RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6058
(235 letters)
>gnl|CDD|233173 TIGR00892, 2A0113, monocarboxylate transporter 1. [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 455
Score = 117 bits (295), Expect = 1e-30
Identities = 50/143 (34%), Positives = 82/143 (57%), Gaps = 1/143 (0%)
Query: 1 MAVPLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGL 60
+AV GP++S V+++GCR + I GG+++ G +L A+ ++++ Y+T G I G GL
Sbjct: 64 LAVLYAGGPISSILVNRFGCRPVVIAGGLLASLGMIL-ASFSSNVIELYLTAGFITGLGL 122
Query: 61 SLAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGT 120
+ + ++ + +F ++R LA L G+ + APL QY E +GWRG+ L+L G
Sbjct: 123 AFNFQPSLTMLGKYFYRRRPLANGLAMAGSPVFLSTLAPLNQYLFESFGWRGSFLILGGL 182
Query: 121 FLQMCICGALMKDPEWWIREQKR 143
L C+CGALM+ R K
Sbjct: 183 LLHCCVCGALMRPVGPSQRVSKS 205
>gnl|CDD|233171 TIGR00890, 2A0111, oxalate/formate antiporter family transporter.
This subfamily belongs to the major facilitator family.
Members include the oxalate/formate antiporter of
Oxalobacter formigenes, where one substrate is
decarboxylated in the cytosol into the other to consume
a proton and drive an ion gradient [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 377
Score = 75.2 bits (185), Expect = 8e-16
Identities = 45/128 (35%), Positives = 70/128 (54%), Gaps = 3/128 (2%)
Query: 9 PVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTAV 68
PV DK+G R + +LGGI+ G GF A +A+S+ A Y+T+G +A G+ +AY A+
Sbjct: 56 PVGGLLADKFGPRAVAMLGGILYGLGFTFYA-IADSLAALYLTYG-LASAGVGIAYGIAL 113
Query: 69 VSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFLQMCICG 128
+ WF KR LA+ + G G+G+F+ +PL I G + + FL + + G
Sbjct: 114 NTAVKWFPDKRGLASGIIIGGYGLGSFILSPLITSVINLEGVPAAFIYMGIIFLLVIVLG 173
Query: 129 A-LMKDPE 135
A L+ P
Sbjct: 174 AFLIGYPP 181
>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 = 69.3 bits (170), Expect = 8e-14
Identities = 34/132 (25%), Positives = 53/132 (40%), Gaps = 3/132 (2%)
Query: 1 MAVPLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGL 60
L +A D++G R + +LG ++ G +L A ++ + + G G
Sbjct: 44 SLGYALGSLLAGYLSDRFGRRRVLLLGLLLFALGSLLLAFASSL--WLLLVGRFLLGLGG 101
Query: 61 SLAYVTAVVSIAYWFDKK-RTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAG 119
Y A IA WF K R A L + G G+G + L E GWR L+LA
Sbjct: 102 GALYPAAAALIAEWFPPKERGRALGLFSAGFGLGALLGPLLGGLLAESLGWRWLFLILAI 161
Query: 120 TFLQMCICGALM 131
L + + +
Sbjct: 162 LGLLLALLLLFL 173
Score = 42.3 bits (100), Expect = 1e-04
Identities = 25/119 (21%), Positives = 48/119 (40%), Gaps = 2/119 (1%)
Query: 5 LLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAY 64
+L + D+ G R + +L G++ +L +A S+ A + + G GL A+
Sbjct: 225 ILGALLGGLLSDRLGRRRLLLLIGLLLAALGLLLLALAPSL-ALLLVALLLLGFGLGFAF 283
Query: 65 VTAVVSIA-YWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFL 122
+ + + R A+ L +G + L ++ G+ G L+LA L
Sbjct: 284 PALLTLASELAPPEARGTASGLFNTFGSLGGALGPLLAGLLLDTGGYGGVFLILAALAL 342
Score = 35.4 bits (82), Expect = 0.016
Identities = 20/137 (14%), Positives = 44/137 (32%), Gaps = 6/137 (4%)
Query: 4 PLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGC--GLS 61
LL + + G RW+ ++ I+ +L + + + F ++ GL
Sbjct: 136 ALLGPLLGGLLAESLGWRWLFLILAILGLLLALLLLFLLRLLLLLALAFFLLSFGYYGLL 195
Query: 62 LAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTF 121
+ + + L SL G +G + L+ G R +LL+
Sbjct: 196 TYLPLYLQEVLGLSAAEAGLLLSLFGLGGILGALLGGLLSDRL----GRRRLLLLIGLLL 251
Query: 122 LQMCICGALMKDPEWWI 138
+ + + +
Sbjct: 252 AALGLLLLALAPSLALL 268
>gnl|CDD|219516 pfam07690, MFS_1, Major Facilitator Superfamily.
