RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy799
(209 letters)
>gnl|CDD|233179 TIGR00911, 2A0308, L-type amino acid transporter. [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 501
Score = 82.9 bits (205), Expect = 1e-18
Identities = 36/82 (43%), Positives = 49/82 (59%)
Query: 6 EMIASPAVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAF 65
E++AS AVAV F ER+LG + +P V L+ FG F +RL + GREGH+
Sbjct: 298 ELLASLAVAVDFGERLLGVMSWAMPALVGLSCFGSVNGSLFSSSRLFFVGGREGHLPSLL 357
Query: 66 SFVHVKRLTPAPAVLFQVPLVI 87
S +HVKRLTP P++L L +
Sbjct: 358 SMIHVKRLTPLPSLLIVCTLTL 379
>gnl|CDD|223605 COG0531, PotE, Amino acid transporters [Amino acid transport and
metabolism].
Length = 466
Score = 51.3 bits (123), Expect = 9e-08
Identities = 28/115 (24%), Positives = 55/115 (47%)
Query: 12 AVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAFSFVHVK 71
+A+A I+ + +L+ FG L+ V+R+ YA R+G + + F+ V+ K
Sbjct: 273 PLALAALFGGGNWGAIIIAILALLSLFGSLLAWILAVSRVLYAMARDGLLPKFFAKVNPK 332
Query: 72 RLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYI 126
TP A++ + + + +L ++ +V+ + FLIA + L +LV
Sbjct: 333 GRTPVIALILTGIISLILLLLFPLSSIAFNALVSLASVAFLIAYLLVALALLVLR 387
>gnl|CDD|222193 pfam13520, AA_permease_2, Amino acid permease.
Length = 425
Score = 40.0 bits (94), Expect = 5e-04
Identities = 30/137 (21%), Positives = 62/137 (45%), Gaps = 8/137 (5%)
Query: 10 SPAVAVAFSERVLGP-FQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAFSFV 68
P+VA E V GP IV + + L+ G + +R+ A R+G + + F+ V
Sbjct: 256 LPSVAALLFEAVGGPWGAIIVVILLALSLLGAVNTAIVASSRVLEALARDGVLPKFFAKV 315
Query: 69 HVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPF 128
+ K +P A++ L + + +L + + +++ L AV ++++ +L+ I
Sbjct: 316 N-KFGSPVRALILTAILSLILLLLFLLSGAAYNALLS------LSAVGYLLVYLLLIIGL 368
Query: 129 VYYQYRMPYLDNITYFI 145
+ + + P L I
Sbjct: 369 LILRKKRPDLPRIKGRW 385
>gnl|CDD|129984 TIGR00906, 2A0303, cationic amino acid transport permease.
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 557
Score = 35.9 bits (83), Expect = 0.012
Identities = 29/136 (21%), Positives = 54/136 (39%), Gaps = 5/136 (3%)
Query: 1 MDPVFEMIASPAVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGH 60
M P + + VAF GP ++IV +G + L F + R+ YA R+G
Sbjct: 289 MMPYYLLDPDAPFPVAFEYVGWGPAKYIVAVGALCGMSTSLLGGMFPLPRVIYAMARDGL 348
Query: 61 MLQAFSFVHVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVL 120
+ + + ++ K TP A +V +M+ + L +V + L+A + +
Sbjct: 349 LFKWLAQINSKTKTPINAT-----VVSGAIAALMAFLFDLKALVDLLSIGTLLAYSLVAA 403
Query: 121 GILVYIPFVYYQYRMP 136
+L+ Y
Sbjct: 404 CVLILRYQPGLVYGQA 419
>gnl|CDD|129987 TIGR00909, 2A0306, amino acid transporter. [Transport and binding
proteins, Amino acids, peptides and amines].
