RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17792
(116 letters)
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 95.4 bits (238), Expect = 2e-24
Identities = 45/108 (41%), Positives = 65/108 (60%), Gaps = 2/108 (1%)
Query: 9 QSESKISMSELLCSSTLRKPLIIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFT 68
K S EL T+R+ L++G+++Q+ QQ +GINA+FYYS +FE+ GLS+
Sbjct: 234 VEAEKASWLELFRGKTVRQRLLMGVMLQIFQQLTGINAIFYYSPTIFETLGLSDSLL--V 291
Query: 69 TIGIGAVMVTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITISLLI 116
TI +G V T I+I L+DR GRR L L G GM I + + ++LL
Sbjct: 292 TIIVGVVNFVFTFIAIFLVDRFGRRPLLLLGAAGMAICFLVLGVALLG 339
>gnl|CDD|233165 TIGR00879, SP, MFS transporter, sugar porter (SP) family. This
model represent the sugar porter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 481
Score = 84.3 bits (209), Expect = 2e-20
Identities = 40/96 (41%), Positives = 58/96 (60%)
Query: 17 SELLCSSTLRKPLIIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFTTIGIGAVM 76
S + +R+ L +G+V+Q QQF+GINA+ YYS +FE++G+S A +I +GAV
Sbjct: 273 SLFSSTRRIRRRLFLGVVLQWFQQFTGINAIMYYSPTIFENAGVSTDHAFLVSIIVGAVN 332
Query: 77 VTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITI 112
T ++I L+DR GRR L L G GM I + I
Sbjct: 333 FAFTFVAIFLVDRFGRRPLLLIGAAGMAICLFVLGI 368
>gnl|CDD|182225 PRK10077, xylE, D-xylose transporter XylE; Provisional.
Length = 479
Score = 63.9 bits (156), Expect = 3e-13
Identities = 29/77 (37%), Positives = 49/77 (63%)
Query: 29 LIIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFTTIGIGAVMVTMTIISIPLMD 88
++IG+++ + QQF GIN V YY+ +F++ G S A TI +G + +T T+++I +D
Sbjct: 272 IVIGVMLSVFQQFVGINVVLYYAPEIFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVD 331
Query: 89 RMGRRTLHLYGLGGMFI 105
+ GR+ L + G GM I
Sbjct: 332 KFGRKPLQIIGALGMAI 348
>gnl|CDD|119392 cd06174, MFS, The Major Facilitator Superfamily (MFS) is a large
and diverse group of secondary transporters that
includes uniporters, symporters, and antiporters. MFS
proteins facilitate the transport across cytoplasmic or
internal membranes of a variety of substrates including
ions, sugar phosphates, drugs, neurotransmitters,
nucleosides, amino acids, and peptides. They do so using
the electrochemical potential of the transported
substrates. Uniporters transport a single substrate,
while symporters and antiporters transport two
substrates in the same or in opposite directions,
respectively, across membranes. MFS proteins are
typically 400 to 600 amino acids in length, and the
majority contain 12 transmembrane alpha helices (TMs)
connected by hydrophilic loops. The N- and C-terminal
halves of these proteins display weak similarity and may
be the result of a gene duplication/fusion event. Based
on kinetic studies and the structures of a few bacterial
superfamily members, GlpT (glycerol-3-phosphate
transporter), LacY (lactose permease), and EmrD
(multidrug transporter), MFS proteins are thought to
function through a single substrate binding site,
alternating-access mechanism involving a rocker-switch
type of movement. Bacterial members function primarily
for nutrient uptake, and as drug-efflux pumps to confer
antibiotic resistance. Some MFS proteins have medical
significance in humans such as the glucose transporter
Glut4, which is impaired in type II diabetes, and
glucose-6-phosphate transporter (G6PT), which causes
glycogen storage disease when mutated.
Length = 352
Score = 33.1 bits (76), Expect = 0.018
Identities = 20/96 (20%), Positives = 32/96 (33%)
Query: 19 LLCSSTLRKPLIIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFTTIGIGAVMVT 78
L L + L++ + F + Y L E GLS A G +
Sbjct: 167 ALLLLFLLRLLLLLALAFFLLSFGYYGLLTYLPLYLQEVLGLSAAEAGLLLSLFGLGGIL 226
Query: 79 MTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITISL 114
++ L DR+GRR L L + + +
Sbjct: 227 GALLGGLLSDRLGRRRLLLLIGLLLAALGLLLLALA 262
>gnl|CDD|227437 COG5106, RPF2, Uncharacterized conserved protein [Function
unknown].
