RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8844
(353 letters)
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the two
membrane helix type ion channels found in bacteria.
Length = 74
Score = 64.5 bits (158), Expect = 2e-13
Identities = 24/57 (42%), Positives = 34/57 (59%)
Query: 73 KAGQQWKFAGSFYYATTVLTTIGYGHSTPNTIGGKLFTMFYAMVGIPLGLVMFQSIG 129
+ G W F + Y++ LTTIGYG P T G+LFT+ Y ++GIPL L+ +G
Sbjct: 18 EEGWGWDFLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLAVLG 74
Score = 56.4 bits (137), Expect = 1e-10
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 11/82 (13%)
Query: 165 TLSSLTIAVGAAAFSRYE---GWTYFDSVYYCFITLTTIGFGDMVALQKDNALDTKPEYV 221
L L + G +S E GW + D++Y+ F+TLTTIG+GD+V L
Sbjct: 1 ILLLLVLIFGTVYYSLEEEGWGWDFLDALYFSFVTLTTIGYGDIVPLT--------DAGR 52
Query: 222 IFALIFILFGLAIVAASLNLLV 243
+F +I+IL G+ + L +L
Sbjct: 53 LFTIIYILIGIPLFLLFLAVLG 74
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 35.7 bits (83), Expect = 0.019
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 185 TYFDSVYYCFITLTTIGFGDMVALQKDNALDTKPEYVIFALIFILFGLAIVAASLNLLV 243
+Y +++ + F TLTT G+GD++ D + IF +IFI+ G ++ LNLL+
Sbjct: 139 SYGEALLWLFRTLTTEGWGDVMY---DTLVPGTVLGKIFFVIFIILGGVLL---LNLLI 191
Score = 28.8 bits (65), Expect = 2.9
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 79 KFAGSFYYATTVLTTIGYG-----HSTPNTIGGKLFTMFYAMVGIPLGLVMF 125
+ + + LTT G+G P T+ GK+F + + ++G L L +
Sbjct: 139 SYGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLL 190
>gnl|CDD|216326 pfam01142, TruD, tRNA pseudouridine synthase D (TruD). TruD is
responsible for synthesis of pseudouridine from
uracil-13 in transfer RNAs. The structure of TruD
reveals an overall V-shaped molecule which contains an
RNA-binding cleft.
Length = 336
Score = 35.3 bits (82), Expect = 0.041
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 15/66 (22%)
Query: 41 LSDIEKMIMNKYNISPDDFKLLETLILKSE-------PHKAGQQWKFAG---SFY----- 85
++E+ I+ + I+P+DF+LL L LK E P QW G SF
Sbjct: 268 AGELEQEILAEEGITPEDFELLPKLGLKGERRPLRLKPENLSWQWDDEGLVLSFSLPKGS 327
Query: 86 YATTVL 91
YAT+VL
Sbjct: 328 YATSVL 333
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 35.2 bits (81), Expect = 0.060
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 8/51 (15%)
Query: 186 YFDSVYYCFITLTTIGFGDMVALQKDNALDTKPEYVIFALIFILFGLAIVA 236
Y ++Y+ T+TT+G+GD+ A+ N ++ +IF + ++LF L + A
Sbjct: 251 YISAIYWSITTMTTVGYGDLHAV---NTIE-----MIFIIFYMLFNLGLTA 293
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 31.1 bits (71), Expect = 0.97
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 13/71 (18%)
Query: 84 FYYATTVLTTIGYGHSTPNTIGGKLFTMFYAMVGIPLGLVMFQS---------IGERLNK 134
FY++ ++T+GYG P + +LFT+ I LG+ +F + I L +
Sbjct: 173 FYFSIVTMSTVGYGDIVPVSESARLFTISV----IILGITVFATSISAIFGPVIRGNLKR 228
Query: 135 LSSVVIRKAKR 145
L I R
Sbjct: 229 LVKGRISHMHR 239
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 30.6 bits (70), Expect = 1.2
Identities = 17/90 (18%), Positives = 29/90 (32%), Gaps = 13/90 (14%)
Query: 198 TTIGF----GDMV-------ALQKDNALDTKPEYVI--FALIFILFGLAIVAASLNLLVL 244
+ +GF GD V + + P + F + L A++ L VL
Sbjct: 399 SAVGFDAKRGDSVNVVNVPFDEEAEEEAAELPFWQQPWFMDLIKLAAGALLILILIFFVL 458
Query: 245 RFVTMNTEDERRDEAEALQAAQGAVRLEGD 274
R E E A + A+ + +
Sbjct: 459 RPRLRPLLPEEELAEEEAAAEEAALEEDEE 488
>gnl|CDD|143496 cd06822, PLPDE_III_YBL036c_euk, Pyridoxal 5-phosphate (PLP)-binding
TIM barrel domain of Type III PLP-Dependent Enzymes,
Eukaryotic YBL036c-like proteins. This subfamily
contains mostly uncharacterized eukaryotic proteins with
similarity to the yeast hypothetical protein YBL036c,
which is homologous to a Pseudomonas aeruginosa gene
that is co-transcribed with a known proline biosynthetic
gene. YBL036c is a single domain monomeric protein with
a typical TIM barrel fold. It binds the PLP cofactor and
has been shown to exhibit amino acid racemase activity.
