RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 010004
(520 letters)
>gnl|CDD|233147 TIGR00840, b_cpa1, sodium/hydrogen exchanger 3. The Monovalent
Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The
CPA1 family is a large family of proteins derived from
Gram-positive and Gram-negative bacteria, blue green
bacteria, yeast, plants and animals.Transporters from
eukaryotes have been functionally characterized, and all
of these catalyze Na+:H+ exchange. Their primary
physiological functions may be in(1) cytoplasmic pH
regulation, extruding the H+ generated during
metabolism, and (2) salt tolerance (in plants), due to
Na+ uptake into vacuoles.This model is specific for the
eukaryotic members members of this family [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 559
Score = 221 bits (566), Expect = 1e-65
Identities = 143/471 (30%), Positives = 220/471 (46%), Gaps = 50/471 (10%)
Query: 11 TQEHTQV-VPISLFVAILCLCLIVGHLLEE-NRWVNESITAILIGCVSGIIILSITKWKS 68
EH Q L++ + L I HL + R V ES+ I+ G + G II S
Sbjct: 1 DYEHVQSPYEFILWILLASLAKIGFHLTHKVIRAVPESVLLIVYGLLVGGII-----KAS 55
Query: 69 SHI--LRFDEELFFIYLLPPIIFNAGFQVKKKQFFHNFLTIMMFGVIGVFISVSIITVGS 126
HI D FF+YLLPPI+ +AG+ + ++ FF N +I++F V+G I+ +I +
Sbjct: 56 PHIDPPTLDSSYFFLYLLPPIVLDAGYFMPQRNFFENLGSILIFAVVGTLINAFVIGLSL 115
Query: 127 WWLFPKLGFMGLSIQ--DYLALGTIFSSTDTVCTLQILNQ-DETPLLYSLVFGEGVVNDA 183
+ + GF + I D L G++ S+ D V L + + LY ++FGE ++NDA
Sbjct: 116 YGICLIGGFGSIDIGLLDNLLFGSLISAVDPVAVLAVFEEYHVNEKLYIIIFGESLLNDA 175
Query: 184 TSVVLFNAVQKIDVRELNGKAALRIFRDFLYLFST---STILGVTAGLLTALVLKTLYFG 240
+VVL+N K + +F F ++GV G L A + + F
Sbjct: 176 VTVVLYNTFIKFHKTADEPVTIVDVFEGCASFFVVTCGGLLVGVVFGFLVAFITR---FT 232
Query: 241 KHSSVREIALMVLMAYLSYILAELLELSGILTVFFCGIFMSHYAWHNMTDSSRITTRHTF 300
H E + L++YLSY+ AE L LSGIL + FCGI M Y NM+ S+ T ++
Sbjct: 233 HHIRQIEPLFVFLISYLSYLFAETLHLSGILALIFCGITMKKYVEANMSRRSQTTIKYFM 292
Query: 301 AMMSFIAETFIFLYVGMDAFD-IEKWRMSKLSFVTSLGVYSALILMILLGRAAFVFPLSL 359
M+S ++ET IF+++G+ +W +FV A + ++ R V
Sbjct: 293 KMLSSLSETLIFIFLGVSLVTENHEW---NWAFVV------ATLSFCVIYRVLGVR---T 340
Query: 360 LSNYMNSHRSPSISFNHQVVIWWAGLMRGAVSIALAF----KQFTYSGVTSDPDSATMIT 415
LS N R I + Q+VI++AGL RGAV+ ALA K F P +T
Sbjct: 341 LSWITNEFRPVEIPYKDQLVIFYAGL-RGAVAFALALLLDEKIF--------PYKFLFVT 391
Query: 416 ATIIIVLFTTLVFGFLTRPLVKYLLPHPQHATNNSCREPKSPNEDMNLPLL 466
T+++V FT + G +PLV+ L C NE+++
Sbjct: 392 TTLVVVFFTVIFQGGTIKPLVEVL------KVKKGCISKTKINEELHDREF 436
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 155 bits (394), Expect = 4e-42
Identities = 93/396 (23%), Positives = 166/396 (41%), Gaps = 30/396 (7%)
Query: 47 ITAILIGCVSGIIILSITKWKSSHILRFDEELFFIYLLPPIIFNAGFQVKKKQFFHNFLT 106
