RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1432
(850 letters)
>gnl|CDD|233190 TIGR00926, 2A1704, Peptide:H+ symporter (also transports b-lactam
antibiotics, the antitumor agent, bestatin, and various
protease inhibitors). [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 641
Score = 295 bits (758), Expect = 2e-89
Identities = 157/391 (40%), Positives = 221/391 (56%), Gaps = 42/391 (10%)
Query: 253 FSFCGLRTMLSLYLRDVLKFSEKDATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVF 312
FS+ G++T+L LYL + L ++E AT +YH F LCY P+IGA++ADS+ G+++TI
Sbjct: 1 FSYYGMKTILVLYLLNFLGWNEDTATNIYHTFTYLCYLTPLIGALIADSWLGKFKTI--- 57
Query: 313 SFDATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLAL 372
LY S VYV+G+ L LGAVP+L
Sbjct: 58 ------LY------------------------------LSLVYVVGHALASLGAVPSLGH 81
Query: 373 P-TIKTTLLGLIFIGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLG 431
P +L+GL I +GTGGIKPCV+A G+QF Q RFFS +YF IN G
Sbjct: 82 PLHDALSLVGLALIALGTGGIKPCVSAFGGDQF-EERQLSLRFRFFSFFYFAINAGSLFS 140
Query: 432 MIFIPMIRKSIPCYGGESCYALGFVVPAVLMVLALVMFVVGKPMYTIRCPKKNIILQFLK 491
I P++R + C+G + C+ L F VP +LM LAL++F +G MY + P NI+ + +K
Sbjct: 141 TIITPILRGDVGCFGCQDCFPLAFGVPGILMTLALIVFSMGSKMYKKKPPVGNIVSKVMK 200
Query: 492 CMFYSLSKKLSS-SPYQKKAHWLDYAEDEYSPRLISDMKTVLAILFVFIPLPLFWSLFDQ 550
C+ ++L K+ + S + HWLD+A +Y R+I K +L +LF+FIPLP+FW+LFDQ
Sbjct: 201 CIVFALKKRFRTRSEDWPRLHWLDWAAPKYLIRMIRSTKRLLRVLFLFIPLPMFWALFDQ 260
Query: 551 LGSSWTFQAARTDSQIFGIHILPDQMQVISPMLSLILIPLFDNCIYPALDKIRILENPLR 610
GS WT QA R D + I PDQMQ ++P+L LIL+P+FD +YPAL K LR
Sbjct: 261 QGSRWTLQATRMDGDVGLFPIQPDQMQAVNPLLVLILVPIFDYVVYPALAKCGTRFTSLR 320
Query: 611 RMVCGGCIAGFAFISAGYVELNLQENPPEST 641
+M G +A AF A ++ + PE
Sbjct: 321 KMAVGMLLAALAFAVAALLQNKINPTLPEEP 351
Score = 92.9 bits (231), Expect = 2e-19
Identities = 40/105 (38%), Positives = 64/105 (60%), Gaps = 1/105 (0%)
Query: 710 NITSKFQVFSKLLILSPGRTVKLIYMVPQYVLMSIGEVMFAIAGLHFSFTQAPRSMKTVT 769
N T + + TV +++ +PQYVL + GEVMF++ GL FS++QAP +MK+V
Sbjct: 531 NPTIDGLQLQIVEDVPVN-TVSILWQLPQYVLATAGEVMFSVTGLEFSYSQAPPNMKSVL 589
Query: 770 IAAWQLSVALGNLIIICIEQLRGYVGQAGEFFLYACLIFLDMLLF 814
A W L+VA+GN+I++ I + Q EF L++ L+ + M +F
Sbjct: 590 QALWLLTVAIGNIIVLIIAEFENMAVQWAEFVLFSSLMLVVMAIF 634
>gnl|CDD|216153 pfam00854, PTR2, POT family. The POT (proton-dependent
oligopeptide transport) family all appear to be proton
dependent transporters.
Length = 372
Score = 198 bits (505), Expect = 2e-56
Identities = 95/295 (32%), Positives = 138/295 (46%), Gaps = 9/295 (3%)
Query: 345 YRTIRVFSFVYVLGNILLCLGAVPTLALPTIKT-TLLGLIFIGIGTGGIKPCVAALCGEQ 403
++TI + S +Y +G++LL LGA+P P +GL I +GTGGIKP V+A +Q
Sbjct: 1 FKTILLGSIIYAIGHVLLTLGAIPPSLSPVQVALFYIGLYLIALGTGGIKPNVSAFGADQ 60
Query: 404 FCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMV 463
F Q + FFS +YF IN G + I P +++ Y LGF +PAV M+
Sbjct: 61 F-DETQDPRRDGFFSWFYFSINAGSLIATIITPYLQQ-------NVGYPLGFGLPAVGML 112
Query: 464 LALVMFVVGKPMYTIRCPKKNIILQFLKCMFYSLSKKLSSSPYQKKAHWLDYAEDEYSPR 523
LAL++F++G Y + P + + K K +HWL +A ++Y+ R
Sbjct: 113 LALLVFLLGSRRYKKKAPPGGSPFTVCIAFIITAAGKNRKLQLPKDSHWLYWALEKYNKR 172
Query: 524 LISDMKTVLAILFVFIPLPLFWSLFDQLGSSWTFQAARTDSQIFGIHILPDQMQVISPML 583
IS K + +FIPLP FW+LFDQ GS W QA I+ ILPDQM L
Sbjct: 173 SISQTKVHTRVAVIFIPLPKFWALFDQQGSVWLLQAILLMLPIWAFWILPDQMWTQLATL 232
Query: 584 SLILIPLFDNCIYPALDKIRILENPLRRMVCGGCIAGFAFISAGYVELNLQENPP 638
+ +P D IYP + + + F+ + L P
Sbjct: 233 IVRQVPTMDRIIYPLFEIPPASFQSFNPLAVLILLPILDFLVYPLLRLKRGLTLP 287
>gnl|CDD|225646 COG3104, PTR2, Dipeptide/tripeptide permease [Amino acid transport
and metabolism].
