RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 041074
(452 letters)
>gnl|CDD|233145 TIGR00836, amt, ammonium transporter. The Ammonium Transporter
(Amt) Family (TC 2.A.49) All functionally characterized
members of the Amt family are ammonia or ammonium uptake
transporters. Some, but not others, also transport
methylammonium. The mechanism of energy coupling, if
any, to methyl-NH2 or NH3 uptake by the AmtB protein of
E. coli is not entirely clear. NH4+ uniport driven by
the pmf, energy independent NH3 facilitation, and
NH4+/K+ antiport have been proposed as possible
transport mechanisms. In Corynebacterium glutamicum and
Arabidopsis thaliana, uptake via the Amt1 homologues of
AmtB has been reported to be driven by the pmf
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 403
Score = 346 bits (889), Expect = e-116
Identities = 158/430 (36%), Positives = 228/430 (53%), Gaps = 31/430 (7%)
Query: 15 NAWQMISATLVGLQSVPGLVILYGSIVKKKWAVNSAFMALYAFAAVVICWATWAYKMSFG 74
AW +I+A LV PG +LY +V+ K +N L FA + W + Y ++FG
Sbjct: 1 TAWLLIAAALVFFM-QPGFALLYAGLVRSKNVLNIMMKNLLDFAIGSLLWWLFGYSLAFG 59
Query: 75 DKLLPFWGKAGPALGQKFLIKQSALPETTQFHDDGSVETAMVLPFYPMASMVWFQCVFAA 134
+ P G G G L + + + P FQ +FAA
Sbjct: 60 EDN-PINGFIGT--GGFGLKNFLYPGKIS------------LAGTLPDLLFFLFQMMFAA 104
Query: 135 ITLVILAGSVLGRMNIKAWMAFVPLWLTFSYTVGAFSLWG-GGFLFHWGVMDYSGGYVIH 193
I I++G+V RM A++ F LW T Y A +WG GG+L+ GV+D++GG V+H
Sbjct: 105 IAATIISGAVAERMKFSAYLLFSVLWTTLVYPPVAHWVWGGGGWLYKLGVLDFAGGGVVH 164
Query: 194 LSSGIAGFTAAYWVGPRSTKDRE--RFPPNNVIMMLAGAGLLWMGWAGFNGGDPYTANID 251
+ G+AG AA +GPR + P+NV +++ G +LW GW GFN G AN
Sbjct: 165 IVGGVAGLAAALVLGPRIGRFPRPVAIRPHNVPLVVLGTFILWFGWFGFNAGSALAANGT 224
Query: 252 SSMAVLNTNICAATSLLVWTWLDVIFFKKPSVIGAVQGMITGLVCITPGAGLVQGWAAIV 311
++ A +NTN+ AA L W +D + KP+++GA G++ GLV ITPG G+V W AI+
Sbjct: 225 AAYAAVNTNLAAAAGGLTWLLIDWLKHGKPTLLGACNGILAGLVAITPGCGVVTPWGAII 284
Query: 312 MGILSGSVPWFTMMFIHKRWTLLQKIDDTLSVFHTHAVAGLLGGVLTGLFAEPKLCSLFL 371
+G+++G + + + + K+ KIDD L F H V G+ G + TGLFA PK+ +
Sbjct: 285 IGLVAGVLCYLAVSKLKKK----LKIDDPLDAFAVHGVGGIWGLIATGLFAAPKVGGV-- 338
Query: 372 PVTNSRGGVYGGSGGIQILKQLAGAAFIIGWNVVVTSIICVIINKVIPLRMTEEQLLIGD 431
GG+ GG+G Q+ QL G A II W VVT II I++K I LR++EE+ IG
Sbjct: 339 ----GTGGLLGGNGK-QLGVQLIGIAAIIAWAFVVTFIILKILDKTIGLRVSEEEEKIGL 393
Query: 432 D-AVHGEEAY 440
D A HGE AY
Sbjct: 394 DLAEHGEFAY 403
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 320 bits (822), Expect = e-106
Identities = 157/433 (36%), Positives = 231/433 (53%), Gaps = 33/433 (7%)
Query: 10 LNKGDNAWQMISATLVGLQSVPGLVILYGSIVKKKWAVNSAFMALYAFAAVVICWATWAY 69
++ GD AW ++SA LV L PGL + YG +V+KK +N+ + AFA V + W Y