+ L+G G+ ++S D ELF + L ++F G ++ ++ + +
Sbjct: 37 LLLGLLGGPPGLNLISPDLE-------LDPELFLVLFLAILLFAGGLELDLRELRRVWRS 89
Query: 107 IMMFGVIGVFISVSIITVGSWWLFPKLGFMGLSIQDYLALGTIFSSTDTVCTLQILNQDE 166
I++ + V I+ I + + WL P G+ + LG I S TD V I +
Sbjct: 90 ILVLALPLVLITALGIGLLAHWLLP-----GIPLAAAFLLGAILSPTDPVAVSPIFKRVR 144
Query: 167 TPL-LYSLVFGEGVVNDATSVVLFNAVQKIDVRELNGKAALRIFRDFLYLFSTSTILGVT 225
P + +++ GE ++ND +VLF + FL +LG+
Sbjct: 145 VPKRIRTILEGESLLNDGVGIVLFKVALAALLGTGAFSLGW-ALLLFLIEALGGILLGLL 203
Query: 226 AGLLTALVLKTLYFGKHSSV-REIALMVLMAYLSYILAELLELSGILTVFFCGIFMSHYA 284
G L +L+ L +S E L +L+A+ +Y+LAE L +SGIL V G+ +
Sbjct: 204 LGYLLGRLLRRLDRRGWTSPLLETLLTLLLAFAAYLLAEALGVSGILAVVVAGLVLGEAV 263
Query: 285 WHNMTDSS-RITTRHTFAMMSFIAETFIFLYVGMDAFDIEKWRMSKLSFVTSLGVYSALI 343
N++ +S R+ + ++ F+ +F+ +G + L + +
Sbjct: 264 RINLSPASARLRLSSFWEVLDFLLNGLLFVLLGAQLPLSLLLALGLLGLL-------VAL 316
Query: 344 LMILLGRAAFVFPLSLLSNYMNSHRSPSISFNHQVVIWWAGLMRGAVSIALAFKQFTYSG 403
+ +LL R +VF S N + + ++ + WAG RG VS+ALA
Sbjct: 317 VAVLLARPLWVFLSLKGS---NLKLRDPLPWRERLFLSWAG-PRGVVSLALA---LLIPL 369
Query: 404 VTSDPDSATMITATIIIVLFTTLVFGFLTRPLVKYL 439
P ++ +++LF+ LV G PL K L
Sbjct: 370 ELPGPARELILFIVFLVILFSLLVQGLTLPPLAKKL 405
>gnl|CDD|216235 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family. Na/H
antiporters are key transporters in maintaining the pH
of actively metabolising cells. The molecular mechanisms
of antiport are unclear. These antiporters contain 10-12
transmembrane regions (M) at the amino-terminus and a
large cytoplasmic region at the carboxyl terminus. The
transmembrane regions M3-M12 share identity with other
members of the family. The M6 and M7 regions are highly
conserved. Thus, this is thought to be the region that
is involved in the transport of sodium and hydrogen
ions. The cytoplasmic region has little similarity
throughout the family.
Length = 370
Score = 140 bits (354), Expect = 5e-37
Identities = 105/416 (25%), Positives = 178/416 (42%), Gaps = 48/416 (11%)
Query: 20 ISLFVAILCLCLIVGHLLEENRWVNESITAILIGCVSGIIILSITKWKSSHILRFDEELF 79
L + + L ++ L + + IL G + G L + + L E+
Sbjct: 1 AVLLLLLALLAGLLARRLG----LPPVVGLILAGILLGPSGLGL--VEPDLDL----EVL 50
Query: 80 FIYLLPPIIFNAGFQVKKKQFFHNFLTIMMFGVIGVFISVSIITVGSWWLFPKLGFMGLS 139
LP ++F AG ++ ++ N +I++ ++GV I ++ + L +G+
Sbjct: 51 AELGLPLLLFLAGLELDLRELRKNGKSILLLALLGVLIPF-LLGLLLALLG----GLGIP 105
Query: 140 IQDYLALGTIFSSTDTVCTLQIL-NQDETP-LLYSLVFGEGVVNDATSVVLFNAVQKIDV 197
+ + L G S+T V L IL + L +L+ GE V+NDA +VVL + +
Sbjct: 106 LLEALLFGAALSATSPVVVLAILKERGRLNTRLGTLILGESVLNDAVAVVLLAVLLALAG 165
Query: 198 RELNGKAALRIFRDFLYLFSTSTILGVTAGLLTALVLKTLYFGKHSSVREIALMVLMAYL 257
L + FL + +LG+ G L L+ + F E+ L++ +A L
