RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7379
(465 letters)
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein
which is localized in the photoreceptor outer segment
discs. Mutation/s in its genetic loci is implicated in
the recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 256 bits (655), Expect = 4e-75
Identities = 124/327 (37%), Positives = 188/327 (57%), Gaps = 8/327 (2%)
Query: 10 GRQAIRNEILRSVGNQSQTYNAALNFFDSFFSDQNLTSSLNF-----LNDTQESMQYVVQ 64
+++ I R +G + T A LNF + ++ NF N T ++ Q
Sbjct: 456 QNPTVKDFINRQLGEEGITAEAVLNFLYNGPREKQADDMTNFDWRDIFNITDRFLRLANQ 515
Query: 65 LLQCIDFNKIVPYNDSATAENDAFLRMDNNTLWALINF--TQPGYDKLKPTLTYSIRMST 122
L+C+ +K Y+D A ++ N WA + F P L P + Y IRM
Sbjct: 516 YLECLVLDKFESYDDEVQLTQRALSLLEENRFWAGVVFPDMYPWTSSLPPHVKYKIRMDI 575
Query: 123 ALIGDT-YISDRFYTLDPRSRPLYDLKYITFGFAYLQDMVEQSIIQEHTGRESTPGIVLQ 181
++ T I DR++ PR+ P+ D +YI GFAYLQDMVEQ I + E GI LQ
Sbjct: 576 DVVEKTNKIKDRYWDSGPRADPVEDFRYIWGGFAYLQDMVEQGITRSQMQAEPPVGIYLQ 635
Query: 182 QFPYPCYIEDQFIKAVSKTFPLFMVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGV 241
Q PYPC+++D F+ +++ FP+FMVL+W+++ SM KSIV EK+ RLKE ++ G+SN V
Sbjct: 636 QMPYPCFVDDSFMIILNRCFPIFMVLAWIYSVSMTVKSIVLEKELRLKETLKNQGVSNAV 695
Query: 242 HWTAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLF 301
W WF+DS +M ++ LL++ +++G ++ +S+P I+F+FL++F ATI Q FL S F
Sbjct: 696 IWCTWFLDSFSIMSMSIFLLTIFIMHGRILHYSDPFILFLFLLAFSTATIMQCFLLSTFF 755
Query: 302 DQANIAAASGGIIYFLLYLPYPFLSNW 328
+A++AAA G+IYF LYLP+ W
Sbjct: 756 SKASLAAACSGVIYFTLYLPHILCFAW 782
Score = 52.7 bits (126), Expect = 3e-07
Identities = 26/65 (40%), Positives = 37/65 (56%)
Query: 363 DVTQLIRSFLPAANIHKISGSEVTYVLPQDPASMGAYVSLFESLSENRAKLGIDSYGISD 422
++ L+ +P A + + G E+ ++LP AY SLF L E A LG+ S+GISD
Sbjct: 1207 ELMDLVYHHVPEAKLVECIGQELIFLLPNKNFKQRAYASLFRELEETLADLGLSSFGISD 1266
Query: 423 TSLEE 427
T LEE
Sbjct: 1267 TPLEE 1271
>gnl|CDD|221721 pfam12698, ABC2_membrane_3, ABC-2 family transporter protein. This
family is related to the ABC-2 membrane transporter
family pfam01061.
Length = 278
Score = 64.7 bits (158), Expect = 1e-11
Identities = 31/122 (25%), Positives = 58/122 (47%), Gaps = 1/122 (0%)
Query: 201 FPLFMVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIVVMIITAVL 260
L + L + +I SIV EK+ R+KE + V G+S + + +++ + +L
Sbjct: 98 LGLLLFLLILIGALIIALSIVEEKESRIKERLLVSGVSPLKYLLGKIL-GDLLVGLIQLL 156
Query: 261 LSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQANIAAASGGIIYFLLYL 320
+ LLL++G I N +++ + + + +A IA L LF + A I+ LL
Sbjct: 157 IILLLLFGLGIPFGNLLLLLLLFLLYGLAYIALGALLGSLFKNSEAAILVISILILLLSG 216
Query: 321 PY 322
+
Sbjct: 217 FF 218
>gnl|CDD|223912 COG0842, COG0842, ABC-type multidrug transport system, permease
component [Defense mechanisms].
Length = 286
Score = 36.4 bits (84), Expect = 0.025
Identities = 30/154 (19%), Positives = 60/154 (38%), Gaps = 7/154 (4%)
Query: 177 GIVLQQFPYPCYIEDQFIKAVSKTFPLFMVLSWVF-ACSMICKSIVYEKQERLKEMMRVM 235
G+ + + + ++ P +++S +F ++ E++ E + V
Sbjct: 67 GLREGLSGRLYHWSNPSLDYLAFIVPGVILMSVLFSGIFSFSSALFREREFGTLERLLVS 126
Query: 236 GLSNGVHWTAWFIDSIVV--MIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQ 293
+S + +VV +I VLL + + G V + +++ + L+ +AT+A
Sbjct: 127 PVSRLFILLGKIVPYLVVASLIAGLVLLVIAFLLG-VPFLGSLLLLLLLLLLLLLATVAL 185
Query: 294 SFLYSVLFDQANIAAASGGIIYFLLYLPYPFLSN 327
L S A + LL LP FLS
Sbjct: 186 GLLLSTF---AKSQLQCASAVGNLLILPLGFLSG 216
>gnl|CDD|221706 pfam12679, ABC2_membrane_2, ABC-2 family transporter protein. This
family is related to the ABC-2 membrane transporter
family.