Length = 346
Score = 65.9 bits (161), Expect = 1e-12
Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 3/131 (2%)
Query: 1 MAVPLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGL 60
L P+A D++G R + ++G ++ G +L ++ + + G G
Sbjct: 42 SLGYALAQPLAGRLSDRFGRRRVLLIGLLLFALGLLLLLFASSL--WLLLVLRVLQGLGG 99
Query: 61 SLAYVTAVVSIAYWFDKK-RTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAG 119
+ A IA WF + R A L + G G+G + L +GWR L+LA
Sbjct: 100 GALFPAAAALIADWFPPEERGRALGLLSAGFGLGAALGPLLGGLLASLFGWRAAFLILAI 159
Query: 120 TFLQMCICGAL 130
L + AL
Sbjct: 160 LALLAAVLAAL 170
>gnl|CDD|234525 TIGR04259, oxa_formateAnti, oxalate/formate antiporter. This model
represents a subgroup of the more broadly defined model
TIGR00890, which in turn belongs to the Major
Facilitator transporter family. Seed members for this
family include the known oxalate/formate antiporter of
Oxalobacter formigenes, as well as transporter subunits
co-clustered with the two genes of a system that
decarboxylates oxalate into formate. In many of these
cassettes, two subunits are found rather than one,
suggesting the antiporter is sometimes homodimeric,
sometimes heterodimeric.
Length = 405
Score = 62.1 bits (151), Expect = 2e-11
Identities = 40/109 (36%), Positives = 55/109 (50%), Gaps = 2/109 (1%)
Query: 7 LGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVT 66
L P+ FVDKYG R + + GGI+ G G+VL+A A+S+ A Y +AG G Y T
Sbjct: 54 LVPIEGWFVDKYGPRIVVMFGGIMCGLGWVLNA-YADSLPALYAAA-VVAGIGAGAVYGT 111
Query: 67 AVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTIL 115
V + WF KR LA L A G G G + I+ G++ +
Sbjct: 112 CVGNALKWFPDKRGLAAGLTAAGFGAGAALTVVPIAAMIKVSGYQAAFM 160
>gnl|CDD|233175 TIGR00895, 2A0115, benzoate transport. [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 398
Score = 43.5 bits (103), Expect = 4e-05
Identities = 45/188 (23%), Positives = 77/188 (40%), Gaps = 16/188 (8%)
Query: 5 LLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAY 64
L GP+A D+ G R + +L I+ + F L +A ++ Q + +AG GL
Sbjct: 70 LFFGPLA----DRIGRRRV-LLWSILLFSVFTLLCALATNVT-QLLILRFLAGLGLGGLM 123
Query: 65 --VTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFL 122
+ A+VS Y + R A L CG IG V L + I +GWR L G
Sbjct: 124 PNLNALVS-EYAPKRFRGTAVGLMFCGYPIGAAVGGFLAGWLIPVFGWR--SLFYVGGIA 180
Query: 123 QMCICGALMK---DPEWWIREQKRLQNPTPSHSIATKSNRNSIAESAAVDPGLVAVEIKE 179
+ + LM+ + ++ ++ ++IA + A+SA + +
Sbjct: 181 PLLLLLLLMRFLPESIDFLVSKRPETVRRIVNAIAPQMQAE--AQSALPEQKATQGTKRS 238
Query: 180 IRRVLMDG 187
+ + L G
Sbjct: 239 VFKALFQG 246
>gnl|CDD|233166 TIGR00880, 2_A_01_02, Multidrug resistance protein.