Sbjct: 166 VGGLSDLGL-LLLIFLVVALGGLLLGLVFGWLLRLITR---FTSGDRELEVLLVLALALL 221
Query: 258 SYILAELLELSGILTVFFCGIFMSHYAWHNMTDSSRITTRHTFAMMSFIAETFIFLYVGM 317
+ +LAELL LSGIL F G+ +S+YA+ N + F+ VG+
Sbjct: 222 AALLAELLGLSGILGAFLAGLVLSNYAFANELSEK------LEPFGYGLFLPLFFVSVGL 275
Query: 318 DAFDIEKWRMSKLSFVTSLGVYSALILMILLGRAAFVFPLSLLSNYMNSHRSPSISFNHQ 377
+ D+ +S L V L++ ILLG+ VF L+ L S
Sbjct: 276 -SLDLSSLLLSLLLLVL------LLLVAILLGKLLGVFLLARLLGL---------SLREA 319
Query: 378 VVIWWAGLMRGAVSIALAFKQFTYSGVTSDPDSATMITATIIIVLFTTLVFGFLTR 433
+++ + GL RGAVS+ALA G+ + T + +VL TTL+ L +
Sbjct: 320 LIVGFGGLQRGAVSLALAA-----IGLQLGLIDRELYTLLVAVVLLTTLLKPLLKK 370
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. The
Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC
2.A.36) The CPA1 family is a large family of proteins
derived from Gram-positive and Gram-negative bacteria,
blue green bacteria, yeast, plants and animals.
Transporters from eukaryotes have been functionally
characterized, and all of these catalyze Na+:H+
exchange. Their primary physiological functions may be
in (1) cytoplasmic pH regulation, extruding the H+
generated during metabolism, and (2) salt tolerance (in
plants), due to Na+ uptake into vacuoles. This model is
specific for the bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 112 bits (282), Expect = 1e-26
Identities = 88/384 (22%), Positives = 158/384 (41%), Gaps = 42/384 (10%)
Query: 74 FDEELFFIYLLPPIIFNAGFQVKKKQFFHNFLTIMMFGVIGVFISVSIITVGSWWLFPKL 133
D E+ LPP++F A ++ NF I + + V ++ ++ W+
Sbjct: 46 LDREIVLFLFLPPLLFEAAMNTDLRELRENFRPIALIAFLLVVVTTVVVGFSLNWI---- 101
Query: 134 GFMGLSIQDYLALGTIFSSTDTVCTLQILNQDETP-LLYSLVFGEGVVNDATSVVLFNAV 192
+G+ + L LG + S TD V L P L L+ GE ++ND ++V+F
Sbjct: 102 --LGIPLALALILGAVLSPTDAVAVLGTFKSIRAPKKLSILLEGESLLNDGAALVVF--- 156
Query: 193 QKIDVRELNGKAALRIFRDFLYLFSTSTILGVTAGLLTA-LVLKTLYFGKHSSVREIALM 251
I V GK L F+ + G+ AGL L + L + EIAL
Sbjct: 157 -AIAVAVALGKGVFDPLNAALD-FAVVCVGGIAAGLAVGYLAYRLLRAKIDDPLVEIALT 214
Query: 252 VLMAYLSYILAELLELSGILTVFFCGIFMSHYA-WHNMTDSSRITTRHTFAMMSFIAETF 310
+L + ++LAE SG++ V G+ +++Y +M+ ++R+ ++++ F+
Sbjct: 215 ILAPFAGFLLAERFHFSGVIAVVAAGLILTNYGRDFSMSPTTRLIALDFWSVIVFLVNGI 274
Query: 311 IFLYVGMD--------------AFDIEKWRMSKLSFVTSLGVYSALILMILLGRAAFVFP 356
IF+ +G+ A + F + +Y + + F++
Sbjct: 275 IFILIGVQTPGTIFSAWKEILVAPAAVILAL----FTNAFVIYPVMTYV------RFLWT 324
Query: 357 LSLLSNYMNSHRSPSISFNHQVVIWWAGLMRGAVSIA--LAFKQFTYSGVTSDPDSATMI 414
+ SN + + V+ WAGL RGA+ +A L+F SG+ P ++
Sbjct: 325 MKPFSNRFLKKKPMEFGTRWKHVVSWAGL-RGAIPLALALSFPNQLLSGMAF-PARYELV 382
Query: 415 TATIIIVLFTTLVFGFLTRPLVKY 438
++LF+ LV G VK
Sbjct: 383 FLAAGVILFSLLVQGISLPIFVKR 406
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 66.3 bits (162), Expect = 2e-11