Length = 429
Score = 34.0 bits (78), Expect = 0.052
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 2/94 (2%)
Query: 28 IVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAFSFVHVKRLTPAPAVLFQVPLVI 87
I+ G V + L+ +G +R+ +A R+G + + S VH K TP +++
Sbjct: 281 ILTAGAVFSIASVMLAGIYGTSRVLFAMSRDGLLPGSLSKVHPKTGTPHMSIIIFSLTAA 340
Query: 88 PIFVLI-MSIVLSLTPIVTKPAPQFLIAVAFIVL 120
+ L+ + + LT I T + VA I+L
Sbjct: 341 LLASLVPLEGLAELTSIGTL-IAFAAVNVAVIIL 373
>gnl|CDD|224038 COG1113, AnsP, Gamma-aminobutyrate permease and related permeases
[Amino acid transport and metabolism].
Length = 462
Score = 32.6 bits (75), Expect = 0.11
Identities = 30/136 (22%), Positives = 51/136 (37%), Gaps = 30/136 (22%)
Query: 4 VFEMIASPAVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQ 63
VF +I P A G F+V A S + +R+ Y+ ++G +
Sbjct: 277 VFSLIGIPFAA--------GIMNFVVLT----AALSALNSGLYSTSRMLYSLAKQGDAPK 324
Query: 64 AFSFVHVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQ--FLIAVAFIVLG 121
AF+ + KR P A+L ++VL L ++ P+ F + + LG
Sbjct: 325 AFAKL-SKRGVPVNAILL------------SAVVLLLGVVLNYILPEKVFELVTSSSGLG 371
Query: 122 ILV---YIPFVYYQYR 134
+L I + R
Sbjct: 372 LLFVWLMILLSQLKLR 387
>gnl|CDD|218809 pfam05915, DUF872, Eukaryotic protein of unknown function (DUF872).
This family consists of several uncharacterized
eukaryotic proteins. The function of this family is
unknown.
Length = 108
Score = 30.1 bits (68), Expect = 0.28
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 85 LVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQY 133
L++ +L++ + + P+ Q A F VLGIL++IP Y+
Sbjct: 44 LLLGALLLVIGVFIFTGPME-GDGSQ---AYVFFVLGILLFIPGFYHVR 88
>gnl|CDD|132469 TIGR03428, ureacarb_perm, permease, urea carboxylase system. A
number of bacteria obtain nitrogen by biotin- and
ATP-dependent urea degradation system distinct from
urease. The two characterized proteins of this system
are the enzymes urea carboxylase and allophanate
hydrolase, but other, uncharacterized proteins co-occur
as genes encoded nearby in multiple organisms. This
family includes predicted permeases of the amino acid
permease family, likely to transport either urea or a
compound from which urea is derived. It is found so far
only Actinobacteria, whereas a number of other species
with the urea carboxylase have an adjacent ABC
transporter operon.
Length = 475
Score = 31.0 bits (70), Expect = 0.41
Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 7 MIASPAVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHM--LQA 64
+A+ + S + P+ ++ + V +A C L++Q +RL ++ R+G +
Sbjct: 279 RLAAEGLPYVLSAVLDSPWGTVLLVDVAIAILVCTLAIQTAGSRLMFSMARDGKLPASAQ 338
Query: 65 FSFVHVKRLTP-APAVLFQV 83
S VH + TP P+++ V
Sbjct: 339 LSRVHPRTGTPILPSIVIGV 358
>gnl|CDD|183096 PRK11357, frlA, putative fructoselysine transporter; Provisional.