The YBL036c structure is similar to the N-terminal
domain of the fold type III PLP-dependent enzymes,
bacterial alanine racemase and eukaryotic ornithine
decarboxylase, which are two-domain dimeric proteins.
The lack of a second domain in YBL036c may explain
limited D- to L-alanine racemase or non-specific
racemase activity. Some members of this subfamily are
also referred to as PROSC (Proline synthetase
co-transcribed bacterial homolog).
Length = 227
Score = 29.5 bits (67), Expect = 2.2
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 21 IGASVFDALESQTENRRWTTLSDIEKMIMNKYNISPDDFKL 61
IG+ F S N + L D K + K I+PDD +L
Sbjct: 162 IGS--FGYSLSSGPNPDFLCLVDCRKKVCEKLGINPDDLEL 200
>gnl|CDD|206509 pfam14341, PilX_N, PilX N-terminal. This domain is found at the
N-terminus of the PilX prepilin-like proteins which are
involved in type 4 fimbrial biogenesis.
Length = 51
Score = 26.7 bits (60), Expect = 2.4
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 223 FALIFILFGLAIVAASLNLLVLRFVTMNTEDER-----RDEAEALQAAQGAVR 270
AL+ L L + L LL + + + +ER RD +A AA+ +
Sbjct: 3 AALVVALLLLLV----LTLLGVAAIQGSLLEERMAANDRDRNQAFYAAEAGLE 51
>gnl|CDD|212155 cd11586, VbhA_like, VbhA antitoxin and related proteins. VbhA is
the antitoxin to VbhT. The VbhT toxin of the mammalian
pathogen Bartonella schoenbuchensis is responsible for
the disruptive adenylation of host proteins. VbhT also
induces FIC-domain-mediated growth arrest in bacteria;
it is inhibited by this antitoxin which binds to block
the ATP binding site of the VbhT FIC domain.
Length = 54
Score = 26.7 bits (60), Expect = 3.3
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 252 EDERRDEAEALQAAQGAVRLEGDVITADG 280
E+E+ + EA+ +A + RLEG + +
Sbjct: 1 EEEQAERREAVASAIASNRLEGLEPSPEA 29
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.3 bits (66), Expect = 3.4
Identities = 20/107 (18%), Positives = 39/107 (36%), Gaps = 21/107 (19%)
Query: 194 FITLTTI-GFGDMVALQKDNALDTKPEYVIF------ALIFILFGLAIVAASLNLLVLRF 246
F+ L I + + L + + F A+ F+L +V
Sbjct: 571 FLPLDRIKPLRSLKSDAAPGFLGLASDLIDFDPKYEPAVRFVLGDTLVV----------- 619
Query: 247 VTMNTEDERRDEAEALQAAQGAVRLEGDVITADGSILSGQLGENNAV 293
+ ++ R A L+ V L+GD++ GSI G + +++
Sbjct: 620 ---DDLEQARRLARKLRIKYRIVTLDGDLVEPSGSITGGSRNKRSSL 663
>gnl|CDD|226667 COG4211, MglC, ABC-type glucose/galactose transport system,
permease component [Carbohydrate transport and
metabolism].
Length = 336
Score = 29.0 bits (65), Expect = 3.5
Identities = 14/52 (26%), Positives = 22/52 (42%)
Query: 205 MVALQKDNALDTKPEYVIFALIFILFGLAIVAASLNLLVLRFVTMNTEDERR 256
M AL K LD E I+ ++ +L + IV L + + T+ R
Sbjct: 1 MSALNKKFFLDYLKENGIYVVLLVLLAIIIVQDPTFLSLRNLSNILTQSSVR 52
>gnl|CDD|151252 pfam10802, DUF2540, Protein of unknown function (DUF2540). This
family of proteins with unknown function appears to be
restricted to Methanococcus.