Identities = 79/362 (21%), Positives = 133/362 (36%), Gaps = 53/362 (14%)
Query: 87 IIFNAGFQVKKKQFFHNFLTIMMFGVIGVFISVSIITVGSWWLFPKLGFMGLSIQDYLAL 146
I+F+ GF + F + +GV I+ + V + +L L + L +
Sbjct: 71 ILFDGGFGTQLSSFRVAAGPALSLATLGVLITSGLTGVAAAYLL------NLDWLEGLLI 124
Query: 147 GTIFSSTDTVCTLQILN-QDETPLLYSLVFGEGVVNDATSVVLFNAVQKIDVRELNGKAA 205
G I STD +L ++ + S + E ND +V L I + EL
Sbjct: 125 GAIVGSTDAAAVFSLLGGKNLNERVASTLEIESGSNDPMAVFL-----TITLIELIAGGE 179
Query: 206 LRIFRDFLYLFSTSTILGVTAGLLTALVLKTLYFGKHSSVREIAL-----MVLM---AYL 257
+ FL F LG+ GL +L L + I L +L L
Sbjct: 180 TNLSWGFLLGFLQQFGLGLLLGLGGGKLLLQL-------INRINLDSGLYPILALAGGLL 232
Query: 258 SYILAELLELSGILTVFFCGIFMSHYAWHNMTDSSRITTRHTFAMMSFIAETFIFLYVGM 317
+ L + SGIL V+ G+ + N +R F ++++A+ +FL +G+
Sbjct: 233 IFSLTGAIGGSGILAVYLAGLLLG-----NRPIRARHGILRFFDGLAWLAQILMFLVLGL 287
Query: 318 DAFDIEKWRMSKLSFVTSLGVYSALILMILLGRAAFVFPLSLLSNYMNSHRSPSISFNHQ 377
+ ++ + + SL MI + R VF L +R +
Sbjct: 288 LVTPSQLLPIAIPAILLSLW-------MIFVARPLAVF---LGLIPFRFNR------REK 331
Query: 378 VVIWWAGLMRGAVSIALAFKQFTYSGVTSDPDSATMITATIIIVLFTTLVFGFLTRPLVK 437
+ + W GL RGAV I LA + + ++ +VL + L+ G K
Sbjct: 332 LFVSWVGL-RGAVPIILA----IFPMMAGLENARLFFNVAFFVVLVSLLIQGSTLPWAAK 386
Query: 438 YL 439
L
Sbjct: 387 KL 388
>gnl|CDD|235410 PRK05326, PRK05326, potassium/proton antiporter; Reviewed.
Length = 562
Score = 59.1 bits (144), Expect = 3e-09
Identities = 81/337 (24%), Positives = 134/337 (39%), Gaps = 52/337 (15%)
Query: 113 IGVFISVSIITVGSWWLFPKLGFMGLSIQDYLALGTIFSSTDTVCTLQILNQDETPL--- 169
+GV I+ + + + WL GL + L LG I STD +L L
Sbjct: 96 LGVLITAGLTGLFAHWLL------GLDWLEGLLLGAIVGSTDAAAVFSLLRGKGLNLKER 149
Query: 170 LYSLVFGEGVVNDATSVVLFNAVQKIDVRELNGKAALRIFRDFLYLFSTSTILGVTAGLL 229
+ S + E ND +V L + ++ G + FL F ++G+ G L
Sbjct: 150 VASTLEIESGSNDPMAVFLTITLIELITGGETG-LSWGFLLLFLQQFGLGALIGLLGGWL 208
Query: 230 TALVLKTLYF---GKHSSVREIALMVLMAYLSYILAELLELSGILTVFFCGIFMSHYAWH 286
+L + G + L++ A L + L L SG L V+ G+ +
Sbjct: 209 LVQLLNRIALPAEGLYP-----ILVLAGALLIFALTAALGGSGFLAVYLAGLVLG----- 258
Query: 287 NMTDSSRITTRHTFAMMSFIAETFIFLYVGMDAFDIEKWRMSKLSFVTSLGVYSALILMI 346
N R + F ++++A+ +FL +G+ S+L + + AL +I
Sbjct: 259 NRPIRHRHSILRFFDGLAWLAQIGMFLVLGLLVTP------SRLLDIALPALLLALF-LI 311
Query: 347 LLGRAAFVFPLSLLSNYMNSHRSP-SISFNHQVVIWWAGLMRGAVSIALAFKQFTY---S 402
L+ R VF LSLL P + ++ I W GL RGAV I LA T+ +
Sbjct: 312 LVARPLAVF-LSLL---------PFRFNLREKLFISWVGL-RGAVPIVLA----TFPMMA 356
Query: 403 GVTSDPDSATMITATIIIVLFTTLVFGFLTRPLVKYL 439
G+ P++ + +VL + L+ G + L
Sbjct: 357 GL---PNAQLIFNVVFFVVLVSLLLQGTTLPWAARKL 390
>gnl|CDD|223551 COG0475, KefB, Kef-type K+ transport systems, membrane components
[Inorganic ion transport and metabolism].