Sbjct: 1 MDSGDTAWMLLSAALVLLM-TPGLALFYGGLVRKKNVLNTLMQSFVAFAIVTLLWIFVGY 59
Query: 70 KMSFGDKLLPFWGKAGPALGQKFLIKQSALPETTQFHDDGSVETAMVLPFYPMASMVWFQ 129
++FG F G L Q FL F P FQ
Sbjct: 60 SLAFGPDGNGFIGN----LDQFFLN-------GLGFAAVAGGAG------IPELVFFAFQ 102
Query: 130 CVFAAITLVILAGSVLGRMNIKAWMAFVPLWLTFSYTVGAFSLWG-GGFLFHWGVMDYSG 188
+FAAIT +++G+V RM A++ F LW T Y A +WG GG+L G +D++G
Sbjct: 103 MMFAAITPALISGAVAERMKFSAYLLFSVLWSTLVYPPVAHWVWGGGGWLALLGALDFAG 162
Query: 189 GYVIHLSSGIAGFTAAYWVGPRSTKDRERFPPNNVIMMLAGAGLLWMGWAGFNGGDPYTA 248
G V+H+++G A AA +G R PP+N+ +++ GA LLW GW GFN G A
Sbjct: 163 GTVVHINAGFAALAAALVLGKRIGGKPVAIPPHNLPLVVLGAALLWFGWFGFNAGSALAA 222
Query: 249 NIDSSMAVLNTNICAATSLLVWTWLDVIFFKKPSVIGAVQGMITGLVCITPGAGLVQGWA 308
N +++A +NTN+ AA L W ++ + KPS++GA G + GLV ITP AG V W
Sbjct: 223 NGVAALAFVNTNLAAAAGALGWMLIEWLRNGKPSLLGAASGAVAGLVAITPAAGFVSPWG 282
Query: 309 AIVMGILSGSVPWFTMMFIHKRWTLLQKIDDTLSVFHTHAVAGLLGGVLTGLFAEPKLCS 368
A+++G+++G + +F + + K+ +DD L VF H V G++G +LTG+FA P
Sbjct: 283 ALIIGLIAGVICYFAVKLLKKKL----GVDDALDVFGVHGVGGIVGAILTGIFAAPA--- 335
Query: 369 LFLPVTNSRGGVYGGSGGIQILKQLAGAAFIIGWNVVVTSIICVIINKVIPLRMTEEQLL 428
GG++ G GG+Q+ QL G I + VVT II ++ +I LR++EE+ L
Sbjct: 336 -----VGGGGGLFYG-GGVQLGVQLLGVLVTIVYAFVVTFIILKVLKLIIGLRVSEEEEL 389
Query: 429 IG-DDAVHGEEAY 440
G D + HGE AY
Sbjct: 390 EGLDISEHGESAY 402
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 222 bits (567), Expect = 4e-68
Identities = 138/432 (31%), Positives = 211/432 (48%), Gaps = 40/432 (9%)
Query: 16 AWQMISATLVGLQSVPGLVILYGSIVKKKWAVNSAFMALYAFAAVVICWATWAYKMSFGD 75
A+ +++A LV PG +L +V+ K +N + A V+ + + Y ++FG
Sbjct: 1 AFILLAAALVIF-MQPGFALLESGLVRSKNVLNILYKNFQDVAIGVLAYWGFGYSLAFGK 59
Query: 76 KLLPFWGKAGPALGQKFLIKQSALPETTQFHDDGSVETAMVLPFYPMASMVWFQCVFAAI 135
+ F G G I+ LP+ FQ +FAA
Sbjct: 60 R-YGFSGFIGNLGVSAAGIQWGTLPD---------------------GLFFLFQMMFAAT 97
Query: 136 TLVILAGSVLGRMNIKAWMAFVPLWLTFSYTVGAFSLWG-GGFLFHWGVM-DYSGGYVIH 193
+ I++G+V R+ A++ F L T Y A +WG GG+L GV+ D++G V+H
Sbjct: 98 AITIVSGAVAERIKFSAYLLFSALLGTLVYPPVAHWVWGEGGWLAKLGVLVDFAGSTVVH 157
Query: 194 LSSGIAGFTAAYWVGPR---STKDRERFPPNNVIMMLAGAGLLWMGWAGFNGGDPYTAN- 249
+ G AG AA +GPR T E P+N+ + G LLW GW GFN G TAN
Sbjct: 158 IFGGYAGLAAALVLGPRIGRFTDKNEAITPHNLPFAVLGTFLLWFGWFGFNAGSALTANG 217
Query: 250 IDSSMAVLNTNICAATSLLVWTWLDVIFFKKPSVIGAVQGMITGLVCITPGAGLVQGWAA 309
++A +NTN+ AA L + + KP+++G G + GLV IT G+V W A
Sbjct: 218 RARAIAAVNTNLAAAGGGLTALLISRLKTGKPNMLGLANGALAGLVAITAACGVVTPWGA 277
Query: 310 IVMGILSGSVPWFTMMFIHKRWTLLQKIDDTLSVFHTHAVAGLLGGVLTGLFAEPKLCSL 369
+++G+++G V +K+ IDD L VF H V G+ GG+ G+FA P
Sbjct: 278 LIIGLIAGVVSVLG----YKKLKEKLGIDDPLDVFPVHGVGGIWGGIAVGIFAAPY---- 329