Length = 498
Score = 191 bits (487), Expect = 1e-52
Identities = 106/430 (24%), Positives = 180/430 (41%), Gaps = 83/430 (19%)
Query: 228 LMKEMTSANYPKSIYLILTIEFCERFSFCGLRTMLSLYLR----DVLKFSEKDATVLYHI 283
EM P+ +YLI +E ERFS+ G+R +L LYL D L F E AT L+
Sbjct: 10 TTLEMKFFGQPRGLYLIFFVELWERFSYYGMRAILILYLYYQLGDGLGFDETHATGLFSA 69
Query: 284 FYALCYFVPIIGAILADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAILADSFYG 343
+ +L Y PIIG LAD G RTI ++GAIL
Sbjct: 70 YGSLVYLTPIIGGWLADRVLGTRRTI----------------------VLGAIL------ 101
Query: 344 RYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAALCGEQ 403
+G+++L A+ +++ P +GL I +GTG KP +++L GE
Sbjct: 102 -----------MAIGHLVL---AISSVSGPGG--LYIGLALIIVGTGLFKPNISSLLGEL 145
Query: 404 FCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMV 463
+ P+ + F+++Y INIG + I ++ + +GF + AV M+
Sbjct: 146 Y--PKDDPRRDGGFTLFYMGINIGSLIAPIITGLL-------AINYGWHVGFGLAAVGMI 196
Query: 464 LALVMFVVGKPMYTIR--------CPKKNIILQFLKCMFYSLSKKLSSSPYQKKAHW--- 512
+ LV+F++G+ ++ + L+ L+ Q
Sbjct: 197 IGLVIFLLGRRHVKGIGGVPDPNPLSFNFLLPVLGGLVVMILAALLTLLLNQNTFSGVLL 256
Query: 513 --------LDYAEDEYSPRLISDMKTVLAILFVFIPLPLFWSLFDQLGSSWTFQAART-D 563
+ +AE SP++ + + +LA + +F+ +FW+L++Q+GSS A R +
Sbjct: 257 VISILIAIIYFAEAFRSPKVFDERRRLLAAIPLFLFAVIFWALYEQMGSSLNLYADRNVN 316
Query: 564 SQIFGIHILPDQMQVISPMLSLILIPLFDNCIYPALDKIRILENPLR----RMVCGG--C 617
QIFG + P Q ++P ++ P+ + P++ ++ G
Sbjct: 317 RQIFGFEVPPAWFQSLNPFFIILFSPILAALWTKLGRGNKQPSTPIKFALGLILAGLGFL 376
Query: 618 IAGFAFISAG 627
I A I G
Sbjct: 377 ILLLAGIWFG 386
Score = 53.1 bits (128), Expect = 4e-07
Identities = 20/71 (28%), Positives = 35/71 (49%)
Query: 717 VFSKLLILSPGRTVKLIYMVPQYVLMSIGEVMFAIAGLHFSFTQAPRSMKTVTIAAWQLS 776
+ + + P V + ++V YVL S GE+ + GL AP ++K+ +A W L+
Sbjct: 379 LLAGIWFGGPSGLVSVWWLVLSYVLQSFGELFISPVGLSMVTKLAPPALKSFIMAMWFLT 438
Query: 777 VALGNLIIICI 787
VA G + +
Sbjct: 439 VAAGQTLGGQV 449
>gnl|CDD|233189 TIGR00924, yjdL_sub1_fam, amino acid/peptide transporter
(Peptide:H+ symporter), bacterial. The model describes
proton-dependent oligopeptide transporters in bacteria.
This model is restricted in its range in recognizing
bacterial proton-dependent oligopeptide transporters,
although they are found in yeast, plants and animals.