Length = 397
Score = 52.2 bits (126), Expect = 3e-07
Identities = 84/440 (19%), Positives = 159/440 (36%), Gaps = 60/440 (13%)
Query: 14 HTQVVPISLFVAILCLCLIVGHLLEENRWVNESITAILIGCVSGIIILSITKWKSSHILR 73
+ + + +L + +I+G L + + + +L G + G L + SS I+
Sbjct: 2 EMLSLILLQLLILLLVAVILGPLFKRLG-LPPVLGYLLAGIILGPWGLLLIIE-SSEIIE 59
Query: 74 FDEELFFIYLLPPIIFNAGFQVKKKQFFHNFLTIMMFGVIGVFISVSIITVGSWWLFPKL 133
EL ++LL F G + ++ ++ G+ + ++ + L L
Sbjct: 60 LLAELGVVFLL----FLIGLEFDLERLKKVGRSV---GLGVAQVGLTAPFLLGLLLL--L 110
Query: 134 GFMGLSIQDYLALGTIFSSTDTVCTLQIL---NQDETPLLYSLVFGEGVVNDATSVVLFN 190
G +GLS+ L LG + + T L+IL +T L+ G V +D +++L
Sbjct: 111 GILGLSLIAALFLGAALALSSTAIVLKILMELGLLKTREG-QLILGALVFDDIAAILLLA 169
Query: 191 AVQKIDVRELNGKAALRIFRDFLYLFSTSTILGVTAGLLTALVLKTL-YFGKHSSVREIA 249
V + L L LL +L L + E+
Sbjct: 170 IVPAL------AGGGSGSVGFILGLLLAILAFLALLLLLGRYLLPPLFRRVAKTESSELF 223
Query: 250 LMVLMAY--LSYILAELLELSGILTVFFCGIFMSHYAWHNMTDSSRITTRHTFAMMSFIA 307
++ ++ + LAELL LS IL F G+ +S S +
Sbjct: 224 ILFVLLLVLGAAYLAELLGLSMILGAFLAGLLLSE---------SEYRKHELEEKIEPFG 274
Query: 308 ETFI----FLYVGMDAFDIEKWRMSKLSFVTSLGVYSALILMILLGRAAFVFPLSLLSNY 363
+ F+ VGM + D+ + +L + L+ + +LG+ + + L
Sbjct: 275 DGLFIPLFFISVGM-SLDLGV-------LLENLLLILLLVALAILGKILGAYLAARL--- 323
Query: 364 MNSHRSPSISFNHQVVIWWAGLMRGAVSIALAFKQFTYSGVTSDPDSATMITATIIIVLF 423
+ F+ ++ + L+R A S ++TA +I+ +
Sbjct: 324 --------LGFSKRLALGIGLLLRQGGEFAFVLAGIALGS----AISEALLTAVVILSMI 371
Query: 424 TTLVFGFLTRPLVKYLLPHP 443
TT + LT L+K LL
Sbjct: 372 TTPILPLLTPILLKRLLKKS 391
>gnl|CDD|233195 TIGR00932, 2a37, transporter, monovalent cation:proton antiporter-2
(CPA2) family. [Transport and binding proteins, Cations
and iron carrying compounds].