Length = 263
Score = 36.1 bits (84), Expect = 0.026
Identities = 19/105 (18%), Positives = 40/105 (38%), Gaps = 5/105 (4%)
Query: 250 SIVVMIITAVLLSLLLVYGHVIQHSN----PVIIFIFLVSFCVATIAQSFLYSVLFDQAN 305
+ + I+ VLL+L + S +++ L+ + ++ L S +
Sbjct: 117 ILAIAILVGVLLALAVTAALGDSLSLGDLLLLVLASVLLLLALLFLSLGLLISTVLRSTA 176
Query: 306 IAAASGGIIYFLLYLPYP-FLSNWLNVLPPLVNYFITIPQDHNHT 349
AAA+ ++F+L + L+ L + L P +T
Sbjct: 177 TAAAAALGLFFVLSILSGILLAGILKLEELLDFLLFLNPTSPYNT 221
>gnl|CDD|216561 pfam01545, Cation_efflux, Cation efflux family. Members of this
family are integral membrane proteins, that are found to
increase tolerance to divalent metal ions such as
cadmium, zinc, and cobalt. These proteins are thought to
be efflux pumps that remove these ions from cells.
Length = 273
Score = 34.6 bits (80), Expect = 0.090
Identities = 14/101 (13%), Positives = 31/101 (30%), Gaps = 13/101 (12%)
Query: 241 VHWTAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFC---------VATI 291
+ + +++ +++ +L L G I + + L + + +
Sbjct: 90 IEPGGILLVALISLVVNLLLALYLRRAGRKIGKKSSALRADALHALVDVLGSLAVLIGLL 149
Query: 292 AQSFLYSVLFDQANIAAASGGIIYFLLYLPYPFLSNWLNVL 332
+ D AS I +LY L L+ L
Sbjct: 150 LILLTGLPIAD----PLASLLIALLILYTGLRLLKESLSEL 186
>gnl|CDD|224582 COG1668, NatB, ABC-type Na+ efflux pump, permease component [Energy
production and conversion / Inorganic ion transport and
metabolism].
Length = 407
Score = 34.0 bits (78), Expect = 0.17
Identities = 25/159 (15%), Positives = 52/159 (32%), Gaps = 17/159 (10%)
Query: 201 FPLFMVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIVVMIITAVL 260
L + +A M+ S+ EK+ R E++ +S + + +V + L
Sbjct: 191 IFLLFFIPLSYAGQMVADSVAGEKERRTLEVLLSSPVSRSEIVFGKILGAALVGLTQIAL 250
Query: 261 LSLLLVY-----------GHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFD------Q 303
L L G + ++ L F + + + L + L +
Sbjct: 251 WLLALTIATFLSLAVALAGTGLALLPAYLLLFALSLFLLGLLLYAALAAFLGAMAGSIKE 310
Query: 304 ANIAAASGGIIYFLLYLPYPFLSNWLNVLPPLVNYFITI 342
A + + + +LP F+S + L+ I
Sbjct: 311 AQTLISPLTFLAIIAFLPLSFISAAPDNAVALILSAIPF 349
>gnl|CDD|216716 pfam01810, LysE, LysE type translocator. This family consists of
various hypothetical proteins and an l-lysine exporter
LysE from Corynebacterium glutamicum which is proposed
to be the first of a novel family of translocators. LysE
exports l-lysine from the cell into the surrounding
medium and is predicted to span the membrane six times.
The physiological function of the exporter is to excrete
excess l-Lysine as a result of natural flux imbalances
or peptide hydrolysis; and also after artificial
deregulation of l-Lysine biosynthesis as used by the
biotechnology. industry for the production of l-lysine.
Length = 191
Score = 31.5 bits (72), Expect = 0.63
Identities = 17/94 (18%), Positives = 35/94 (37%), Gaps = 8/94 (8%)
Query: 231 MMRVMGLSN--GVHWTAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCV 288
++ LSN + + + + + G V+ +I+ L++F
Sbjct: 102 RGLLVSLSNPKVILFWLSVGSAFLDKQQYGDAGRIAFAAGLVVA----SLIWFSLLAFLA 157
Query: 289 ATIAQSFLYSVLFDQANIAAASGGIIYFLLYLPY 322
+ +A+ + IA A +I F +YL Y
Sbjct: 158 SRLARRLSTKKVRIINVIAGAL--LIGFGVYLLY 189
>gnl|CDD|217790 pfam03916, NrfD, Polysulphide reductase, NrfD. NrfD is an integral
transmembrane protein with loops in both the periplasm
and the cytoplasm. NrfD is thought to participate in the
transfer of electrons, from the quinone pool into the
terminal components of the Nrf pathway.