They function by proton symport in a 1:1 stoichiometry,
which is variable in different species. All of them are
predicted to contain 12 transmembrane domains, for which
limited experimental evidence exists [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 475
Score = 94.5 bits (235), Expect = 3e-20
Identities = 92/441 (20%), Positives = 165/441 (37%), Gaps = 110/441 (24%)
Query: 231 EMTSANYPKSIYLILTIEFCERFSFCGLRTMLSLYL--RDVLKFSEKDATVLYHIFYALC 288
E T +PK ++ + +E ERFS+ G++ +L++YL + L FS++ A +++ + AL
Sbjct: 2 EKTFFGHPKPLFTLFFVELWERFSYYGMQGILAVYLVQQAGLGFSQEQAFIIFGAYSALV 61
Query: 289 YFVPIIGAILADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAILADSFYGRYRTI 348
Y + +G D +G +T+
Sbjct: 62 YLLTSVGWWFGDRVWGTKKTM--------------------------------------- 82
Query: 349 RVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAALCGEQFCVPE 408
VLG I+L LG GL I +G+G K +++ G+ + +
Sbjct: 83 -------VLGGIVLMLGHFMLAMSIYPDLIFYGLGTIAVGSGLFKANPSSMVGKLYERGD 135
Query: 409 QRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMVLALVM 468
+ F+++Y INIG F+ + +I ++ Y +GF + AV MV+ L+
Sbjct: 136 MPR-RDGGFTLFYMSINIGSFISPLLAGVIAENYG-------YHVGFNLAAVGMVIGLLT 187
Query: 469 FVVGKPMYTIRCPKKNIILQFLKCMFYSLSKKLSSSPYQKKAHWLDYAEDEYSPRLISD- 527
F G+ M L+ + + LS + + A A + L+
Sbjct: 188 FFAGRHM-----------LRDIGSVPDPLSGQGKTYGKLLLALLAALALVFFCAWLMHHV 236
Query: 528 -------MKTVLAI--------------------LFVFIPLPL----FWSLFDQLGSSWT 556
M LA+ ++ +I L L FW L+ Q+ +S
Sbjct: 237 VIANILLMTVTLAVIIFFFRLAFKPRLDAVARNKMYAYIVLFLEAVVFWVLYAQMPTSLN 296
Query: 557 FQAART-DSQIFGIHILPDQMQVISPMLSLILIPLFDNCIYPALD-KIRILENPLR---- 610
F A ++ G+ + Q ++P ++ P+ I+ L K + PL+
Sbjct: 297 FFADNNMHHEMLGMSVPVIWFQSLNPFWVVVGSPVL-AMIWTRLGRKGKDPTTPLKFTLG 355
Query: 611 RMVCGGCIAGFA----FISAG 627
+ CG FA F AG
Sbjct: 356 MLFCGASFLTFAASIWFADAG 376
Score = 34.8 bits (80), Expect = 0.18
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 7/78 (8%)
Query: 721 LLILSPGRTVKLIYMVPQYVLMSIGEVMFAIAGLHFSFTQAPRSMKTVTIAAWQLSVALG 780
+ G +MV Y+ ++GE+M + GL + AP+ + + W L+ A+G
Sbjct: 370 IWFADAGGLTSPWFMVLIYLFQTLGELMISPLGLSWWTKIAPQRLMGQMLGMWFLAQAMG 429
Query: 781 NLIIICIEQLRGYVGQAG 798
+L L GY+ G
Sbjct: 430 SL-------LGGYLATFG 440
>gnl|CDD|181969 PRK09584, tppB, putative tripeptide transporter permease; Reviewed.
Length = 500
Score = 85.6 bits (212), Expect = 3e-17
Identities = 87/395 (22%), Positives = 160/395 (40%), Gaps = 85/395 (21%)
Query: 217 DNSSDIPVNLSLMKEMTSANYPKSIYLILTIEFCERFSFCGLRTMLSLYLRDVLKFSEKD 276
+ V+L+ K+ PK+ YLI +IE ERF + GL+ ++++YL L SE D
Sbjct: 5 NQKPTESVSLNAFKQ------PKAFYLIFSIELWERFGYYGLQGIMAVYLVKQLGMSEAD 58
Query: 277 ATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAI 336
+ L+ F AL Y + IG L D G R I
Sbjct: 59 SITLFSSFSALVYGLVAIGGWLGDKVLGTKRVI--------------------------- 91
Query: 337 LADSFYGRYRTIRVFSFVYVLGNILLCLG-AVPTLALPTIKTTLLGLIFIGIGTGGIKPC 395
+LG I+L +G A+ + +G+ I +G G K
Sbjct: 92 -------------------MLGAIVLAIGYALVAWSGHDAGIVYMGMATIAVGNGLFKAN 132
Query: 396 VAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGF 455
++L C + L+ F++YY INIG F M+ P + YG +++ F
Sbjct: 133 PSSLLST--CYEKDDPRLDGAFTMYYMSINIGSFFSMLATPWLAAK---YG----WSVAF 183
Query: 456 VVPAVLMVLALVMFVVGKPMYTIRCPKKNII-LQFLKCM--------FYSLSKKLSSSPY 506
+ V M++ +V F + K + + + K + +++ L +
Sbjct: 184 ALSVVGMLITVVNFAFCQRWVKQYGSKPDFEPINYRKLLLTIVGVVALIAIATWLLHN-- 241
Query: 507 QKKAHW----------LDYAEDEYSPRLISDMKTVLAILFVFIPLPLFWSLFDQLGSSWT 556
Q+ A + + ++ ++ + + K ++A + + + +F+ L+ Q+ +S
Sbjct: 242 QEIARMALGVVALGIVVIFGKEAFAMKGAARRKMIVAFILMLEAI-IFFVLYSQMPTSLN 300
Query: 557 FQAAR-TDSQIFGIHILPDQMQVISPMLSLILIPL 590
F A R + I GI + P+Q Q ++P +I P+
Sbjct: 301 FFAIRNVEHSILGIAVEPEQYQALNPFWIMIGSPI 335
>gnl|CDD|237971 PRK15462, PRK15462, dipeptide/tripeptide permease D; Provisional.