Length = 445
Score = 31.0 bits (70), Expect = 0.42
Identities = 36/160 (22%), Positives = 57/160 (35%), Gaps = 35/160 (21%)
Query: 3 PVFEMIASPA-VAVAFSE-----RVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAG 56
P ++ S ++ A + G F I + V+L + + Q RL YA
Sbjct: 255 PFDKLANSETPISDALTWIPALGSTAGIFVAITAMIVILGSLSSCVMYQ---PRLEYAMA 311
Query: 57 REGHMLQAFSFVHVKRLTPAPAVLFQVPLVI------------PIFVLIMSIVLSLT--- 101
++ + F VH K TP +++ Q L I F L+M +LT
Sbjct: 312 KDNLFFKCFGHVHPKYNTPDVSIILQGALGIFFIFVSDLTSLLGYFTLVMCFKNTLTFGS 371
Query: 102 -----------PIVTKPAPQFLIAVAFIVLGILVYIPFVY 130
P+ PA + +A ILV FV+
Sbjct: 372 IIWCRKRDDYKPLWRTPAFGLMTTLAIASSLILVASTFVW 411
>gnl|CDD|236185 PRK08205, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 583
Score = 30.0 bits (68), Expect = 0.89
Identities = 14/25 (56%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 48 VTRLCYAAGREGHM-LQAFSFVHVK 71
V R CYAA R GHM LQ VK
Sbjct: 128 VRRACYAADRTGHMILQTLYQNCVK 152
>gnl|CDD|233178 TIGR00907, 2A0304, amino acid permease (GABA permease). [Transport
and binding proteins, Amino acids, peptides and amines].
Length = 482
Score = 30.1 bits (68), Expect = 0.90
Identities = 25/101 (24%), Positives = 45/101 (44%), Gaps = 8/101 (7%)
Query: 28 IVPLGVVL-ATFGCALSVQFGVTRLCYAAGREGHMLQAFSFVHVKRLTPAPAVLFQVPLV 86
I L ++L +F CA++ +R+ YA R+G + + + V T QVPL
Sbjct: 306 IFLLCLILVTSFFCAITCMTANSRMIYAFSRDGGLPFSPLWSRVNPRT-------QVPLN 358
Query: 87 IPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIP 127
+ I++ L + + A Q + +V + L + IP
Sbjct: 359 AVWLSAVWIILIGLLGLGSSTAFQAIFSVCTVALDVSYVIP 399
>gnl|CDD|182670 PRK10715, flk, flagella biosynthesis regulator; Provisional.
Length = 335
Score = 29.6 bits (67), Expect = 1.0
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 67 FVHVKRLTPAPAVLFQVPLVIPIFV-LIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVY 125
+ +R+ L PL P+ LI + +L P+ +P L V IV+ +L++
Sbjct: 276 QLFQRRVERIQEALEPRPL-QPLINPLIAPLPDTLQPLAARPG--LLALVLVIVILLLLW 332
Query: 126 I 126
+
Sbjct: 333 L 333
>gnl|CDD|118668 pfam10140, YukC, WXG100 protein secretion system (Wss), protein
YukC. Members of this family of proteins include
predicted membrane proteins homologous to YukC in B.
subtilis. The YukC protein family would participate to
the formation of a translocon required for the secretion
of WXG100 proteins (pfam06013) in monoderm bacteria, the
WXG100 protein secretion system (Wss). This family
includes EssB in Staphylococcus aureus.
Length = 359
Score = 29.6 bits (67), Expect = 1.3
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 112 LIAVAFIVLGILVYIPFVYYQY-RMPYLDNI----TYFIQV 147
+ + I L + + IP +Y + P + I T F+ V
Sbjct: 196 YLGIGLIALLVPLIIPLIYLLFFAQPKQEAILEANTAFLNV 236
>gnl|CDD|100080 cd06159, S2P-M50_PDZ_Arch, Uncharacterized Archaeal homologs of
Site-2 protease (S2P), zinc metalloproteases (MEROPS
family M50) which cleave transmembrane domains of
substrate proteins, regulating intramembrane proteolysis
(RIP) of diverse signal transduction mechanisms. Members
of the S2P/M50 family of RIP proteases use proteolytic
activity within the membrane to transfer information
across membranes to integrate gene expression with
physiologic stresses occurring in another cellular
compartment. In eukaryotic cells they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum stress responses. In prokaryotes
they regulate such processes as sporulation, cell
division, stress response, and cell differentiation.
This group appears to be limited to Archaeal S2P/M50s
homologs with additional putative N-terminal
transmembrane spanning regions, relative to the core
protein, and either one or two PDZ domains present.