Length = 313
Score = 31.6 bits (72), Expect = 0.84
Identities = 19/105 (18%), Positives = 43/105 (40%), Gaps = 6/105 (5%)
Query: 201 FPLFMVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGVHW---TAWFIDSIVVMIIT 257
L+MV+ ++ + K + L + +++ L+ V I ++++ T
Sbjct: 98 LSLYMVVLVLWLAVIFEKDLAALGLPALGFLAKLISLAERVARGLAIIALILAVLLGAYT 157
Query: 258 AVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFD 302
LLS + ++P++ +FL S + +A L +L
Sbjct: 158 GFLLSAVYSR---PLWNSPLLPPLFLASAISSGLAVLLLAMLLAF 199
>gnl|CDD|233146 TIGR00837, araaP, aromatic amino acid transport protein. The
Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family-
tyrosine/tryptophan subfamily (TC 2.A.42.1) The HAAAP
family includes well characterized aromatic amino
acid:H+ symport permeases and hydroxy amino acid
permeases. This subfamily is specific for aromatic amino
acid transporters and includes the tyrosine permease,
TyrP, of E. coli, and the tryptophan transporters TnaB
and Mtr of E. coli [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 381
Score = 31.5 bits (72), Expect = 0.92
Identities = 24/112 (21%), Positives = 44/112 (39%), Gaps = 10/112 (8%)
Query: 231 MMRVMGLSNGVHWTAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVAT 290
+ R++G G W+A +V+I T + S + + + V+IF +++F +
Sbjct: 100 LSRLIGEYFGFPWSA----RAIVLIFTVLFGSFVWLSTSAVDRITRVLIFGKIIAFALVF 155
Query: 291 IAQSFL--YSVLFDQANIAAASGGIIYFLLYLPYPFLS-NWLNVLPPLVNYF 339
+L D A + Y L LP S + +P L Y+
Sbjct: 156 SGLLPHVKGDLLLDVALDTSYWP---YILSALPVCLTSFGFHGNVPSLYKYY 204
>gnl|CDD|224196 COG1277, NosY, ABC-type transport system involved in multi-copper
enzyme maturation, permease component [General function
prediction only].
Length = 278
Score = 31.3 bits (71), Expect = 1.1
Identities = 16/95 (16%), Positives = 40/95 (42%), Gaps = 1/95 (1%)
Query: 245 AWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQ-SFLYSVLFDQ 303
+ I++ I+ + L LL + + + +++F+ + S L S LF
Sbjct: 115 LVILIIILISFISLLTLLLLFGFPGNVSSISRLLLFLGSSLLYGLVLLSISLLISSLFSS 174
Query: 304 ANIAAASGGIIYFLLYLPYPFLSNWLNVLPPLVNY 338
+++A I+ L + + + +++VL +
Sbjct: 175 SSLALLVSIILLLLFIIAFSLILLFISVLLIGIAP 209
>gnl|CDD|237929 PRK15238, PRK15238, inner membrane transporter YjeM; Provisional.
Length = 496
Score = 31.4 bits (72), Expect = 1.1
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 12/50 (24%)
Query: 277 VIIFIFLVSFCVATIAQSFLYSVLFDQANIAAASGGIIYFLLYLPYPFLS 326
V +FI LVSF A +F +++L AN++ + LPY FL+
Sbjct: 376 VSVFILLVSFG-GDAASAF-FNILTLMANVS----------MTLPYLFLA 413
>gnl|CDD|112053 pfam03222, Trp_Tyr_perm, Tryptophan/tyrosine permease family.
Length = 393
Score = 31.5 bits (72), Expect = 1.1
Identities = 22/111 (19%), Positives = 40/111 (36%), Gaps = 11/111 (9%)
Query: 232 MRVMGLSNGVHWTAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATI 291
RV+ G+ W +I T + + + N V+IF +++F +
Sbjct: 107 SRVIPEMFGIPW----SARAAPLIFTLLFGPFVWAGTKAVDRINRVLIFGKIIAFALVFS 162
Query: 292 AQSFL--YSVLFDQANIAAASGGIIYFLLYLPYPFLS-NWLNVLPPLVNYF 339
+L D + + Y L+ LP F S + +P L Y+
Sbjct: 163 GLLPKIKGDLLLDALDTSYWP----YILMALPVFFTSFGFHGNVPSLYKYY 209
>gnl|CDD|234038 TIGR02865, spore_II_E, stage II sporulation protein E. Stage II
sporulation protein E (SpoIIE) is a multiple membrane
spanning protein with two separable functions. It plays
a role in the switch to polar cell division during
sporulation. By means of it protein phosphatase
activity, located in the C-terminal region, it activates
sigma-F. All proteins that score above the trusted
cutoff to this model are found in endospore-forming
Gram-positive bacteria. Surprisingly, a sequence from
the Cyanobacterium-like (and presumably
non-spore-forming) photosynthesizer Heliobacillus
mobilis is homologous, and scores between the trusted
and noise cutoffs [Cellular processes, Sporulation and
germination].