Query: 370 FLPVTNSRGGVYGGSGGIQILKQLAGAAFIIGWNVVVTSIICVIINKVIPLRMTEEQLLI 429
+P + GG+ GG G Q+ QL G A I+ + VT I+ +++ + LR++EE+ +
Sbjct: 330 -VPTSGIYGGLLGG-GFKQLGVQLIGIAVILAYAFGVTFILGLLLGLTLGLRVSEEEEEV 387
Query: 430 GDD-AVHGEEAY 440
G D A HGE AY
Sbjct: 388 GLDVAEHGETAY 399
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 216 bits (551), Expect = 2e-65
Identities = 149/445 (33%), Positives = 227/445 (51%), Gaps = 41/445 (9%)
Query: 1 GTSAAVPDWLNKGDNAWQMISATLVGLQSVPGLVILYGSIVKKKWAVNSAFMALYAFAAV 60
G + A P +K DNA+ MI LV ++PG+ + YG +++ K ++ FA V
Sbjct: 18 GLAMAAPAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALV 77
Query: 61 VICWATWAYKMSFGDKLLPFWGKAGPALGQKFLIKQSALPETTQFHDDGSVETAMVLPFY 120
I W + Y ++FG+ F+G ++K L TA++ Y
Sbjct: 78 CILWVVYGYSLAFGEGN-AFFGNF-----NWLMLKNIEL-------------TAVMGSIY 118
Query: 121 PMASMVWFQCVFAAITLVILAGSVLGRMNIKAWMAFVPLWLTFSYTVGAFSLWGGGFLFH 180
+ FQ FA IT+ ++ G++ R+ A + FV +WLT SY A +WGGG L
Sbjct: 119 QYIHVA-FQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLAS 177
Query: 181 WGVMDYSGGYVIHLSSGIAGFTAAYWVGPRSTKDRERFPPNNVIMMLAGAGLLWMGWAGF 240
G +D++GG V+H+++ +AG AY +G R +E F P+N+ M+ G +L++GW GF
Sbjct: 178 DGALDFAGGTVVHINAAVAGLVGAYLLGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGF 237
Query: 241 NGGDPYTANIDSSMAVLNTNICAATSLLVWTWLDVIFFKKPSVIGAVQGMITGLVCITPG 300
N G AN +++A +NT + A ++L W + + KPS++GA G I GLV +TP
Sbjct: 238 NAGSAGAANEIAALAFVNTVVATAAAILGWVFGEWALRGKPSLLGACSGAIAGLVGVTPA 297
Query: 301 AGLVQGWAAIVMGILSGSVP-WFTMMFIHKRWTLLQKIDDTLSVFHTHAVAGLLGGVLTG 359
G V A+++G+++G W M KRW ++DD VF H V G++G +LTG
Sbjct: 298 CGYVGVGGALIIGVVAGLAGLWGVTML--KRWL---RVDDPCDVFGVHGVCGIVGCILTG 352
Query: 360 LFAEPKLCSLFLPVTNSRGGVYGGSG---GIQILKQLAGAAFIIGWNVVVTSIICVIINK 416
+FA +S GGV G G Q+L QL A I W+ VV I + +
Sbjct: 353 IFA-----------ASSLGGVGYAEGVTMGHQVLVQLESIAITIVWSGVVAFIGYKLADL 401
Query: 417 VIPLRMTEEQLLIGDDA-VHGEEAY 440
+ LR+ EEQ G D HGE AY
Sbjct: 402 TVGLRVPEEQEREGLDVNSHGENAY 426
>gnl|CDD|234292 TIGR03644, marine_trans_1, probable ammonium transporter, marine
subtype. Members of this protein family are well
conserved subclass of putative ammonimum transporters,
belonging to the much broader set of
ammonium/methylammonium transporter described by
TIGR00836. Species with this transporter tend to be
marine bacteria. Partial phylogenetic profiling (PPP)
picks a member of this protein family as the single
best-scoring protein vs. a reference profile for the
marine environment Genome Property for a large number of
different query genomes. This finding by PPP suggests
that this transporter family represents an important
adaptation to the marine environment.