Length = 493
Score = 69.6 bits (170), Expect = 3e-12
Identities = 64/245 (26%), Positives = 103/245 (42%), Gaps = 54/245 (22%)
Query: 233 TSANYPKSIYLILTIEFCERFSFCGLRTMLSLYLRDVLKFSEKDATVLYHIFYALCYFVP 292
A+ P++IY ++ ++ E FSF G+R +L LYL + LK+ + A Y +F A C
Sbjct: 3 KHASQPRAIYYVVALQIWEYFSFYGMRALLILYLTNQLKYDDNHA---YELFSAYC---- 55
Query: 293 IIGAILADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVFS 352
+L Y PI+G LAD G + + +
Sbjct: 56 --------------------------------SLVYVTPILGGFLADKVLGNRMAVMLGA 83
Query: 353 FVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAALCGEQFCVPEQRFY 412
+ +G+ + LGA P+ L L I G G K V+ L GE + + R
Sbjct: 84 LLMAIGH--VVLGASEI--HPSF--LYLSLAIIVCGYGLFKSNVSCLLGELYEPTDPR-- 135
Query: 413 LERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMVLALVMFVVG 472
+ FS+ Y N+G + I ++ E +A+GF + AV M+ LV+F+ G
Sbjct: 136 RDGGFSLMYAAGNVGSIIAPIACGYAQE-------EYSWAMGFGLAAVGMIAGLVIFLCG 188
Query: 473 KPMYT 477
+T
Sbjct: 189 NRHFT 193
>gnl|CDD|182306 PRK10207, PRK10207, dipeptide/tripeptide permease B; Provisional.
Length = 489
Score = 55.2 bits (133), Expect = 8e-08
Identities = 54/239 (22%), Positives = 99/239 (41%), Gaps = 56/239 (23%)
Query: 238 PKSIYLILTIEFCERFSFCGLRTMLSLYLRDVLKFSEKDATVLYHIFYALCYFVPIIGAI 297
P+ ++I +E ERF + G++ +L+++ L FS++ A + + F AL Y + IG
Sbjct: 13 PRPFFMIFFVELWERFGYYGVQGILAVFFVKQLGFSQEQAFITFGAFAALVYGLISIGGY 72
Query: 298 LADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVFSFVYVL 357
+ D G RTI VL
Sbjct: 73 VGDHLLGTKRTI----------------------------------------------VL 86
Query: 358 GNILLCLGAVPT-LALPTIKTTLLGLIFIGIGTGGIKPCVAALCGEQFCVPEQRFYLERF 416
G I+L +G T ++L + L I +G G K A+L + C P + L+
Sbjct: 87 GAIVLAIGYFMTGMSLLKPDLIFIALGTIAVGNGLFKANPASLLSK--CYPPKDPRLDGA 144
Query: 417 FSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMVLALVMFVVGKPM 475
F+++Y INIG + + P+I +G Y++ + + +++AL+++ + M
Sbjct: 145 FTLFYMSINIGSLISLSLAPVIADK---FG----YSVTYNLCGAGLIIALLVYFACRGM 196
>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 = 49.6 bits (119), Expect = 4e-06
Identities = 32/148 (21%), Positives = 62/148 (41%), Gaps = 15/148 (10%)
Query: 322 IFYALCYFVPIIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLG 381
F ++ L+D +GR R + + ++ LG++LL + L L +G
Sbjct: 42 AFSLGYALGSLLAGYLSD-RFGRRRVLLLGLLLFALGSLLLAFASSLWLLL-------VG 93
Query: 382 LIFIGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKS 441
+G+G G + P AAL E F E+ R ++ +G LG + ++ +S
Sbjct: 94 RFLLGLGGGALYPAAAALIAEWFPPKERG----RALGLFSAGFGLGALLGPLLGGLLAES 149
Query: 442 IPCYGGESCYALGFVVPAVLMVLALVMF 469
G + + ++ +L +L L +
Sbjct: 150 ---LGWRWLFLILAILGLLLALLLLFLL 174
Score = 31.1 bits (71), Expect = 2.7
Identities = 35/250 (14%), Positives = 76/250 (30%), Gaps = 40/250 (16%)
Query: 241 IYLILTIEFCERFSFCGLRTMLSLYLRDVLKFSEKDATVLYHIFYALCYFVPIIGAILAD 300
+ L+ F L L L D L S A ++ F ++ L+D
Sbjct: 1 LLLLFLGFFLSGLDRGLLSPALPLLAED-LGLSASQAGLIVSAFSLGYALGSLLAGYLSD 59
Query: 301 SFYGRYRTIRVFSFDATVLYHIFYALCYFV---------------------PIIGAILAD 339
+GR R + + +L+ + L F P A++A+
Sbjct: 60 -RFGRRRVLLL----GLLLFALGSLLLAFASSLWLLLVGRFLLGLGGGALYPAAAALIAE 114
Query: 340 SFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAAL 399
F + R R + LG + L + + I +
Sbjct: 115 WFPPKERG-RALGLFSAGFGLGALLGPLLGGLLAESLGWRWLFLILAI------LGLLLA 167
Query: 400 CGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPA 459
F + L ++ +F+++ G + + ++P+ + + L +
Sbjct: 168 LLLLFLLR--LLLL---LALAFFLLSFGYYGLLTYLPLYLQEVLGLSAAE-AGLLLSLFG 221
Query: 460 VLMVLALVMF 469
+ +L ++
Sbjct: 222 LGGILGALLG 231
>gnl|CDD|219516 pfam07690, MFS_1, Major Facilitator Superfamily.