Length = 273
Score = 34.9 bits (81), Expect = 0.080
Identities = 49/236 (20%), Positives = 90/236 (38%), Gaps = 21/236 (8%)
Query: 50 ILIGCVSGIIILSITKWKSSHILRFDEELFFIYLLPPIIFNAGFQVKKKQFFHNFLTIMM 109
+L G + G L + + + E I L+ F G ++ ++ +
Sbjct: 23 LLAGVLIGPSGLGLIS--NVEGVNHLAEFGVILLM----FLIGLELDLERLWKLRKAAFG 76
Query: 110 FGVIGVFISVSIITVGSWWLFPKLGFMGLSIQDYLALGTIFSSTDTVCTLQILNQDETPL 169
GV+ V + ++ + L GL++ + +G I + + T +Q+L E L
Sbjct: 77 VGVLQVLVPGVLLGLLLGHLL------GLALGAAVVIGIILALSSTAVVVQVLK--ERGL 128
Query: 170 LYS----LVFGEGVVNDATSVVLFNAVQKIDVRELNGKAALRIFRDFLYLFSTSTILGVT 225
L + V G + D V L + + AL + L +F +L +
Sbjct: 129 LKTPFGQTVLGILLFQDIAVVPLLALLPLLATSASTEHVALALL--LLKVFLAFLLLVLL 186
Query: 226 AGLLTALVLKTLYFGKHSSVREIALMVLMAYLSYILAELLELSGILTVFFCGIFMS 281
L VL+ + S + ++LM + S A+LL LS L F G+ +S
Sbjct: 187 GRWLLRPVLRLTAELRPSELFTAGSLLLM-FGSAYFADLLGLSMALGAFLAGVVLS 241
>gnl|CDD|241044 cd12600, RRM2_SRSF4_like, RNA recognition motif 2 in
serine/arginine-rich splicing factor 4 (SRSF4) and
similar proteins. This subfamily corresponds to the
RRM2 of three serine/arginine (SR) proteins:
serine/arginine-rich splicing factor 4 (SRSF4 or SRp75
or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5
or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing
factor 6 (SRSF6 or SRp55). SRSF4 plays an important role
in both, constitutive and alternative, splicing of many
pre-mRNAs. It can shuttle between the nucleus and
cytoplasm. SRSF5 regulates both alternative splicing and
basal splicing. It is the only SR protein efficiently
selected from nuclear extracts (NE) by the splicing
enhancer (ESE) and is essential for enhancer activation.
SRSF6 preferentially interacts with a number of
purine-rich splicing enhancers (ESEs) to activate
splicing of the ESE-containing exon. It is the only
protein from HeLa nuclear extract or purified SR
proteins that specifically binds B element RNA after UV
irradiation. SRSF6 may also recognize different types of
RNA sites. Members in this family contain two N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
followed by a C-terminal RS domains rich in
serine-arginine dipeptides. .
Length = 72
Score = 30.4 bits (69), Expect = 0.30
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 176 GEGVVNDATSVVLFNAVQKIDVRELNGKAALRIFRD 211
EGVV AT + A++K+D ELNG+ +++ D
Sbjct: 38 NEGVVEFATYSDMKRAIEKLDGTELNGR-KIKLIED 72
>gnl|CDD|129983 TIGR00905, 2A0302, transporter, basic amino acid/polyamine
antiporter (APA) family. This family includes several
families of antiporters that, rather commonly, are
encoded next to decarboxylases that convert one of the
antiporter substrates into the other. This arrangement
allows a cycle that can remove proteins from the
cytoplasm and thereby protect against acidic conditions
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 473
Score = 32.7 bits (75), Expect = 0.51
Identities = 32/118 (27%), Positives = 49/118 (41%), Gaps = 20/118 (16%)
Query: 328 SKLSFVTSLGVYSALILMILLGRAAFVFPLSLLSNYMNSHRSPSI-SFNHQV-----VIW 381
+ ++ +T++ L L I++G F F L L + H PS+ S QV V
Sbjct: 152 AFINTITTIAKLIPLFLFIIIG--WFWFKLDLFTADFWGHDVPSLGSVFSQVKNTMLVTL 209
Query: 382 WA--GLMRGAVSIALAFKQFTYSGVTSDPDSATMI---TATIIIVLFTTLVFGFLTRP 434
W G+ VS A + SD AT++ A +I +L T L G L +
Sbjct: 210 WVFIGIEGAVVSSGRAKNK-------SDVGKATVLGTLGALVIYILITLLSLGVLPQQ 260
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 31.8 bits (72), Expect = 0.96
Identities = 16/41 (39%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 457 PNEDMNLPLLSFDESTATNLLRAKDSLSMLLDRPVYTIHSF 497
P DM LP SFD R + S LL RPV H +
Sbjct: 489 PLPDMVLPA-SFDSDNPAYRYRYLEPSSQLLTRPVLDTHGW 528
>gnl|CDD|171522 PRK12468, flhB, flagellar biosynthesis protein FlhB; Reviewed.