Length = 764
Score = 31.6 bits (72), Expect = 1.2
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 9/88 (10%)
Query: 247 FIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSV--LFDQ- 303
S+ +++ AV++ L V ++ V+ I + F A + F Y L
Sbjct: 56 PKHSLKYLLLVAVIILLSYVLKNLTDKKKTVVPPIVV--FLEAAVYAIFGYLQNKLVTPL 113
Query: 304 ----ANIAAASGGIIYFLLYLPYPFLSN 327
+ + A+ ++Y++ P L N
Sbjct: 114 DFILSIVEASLSFVLYYIFNYSIPCLKN 141
>gnl|CDD|219154 pfam06738, DUF1212, Protein of unknown function (DUF1212). This
family represents a conserved region within a number of
hypothetical membrane proteins of unknown function found
in eukaryotes, bacteria and archaea.
Length = 193
Score = 30.2 bits (69), Expect = 1.7
Identities = 11/69 (15%), Positives = 24/69 (34%), Gaps = 2/69 (2%)
Query: 250 SIVVMIITAVLLSLL-LVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQANIAA 308
+ +I + L L+ + + +F L +F + IA + L +
Sbjct: 124 DWIDFLIAFLAGLLGGLLRQILAKRGLNPFVFEALAAFVASLIALLAVSLGLGINPDAII 183
Query: 309 ASGGIIYFL 317
G I+ +
Sbjct: 184 I-GSIMLLV 191
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 31.0 bits (70), Expect = 1.9
Identities = 26/90 (28%), Positives = 38/90 (42%), Gaps = 17/90 (18%)
Query: 374 AANIHKISGSEVTYVLPQDPASMGAYVSLFESLSENRAKLGIDSYGISDTSLEEKWGSLQ 433
NI +I EVT A + A + + ENR K I +E++W +
Sbjct: 729 GPNIKRIEFHEVT-----RRAILKA-IKEARDIDENRVKAQIVR------RIEDRWIGFE 776
Query: 434 LGRKLWLFVG--NVSYKKV---CLGWELTR 458
L +KLW N+S +V LGW + R
Sbjct: 777 LSQKLWEVFEDRNLSAGRVQTPVLGWIIQR 806
>gnl|CDD|176861 cd07819, SRPBCC_2, Ligand-binding SRPBCC domain of an
uncharacterized subfamily of proteins. Uncharacterized
group of the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
SRPBCC domains include the steroidogenic acute
regulatory protein (StAR)-related lipid transfer (START)
domains of mammalian STARD1-STARD15, the C-terminal
catalytic domains of the alpha oxygenase subunit of
Rieske-type non-heme iron aromatic ring-hydroxylating
oxygenases (RHOs_alpha_C), Class I and II
phosphatidylinositol transfer proteins (PITPs), Bet v 1
(the major pollen allergen of white birch, Betula
verrucosa), CoxG, CalC, and related proteins. Other
members of the superfamily include PYR/PYL/RCAR plant
proteins, the aromatase/cyclase (ARO/CYC) domains of
proteins such as Streptomyces glaucescens
tetracenomycin, and the SRPBCC domains of Streptococcus
mutans Smu.440 and related proteins.
Length = 140
Score = 29.5 bits (67), Expect = 2.1
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 410 RAKLGIDSYGISDT-SLEEKW-GSLQLGRKLWLFVGNVSYKKVCLGWELTRMGYQTLV 465
++G+ +YGI DT +LE W G+ + W V + + LT G T V
Sbjct: 50 MVRIGVGAYGIKDTYALEYTWDGAGSVS---WTLVEGEGNRSQEGSYTLTPKGDGTRV 104
>gnl|CDD|144205 pfam00528, BPD_transp_1, Binding-protein-dependent transport system
inner membrane component. The alignments cover the most
conserved region of the proteins, which is thought to be
located in a cytoplasmic loop between two transmembrane
domains. The members of this family have a variable
number of transmembrane helices.
Length = 183
Score = 29.6 bits (67), Expect = 2.1
Identities = 23/126 (18%), Positives = 46/126 (36%), Gaps = 6/126 (4%)
Query: 205 MVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIVVMIITAVLLSLL 264
+L W +I ++ + L E R +G S W F I+ + +L L
Sbjct: 59 ALLGWAGYARLIRRAALRSLPSDLVEAARALGAS---RWQI-FRKIILPNALPPILTGLA 114
Query: 265 LVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQANIAAASGGIIYFLLYLPYPF 324
L +G + + ++ F+ + ++ L + + + +I LL L
Sbjct: 115 LAFGGALGGA-VLLEFLGSWPGLGLLLIEAILGY-DYPEIQGPVLAAALILLLLNLLVDI 172
Query: 325 LSNWLN 330
L L+
Sbjct: 173 LQRLLD 178
>gnl|CDD|219078 pfam06541, DUF1113, Protein of unknown function (DUF1113). This
family consists of several bacterial proteins of unknown
function.