Length = 141
Score = 40.3 bits (95), Expect = 1e-04
Identities = 28/118 (23%), Positives = 51/118 (43%), Gaps = 3/118 (2%)
Query: 2 AVPLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLS 61
L+ P++ D++G + + ++G I + A +++I I + G G +
Sbjct: 9 LGQLIYSPLSGLLTDRFGRKPVLLVGLFIFVLSTAMFAL-SSNITVLIIAR-FLQGFGAA 66
Query: 62 LAYVTAVVSIAYWFD-KKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLA 118
A V IA + ++R +A L + G +G + PL + GWR L LA
Sbjct: 67 FALVAGAALIADIYPPEERGVALGLMSAGIALGPLLGPPLGGVLAQFLGWRAPFLFLA 124
>gnl|CDD|223553 COG0477, ProP, Permeases of the major facilitator superfamily
[Carbohydrate transport and metabolism / Amino acid
transport and metabolism / Inorganic ion transport and
metabolism / General function prediction only].
Length = 338
Score = 37.7 bits (86), Expect = 0.003
Identities = 28/133 (21%), Positives = 45/133 (33%), Gaps = 2/133 (1%)
Query: 1 MAVPLLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGL 60
+ +A D+YG R + I+G ++ G +L A N A + + G G
Sbjct: 49 FLGYAIGSLLAGPLGDRYGRRKVLIIGLLLFLLGTLLLALAPNVGLALLLILRLLQGLGG 108
Query: 61 SLAYVTAVVSIAYWFDK--KRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLA 118
A ++ WF + +R LA L G G PL + G
Sbjct: 109 GGLLPVASALLSEWFPEATERGLAVGLVTLGAGALGLALGPLLAGLLLGALLWGWRAAFL 168
Query: 119 GTFLQMCICGALM 131
L + L+
Sbjct: 169 LAALLGLLLLILV 181
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 36.1 bits (84), Expect = 0.012
Identities = 27/140 (19%), Positives = 48/140 (34%), Gaps = 4/140 (2%)
Query: 10 VASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTAVV 69
A D++G + ++G ++ G +L I I G G+ V +
Sbjct: 65 FAGKLGDRFGRKKSLLIGNVLFVIGALLQGFAKGKSFYMLIVGRVIVGLGVGGISVLVPM 124
Query: 70 SIA-YWFDKKRTLATSLGACGTGIGTFVYA---PLTQYWIEEYGWRGTILLLAGTFLQMC 125
I+ K R SL G G V A + GWR + L + +
Sbjct: 125 YISEIAPKKLRGALGSLYQLGITFGILVAAIIGLGLNKYSNSDGWRIPLGLQFVPAILLL 184
Query: 126 ICGALMKDPEWWIREQKRLQ 145
I + + W+ + +L+
Sbjct: 185 IGLLFLPESPRWLVLKGKLE 204
Score = 29.6 bits (67), Expect = 1.5
Identities = 21/131 (16%), Positives = 37/131 (28%), Gaps = 16/131 (12%)
Query: 9 PVASSFVDKYGCRWMTILGGII-SGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTA 67
+A VD++G R + +LG + VL + +++ I L +A+
Sbjct: 304 FIAIFLVDRFGRRPLLLLGAAGMAICFLVLGVALLGVAKSKGAGIVAIVFILLFIAFFAL 363
Query: 68 VVSIAYWF-------DKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGT 120
W R A ++ + F+ L G
Sbjct: 364 GWGPVPWVIVSELFPLGVRPKAMAIATAANWLANFLIGFLFPIITGAIGG--------YV 415
Query: 121 FLQMCICGALM 131
FL L
Sbjct: 416 FLVFAGLLVLF 426
>gnl|CDD|237051 PRK12307, PRK12307, putative sialic acid transporter; Provisional.