Length = 346
Score = 45.5 bits (108), Expect = 8e-05
Identities = 31/153 (20%), Positives = 60/153 (39%), Gaps = 15/153 (9%)
Query: 322 IFYALCYFVPIIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLG 381
F + L+D +GR R V ++G +L LG + L ++ L+
Sbjct: 40 AFSLGYALAQPLAGRLSD-RFGRRR-------VLLIGLLLFALGLLLLLFASSLWLLLVL 91
Query: 382 LIFIGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKS 441
+ G+G G + P AAL + F P + R + +G LG + ++
Sbjct: 92 RVLQGLGGGALFPAAAALIADWF--PPEE--RGRALGLLSAGFGLGAALGPLLGGLL--- 144
Query: 442 IPCYGGESCYALGFVVPAVLMVLALVMFVVGKP 474
+G + + + ++ + VLA ++ P
Sbjct: 145 ASLFGWRAAFLILAILALLAAVLAALLLPRPPP 177
Score = 39.7 bits (93), Expect = 0.005
Identities = 32/151 (21%), Positives = 61/151 (40%), Gaps = 12/151 (7%)
Query: 283 IFYALCYFVPIIGAILADSFYGRYRTIRVFS-FDATVLYHIFYALCYFVPIIGAILADSF 341
+ AL F A+L ++ Y+ + S A +L + L ++ L+D
Sbjct: 207 LLLALLLFGFAFFALL--TYLPLYQEVLGLSALLAGLLLGLAGLLGAIGRLLLGRLSDR- 263
Query: 342 YGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAALCG 401
GR R + + + +L + L L ++ +L L+ L+ +G G G + P + AL
Sbjct: 264 LGRRRRLLLALLLLILAALGLALLSLTESSL----WLLVALLLLGFGAGLVFPALNALVS 319
Query: 402 EQFCVPEQRFYLERFFSVYYFIINIGGFLGM 432
+ + +Y ++GG LG
Sbjct: 320 DLA----PKEERGTASGLYNTAGSLGGALGP 346
>gnl|CDD|233165 TIGR00879, SP, MFS transporter, sugar porter (SP) family. This
model represent the sugar porter subfamily of the major
facilitator superfamily (pfam00083) [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 481
Score = 40.8 bits (96), Expect = 0.003
Identities = 39/191 (20%), Positives = 69/191 (36%), Gaps = 13/191 (6%)
Query: 289 YFVPIIGAILADSFYGRYRTIRVFSFDATVLYHIFYALCYFVPIIGAILAD---SFYGRY 345
Y +IG LA + T ++ L+ + ++ IGA+ A +GR
Sbjct: 42 YDTGVIGGALALPAFEFKFTSANSDSYSSSLWGLVVSIFLVGGFIGALFAGWLSDRFGRK 101
Query: 346 RTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGIGTGGIKPCVAALCGEQFC 405
+++ + + ++V+G IL+ L A I +G + +GIG G V E
Sbjct: 102 KSLLIIALLFVIGAILMGLAAFALSVEMLI----VGRVLLGIGVGIASALVPMYLSE-IA 156
Query: 406 VPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESCYALGFVVPAVLMVLA 465
R L S+Y I G + F K LG + ++
Sbjct: 157 PKALRGAL---TSLYQLAITFGILVAYGF--GSGKVSLNNTLGWRIPLGLQLIPAGLLFL 211
Query: 466 LVMFVVGKPMY 476
+ F+ P +
Sbjct: 212 GLFFLPESPRW 222
>gnl|CDD|215702 pfam00083, Sugar_tr, Sugar (and other) transporter.