Length = 157
Score = 29.4 bits (67), Expect = 2.2
Identities = 13/85 (15%), Positives = 29/85 (34%), Gaps = 20/85 (23%)
Query: 278 IIFIFLVSFCVAT--------IAQSFLYSVLFDQANIAAASGGII------------YFL 317
I +FL + T + + ++ +D +++ G I L
Sbjct: 58 PILLFLGGAILTTVLEYITGWLLEKLFHAKWWDYSDLPFNIHGRICLLFSLFWGLLGVLL 117
Query: 318 LYLPYPFLSNWLNVLPPLVNYFITI 342
+ +PF+ + +P Y I +
Sbjct: 118 VKFIHPFVLGLIERIPRKTGYIIAL 142
>gnl|CDD|215078 PLN00150, PLN00150, potassium ion transporter family protein;
Provisional.
Length = 779
Score = 30.6 bits (69), Expect = 2.2
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 12/78 (15%)
Query: 245 AWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQA 304
A+ I + VMIIT L++L+++ +I + ++ +F F A I + +VLF
Sbjct: 438 AYGIAVVGVMIITTCLMTLVMI---IIWRKHILLALLFFTVF--AIIEGIYFSAVLFKVT 492
Query: 305 N-------IAAASGGIIY 315
IAA G ++Y
Sbjct: 493 QGGWVPLVIAAVFGTVMY 510
>gnl|CDD|216818 pfam01970, TctA, Tripartite tricarboxylate transporter TctA family.
This family, formerly known as DUF112, is a family of
bacterial and archaeal tripartite tricarboxylate
transporters of the extracytoplasmic solute binding
receptor-dependent transporter group of families,
distinct from the ABC and TRAP-T families. TctA is part
of the tripartite TctABC system which, as characterized
in S. typhimurium, is a secondary carrier that depends
for activity on the extracytoplasmic
tricarboxylate-binding receptor TctC as well as two
integral membrane proteins, TctA and TctB. complete
three-component systems are found only in bacteria. TctA
is a large transmembrane protein with up to 12 predicted
membrane spanning regions in bacteria and up to 11 such
in archaea, with the N-terminal within the cytoplasm.
TctA is thought to be a permease, and in most other
bacteria functions without TctB and TctC molecules.
Length = 418
Score = 30.1 bits (69), Expect = 2.3
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 18/77 (23%)
Query: 256 ITAVLLSLLLVYGHVIQ------HSNPVIIFIFLVSFCVATIAQSFLYSVLFDQANIAAA 309
+TA+LL LL++G +Q NP +++ + S +A + L +
Sbjct: 308 VTAILLGALLIHG--LQPGPLLFTENPDLVYGLIASLLIANL---LLLILGL-------P 355
Query: 310 SGGIIYFLLYLPYPFLS 326
+ LL +PY L
Sbjct: 356 LIRLFARLLRIPYRILY 372
>gnl|CDD|218966 pfam06271, RDD, RDD family. This family of proteins contain three
highly conserved amino acids: one arginine and two
aspartates, hence the name of RDD family. This region
contains two predicted transmembrane regions. The
arginine occurs at the N terminus of the first helix and
the first aspartate occurs in the middle of this helix.
The molecular function of this region is unknown.
However this region may be involved in transport of an
as yet unknown set of ligands (Bateman A pers. obs.).
Length = 131
Score = 28.8 bits (65), Expect = 2.9
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 245 AWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLF 301
A+ ID +++ ++ L+ LLL + S +++ + L+ V +Y VLF
Sbjct: 10 AFLIDLLLLSLLLL-LIFLLLGALGNLADSGGLLLLLLLLLLLVF-----LVYFVLF 60
>gnl|CDD|217187 pfam02687, FtsX, FtsX-like permease family. This is a family of
predicted permeases and hypothetical transmembrane
proteins. Buchnera aphidicola lolC has been shown to
transport lipids targeted to the outer membrane across
the inner membrane. Both lolC and Streptococcus
cristatus tptD have been shown to require ATP. This
region contains three transmembrane helices.
Length = 121
Score = 28.4 bits (64), Expect = 3.4
Identities = 20/109 (18%), Positives = 40/109 (36%), Gaps = 21/109 (19%)
Query: 203 LFMVLSWVFACSMICKSIVYEKQERLKEM--MRVMGLSNG-----VHWTAWFIDSIVVMI 255
L VL + A ++ + ER +E+ ++ +G S + A + ++
Sbjct: 2 LLSVLILLLALLILLNLLSISISERRREIGILKALGASKKQIFKLLLLEALLL--GLIGS 59
Query: 256 ITAVLLSLLLVY------------GHVIQHSNPVIIFIFLVSFCVATIA 292
+ +LL LL Y + VI+ L+ +A +A
Sbjct: 60 LLGLLLGFLLAYLLSSAIASFLGFSLPLSIDPIVILLSLLLILLIALLA 108
>gnl|CDD|223690 COG0617, PcnB, tRNA nucleotidyltransferase/poly(A) polymerase
[Translation, ribosomal structure and biogenesis].