Length = 426
Score = 34.9 bits (80), Expect = 0.030
Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 3/110 (2%)
Query: 8 GPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTA 67
G + DK+G + + + + G LS + I F I G G++ Y A
Sbjct: 70 GALFGLLADKFGRKPLMMWSIVAYSVGTGLSGLASGVIMLTLSRF--IVGMGMAGEYACA 127
Query: 68 -VVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILL 116
++ W ++ A++ G GIG + A + E YGWR +
Sbjct: 128 STYAVESWPKHLKSKASAFLVSGFGIGNIIAAYFMPSFAEAYGWRAAFFV 177
>gnl|CDD|225646 COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport
and metabolism].
Length = 498
Score = 32.3 bits (74), Expect = 0.21
Identities = 27/107 (25%), Positives = 45/107 (42%), Gaps = 5/107 (4%)
Query: 9 PVASSFV-DKYGCRWMTI-LGGIISGTG-FVLSATVANSIEAQYITFGCIA-GCGLSLAY 64
P+ ++ D+ TI LG I+ G VL+ + + YI I G GL
Sbjct: 78 PIIGGWLADRVLGTRRTIVLGAILMAIGHLVLAISSVSGPGGLYIGLALIIVGTGLFKPN 137
Query: 65 VTAVVSIAYWFDK-KRTLATSLGACGTGIGTFVYAPLTQYWIEEYGW 110
+++++ Y D +R +L G IG+ + +T YGW
Sbjct: 138 ISSLLGELYPKDDPRRDGGFTLFYMGINIGSLIAPIITGLLAINYGW 184
>gnl|CDD|225133 COG2223, NarK, Nitrate/nitrite transporter [Inorganic ion transport
and metabolism].
Length = 417
Score = 31.5 bits (72), Expect = 0.34
Identities = 30/120 (25%), Positives = 51/120 (42%), Gaps = 13/120 (10%)
Query: 2 AVPLLLGPVA----SSFVDKYGCRWMTILGGIISGT-GFVLSATVANSIEAQYITFGCIA 56
A+P+L+G + D++G R TIL ++ L+ V Q + G
Sbjct: 56 AIPILVGALLRLPYGFLTDRFGGRKWTILSMLLLLIPCLGLAFAVTYPSTWQLLVIG--L 113
Query: 57 GCGLSLA-YVTAVVSIAYWFDKKRTLATSLGACGTG-IGTFV---YAPLTQYWIEEYGWR 111
GL+ A + + + +++F K++ +LG G G +G V APL WR
Sbjct: 114 LLGLAGASFAVGMPNASFFFPKEKQ-GLALGIAGAGNLGVAVAQLVAPLVAVAFGFLAWR 172
>gnl|CDD|182559 PRK10573, PRK10573, type IV pilin biogenesis protein; Provisional.