Length = 386
Score = 31.5 bits (71), Expect = 1.1
Identities = 26/89 (29%), Positives = 33/89 (37%), Gaps = 17/89 (19%)
Query: 256 YLSYILAELLELSGILTVFFCGIFMSHYAWHNMTDSSRITTRHTFAMMSFIAETFIFL-- 313
+ S LAELL+ IL G + WHN D R+ A + IF
Sbjct: 138 FSSQALAELLK--AILKATLVGWVTGLFLWHNWPDMMRLIAAPPVAALGDALHLIIFCGL 195
Query: 314 --------YVGMDAF-----DIEKWRMSK 329
VG D F I+K RM+K
Sbjct: 196 VVVLGLSPMVGFDVFYQITSHIKKLRMTK 224
>gnl|CDD|221288 pfam11882, DUF3402, Domain of unknown function (DUF3402). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 350 to 473 amino acids in length. This domain is
found associated with pfam07923.
Length = 402
Score = 30.8 bits (70), Expect = 1.9
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 50 ILIGCVSGIIILSITKW-KSSHILRF 74
I + VS I++L + KW K SH+L+F
Sbjct: 159 ITLKAVSAILLL-LLKWFKLSHVLKF 183
>gnl|CDD|240537 cd13132, MATE_eukaryotic, Eukaryotic members of the multidrug and
toxic compound extrusion (MATE) family. The integral
membrane proteins from the MATE family are involved in
exporting metabolites across the cell membrane and are
responsible for multidrug resistance (MDR) in many
bacteria and animals. MATE has also been identified as a
large multigene family in plants, where the proteins are
linked to disease resistance. A number of family members
are involved in the synthesis of peptidoglycan
components in bacteria. This subfamily, which is
restricted to eukaryotes, contains vertebrate solute
transporters responsible for secretion of cationic drugs
across the brush border membranes, yeast proteins
located in the vacuole membrane, and plant proteins
involved in disease resistance and iron homeostatis
under osmotic stress.
Length = 436
Score = 30.6 bits (70), Expect = 2.0
Identities = 20/107 (18%), Positives = 45/107 (42%), Gaps = 22/107 (20%)
Query: 48 TAILIGCVSGIIILSITKWKSSHILRF---DEEL------FFIYLLPPIIFNAGFQVKKK 98
IL+ C + +S+ + IL D E+ + +L+P + A F+ K+
Sbjct: 87 LVILLLCC---VPISLLWLNTEPILLLLGQDPEIARLAGEYLRWLIPGLFAYALFEPLKR 143
Query: 99 --QFFHNFLTIMMFGVIGVFISVSIITVGSWWLF---PKLGFMGLSI 140
Q L ++ ++ + +++ + +L LGF+G ++
Sbjct: 144 YLQAQGIVLPLVYISLVALLLNILL-----NYLLVFVLGLGFIGAAL 185
>gnl|CDD|221310 pfam11913, DUF3431, Protein of unknown function (DUF3431). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 291 to 390 amino acids in
length. This protein has a conserved NLRC sequence
motif.
Length = 220
Score = 30.3 bits (69), Expect = 2.0
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 254 MAYLSYILAELLELSGILTVFFCGIFM-SH-YAWHN 287
M YL+YI+ L +F+ SH +AWHN
Sbjct: 49 MVYLTYIIDHYDHLPDTT------VFIHSHRFAWHN 78
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 30.5 bits (69), Expect = 2.8
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 240 GKHSSVREIALMVLMAYL-SYILAELLELS---GILT 272
GK + +R+ AL+ L+A + S++ AE EL I T
Sbjct: 604 GKSTYMRQTALIALLAQIGSFVPAESAELPLFDRIFT 640
>gnl|CDD|233192 TIGR00928, purB, adenylosuccinate lyase. This family consists of
adenylosuccinate lyase, the enzyme that catalyzes step 8
in the purine biosynthesis pathway for de novo synthesis
of IMP and also the final reaction in the two-step
sequence from IMP to AMP [Purines, pyrimidines,
nucleosides, and nucleotides, Purine ribonucleotide
biosynthesis].