Length = 263
Score = 29.2 bits (66), Expect = 1.5
Identities = 11/46 (23%), Positives = 24/46 (52%)
Query: 85 LVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVY 130
V IF+L++ ++ ++ + PAP ++ G+ ++IP Y
Sbjct: 67 FVGMIFMLLLILLSAIIILSGPPAPLNAPRNVLVIPGVNIFIPLPY 112
>gnl|CDD|225646 COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport
and metabolism].
Length = 498
Score = 29.2 bits (66), Expect = 1.7
Identities = 26/118 (22%), Positives = 47/118 (39%), Gaps = 32/118 (27%)
Query: 1 MDPVFEMIASPAVAVAFSERVLGPFQFIVP----LGVVLATFGCALSVQFGVTRLCYAAG 56
++P F ++ SP +A +++ G Q P LG++LA G + + G+ + G
Sbjct: 332 LNPFFIILFSPILAALWTKLGRGNKQPSTPIKFALGLILAGLGFLILLLAGI----WFGG 387
Query: 57 REGHMLQAFSFVHVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPI----VTKPAPQ 110
G + V ++ +VL L ++P+ VTK AP
Sbjct: 388 PSGLV--------------------SVWWLVLSYVLQSFGELFISPVGLSMVTKLAPP 425
>gnl|CDD|215858 pfam00324, AA_permease, Amino acid permease.
Length = 473
Score = 28.8 bits (65), Expect = 2.1
Identities = 22/118 (18%), Positives = 40/118 (33%), Gaps = 11/118 (9%)
Query: 6 EMIASPAVAVAFSERVLGPFQFIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAF 65
A+ + F + ++ ++ A A S + +R+ YA R+G +
Sbjct: 265 SASAASPFVIFFKSLGISGLAPLINAVILTAALSAANSSLYSGSRVLYALARDGLAPKFL 324
Query: 66 SFVHVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGIL 123
K P A+L L+ ++ SL P + F +A L L
Sbjct: 325 K-KVDKSGVPLRAILLST-----AISLLAVLLASLNPAIV-----FNFLLAISGLIGL 371
>gnl|CDD|217315 pfam03006, HlyIII, Haemolysin-III related. Members of this family
are integral membrane proteins. This family includes a
protein with hemolytic activity from Bacillus cereus. It
has been proposed that YOL002c encodes a Saccharomyces
cerevisiae protein that plays a key role in metabolic
pathways that regulate lipid and phosphate metabolism.
In eukaryotes, members are seven-transmembrane pass
molecules found to encode functional receptors with a
broad range of apparent ligand specificities, including
progestin and adipoQ receptors, and hence have been
named PAQR proteins. The mammalian members include
progesterone binding proteins. Unlike the case with GPCR
receptor proteins, the evolutionary ancestry of the
members of this family can be traced back to the
Archaea.
Length = 207
Score = 28.0 bits (63), Expect = 2.8
Identities = 10/65 (15%), Positives = 29/65 (44%)
Query: 85 LVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQYRMPYLDNITYF 144
++ IF+ ++++ L + ++L V ++++G L IP + + +
Sbjct: 105 WILLIFIWGLALLGILLKLFWLKRFRWLRTVLYLLMGWLGIIPIKHLILALGGGGLVLLV 164
Query: 145 IQVLL 149
+ +L
Sbjct: 165 LGGVL 169
>gnl|CDD|130875 TIGR01816, sdhA_forward, succinate dehydrogenase, flavoprotein
subunit, E. coli/mitochondrial subgroup. Succinate
dehydrogenase and fumarate reductase are homologous
enzymes reversible in principle but favored under
different circumstances. This model represents a
narrowly defined clade of the succinate dehydrogenase
flavoprotein subunit as found in mitochondria, in
Rickettsia, in E. coli and other Proteobacteria, and in
a few other lineages. However, This model excludes all
known fumarate reductases. It also excludes putative
succinate dehydrogenases that appear to diverged before
the split between E. coli succinate dehydrogenase and
fumarate reductase [Energy metabolism, TCA cycle].