Length = 399
Score = 29.9 bits (68), Expect = 1.2
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 104 WIEEYGWRGTILLLAGTFLQMCICGALMKDPEWWIREQKRL 144
++ +YGW +LLL L + K P W IREQ+ L
Sbjct: 213 FLIQYGW---LLLLLLFLLAIAYKRLRRKKPTWQIREQRLL 250
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 29.4 bits (66), Expect = 2.0
Identities = 15/66 (22%), Positives = 26/66 (39%), Gaps = 7/66 (10%)
Query: 145 QNPTPSHSIATKSNRNSIAESAAVDPG-------LVAVEIKEIRRVLMDGGNIESLLFTE 197
+ P P+ + A S+ N+ AE + G L V K R + +I L
Sbjct: 728 EEPDPATAAALGSDENTTAEGLKFNDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLS 787
Query: 198 EEEMTK 203
+ E+ +
Sbjct: 788 QNELNE 793
>gnl|CDD|233174 TIGR00893, 2A0114, D-galactonate transporter. [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 399
Score = 29.2 bits (66), Expect = 2.1
Identities = 18/108 (16%), Positives = 37/108 (34%), Gaps = 3/108 (2%)
Query: 5 LLLGPVASSFVDKYGCRWMTILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAY 64
++ +D++G R L I G + G + +
Sbjct: 43 VVGQFPGGWLLDRFGAR--KTLAVFIVIWGVFTGLQAFAGAYVSLYILRVLLGAAEAPFF 100
Query: 65 VTAVVSIAYWF-DKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWR 111
++ +A WF +R A S+ G+G + PL + + + W+
Sbjct: 101 PGIILIVASWFPASERATAVSIFNSAQGLGGIIGGPLVGWILIHFSWQ 148
>gnl|CDD|131765 TIGR02718, sider_RhtX_FptX, siderophore transporter, RhtX/FptX
family. RhtX from Sinorhizobium meliloti 2011 and FptX
from Pseudomonas aeruginosa appear to be single
polypeptide transporters, from the major facilitator
family (see pfam07690) for import of siderophores as a
means to import iron. This function was suggested by
proximity to siderophore biosynthesis genes and then
confirmed by study of knockout and heterologous
expression phenotypes [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 390
Score = 29.1 bits (65), Expect = 2.1
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 79 RTLA--TSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFLQMCICGALMKDPE 135
RTLA ++ G IG F T ++G R LL+A L +C +KD
Sbjct: 129 RTLAKGNAVQIAGVMIGFFGGGAGTLVLFGKFGQRPAFLLVACVPLASLVCVLWLKDRA 187
>gnl|CDD|235958 PRK07194, fliG, flagellar motor switch protein G; Reviewed.
Length = 334
Score = 28.8 bits (65), Expect = 2.2
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 176 EIKEIRRVLMDGGNIESLLFTEEE 199
EI + R L + G IE LF E+
Sbjct: 309 EIMALVRELAEAGEIELQLFEEQV 332
>gnl|CDD|225371 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport
and metabolism].
Length = 394
Score = 28.0 bits (63), Expect = 4.3
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 59 GLSLAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLA 118
++ A +V KR A +L G + T + PL + + +GWR T L +A
Sbjct: 120 SIAAALAARLVP-----PGKRGRALALVFTGLTLATVLGVPLGTFLGQLFGWRATFLAIA 174
Query: 119 G 119
Sbjct: 175 V 175
>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 505
Score = 28.1 bits (63), Expect = 4.3
Identities = 34/143 (23%), Positives = 60/143 (41%), Gaps = 19/143 (13%)
Query: 5 LLLGPVASSFVDKYGCRWM---TILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLS 61
LL V D++G + + + L +SG VL+A + + ++ F + G G+
Sbjct: 141 LLGSFVFGYLSDRFGRKKVLLLSTLVTAVSG---VLTA-FSPNYTV-FLVFRLLVGMGIG 195
Query: 62 LAYVTAVVSIAYWFDKK-RTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGT 120
+V AVV + KK R + +L +G + PL Y+I + WR L ++
Sbjct: 196 GIWVQAVVLNTEFLPKKQRAIVGTLIQVFFSLGLVLL-PLVAYFIPD--WRWLQLAVSLP 252
Query: 121 FLQMCICGALMKDPEWWIREQKR 143
+ L W++ E R
Sbjct: 253 TF---LFFLLS----WFVPESPR 268
>gnl|CDD|215415 PLN02776, PLN02776, prenyltransferase.
