RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780342|ref|YP_003064755.1| substrate-binding region of
ABC-type glycine betaine transport system [Candidatus Liberibacter
asiaticus str. psy62]
(309 letters)
>gnl|CDD|32296 COG2113, ProX, ABC-type proline/glycine betaine transport systems,
periplasmic components [Amino acid transport and
metabolism].
Length = 302
Score = 236 bits (604), Expect = 5e-63
Identities = 96/295 (32%), Positives = 144/295 (48%), Gaps = 3/295 (1%)
Query: 4 ILAVCLFLTTFSISYARDADSCTPVRFADTGWTDIAATTAMTSVILEEILGYKTNIKLLA 63
L + + A A++ VR AD GWT ATT + IL+ LGY + L
Sbjct: 9 AAVAAAALLAAAAAAAAAAEAGKTVRIADVGWTSGTATTNVAKKILKG-LGYTVELVTLD 67
Query: 64 VPVTFRSLKNKGIDIFMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFAL 123
V ++SL +D+F W P+ +++ ++L NL+GAK AV
Sbjct: 68 TAVMYQSLAKGDLDVFPEAWLPTTPDDYKKAVKDKKVELGGTNLEGAKQGWAVPKYVADA 127
Query: 124 GIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQI 183
GIKS D+AK+K + G KIYGIEPG + I D I LKGF L+E+SE A +
Sbjct: 128 GIKSIADLAKFKDKFGGKIYGIEPGWGCMRVIEDAIKAYGLGLKGFELVESSEAAMLAAA 187
Query: 184 RRDQRNNIPAVFLSWEPHPINSDLNIHYLPGGEEISG--FGEASVYTVVRSDYLDKCPNI 241
R + P VF W PH + ++ YL G G +V+TVVR + ++ PN+
Sbjct: 188 IRAAKRKEPIVFYGWSPHWMFGKYDLKYLEDPGPPKGANGGWETVHTVVRKGFAEEAPNV 247
Query: 242 SRLLKNIKFSVALENEMMKLILNNKQDRQFVGRTMLRTHPDLLKNWLIGVTTFDG 296
++LL N F +A EN +M + + + + L+ +P++ W+ GV DG
Sbjct: 248 AKLLANFSFPLAEENALMAAMDDGGATPEEAAKQWLKANPEIWDGWVSGVAAADG 302
>gnl|CDD|146609 pfam04069, OpuAC, Substrate binding domain of ABC-type glycine
betaine transport system. Part of a high affinity
multicomponent binding-protein-dependent transport
system involved in bacterial osmoregulation. This domain
is often fused to the permease component of the
transporter complex. Family members are often integral
membrane proteins or predicted to be attached to the
membrane by a lipid anchor. Glycine betaine is involved
in protection from high osmolarity environments for
example in Bacillus subtilis. The family member OpuBC is
closely related, and involved in choline transport.
Choline is necessary for the biosynthesis of glycine
betaine. L-carnitine is important for osmoregulation in
Listeria monocytogenes. Family also contains proteins
binding l-proline (ProX), histidine (HisX) and taurine
(TauA).
Length = 256
Score = 139 bits (352), Expect = 9e-34
Identities = 54/248 (21%), Positives = 95/248 (38%), Gaps = 10/248 (4%)
Query: 27 PVRFADTGWTDIAATTAMTSVILEEILGYKTNI-KLLAVPVTFRSLKNKGIDIFMGYWYP 85
+ WT+ + + +LE LGY + L + V F +L + ID++ W
Sbjct: 2 TIVIGSKNWTEQEILANIAAQLLEA-LGYVVELVGLGSTAVLFAALASGDIDLYPEEWTG 60
Query: 86 SLEKFIAPYLEEGSIKLVA-ENLQGAKYMLAVN-DVGFALGIKSYQDIAKYKKE---LGA 140
+ + +EE LV G Y LAV V GIKS D+AK +
Sbjct: 61 TTYEAYKKAVEEKLGLLVLGPLGAGNTYGLAVPKYVAEKPGIKSISDLAKPADDELGFKG 120
Query: 141 KIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQIRRDQRNNIPAVFLSWEP 200
+ G G + ++ + L + L+E SE A + + + P V +W P
Sbjct: 121 EFIGRPDGWGCTRSTEGLLK--AYGLDKYELVEGSEAAMDALLYAAIKRGEPDVVYAWTP 178
Query: 201 HPINSDLNIHYLPGGEEISGFGEASVYTVVRSDYLDKCPNISRLLKNIKFSVALENEMMK 260
+ ++ L + + +V VVR + +K P ++ L + NE+
Sbjct: 179 DWMIKKYDLVVLEDPKGLFPPAY-NVVPVVRKGFAEKHPEVAAFLNKLSLDTEDLNELNA 237
Query: 261 LILNNKQD 268
+ +D
Sbjct: 238 QVDVEGKD 245
>gnl|CDD|147350 pfam05128, DUF697, Domain of unknown function (DUF697). Family of
bacterial hypothetical proteins that is sometimes
associated with GTPase domains.
Length = 162
Score = 27.1 bits (61), Expect = 5.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 140 AKIYGIEPGNEGNQRILDMI 159
AK+YGIE G EG R+ +
Sbjct: 62 AKLYGIELGYEGAIRLARSV 81
>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 167
Score = 26.8 bits (60), Expect = 7.6
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 154 RILDMINNNKFSLKGFRLI---EASELAS------FSQIRRDQRNNIPAVFLS 197
R+LD++ LK +L+ EA L +I R + LS
Sbjct: 105 RLLDLLERGGLLLKNLKLLVLDEAHRLLDQGFGDDLEEILRRLPPKRQILLLS 157
>gnl|CDD|33735 COG3954, PrkB, Phosphoribulokinase [Energy production and
conversion].
Length = 289
Score = 26.5 bits (58), Expect = 9.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 189 NNIPAVFLSWEPHPINSDL 207
N +P F W+P P +D+
Sbjct: 108 NQVPGTFTPWQPLPEPTDV 126
>gnl|CDD|38590 KOG3380, KOG3380, KOG3380, Actin-related protein Arp2/3 complex,
subunit ARPC5 [Cytoskeleton].
Length = 152
Score = 26.4 bits (58), Expect = 9.3
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 57 TNIKLLAVPVTFRSLKNKGIDIFMGYWYPSLEK 89
T+IK + + L + IDI M Y Y +E
Sbjct: 84 TSIKQADIEAAVKKLSTEEIDILMKYIYKGMEI 116
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
0.321 0.138 0.405
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,742,507
Number of extensions: 196299
Number of successful extensions: 412
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 16
Length of query: 309
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 215
Effective length of database: 4,232,491
Effective search space: 909985565
Effective search space used: 909985565
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.6 bits)