Length = 565
Score = 28.2 bits (63), Expect = 3.4
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 30 PLGVVLATFGCALSVQFGVTRLCYAAGREGHML 62
P G FG + + R C AA R GH +
Sbjct: 93 PFGGHTRDFGKGGAAE----RACAAADRTGHAI 121
>gnl|CDD|225142 COG2233, UraA, Xanthine/uracil permeases [Nucleotide transport and
metabolism].
Length = 451
Score = 28.3 bits (64), Expect = 3.4
Identities = 26/125 (20%), Positives = 44/125 (35%), Gaps = 37/125 (29%)
Query: 21 VLGP-FQFIVPLGVVLATFGCALSVQFG---VTRLCYAAGREGHMLQAFSF-VHVKRLTP 75
LG F F+ P+ + T G ++ G L Y L + + + RL P
Sbjct: 83 YLGSSFAFVAPMIAIGGTTGDGIAALLGGIIAAGLVY-------FLISPIVKIRLARLFP 135
Query: 76 APAVLFQVPLVIPIFVLIMSIVLSLTPI--------------VTKPAPQFLIAVAFIVLG 121
P+V ++ I LSL P+ + + L +A + L
Sbjct: 136 --------PVVTGPV--VLVIGLSLAPVAINMAGGGPGAAGNPDFGSLENLG-LALVTLL 184
Query: 122 ILVYI 126
I++ I
Sbjct: 185 IILLI 189
>gnl|CDD|232983 TIGR00460, fmt, methionyl-tRNA formyltransferase. The top-scoring
characterized proteins other than methionyl-tRNA
formyltransferase (fmt) itself are
formyltetrahydrofolate dehydrogenases. The mitochondrial
methionyl-tRNA formyltransferases are so divergent that,
in a multiple alignment of bacterial fmt, mitochondrial
fmt, and formyltetrahydrofolate dehydrogenases, the
mitochondrial fmt appears the most different. However,
because both bacterial and mitochondrial fmt are
included in the seed alignment, all credible fmt
sequences score higher than any non-fmt sequence. This
enzyme modifies Met on initiator tRNA to f-Met [Protein
synthesis, tRNA aminoacylation].
Length = 313
Score = 27.7 bits (62), Expect = 4.6
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 71 KRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAF 117
K+LTP P + IP+F L P+V + P ++ V+F
Sbjct: 41 KKLTPPPVKVLAEEKGIPVFQPEKQRQLEELPLVRELKPDVIVVVSF 87
>gnl|CDD|183863 PRK13107, PRK13107, preprotein translocase subunit SecA; Reviewed.
Length = 908
Score = 27.6 bits (61), Expect = 5.1
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 186 EKHALLEVEVRTPIVINGAVKDSN 209
E ++L E RTP++I+GA +DS+
Sbjct: 210 EVDSILIDEARTPLIISGAAEDSS 233
>gnl|CDD|224104 COG1183, PssA, Phosphatidylserine synthase [Lipid metabolism].
Length = 234
Score = 27.2 bits (61), Expect = 5.3
Identities = 29/134 (21%), Positives = 45/134 (33%), Gaps = 27/134 (20%)
Query: 2 DPVFEMIASPAVAVAFSERVLGPFQFIVPLGVVLATFG-CALSVQFGVTRLCYAAGREGH 60
F + PA AV VL L VL + LS+
Sbjct: 123 KNFFIGLPIPAAAVVVVLLVLLYHSLPTGLATVLLSGILLLLSIL--------------- 167
Query: 61 MLQAFSFVHVKRLTPAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVL 120
M+ F +K+L LV + +L ++L+L +V P + + I
Sbjct: 168 MVSNIPFPSLKKLN---------ALVRVVLLLAGILLLALLALVLILYP--WLLLLVIAS 216
Query: 121 GILVYIPFVYYQYR 134
G L+ IP Q+
Sbjct: 217 GYLLSIPIRVRQWF 230
>gnl|CDD|185726 cd08985, GH43_6, Glycosyl hydrolase family 43. This glycosyl
hydrolase family 43 (GH43) includes enzymes with
beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC
3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-),
alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase
(EC 3.2.1.99), xylanase (EC 3.2.1.8),
endo-alpha-L-arabinanase and galactan
1,3-beta-galactosidase (EC 3.2.1.145) activities. These
are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
enzymes in this family display both
alpha-L-arabinofuranosidase and beta-D-xylosidase
activity using aryl-glycosides as substrates. A common
structural feature of GH43 enzymes is a 5-bladed
beta-propeller domain that contains the catalytic acid
and catalytic base. A long V-shaped groove, partially
enclosed at one end, forms a single extended
substrate-binding surface across the face of the
propeller.