Length = 412
Score = 29.7 bits (67), Expect = 3.5
Identities = 8/29 (27%), Positives = 16/29 (55%)
Query: 2 GRFLDVPNGRQAIRNEILRSVGNQSQTYN 30
G +D G + + N +LR +G+ S+ +
Sbjct: 127 GEIIDPFGGLKDLENRVLRHIGDASERFR 155
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 29.4 bits (67), Expect = 3.8
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 19/77 (24%)
Query: 2 GRFLDVPNGRQAIRNEILRSVGNQSQTYNA-------ALNFFDSFFSDQNLTSSLNFL-- 52
G +D+ +G + ++N ++R+VGN + + A+ F S L F
Sbjct: 125 GEIIDLFDGLEDLKNRLIRAVGNAEERFQEDALRMMRAVRF----------ASQLGFDLE 174
Query: 53 NDTQESMQYVVQLLQCI 69
+T E+M+ LL+ I
Sbjct: 175 TETFEAMKTQAPLLEKI 191
>gnl|CDD|219524 pfam07698, 7TM-7TMR_HD, 7TM receptor with intracellular HD
hydrolase. These bacterial 7TM receptor proteins have
an intracellular pfam01966. This entry corresponds to
the 7 helix transmembrane domain. These proteins also
contain an N-terminal extracellular domain.
Length = 189
Score = 29.0 bits (66), Expect = 3.8
Identities = 20/97 (20%), Positives = 36/97 (37%), Gaps = 17/97 (17%)
Query: 250 SIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIA------QSFLYSVLFDQ 303
++VV ++ A+LL L+ +++ L A L + L
Sbjct: 80 ALVVSVLLALLLGLMFGNNLEF------LLYALLGGLVGALSVRRLRSRSQLLQAGLL-- 131
Query: 304 ANIAAASGGIIYFLLYLPYPFLSNWLNVLPPLVNYFI 340
+A + ++Y L L +WL +L L FI
Sbjct: 132 --VALVNV-LLYLALGLIQGGSFSWLEILTDLGLGFI 165
>gnl|CDD|218122 pfam04515, Choline_transpo, Plasma-membrane choline transporter.
This family represents a high-affinity plasma-membrane
choline transporter in C.elegans which is thought to be
rate-limiting for ACh synthesis in cholinergic nerve
terminals.
Length = 327
Score = 29.5 bits (67), Expect = 4.0
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 247 FIDSIVVMIITAVLLSLLLVYGHVIQHSNP--VIIFIFLVSFCVATI 291
F+ + V +T +L L L Y S + FL+S+ +A++
Sbjct: 254 FLGKLFVSALTGLLAYLWLTYTDNSDLSYYAVPVALAFLISYLIASV 300
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 29.5 bits (67), Expect = 4.2
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 137 LDPRSRPLYD-LKYITFGFAYLQDMVEQSII 166
+DP RPLYD L I G ++ + E+ +I
Sbjct: 200 VDPYLRPLYDALYDI-LGAERVEALDERGVI 229
>gnl|CDD|212522 cd09998, HDAC_Hos3, Class II histone deacetylases Hos3 and related
proteins. Fungal histone deacetylase Hos3 from
Saccharomyces cerevisiae is a Zn-dependent enzyme
belonging to HDAC class II. It catalyzes hydrolysis of
an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Hos3 deacetylase is homodimer, in vitro it
shows specificity to H4, H3 and H2A.
Length = 353
Score = 29.3 bits (66), Expect = 4.2
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 219 SIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIV 252
S + E+ ERL+ V+GLS VH + W + I
Sbjct: 20 STIVERPERLRAS--VLGLSAAVHGSKWSAELIE 51
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 29.2 bits (66), Expect = 5.5
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 13/67 (19%)
Query: 244 TAWFIDSIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQ 303
AW I SI++++ + + FL+ +C+ + +Y FD+
Sbjct: 84 LAWAI-SILLLLAALAITLHFYPWLK------------FLIGYCIVLLVALLIYRRDFDR 130
Query: 304 ANIAAAS 310
+++AA +
Sbjct: 131 SSLAAGT 137
>gnl|CDD|226078 COG3548, COG3548, Predicted integral membrane protein [Function
unknown].