Length = 316
Score = 28.4 bits (63), Expect = 0.72
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 6 IAQQSESKISMSELLCSSTLRKPLIIGIV 34
SE K + + + L+KP IG +
Sbjct: 33 YPGMSERKTLLDVICDTEALKKPKEIGFI 61
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 28.4 bits (64), Expect = 0.81
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 85 PLMDRMGRRTLHLYGL 100
PLMD GR T HL GL
Sbjct: 46 PLMDSRGRITSHLSGL 61
>gnl|CDD|219516 pfam07690, MFS_1, Major Facilitator Superfamily.
Length = 346
Score = 28.2 bits (63), Expect = 0.99
Identities = 19/92 (20%), Positives = 36/92 (39%)
Query: 25 LRKPLIIGIVMQLSQQFSGINAVFYYSTALFESSGLSEKTAKFTTIGIGAVMVTMTIISI 84
L + ++ +++ L A+ Y E GLS A G + ++
Sbjct: 199 LLRDPVLWLLLALLLFGFAFFALLTYLPLYQEVLGLSALLAGLLLGLAGLLGAIGRLLLG 258
Query: 85 PLMDRMGRRTLHLYGLGGMFIFSIFITISLLI 116
L DR+GRR L L + + ++ + + L
Sbjct: 259 RLSDRLGRRRRLLLALLLLILAALGLALLSLT 290
>gnl|CDD|222060 pfam13347, MFS_2, MFS/sugar transport protein. This family is part
of the major facilitator superfamily of membrane
transport proteins.
Length = 425
Score = 27.6 bits (62), Expect = 1.4
Identities = 20/112 (17%), Positives = 42/112 (37%), Gaps = 8/112 (7%)
Query: 2 RVEQIAQQSES---KISMSELLCSSTLRKPLIIGIVMQLSQQFSGINAVFYYSTALFESS 58
RV +Q E + L + L L++ ++ L+ ++Y++ L
Sbjct: 198 RVSVPPEQKEKVSLRDMFKALFKNRPLLILLLLYLLNALAMAVRNGLLLYYFTYVL---- 253
Query: 59 GLSEKTAKFTTIGIGAVMVTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFI 110
G + + IG A ++ + L R G++ L G+ I + +
Sbjct: 254 GNAGLFSVLLLIGTIAAILGAPLWP-WLAKRFGKKRTFLLGMLLAAIGLVLL 304
>gnl|CDD|227557 COG5232, SEC62, Preprotein translocase subunit Sec62 [Intracellular
trafficking and secretion].
Length = 259
Score = 27.6 bits (61), Expect = 1.6
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 60 LSEKTAKFT-TIGIGAVMVTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITISLL 115
E T+ + + V+VT+ ++ PL R R+ L G + F +++L
Sbjct: 143 AYEPTSNISLVLCGVFVLVTLALVLFPLWPRNMRQGLFYMSYGLGGFITFFFVLAIL 199
>gnl|CDD|218149 pfam04558, tRNA_synt_1c_R1, Glutaminyl-tRNA synthetase,
non-specific RNA binding region part 1. This is a
region found N terminal to the catalytic domain of
glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes
but not in Escherichia coli. This region is thought to
bind RNA in a non-specific manner, enhancing
interactions between the tRNA and enzyme, but is not
essential for enzyme function.
Length = 164
Score = 26.8 bits (60), Expect = 2.3
Identities = 8/16 (50%), Positives = 8/16 (50%)
Query: 51 STALFESSGLSEKTAK 66
LF GL EK AK
Sbjct: 6 LLKLFSKIGLDEKKAK 21
>gnl|CDD|225121 COG2211, MelB, Na+/melibiose symporter and related transporters
[Carbohydrate transport and metabolism].
Length = 467
Score = 26.8 bits (60), Expect = 2.8
Identities = 24/118 (20%), Positives = 47/118 (39%), Gaps = 12/118 (10%)
Query: 3 VEQIAQQSESKISMSELLCSSTLRKPLIIGIVMQL----SQQFSGINAVFYYSTALFESS 58
VE ++ K+ + + +PL++ ++M L + G V+Y + L
Sbjct: 212 VETQPTKTGVKLKLKDSFLLIFKNRPLLLLLLMNLLLFIAFNIRGSIMVYYVTYVL---- 267
Query: 59 GLSEKTAKFTTIGIGAVMVTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITISLLI 116
G E A + GA ++ I+ L+ + G++ L L GL + + L
Sbjct: 268 GDPELFAYLLLLASGAGLLIGLILWPRLVKKFGKKKLFLIGL----LLLAVGYLLLYF 321
>gnl|CDD|233160 TIGR00869, sec62, protein translocation protein, Sec62 family.