Length = 265
Score = 27.2 bits (61), Expect = 5.4
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 9 ASPAVAVAFSERVLGPFQFI---VPLG 32
+ V VA S+ GP+ ++ PLG
Sbjct: 91 SDARVGVATSDTPTGPYTYLGSFRPLG 117
>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 = 27.4 bits (62), Expect = 5.4
Identities = 30/122 (24%), Positives = 52/122 (42%), Gaps = 7/122 (5%)
Query: 29 VPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAF---SFVHVKRLTPAPAVLFQVPL 85
+ LG + A L++ FGVT + A E +ML A+ + + L A+L + +
Sbjct: 2 LALGAIYALIALGLTLIFGVTGVINFAHGEFYMLGAYVAYTLLVALGLPFWLALLLALLV 61
Query: 86 VIPIFVLIMSIVLSLTPIVTKPAPQFLIA--VAFIVLGILVYIPFVYYQYRMPYLDNITY 143
+ VL+ +VL P+ P LI I+L L+ I + P L + +
Sbjct: 62 AALLGVLLERLVLR--PLRGAPLLTLLITFGGLLILLQGLLLIFGGDPRVPPPPLLSGSV 119
Query: 144 FI 145
+
Sbjct: 120 EL 121
>gnl|CDD|237167 PRK12667, PRK12667, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 520
Score = 27.2 bits (61), Expect = 8.1
Identities = 9/47 (19%), Positives = 21/47 (44%)
Query: 87 IPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQY 133
PI +++ + +L L I+ K + A +V I + + + +
Sbjct: 9 TPILLVLFAFLLPLLSILLKGNRKIQKIYALLVSLITLILSILLFIQ 55
>gnl|CDD|224191 COG1272, COG1272, Predicted membrane protein, hemolysin III homolog
[General function prediction only].
Length = 226
Score = 26.8 bits (60), Expect = 8.8
Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 74 TPAPAVLFQVPLVIPIFVLIMSIVL--SLTPIVTKPAPQFLIAVAFIVLGILVYIPF 128
TP V PL + LI + L L + K + L V ++ +G L I
Sbjct: 105 TPFLLVGLYGPLGWILLGLIWGLALAGILFKLFFKKRFRKLSLVLYLAMGWLGLIVI 161
>gnl|CDD|233737 TIGR02123, TRAP_fused, TRAP transporter, 4TM/12TM fusion protein.
In some species, the 12-transmembrane spanning and
4-transmembrane spanning components of tripartite
ATP-independent periplasmic (TRAP)-type transporters are
fused. This model describes such transporters, found in
the Archaea and in Bacteria [Transport and binding
proteins, Unknown substrate].
Length = 613
Score = 26.9 bits (60), Expect = 9.0
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 75 PAPAVLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIV 119
P + L+IP+ +LI+ +++ +PI A + IA+ IV
Sbjct: 323 PKTVLKAGWYLLIPLVLLIVLLLVGYSPIR---AAFYSIALTLIV 364
>gnl|CDD|119394 cd06261, TM_PBP2, Transmembrane subunit (TM) found in Periplasmic
Binding Protein (PBP)-dependent ATP-Binding Cassette
(ABC) transporters which generally bind type 2 PBPs.