Length = 75
Score = 26.8 bits (60), Expect = 3.8
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 28 ALESQTENRRWTTLSDIEKMIMNKY 52
A+E + + +R TLS+ E+ I+ KY
Sbjct: 34 AVELKKKYKRTLTLSEEEEKIIEKY 58
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 29.2 bits (66), Expect = 3.8
Identities = 27/150 (18%), Positives = 54/150 (36%), Gaps = 34/150 (22%)
Query: 114 AMVGIPLGLVMFQSIGERLNKLSSVVIRKAKRLSGCTEIEATEINLICVVTTLSSLTIAV 173
A+ GI LGL+ +G L ++R+ R + + T + +L +A
Sbjct: 194 ALGGILLGLL----LG----YLLGRLLRRLDRRGWTSPLLETLL----------TLLLAF 235
Query: 174 GAAAFSRYEGWTYFDSVYYCFITLTTIGFGDMVALQKDNALDTKPEYVIFAL---IFILF 230
A + G + +V + L ++ L + E + F L +F+L
Sbjct: 236 AAYLLAEALGVSGILAVVVAGLVLGEAVRINLSPASARLRLSSFWEVLDFLLNGLLFVLL 295
Query: 231 GL-------------AIVAASLNLLVLRFV 247
G ++ A + +L+ R +
Sbjct: 296 GAQLPLSLLLALGLLGLLVALVAVLLARPL 325
>gnl|CDD|181195 PRK08008, caiC, putative crotonobetaine/carnitine-CoA ligase;
Validated.
Length = 517
Score = 28.9 bits (65), Expect = 4.8
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 9/35 (25%)
Query: 203 GDMVALQKDNALDTKPEYVIFALIFILFGLAIVAA 237
GD VAL LD PE+ IF FGLA + A
Sbjct: 62 GDKVALH----LDNCPEF-----IFCWFGLAKIGA 87
>gnl|CDD|227177 COG4840, COG4840, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 71
Score = 26.7 bits (59), Expect = 4.9
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 20 LIGASVFDALESQTENRRWTTLSDIEKMIMNKYNISPDDFKLL 62
++ V D + +N + L+DI M+ K N SP + + +
Sbjct: 22 MVNVGVLDPEK--YDNANYEDLTDIYDMVKKKENFSPSEMQAI 62
>gnl|CDD|224698 COG1784, COG1784, Predicted membrane protein [Function unknown].
Length = 395
Score = 28.5 bits (64), Expect = 5.1
Identities = 32/168 (19%), Positives = 58/168 (34%), Gaps = 29/168 (17%)
Query: 99 STPNTIGGKLFTMFYAMVGIPLGLVMFQSIGERLNKLSSVVIRKA------KRLSGCTEI 152
+G L +F + G+PL + N S + KRL +
Sbjct: 171 QGSLPVGSPLLPLFTGLFGLPLLIEAL------SNPSSIPKQEDSKFAISGKRLLKSSFA 224
Query: 153 EATEINLICVVTTLSSLTIAVGAAAFSRY-EGWTYFDSVY--------YCFITLTTIG-- 201
+ L+ + +S A+ A+ + E + +V + + L IG
Sbjct: 225 GSLAGALVSFLPGVSPAQAALLASKLTGDDEDRRFITAVSGINTANAVFSLVALIAIGKP 284
Query: 202 -FGDMVALQKDNALDTKPEYVIFALIFILFGLAIVAASLNLLVLRFVT 248
G VA+Q+ T P LIF++ A++A +L +
Sbjct: 285 RSGVAVAIQRSVGDITLPY-----LIFLVLSAALIAVALAPWLSILAL 327
>gnl|CDD|227070 COG4726, PilX, Tfp pilus assembly protein PilX [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 196
Score = 27.9 bits (62), Expect = 6.3
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 223 FALIFILFGLAIVAASLNLLVLRFVTMNTEDER-----RDEAEALQAAQGAVR 270
FALI +L L +V L L R V + ER RD + A QAA+ A+R
Sbjct: 15 FALIVVLMVL-VVLTLLGLAAARSVLL---QERISANERDRSLAFQAAEAALR 63
>gnl|CDD|151732 pfam11291, DUF3091, Protein of unknown function (DUF3091). This
eukaryotic family of proteins has no known function.
Length = 100
Score = 26.5 bits (59), Expect = 7.3
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 42 SDIEKMIMNK-YNISPDDFKLLETLILKSE 70
S +E M N+ NI D LE LI K +
Sbjct: 39 SKVENMTCNRPENIDEKDLNNLENLIWKKQ 68
>gnl|CDD|226642 COG4174, COG4174, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 364
Score = 28.1 bits (63), Expect = 7.5
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 77 QWKFAGSFYYATTVLTTIGYGHSTPNTIGGKLF-TMFYAMVGIPLGLVMFQSIGERLNKL 135
++ F SF+ +V+ I P +I L+ T+ ++ IPLG+ G R +
Sbjct: 111 RFDFGESFFRDASVIDLIK--EKLPVSISLGLWSTLIIYLISIPLGIRKAVRNGSRFDVW 168
Query: 136 SSVVI 140
SS VI
Sbjct: 169 SSAVI 173
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.135 0.392
Gapped
Lambda K H
0.267 0.0823 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,496,716
Number of extensions: 1671213
Number of successful extensions: 2264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2260
Number of HSP's successfully gapped: 56
Length of query: 353
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 255
Effective length of database: 6,590,910
Effective search space: 1680682050
Effective search space used: 1680682050
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 (21.9 bits)
S2: 59 (26.3 bits)