Length = 341
Score = 27.8 bits (62), Expect = 4.8
Identities = 14/43 (32%), Positives = 18/43 (41%)
Query: 60 LSLAYVTAVVSIAYWFDKKRTLATSLGACGTGIGTFVYAPLTQ 102
++ A V +A K L LGA + FVY PL Q
Sbjct: 79 VAWAVVVGAAGVALLAYKTNMLTAGLGAGNILLYAFVYTPLKQ 121
>gnl|CDD|239659 cd03688, eIF2_gamma_II, eIF2_gamma_II: this subfamily represents
the domain II of the gamma subunit of eukaryotic
translation initiation factor 2 (eIF2-gamma) found in
Eukaryota and Archaea. eIF2 is a G protein that
delivers the methionyl initiator tRNA to the small
ribosomal subunit and releases it upon GTP hydrolysis
after the recognition of the initiation codon. eIF2 is
composed three subunits, alpha, beta and gamma. Subunit
gamma shows strongest conservation, and it confers both
tRNA binding and GTP/GDP binding.
Length = 113
Score = 26.7 bits (60), Expect = 5.2
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 4 PLLLGPVASSF-VDKYGCRWMTILGGIISGT 33
P ++ V SF V+K G + GG+ G+
Sbjct: 6 PRMI--VIRSFDVNKPGTEVDDLKGGVAGGS 34
>gnl|CDD|226775 COG4325, COG4325, Predicted membrane protein [Function unknown].
Length = 464
Score = 27.5 bits (61), Expect = 6.3
Identities = 24/108 (22%), Positives = 32/108 (29%), Gaps = 23/108 (21%)
Query: 24 TILGGIISGTGFVLSATVANSIEAQYITFGCIAGCGLSLAYVTAVVSIAYWFDKKRTLAT 83
+ +IS TG V S TV L LA + F +
Sbjct: 85 VVAASMISVTGIVFSITVV----------------ALQLASSQFSPRLLRTFLRDVPNQV 128
Query: 84 SLGACGTGIGTFVYA--PLTQYWIEEYGWRGTILLLA--GTFLQMCIC 127
L + TFVY+ L E G I +A + L I
Sbjct: 129 VL---AIFLCTFVYSLGVLRTVGEERDGQGAFIPKVAVTVSLLLAIIS 173
>gnl|CDD|146221 pfam03465, eRF1_3, eRF1 domain 3. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif at
an exposed tip of domain 2 suggests that the Gln residue
coordinates a water molecule to mediate the hydrolytic
activity at the peptidyl transferase centre. A conserved
groove on domain 1, 80 A from the GGQ motif, is proposed
to form the codon recognition site. This family also
includes other proteins for which the precise molecular
function is unknown. Many of them are from
Archaebacteria. These proteins may also be involved in
translation termination but this awaits experimental
verification.
Length = 100
Score = 26.4 bits (59), Expect = 6.4
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 167 AVDPGLVAVEIKEIRRVLMDGGNIESLLFTEE 198
A D GL ++E+ + L G +E+LL ++E
Sbjct: 16 AKDTGLAVYGVEEVLKALEMGA-VETLLISDE 46
>gnl|CDD|118307 pfam09775, Keratin_assoc, Keratinocyte-associated protein 2.
Members of this family comprise various
keratinocyte-associated proteins. Their exact function
has not, as yet, been determined.
Length = 131
Score = 26.7 bits (59), Expect = 6.9
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 22 WMTILGGIISGTGFVLSATVANSIEA 47
MTI GG + F+ S T ++E
Sbjct: 35 LMTIFGGFLGSLLFIFSLTAIGNLEE 60
>gnl|CDD|218603 pfam05482, Serendipity_A, Serendipity locus alpha protein (SRY-A).
The Drosophila serendipity alpha (sry alpha) gene is
specifically transcribed at the blastoderm stage, from
nuclear cycle 11 to the onset of gastrulation, in all
somatic nuclei. SRY-A is required for the
cellularisation of the embryo and is involved in the
localisation of the actin filaments just prior to and
during plasma membrane invagination.