Members of the NSCC2 family have been sequenced from
various yeast, fungal and animals species including
Saccharomyces cerevisiae, Drosophila melanogaster and
Homo sapiens. These proteins are the Sec62 proteins,
believed to be associated with the Sec61 and Sec63
constituents of the general protein secretary systems of
yeast microsomes. They are also the non-selective cation
(NS) channels of the mammalian cytoplasmic membrane. The
yeast Sec62 protein has been shown to be essential for
cell growth. The mammalian NS channel proteins has been
implicated in platelet derived growth factor(PGDF)
dependent single channel current in fibroblasts. These
channels are essentially closed in serum deprived
tissue-culture cells and are specifically opened by
exposure to PDGF. These channels are reported to exhibit
equal selectivity for Na+, K+ and Cs+ with low
permeability to Ca2+, and no permeability to anions
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 232
Score = 26.4 bits (58), Expect = 3.1
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 70 IGIGAVMVTMTIISIPLMDRMGRRTLHLYGLGGMFIFSIFITISLL 115
I I V + + ++ PL R RR LG + I F +++L
Sbjct: 122 IVILVVSIILALVLFPLWPRFMRRGSWYLSLGALGIIGGFFAVAIL 167
>gnl|CDD|189037 cd09867, PIN_FEN1, PIN domain of Flap Endonuclease-1, a
structure-specific, divalent-metal-ion dependent, 5'
nuclease and homologs. Flap endonuclease-1 (FEN1) is
involved in multiple DNA metabolic pathways, including
DNA replication processes (5' flap DNA endonuclease
activity and double stranded DNA 5'-exonuclease
activity) and DNA repair processes (long-patch base
excision repair) in eukaryotes and archaea. Interaction
between FEN1 and PCNA (Proliferating cell nuclear
antigen) is an essential prerequisite to FEN1's DNA
replication functionality and stimulates FEN1 nuclease
activity by 10-50 fold. FEN1 belongs to the
FEN1-EXO1-like family of structure-specific, 5'
nucleases. These nucleases contain a PIN (PilT N
terminus) domain with a helical arch/clamp region (I
domain) of variable length (approximately 45 residues in
FEN1 PIN domains) and a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. Nucleases
within this group also have a carboxylate-rich active
site that is involved in binding essential divalent
metal ion cofactors (Mg2+/Mn2+). FEN1 has a C-terminal
extension containing residues forming the consensus
PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1
to PCNA.
Length = 261
Score = 26.7 bits (60), Expect = 3.1
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 85 PLMDRMGRRTLHLYGL 100
PL + G T HL GL
Sbjct: 47 PLTNSAGEVTSHLSGL 62
>gnl|CDD|213286 cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate
forming enzymes. This family contains benzoate CoA
ligase (BCL) and related ligases that catalyze the
acylation of benzoate derivatives, 2-aminobenzoate and
4-hydroxybenzoate. Aromatic compounds represent the
second most abundant class of organic carbon compounds
after carbohydrates. Xenobiotic aromatic compounds are
also a major class of man-made pollutants. Some bacteria
use benzoate as the sole source of carbon and energy
through benzoate degradation. Benzoate degradation
starts with its activation to benzoyl-CoA by benzoate
CoA ligase. The reaction catalyzed by benzoate CoA
ligase proceeds via a two-step process; the first
ATP-dependent step forms an acyl-AMP intermediate, and
the second step forms the acyl-CoA ester with release of
the AMP.
Length = 436
Score = 26.5 bits (59), Expect = 3.7
Identities = 10/49 (20%), Positives = 16/49 (32%), Gaps = 15/49 (30%)
Query: 83 SIPLMDRMGRRTLHL---------------YGLGGMFIFSIFITISLLI 116
+ + R L L YGLG +F +F S ++
Sbjct: 116 PLTFAEAFARELLGLQPGDRIFSSSKLFFAYGLGNSLLFPLFSGASAVL 164
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
0.327 0.138 0.373
Gapped
Lambda K H
0.267 0.0687 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,673,336
Number of extensions: 484346
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 812
Number of HSP's successfully gapped: 83
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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 (21.7 bits)
S2: 53 (24.3 bits)