Length = 449
Score = 36.9 bits (86), Expect = 0.045
Identities = 36/167 (21%), Positives = 71/167 (42%), Gaps = 16/167 (9%)
Query: 316 ATVLYHIFYALCYFVPIIGAILAD---SFYGRYRTIRVFSFVYVLGNILLCLGAVPTLAL 372
+TVL + ++ +IG++ A +GR +++ + + ++V+G +L + +
Sbjct: 44 STVLSGLIVSIFSVGCLIGSLFAGKLGDRFGRKKSLLIGNVLFVIGALLQGFAKGKSFYM 103
Query: 373 PTIKTTLLGLIFIGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGM 432
++G + +G+G GGI V E + R L S+Y I G +
Sbjct: 104 -----LIVGRVIVGLGVGGISVLVPMYISE-IAPKKLRGALG---SLYQLGITFGILVAA 154
Query: 433 IFIPMIRKSIPCYGGESCYALGF-VVPAVLMVLALVMFVVGKPMYTI 478
I + K LG VPA+L+ L ++F+ P + +
Sbjct: 155 IIGLGLNKYS--NSDGWRIPLGLQFVPAILL-LIGLLFLPESPRWLV 198
>gnl|CDD|233170 TIGR00886, 2A0108, nitrite extrusion protein (nitrite facilitator).
[Transport and binding proteins, Anions].
Length = 366
Score = 35.8 bits (83), Expect = 0.091
Identities = 38/153 (24%), Positives = 55/153 (35%), Gaps = 25/153 (16%)
Query: 329 FVPIIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLI----F 384
+ II L D F RY T + L L A+P L + L+ F
Sbjct: 52 VLRIILGFLVDKFGPRYTTT-----------LSLLLLAIPCLWAGLAVQSYSVLLLLRLF 100
Query: 385 IGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPC 444
IGI G C+ F Q L + N+GG + +P I S+
Sbjct: 101 IGIAGGSFASCM-PWISFFFPKKIQGTAL----GLAAGWGNMGGGVAQFVMPPIIGSLIF 155
Query: 445 YGGESCY-----ALGFVVPAVLMVLALVMFVVG 472
G + A V +L++ AL++F VG
Sbjct: 156 GAGLPAHLAWGWAFVIVPAGILLLPALLIFFVG 188
>gnl|CDD|233175 TIGR00895, 2A0115, benzoate transport. [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 398
Score = 34.3 bits (79), Expect = 0.28
Identities = 36/144 (25%), Positives = 61/144 (42%), Gaps = 15/144 (10%)
Query: 332 IIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFI-GIGTG 390
GA+ R RV + +L ++ L AL T T LL L F+ G+G G
Sbjct: 66 AFGALFFGPLADRIGRRRVLLWSILLFSVFTLL-----CALATNVTQLLILRFLAGLGLG 120
Query: 391 GIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIPCYGGESC 450
G+ P + AL E P++ + + IG +G + IP +G S
Sbjct: 121 GLMPNLNALVSEY--APKRFRGT--AVGLMFCGYPIGAAVGGFLAGWL---IPVFGWRSL 173
Query: 451 YALGFVVPAVLMVLALVMFVVGKP 474
+ +G + P +L++ L+M + +
Sbjct: 174 FYVGGIAPLLLLL--LLMRFLPES 195
>gnl|CDD|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. Rrp4 protein is a subunit of
the exosome complex. The exosome plays a central role in
3' to 5' RNA processing and degradation in eukarytes and
archaea. Its functions include the removal of
incorrectly processed RNA and the maintenance of proper
levels of mRNA, rRNA and a number of small RNA species.
In Saccharomyces cerevisiae, the exosome includes nine
core components, six of which are homologous to
bacterial RNase PH. These form a hexameric ring
structure. The other three subunits (RrP4, Rrp40, and
Csl4) contain an S1 RNA binding domain and are part of
the "S1 pore structure".
Length = 86
Score = 29.8 bits (68), Expect = 1.4
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 126 DAVV--IMSIQNK--KLDINFYQESFLPTSGSNKPQLKIIAMNLNH 167
D V+ + + K K+DIN ++ LP S N P+ +N+
Sbjct: 8 DVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRS 53
>gnl|CDD|233556 TIGR01742, SA_tandem_lipo, Staphylococcus tandem lipoproteins.
Members of this family are predicted lipoproteins
(mostly), found in Staphylococcus aureus in several
different tandem clusters in pathogenicity islands.
Members are also found, clustered, in Staphylococcus
epidermidis.
Length = 255
Score = 31.0 bits (70), Expect = 2.4
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 2/49 (4%)
Query: 667 NRALFLTG--DRTNRKNIENGNLGGTSGNMTEVKNGNSSSITNNKNITS 713
N+ + D +K IEN GN+ + N N ++ N N+ S
Sbjct: 135 NKIVLTKDVKDPNLKKEIENFKFFIQYGNLKSLLNYNDGDVSYNPNVPS 183
>gnl|CDD|233168 TIGR00883, 2A0106, metabolite-proton symporter. This model
represents the metabolite:H+ symport subfamily of the
major facilitator superfamily (pfam00083), including
citrate-H+ symporters, dicarboxylate:H+ symporters, the
proline/glycine-betaine transporter ProP, etc [Transport
and binding proteins, Unknown substrate].