Length = 197
Score = 28.4 bits (64), Expect = 5.6
Identities = 24/108 (22%), Positives = 49/108 (45%), Gaps = 15/108 (13%)
Query: 247 FIDSIVVMIITAVLLSLLLVYGHVIQHS---NPVIIFIFLVSFCVATIAQSFLYSVLFDQ 303
F D++ +I+T ++L + + G + + I+ +SF V I F + +F +
Sbjct: 18 FTDAVFAIIMTIMVLEIKVPKGGGRLQALAELLSSLIIYALSFLVVAIFW-FNHHRIFGR 76
Query: 304 ANIAAASGGIIY----FLLYLP-YPFLSNWLNVLP----PLVNYFITI 342
I +G II+ +LL + PF + W+ + P + Y + +
Sbjct: 77 --IKKITGRIIWINFIWLLLVSLLPFSTAWIGEIHTDFLPALLYLVLL 122
>gnl|CDD|235308 PRK04570, PRK04570, cell division protein ZipA; Provisional.
Length = 243
Score = 28.7 bits (64), Expect = 5.7
Identities = 15/35 (42%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 301 FDQANIAAASGGIIYFLLYLPYPF--LSNWLNVLP 333
FD ANI I F L LP P L W +LP
Sbjct: 158 FDMANIREMQTPAIAFFLTLPAPMTALDAWEKMLP 192
>gnl|CDD|237381 PRK13419, PRK13419, F0F1 ATP synthase subunit A; Provisional.
Length = 342
Score = 28.9 bits (65), Expect = 5.8
Identities = 25/90 (27%), Positives = 41/90 (45%), Gaps = 28/90 (31%)
Query: 237 LSNGVHWTAWFIDSIVVMII-----------------TA---VLLSLLLV------YGHV 270
L+ G HW+ W I I + I TA V+LSL+ + Y
Sbjct: 231 LTGGTHWSLWII-MIPIEFIGLFTKPFALTVRLFANMTAGHIVILSLIFISFILKSYIVA 289
Query: 271 IQHSNPVIIFIFLVSFCVATIAQSFLYSVL 300
+ S P IFI+L+ VA + Q++++++L
Sbjct: 290 VAVSVPFAIFIYLLELFVAFL-QAYIFTML 318
>gnl|CDD|235820 PRK06521, PRK06521, hydrogenase 4 subunit B; Validated.
Length = 667
Score = 29.1 bits (66), Expect = 5.9
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 280 FIFLVSFCVATIAQSFLYSVLFDQANIAAASGGIIYFLL 318
F FLV++ +++ FL V+ + G +Y L+
Sbjct: 136 FSFLVAWETMSLSSWFL--VIANHREAEIRRAGFLYLLM 172
>gnl|CDD|212054 cd11485, SLC-NCS1sbd_YbbW-like, uncharacterized
nucleobase-cation-symport-1 (NCS1) transporter
subfamily, YbbW-like; solute-binding domain. NCS1s are
essential components of salvage pathways for nucleobases
and related metabolites; their known substrates include
allantoin, uracil, thiamine, and nicotinamide riboside.
This subfamily includes the putative allantoin
transporter Escherichia coli YbbW (also known as GlxB2).
NCS1s belong to a superfamily which also contains the
solute carrier 5 family sodium/glucose transporters
(SLC5s), and solute carrier 6 family neurotransmitter
transporters (SLC6s).
Length = 459
Score = 29.1 bits (66), Expect = 6.0
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 17/55 (30%)
Query: 254 MIITAVLLSLL---------LVYGHVI--------QHSNPVIIFIFLVSFCVATI 291
+ IT L + + +++G I + NPV + I L++ +AT+
Sbjct: 255 LPITMALFAFVGVAVTSATVVIFGEAIWDPVDLLSRFDNPVAVIIALLAIILATL 309
>gnl|CDD|223650 COG0577, SalY, ABC-type antimicrobial peptide transport system,
permease component [Defense mechanisms].
Length = 419
Score = 28.9 bits (64), Expect = 6.8
Identities = 17/131 (12%), Positives = 49/131 (37%), Gaps = 11/131 (8%)
Query: 192 QFIKAVSKTFPLFMVLSWVFACSMICKSIVYEKQERLKEM--MRVMGLSNGVHWTAWFID 249
+ I+ + V+S + I ++ ER +E+ ++ +G + + ++
Sbjct: 280 KSIQLLLGVDKAIAVISLIVGAIGIYNILLVSVLERTREIGILKALGATRREILLQFLLE 339
Query: 250 SIVVMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATIAQSFLYSVLFDQANIAAA 309
++++ +I LL +LL G + + + L+ + + +A
Sbjct: 340 ALILGLI-GGLLGILLGLG--------LSLLLALLLIASLFFLLALPILLSPLLILLALI 390
Query: 310 SGGIIYFLLYL 320
++ + L
Sbjct: 391 VALLVGVIAGL 401
>gnl|CDD|215303 PLN02552, PLN02552, isopentenyl-diphosphate delta-isomerase.
Length = 247
Score = 28.5 bits (64), Expect = 6.9
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 222 YEKQERLKEMMRVMGLSNGVHWTAWF 247
Y +E LKEMMR +G+ + WF
Sbjct: 194 YVNREELKEMMRK---ESGLKLSPWF 216
>gnl|CDD|215733 pfam00122, E1-E2_ATPase, E1-E2 ATPase.