Length = 549
Score = 27.6 bits (61), Expect = 7.1
Identities = 8/45 (17%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 139 REQKRLQNPTPSHSIATKSNRNSIAESAAVDPGLVAVEIKEIRRV 183
+ Q+ ++ SI+ S + + L++ ++ EI R+
Sbjct: 505 KRQRSFVKQEIDCTVPN-PQNTSISNSISHESDLISFQLTEILRI 548
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 27.5 bits (62), Expect = 7.5
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 4 PLLLGPVASSF-VDKYGCRWMTILGGIISGT 33
P + VA SF V+K G + GG+I G+
Sbjct: 211 PRMY--VARSFDVNKPGTPPEKLKGGVIGGS 239
>gnl|CDD|183602 PRK12573, PRK12573, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 140
Score = 26.4 bits (59), Expect = 7.7
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 5/51 (9%)
Query: 27 GGIISGTGFVLSATVANSIE----AQYITFGCIAGCGLSLAYVTAVVSIAY 73
GG+I+ + V+ +A I+ A F +AG GL A T + SI +
Sbjct: 40 GGLITASALVI-LLLAFDIKTVRRALPFDFKILAGIGLLFAIATGLASIFF 89
>gnl|CDD|221514 pfam12297, EVC2_like, Ellis van Creveld protein 2 like protein.
This family of proteins is found in eukaryotes. Proteins
in this family are typically between 571 and 1310 amino
acids in length. There are two conserved sequence
motifs: LPA and ELH. EVC2 is implicated in Ellis van
Creveld chondrodysplastic dwarfism in humans. Mutations
in this protein can give rise to this congenital
condition. LIMBIN is a protein which shares around 80%
sequence homology with EVC2 and it is implicated in a
similar condition in bovine chondrodysplastic dwarfism.
Length = 429
Score = 27.1 bits (60), Expect = 8.4
Identities = 10/43 (23%), Positives = 16/43 (37%)
Query: 192 SLLFTEEEEMTKRGHNSVLNLPTFFLYDDVSGQHREEFGKLHT 234
++ +T E + K G L LP + S +L T
Sbjct: 5 AVSYTAELDAKKLGCGESLTLPAQLTFRSSSQNQTANSTQLTT 47
>gnl|CDD|179591 PRK03545, PRK03545, putative arabinose transporter; Provisional.
Length = 390
Score = 27.2 bits (61), Expect = 9.4
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 78 KRTLATSLGACGTGIGTFVYAPLTQYWIEEYGWRGTILLLAGTFLQMCIC 127
K+ A SL A GT + + PL + + GWR T L + G L +
Sbjct: 130 KKAQALSLLATGTALAMVLGLPLGRVIGQYLGWRTTFLAIGGGALITLLL 179
>gnl|CDD|130645 TIGR01583, formate-DH-gamm, formate dehydrogenase, gamma subunit.
This model represents the gamma chain of the gamma
proteobacteria (and Aquifex aolicus) formate
dehydrogenase. This subunit is integral to the
cytoplasmic membrane, consisting of 4 transmembrane
helices, and receives electrons from the beta subunit.
The entire E. coli formate dehydrogenase N
(nitrate-inducible form) has been crystallized. The
gamma subunit contains two cytochromes, heme b(P) and
heme b(C) near the periplasmic and cytoplasmic sides of
the membrane respectively. The electron acceptor
quinone binds at the cytoplasmic heme histidine ligand.
NiFe-hydrogenase and thiosulfate reductase contain
homologous gamma subunits, and these can be found
scoring in the noise of this model [Energy metabolism,
Anaerobic, Energy metabolism, Electron transport].
Length = 204
Score = 26.7 bits (59), Expect = 9.4
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 2 AVPLLLGPVASSFVDKYGCRWMTILGGIISG 32
+P+ L KY RWM +GG +S
Sbjct: 63 IIPMFLKWWRRMIPAKYDIRWMMKVGGYLSK 93
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 0.137 0.426
Gapped
Lambda K H
0.267 0.0752 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,143,421
Number of extensions: 1157657
Number of successful extensions: 1222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1210
Number of HSP's successfully gapped: 62
Length of query: 235
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 141
Effective length of database: 6,768,326
Effective search space: 954333966
Effective search space used: 954333966
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: 57 (25.7 bits)