Length = 394
Score = 31.1 bits (71), Expect = 2.4
Identities = 31/173 (17%), Positives = 52/173 (30%), Gaps = 25/173 (14%)
Query: 236 NYPKSIYLILTIEFCERFSFCGLRTMLSLYLRDVLKFSEKDATVLYHIFYALCYFVPIIG 295
+ K L L + +F + T L YL L S A ++ + L + +
Sbjct: 216 KHRKPFLLGLGLVIATTTTFYLITTYLPTYLTQTLGLSANSALLVLMLSLILFFITIPLS 275
Query: 296 AILADSFYGRYRTIRVFSFDATVLYHIFY---------------------ALCYFVPIIG 334
L+D GR + +F+ A +L + +G
Sbjct: 276 GALSDRI-GRRPVLIIFTVLAALLAVPLLMALLDSGSFTLFFFLVLGMALIGGMYTGPMG 334
Query: 335 AILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLIFIGI 387
+ L + F R S Y L + G P +A + IG
Sbjct: 335 SFLPELFPTEVRYTG-ASLAYNLAGAIFG-GFAPYIAAA-LVAMTGDWYAIGY 384
>gnl|CDD|222060 pfam13347, MFS_2, MFS/sugar transport protein. This family is part
of the major facilitator superfamily of membrane
transport proteins.
Length = 425
Score = 31.0 bits (71), Expect = 2.5
Identities = 47/221 (21%), Positives = 82/221 (37%), Gaps = 28/221 (12%)
Query: 266 LRDVLKFSEKDATVLYHIFYALCYFVPIIGAILADSFYGRYRTIRVFSFDATVLYHIFYA 325
LRD+ K K+ +L + L + + +Y Y L+ +
Sbjct: 211 LRDMFKALFKNRPLLILLLLYLLNALAMAVRNGLLLYYFTYV------LGNAGLFSVLLL 264
Query: 326 LCYFVPIIGAILAD---SFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGL 382
+ I+GA L +G+ RT + + +G +LL L ++ L+ +
Sbjct: 265 IGTIAAILGAPLWPWLAKRFGKKRTFLLGMLLAAIGLVLLFF-----LPPGSLWLFLVLV 319
Query: 383 IFIGIGTGGIKPCVAALCGEQFCVPEQRFYLER---FFSVYYFIINIGGFLGMIFIPMIR 439
+ GIG G A+ + E + R FS+Y F +GG LG I +
Sbjct: 320 VLAGIGLGLATLLPWAMLADVVDYGEWKTGKRREGITFSLYSFADKLGGALG-GAIVGLL 378
Query: 440 KSIPCYGGESC----------YALGFVVPAVLMVLALVMFV 470
+ Y + L ++PAVL +LAL++
Sbjct: 379 LAFAGYVANATAQSAAALSGIRLLFTLIPAVLALLALLILR 419
>gnl|CDD|233174 TIGR00893, 2A0114, D-galactonate transporter. [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 399
Score = 30.8 bits (70), Expect = 3.0
Identities = 29/148 (19%), Positives = 51/148 (34%), Gaps = 10/148 (6%)
Query: 325 ALCYFVP-IIGAILADSFYGRYRTIRVFSFVYVLGNILLCLGAVPTLALPTIKTTLLGLI 383
+ F+ I+G L+D R +++ ++ ++L L T I L L+
Sbjct: 261 GIVGFIGMILGGRLSDLLLRRGKSLVFARKTAIIAGLVLSLLMFAT-NYVNIPYAALALV 319
Query: 384 FIGIGTGGIKPCVAALCGEQFCVPEQRFYLERFFSVYYFIINIGGFLGMIFIPMIRKSIP 443
+G G AL + + + N+GG +G I I I +
Sbjct: 320 ALGFFGLGAGAIGWALISDNAPGNIAGLTG----GLINSLGNLGGIVGPIVIGAIAATT- 374
Query: 444 CYGGESCYALGFVVPAVLMVLALVMFVV 471
G AL V L+ + +V
Sbjct: 375 ---GSFAGALMVVAALALIGALSYLLLV 399
>gnl|CDD|211733 TIGR02341, chap_CCT_beta, T-complex protein 1, beta subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
beta chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 518
Score = 30.6 bits (69), Expect = 3.8
Identities = 32/142 (22%), Positives = 65/142 (45%), Gaps = 23/142 (16%)
Query: 124 NTDAVVIMSIQNKKLDINFYQESFL--PTSGSNKPQL----KIIAMNLNHKHDYKIRLTG 177
N +A+ I+ I KL +F E F+ G N+P+ KI+ N D K+++ G
Sbjct: 185 NLEAIQIIKILGGKLSDSFLDEGFILAKKIGVNQPKRIENAKILIANTTMDTD-KVKIFG 243
Query: 178 -KLKSEKSLEVSKQEHAKTFEGVPVEYGMNQIDVVLKDNLDNSSDIPVNLSLMKEMTSAN 236
+++ + + ++++ E A+ E +++ +LK + + +N L+ N
Sbjct: 244 SRVRVDSTAKLAELEKAER------EKMKEKVEKILKHGI----NCFINRQLI-----YN 288
Query: 237 YPKSIYLILTIEFCERFSFCGL 258
YP+ ++ I E F G+
Sbjct: 289 YPEQLFADAGIMSIEHADFEGV 310
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 30.0 bits (68), Expect = 6.2
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 452 ALGFVVPAVLMVLALVMFVVGKPMYTIRC 480
F+ LM++ L +F+VG +YT+ C
Sbjct: 468 GFSFLFSWFLMLVVLALFLVGGNVYTLVC 496
>gnl|CDD|234497 TIGR04199, exosort_xrtJ, exosortase J. Exosortase J occurs as a
three-member paralogous family in Acidobacterium sp.