Length = 435
Score = 29.6 bits (67), Expect = 4.7
Identities = 9/33 (27%), Positives = 12/33 (36%)
Query: 242 HSSVREIALMVLMAYLSYILAELLELSGILTVF 274
SSV I L +L L++ L V
Sbjct: 311 DSSVERIILPDSFILADIMLKTTLKVVKKLVVN 343
>gnl|CDD|225451 COG2898, COG2898, Uncharacterized conserved protein [Function
unknown].
Length = 538
Score = 29.6 bits (67), Expect = 5.3
Identities = 14/86 (16%), Positives = 30/86 (34%), Gaps = 3/86 (3%)
Query: 203 KAALRIFRDFLYLF--STSTILGVTAGLLTALVLKTLY-FGKHSSVREIALMVLMAYLSY 259
LR+ + L S + G L L+ + L K + + + +++L LS
Sbjct: 38 DERLRLLPRIVPLPLIEASHLTASLLGALLLLLARGLRKRLKRAWIAALIVLILGLVLSL 97
Query: 260 ILAELLELSGILTVFFCGIFMSHYAW 285
+ +L + + A+
Sbjct: 98 AKGLAWIEAAVLFLIAVLLLAGRRAF 123
>gnl|CDD|183255 PRK11646, PRK11646, multidrug resistance protein MdtH; Provisional.
Length = 400
Score = 28.9 bits (65), Expect = 7.5
Identities = 28/79 (35%), Positives = 38/79 (48%), Gaps = 20/79 (25%)
Query: 327 MSKLSFVTSLGVYSALI--LMILLGRAAFVFPLSLLSNYMNSHRSPSISFNHQVVIWWAG 384
MS++S +LG Y LI ++++LG VFPL SI F Q + WA
Sbjct: 1 MSRVSQARNLGKYFLLIDNMLVVLGFFV-VFPLI------------SIRFVDQ--LGWAA 45
Query: 385 LMRGAVSIALAFKQFTYSG 403
+M V IAL +QF G
Sbjct: 46 VM---VGIALGLRQFIQQG 61
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin.
Length = 89
Score = 26.7 bits (60), Expect = 7.8
Identities = 9/32 (28%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 94 QVKKKQFFHNF-LTIMMFGVIGVFISVSIITV 124
++K+K ++ N L I++ V+ + I + II +
Sbjct: 56 KLKRKMWWKNMKLKIILGLVVLILILIIIIVI 87
>gnl|CDD|216115 pfam00780, CNH, CNH domain. Domain found in NIK1-like kinase,
mouse citron and yeast ROM1, ROM2. Unpublished
observations.
Length = 266
Score = 28.4 bits (64), Expect = 7.9
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 326 RMSKLSFVTSLGVYSAL-ILMILLGRAAFVFPLSLLSNYMNS 366
R+ KL VT L V +L+ L + +V+PLS L + S
Sbjct: 30 RIVKLFSVTQLAVLEEFNLLLSLSDKQLYVYPLSALDSKELS 71
>gnl|CDD|187873 cd09742, Csm6_III-A, CRISPR/Cas system-associated protein Csm6.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain;
loosely associated with CRISPR/Cas systems; also known
as APE2256 family.
Length = 183
Score = 28.0 bits (63), Expect = 8.1
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 9/63 (14%)
Query: 199 ELNG--KAALRIFR---DFLYLFSTSTILGVTAGLLTALVLKTLYFGKHSSVREIALMVL 253
ELN R D L L ++ T AG L A +LK K + + VL
Sbjct: 41 ELNSILSILERGKLGKDDELVLLASDT----GAGRLCAEILKEYLEEKGNGAQVTVTEVL 96
Query: 254 MAY 256
+
Sbjct: 97 LVT 99
>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 = 28.3 bits (63), Expect = 9.5
Identities = 11/41 (26%), Positives = 20/41 (48%), Gaps = 11/41 (26%)
Query: 104 FLTIMMFGVIGVFISVSIITV-----------GSWWLFPKL 133
+L++ G+IG F +V+I+ + W+FP L
Sbjct: 149 YLSLGALGIIGGFFAVAILRLILFVLTLIVVKPGIWIFPNL 189
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
0.328 0.140 0.424
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,950,241
Number of extensions: 2734162
Number of successful extensions: 4726
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4615
Number of HSP's successfully gapped: 238
Length of query: 520
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 419
Effective length of database: 6,457,848
Effective search space: 2705838312
Effective search space used: 2705838312
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 (21.8 bits)
S2: 61 (27.1 bits)