These types of transporters consist of a PBP, two TMs,
and two cytoplasmic ABC ATPase subunits, 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. For these transporters the ABCs and TMs are on
independent polypeptide chains. These systems transport
a diverse range of substrates. Most are specific for a
single substrate or a group of related substrates;
however some transporters are more promiscuous,
transporting structurally diverse substrates such as the
histidine/lysine and arginine transporter in
Enterobacteriaceae. In the latter case, this is achieved
through binding different PBPs with different
specificities to the TMs. For other promiscuous
transporters such as the multiple-sugar transporter Msm
of Streptococcus mutans, the PBP has a wide substrate
specificity. These transporters include the
maltose-maltodextrin, phosphate and sulfate
transporters, among others.
Length = 190
Score = 26.5 bits (59), Expect = 9.2
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 79 VLFQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQYRM 135
+ + L +P VL + +VL ++ L A ++L +L+ PF R
Sbjct: 39 RIIDLLLSLPSLVLGLLLVLLFGVLLGWGILPGLGLPA-LILALLLIAPFARLIRRA 94
>gnl|CDD|115915 pfam07290, DUF1449, Protein of unknown function (DUF1449). This
family consists of several bacterial proteins of around
210 residues in length. The function of this family is
unknown.
Length = 202
Score = 26.4 bits (58), Expect = 9.7
Identities = 25/108 (23%), Positives = 45/108 (41%), Gaps = 7/108 (6%)
Query: 27 FIVPLGVVLATFGCALSVQFGVTRLCYAAGREGHMLQAFSFVHVKRLTPAPAVLFQVPLV 86
I L VV G +LS Y +G +LQA ++++ R+ PA VL +
Sbjct: 17 IIGSLEVVTLIVGHSLSGALDAHLDHYDHPSDGGVLQALHYLNIGRV-PALVVL----CL 71
Query: 87 IPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQYR 134
+ + I++ I+ P L + + + V +P V+Y +
Sbjct: 72 LAGAFGLTGILIQHVAIMVWQGP--LSNLVAVPGSVAVSVPAVHYASK 117
>gnl|CDD|227881 COG5594, COG5594, Uncharacterized integral membrane protein
[Function unknown].
Length = 827
Score = 27.0 bits (60), Expect = 9.7
Identities = 17/75 (22%), Positives = 31/75 (41%), Gaps = 9/75 (12%)
Query: 81 FQVPLVIPIFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVY---YQYRMPY 137
FQ V+P +L+ +I + + + P AV F IL Y+ + Y Y
Sbjct: 603 FQFGTVLPQPILLFTITICYS--IISPLILLFGAVYF----ILNYLAYKYNLIYVSNHSP 656
Query: 138 LDNITYFIQVLLKVV 152
Y+ + L +++
Sbjct: 657 ESGGGYWPRALFQII 671
>gnl|CDD|220520 pfam10011, DUF2254, Predicted membrane protein (DUF2254). Members
of this family of bacterial proteins comprises various
hypothetical and putative membrane proteins. Their exact
function, has not, as yet, been defined.
Length = 369
Score = 26.7 bits (60), Expect = 10.0
Identities = 10/59 (16%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 89 IFVLIMSIVLSLTPIVTKPAPQFLIAVAFIVLGILVYIPFVYYQYRMPYLDNITYFIQV 147
++ L++ I + P L+ + VL + +Y ++ ++ IQV
Sbjct: 105 VYSLLVLITIRGGAYGFVPRLSVLVTILLAVLSVAA---LIY------FIHHLARLIQV 154
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
0.326 0.141 0.413
Gapped
Lambda K H
0.267 0.0829 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,979,654
Number of extensions: 1073455
Number of successful extensions: 2122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2092
Number of HSP's successfully gapped: 224
Length of query: 209
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 116
Effective length of database: 6,812,680
Effective search space: 790270880
Effective search space used: 790270880
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 (21.6 bits)
S2: 57 (25.5 bits)