MP5ACTX8. It contains an N-terminal
exosortase/archaeosortase domain and a novel C-terminal
domain comprising about half of total protein length.
The presumptive target, found as an adjacent gene for
two of the three paralogs, consists of a possible
lipoprotein signal peptide followed almost immediately
by a C-terminal region with some PEP-CTERM-like
characteristics.
Length = 522
Score = 29.5 bits (66), Expect = 8.1
Identities = 21/113 (18%), Positives = 39/113 (34%), Gaps = 27/113 (23%)
Query: 522 PRLISDMKTVLAILFVFIPLPLFWSLF-----DQLGSSWTFQAARTDSQIFGIHILPDQM 576
RL+ L ++F P+P F++ + AR + + G+++ Q
Sbjct: 112 VRLLRAGIFPLCLMFFVDPVPQFFNSAVDLPLQHASAL----TARAFAHLIGLNLTGAQ- 166
Query: 577 QVISPMLSLILIPLFDNCIYPALDKIRILENPLRRMVCGGCIAGFAFISAGYV 629
L ++ P F I P + +R G G+ + GY
Sbjct: 167 ------LRMMFAPDFGMFIAPGCNGVR-----------GSITLGYLALIFGYS 202
>gnl|CDD|189032 cd09862, PIN_Rrp44, PIN domain of yeast exosome subunit Rrp44
endoribonuclease and other eukaryotic homologs. PIN
(PilT N terminus) domain of the Saccharomyces cerevisiae
exosome subunit Rrp44 (Ribosomal RNA-processing protein
44 or Protein Dis3 homolog) and other similar eukaryotic
homologs are included in this family. The eukaryotic
exosome is a conserved macromolecular complex
responsible for many RNA-processing and RNA-degradation
reactions. It is composed of nine core subunits that
directly binds Rrp44. The Rrp44 nuclease is the
catalytic subunit of the exosome and has endonuclease
activity in the PIN domain and an exoribonuclease
activity in its RNase II-like region. Rrp44 binding to
the exosome is mediated mainly by the PIN domain and by
subunits Rrp41-Rrp45, and binding predictions indicate
that the PIN domain active site is positioned on the
outer surface of the exosome. These PIN domains are
structural homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but lack the extensive arch/clamp region
and the H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule. Recombinant Rrp44 was shown to possess
manganese-dependent endonuclease activity in vitro that
was abolished by point mutations in the putative metal
binding residues of its PIN domain.
Length = 182
Score = 28.8 bits (65), Expect = 8.2
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 652 KNATEWSKNSLSFMGNRALFLTGDRTNR-KNIENG 685
+ AT+W L + + + LT DR NR K E G
Sbjct: 139 RVATKWYSEHLPKLSIKVVLLTNDRANREKAAEEG 173
>gnl|CDD|232953 TIGR00392, ileS, isoleucyl-tRNA synthetase. The isoleucyl tRNA
synthetase (IleS) is a class I amino acyl-tRNA ligase
and is particularly closely related to the valyl tRNA
synthetase. This model may recognize IleS from every
species, including eukaryotic cytosolic and
mitochondrial forms [Protein synthesis, tRNA
aminoacylation].
Length = 861
Score = 29.6 bits (67), Expect = 9.6
Identities = 11/46 (23%), Positives = 14/46 (30%), Gaps = 6/46 (13%)
Query: 267 RDVLKFSEKDA------TVLYHIFYALCYFVPIIGAILADSFYGRY 306
RD L KD T LY+ L + A+ Y
Sbjct: 744 RDRLYCEAKDNDKRAAQTTLYYALLTLVRLLAPFLPHTAEEIYQNL 789
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 0.142 0.431
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: 44,015,034
Number of extensions: 4484289
Number of successful extensions: 5717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5638
Number of HSP's successfully gapped: 134
Length of query: 850
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 745
Effective length of database: 6,280,432
Effective search space: 4678921840
Effective search space used: 4678921840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 63 (28.0 bits)