Length = 222
Score = 28.3 bits (64), Expect = 7.3
Identities = 5/46 (10%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 247 FIDSIV-VMIITAVLLSLLLVYGHVIQHSNPVIIFIFLVSFCVATI 291
+D + +++ + L++L+ + + + + ++ VA
Sbjct: 143 LLDKLAKILVPIVLALAILVFLIWFFRGGDFLEALLRALAVLVAAC 188
>gnl|CDD|132132 TIGR03088, stp2, sugar transferase, PEP-CTERM/EpsH1 system
associated. Members of this family include a match to
the pfam00534 Glycosyl transferases group 1 domain.
Nearly all are found in species that encode the
PEP-CTERM/exosortase system predicted to act in protein
sorting in a number of Gram-negative bacteria. In
particular, these transferases are found proximal to a
particular variant of exosortase, EpsH1, which appears
to travel with a conserved group of genes summarized by
Genome Property GenProp0652. The nature of the sugar
transferase reaction catalyzed by members of this clade
is unknown and may conceivably be variable with respect
to substrate by species, but we hypothesize a conserved
substrate.
Length = 374
Score = 28.5 bits (64), Expect = 7.8
Identities = 26/129 (20%), Positives = 49/129 (37%), Gaps = 15/129 (11%)
Query: 323 PFLSNWLNVLPPLVNYF---ITIP-----QDHNHTDHSSNQPSSDPEPDVTQLIRSFLPA 374
P + +++ V L ++ + +P Q +N D PS + L F
Sbjct: 135 PLIHHYVAVSRDLEDWLRGPVKVPPAKIHQIYNGVDTERFHPSRGDRSPI--LPPDF--F 190
Query: 375 ANIHKISGSEVTYVLPQDPASM-GAYVSLFESLSE--NRAKLGIDSYGISDTSLEEKWGS 431
A+ + G+ +D ++ A+ L L E R +L I G + + E+ +
Sbjct: 191 ADESVVVGTVGRLQAVKDQPTLVRAFALLVRQLPEGAERLRLVIVGDGPARGACEQMVRA 250
Query: 432 LQLGRKLWL 440
L +WL
Sbjct: 251 AGLAHLVWL 259
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 28.2 bits (64), Expect = 8.4
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 137 LDPRSRPLYDLKYITFGFAYLQDMVEQSIIQ 167
+DP RPLYD Y G ++ ++E+ +I+
Sbjct: 76 VDPYLRPLYDALYDMLGAEKVEKLIERGVIE 106
>gnl|CDD|216594 pfam01594, UPF0118, Domain of unknown function DUF20. This
transmembrane region is found in putative permeases and
predicted transmembrane proteins it has no known
function. It is not clear what source suggested that
these proteins may be permeases and this information
should be treated with caution.
Length = 327
Score = 28.3 bits (64), Expect = 9.3
Identities = 11/61 (18%), Positives = 28/61 (45%)
Query: 204 FMVLSWVFACSMICKSIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIVVMIITAVLLSL 263
F +L I + +ER+ ++R + + G + I ++++ ++T + L +
Sbjct: 156 FFLLDGERLRQGIISFLPKRYRERVDAILREINDTLGGYLLGQVIVALIIGVLTFIGLLI 215
Query: 264 L 264
L
Sbjct: 216 L 216
>gnl|CDD|234789 PRK00549, PRK00549, competence damage-inducible protein A;
Provisional.
Length = 414
Score = 28.2 bits (64), Expect = 9.9
Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 1/56 (1%)
Query: 384 EVTYVLPQDPASMGAYVSLFESLSEN-RAKLGIDSYGISDTSLEEKWGSLQLGRKL 438
EVT L S L + L E R ++G YG + SLEE L + L
Sbjct: 217 EVTLRLTAKARSEEEAEKLIDPLEEEIRDRVGDYFYGYDEDSLEEVVAKLLKEKGL 272
>gnl|CDD|237251 PRK12895, ubiA, prenyltransferase; Reviewed.
Length = 286
Score = 28.2 bits (63), Expect = 10.0
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 8/78 (10%)
Query: 209 WVFACSMI--CKSIVYEKQERLKEMMRVMGLSNGVHWTAWFIDSIVVMIITAVLLSLLLV 266
W+ +I I Y+K LK +M G+ NG++ S + I + +L + +
Sbjct: 171 WIAGFDIIYVIPDIEYDKINGLKTIMNTYGIKNGLY------ISDIFHISSLILFWISGI 224
Query: 267 YGHVIQHSNPVIIFIFLV 284
Y + + +II LV
Sbjct: 225 YIRTLWYLAALIIIYTLV 242
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
0.323 0.138 0.417
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,807,009
Number of extensions: 2323353
Number of successful extensions: 2691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2636
Number of HSP's successfully gapped: 176
Length of query: 465
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 365
Effective length of database: 6,502,202
Effective search space: 2373303730
Effective search space used: 2373303730
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (27.2 bits)