Query: 171 LGTNKVYKNLLDASRATEFIIDGKKINIDSAQNMLAELNKIFPKDFEKVQLISSY 225
+ +Y+ L D ++A E ++ + I + +L++L ++ ++ +K Q +
Sbjct: 562 VQIANIYELLEDPAQAIELLMQANSL-IPNDPAILSKLADLYDQEGDKSQAFQCH 615
>gnl|CDD|145974 pfam03116, NQR2_RnfD_RnfE, NQR2, RnfD, RnfE family. This family
of bacterial proteins includes a sodium-translocating
NADH-ubiquinone oxidoreductase (i.e. a respiration
linked sodium pump). In Vibrio cholerae, it negatively
regulates the expression of virulence factors through
inhibiting (by an unknown mechanism) the transcription
of the transcriptional activator ToxT. The family also
includes proteins involved in nitrogen fixation, RnfD
and RnfE. The similarity of these proteins to
NADH-ubiquinone oxidoreductases was previously noted.
Length = 319
Score = 27.4 bits (62), Expect = 5.1
Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 15 NYGWGALGIVSDVALLAIPAAYLGKVLFGLVRGSSIATK 53
+G AL ++ L+A+ A L + LF +R + K
Sbjct: 37 FFGLQALPVI----LVAVVVALLWEALFLKLRKRPVTFK 71
>gnl|CDD|114185 pfam05445, Pox_ser-thr_kin, Poxvirus serine/threonine protein
kinase.
Length = 434
Score = 27.4 bits (61), Expect = 5.3
Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 15/87 (17%)
Query: 161 GINYFRDFKLLGTNKVYKNLLDASRATEFIIDGKKINID--SAQNMLAELNKIFPKDFEK 218
GINY KLL +YK +L + I+DG+ +NI S + ML N+ KD EK
Sbjct: 149 GINY----KLLFLIILYKRVLHMLLLIKQILDGQPLNITYLSFKKMLKIFNER--KDSEK 202
Query: 219 -VQLISSYAHEHIFCKPFTKDLLNLAN 244
V+L S F K +N+ N
Sbjct: 203 FVKLFSY------FYPKVVKSNINVIN 223
>gnl|CDD|111458 pfam02561, FliS, Flagellar protein FliS. FliS is coded for by the
FliD operon and is transcribed in conjunction with FliD
and FliT, however this protein has no known function.
Length = 122
Score = 27.0 bits (60), Expect = 6.1
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 178 KNLLDASRATEFI----IDGKKINIDSAQNMLAELNKIFPKDFEK-----VQLISSYAH 227
K + RA EFI I+ K NI AQN++ EL D EK L++ Y +
Sbjct: 28 KAIKALVRAAEFIENEDIEKKNENISKAQNIITELRSTL--DEEKGGEIAQNLLAIYTY 84
>gnl|CDD|185679 cd02064, FAD_synthetase_N, FAD synthetase, N-terminal domain of the
bifunctional enzyme. FAD synthetase_N. N-terminal
domain of the bifunctional riboflavin biosynthesis
protein riboflavin kinase/FAD synthetase. These enzymes
have both ATP:riboflavin 5'-phosphotransferase and
ATP:FMN-adenylyltransferase activities. The N-terminal
domain is believed to play a role in the adenylylation
reaction of FAD synthetases. The C-terminal domain is
thought to have kinase activity. FAD synthetase is
present among all kingdoms of life. However, the
bifunctional enzyme is not found in mammals, which use
separate enzymes for FMN and FAD formation.
Length = 180
Score = 27.1 bits (61), Expect = 6.8
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 217 EKVQLISSYAHEHIFCKPFTKDLLNLA 243
EK++L+ S +++ PF K+ +L+
Sbjct: 60 EKLELLESLGVDYLLVLPFDKEFASLS 86
>gnl|CDD|144323 pfam00681, Plectin, Plectin repeat. This family includes repeats
from plectin, desmoplakin, envoplakin and bullous
pemphigoid antigen.
Length = 45
Score = 27.0 bits (61), Expect = 6.9
Identities = 10/27 (37%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 178 KNLLDASRATEFIID---GKKINIDSA 201
LL+A AT IID G++++++ A
Sbjct: 1 LRLLEAQAATGGIIDPETGERLSVEEA 27
>gnl|CDD|147208 pfam04925, SHQ1, SHQ1 protein. S. cerevisiae SHQ1 protein is
required for SnoRNAs of the box H/ACA Quantitative
accumulation (unpublished).
Length = 186
Score = 26.8 bits (60), Expect = 8.2
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 9/47 (19%)
Query: 246 NIYQLSNPRYSY--QFNTLKDKTISFVAKEEGLVTYLNGSLHRNYGI 290
I +LS P+ S+ F+ +KD I+F+ + +TY L+RN+ +
Sbjct: 68 TIGKLS-PQLSWLDSFSNVKDALIAFIRR---ALTY---PLYRNFDL 107
>gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 26.7 bits (59), Expect = 8.5
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 148 KMPLEEYPRL-QKIGINYFRDFKLLGTNKVYKN 179
++ E P L ++IG+ F+DF+LL VY+N
Sbjct: 68 RLKGREIPFLRRQIGV-VFQDFRLLPDRTVYEN 99
>gnl|CDD|146010 pfam03172, Sp100, Sp100 domain. The function of this domain is
unknown. It is about 105 amino acid residues in length
and is predicted to be predominantly alpha helical. This
domain is usually found at the amino terminus of protein
that contain a SAND domain pfam01342.
Length = 104
Score = 26.5 bits (59), Expect = 8.7
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 144 AIFQKMPLEEYPRLQKI 160
A+F + LEEYP LQ+I
Sbjct: 78 ALFSDVNLEEYPDLQEI 94
>gnl|CDD|39770 KOG4570, KOG4570, KOG4570, Uncharacterized conserved protein
[Function unknown].
Length = 418
Score = 26.6 bits (58), Expect = 9.9
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 35 AYLGKVLFGLVRGSSIATKIATTGIATVVQEATVMTKTTQEGA 77
YLG+VL + + ++ A V A + T+ +GA
Sbjct: 254 GYLGRVLQVMEKEAASPEDSKACREALDVLAAVLKALTSADGA 296
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
0.315 0.131 0.362
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,364,680
Number of extensions: 166184
Number of successful extensions: 409
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 25
Length of query: 311
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 217
Effective length of database: 4,232,491
Effective search space: 918450547
Effective search space used: 918450547
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 (21.6 bits)
S2: 57 (25.7 bits)