Length = 404
Score = 136 bits (345), Expect = 5e-36
Identities = 95/335 (28%), Positives = 148/335 (44%), Gaps = 38/335 (11%)
Query: 118 PFYPMASMVWFQCVFAAITLVILAGSVLGRMNIKAWMAFVPLWLTFSYTVGAFSLWGGGF 177
Y S +FQ VF A + I++G+V RM + ++ F + F Y + WGGG+
Sbjct: 95 ADYSSGSDFFFQVVFVATAMSIVSGAVAERMKLWPFLLFAVVLTGFIYPIEGSWTWGGGW 154
Query: 178 LFHWGVMDYSGGYVIHLSSGIAGFTAAYWVGPRSTKDRER-----FPPNNVIMMLAGAGL 232
L G D++G ++H++ A +GPR K + P +N+ + G +
Sbjct: 155 LDDLGFSDFAGSGIVHMAGAAAALAGVLLLGPRKGKYGKNGEVNPIPGSNLPLATLGTFI 214
Query: 233 LWMGWAGFNGGDP-YTANIDS----SMAVLNTNICAATSLLVWTWLDVIFFKKPSVIGAV 287
LWMGW GFNGG +++ + NTN AA + L + F K + +
Sbjct: 215 LWMGWFGFNGGSQLALSDVADANAVARIFANTNAAAAGGAIAALLLTKLLFGKADLTMVL 274
Query: 288 QGMITGLVCITPGAGLVQGWAAIVMGILSGSVPWFTMMFIHKRWTLLQKIDDTLSVFHTH 347
G + GLV IT AA ++G + G + F+++ + K KIDD + H
Sbjct: 275 NGALAGLVAITAEPLTPSPLAATLIGAVGGVIVVFSIVLLDK-----LKIDDPVGAISVH 329
Query: 348 AVAGLLGGVLTGLFAEPKLCSLFLPVTNSRGGVYGGSGGIQILKQLAGAAFIIGWNVVVT 407
VAG+ G +L +P+TN G QL GAA I W V +
Sbjct: 330 GVAGIWG-------------TLVVPITN---------GDASFGAQLIGAATIFAWVFVTS 367
Query: 408 SIICVIINKVIPLRMTEEQLLIGDDAVH-GEEAYA 441
I+ I+ + +R++EE+ G D G EAY
Sbjct: 368 LIVWFILKATMGIRVSEEEEYEGLDIAECGMEAYP 402
>gnl|CDD|226439 COG3926, zliS, Lysozyme family protein [General function prediction
only].
Length = 252
Score = 30.5 bits (69), Expect = 1.5
Identities = 8/45 (17%), Positives = 16/45 (35%)
Query: 278 FKKPSVIGAVQGMITGLVCITPGAGLVQGWAAIVMGILSGSVPWF 322
GA G+++GL + + A + + G W+
Sbjct: 199 APADLATGATGGLLSGLYDLQNQLSPLSYALASAVLAIGGLGLWY 243
>gnl|CDD|220569 pfam10101, DUF2339, Predicted membrane protein (DUF2339). This
domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 738
Score = 29.2 bits (66), Expect = 5.1
Identities = 44/245 (17%), Positives = 74/245 (30%), Gaps = 20/245 (8%)
Query: 32 GLVILYGSIVKKKWAVNSAFMALYAFAAV--VICWATWAYKMSFGDKLLPFWGKAGPALG 89
G +L+ + +++ + + + L A + + +F LL W A AL
Sbjct: 305 GAALLWLGVRQRRRLLRAFGLLLQLLALLSLLALLLLGYLNSAFLTGLLL-WALAAAALA 363
Query: 90 QKFLIKQSALPETTQFHDDGSVETAMVLPFYPMASMVWFQ-----CVFAAITLVILAGSV 144
+L+ L ++ L +A + AA LV+ A +
Sbjct: 364 AAWLLLAERLSRRRLRQGLAALFALAALAALALALTMELSDAWLTLALAAQVLVLAALAR 423
Query: 145 LGRMNIKAWMAFV-PLWLTFSYTVGAFSLWGGGFLFHWGVMDYSGGYVIHLSSGIAGFTA 203
W V L T G L HW ++ Y + L A
Sbjct: 424 RYVAPRLRWALKVLAALLLLRLTALPSLQAGTHPLAHWLLLAYGLALALLL--------A 475
Query: 204 AYWVGPRSTKDRERFPPNNVIMMLAGAGLLWMGWAGFNGGDPYTANIDSSMAVLNTNICA 263
A + R + R + LL + GGD A L T +
Sbjct: 476 ALRLLRRDLQLRAWLEAAAL---HLWLLLLVLTRYLLWGGDGLAGAYSLWEAALLTLLAL 532
Query: 264 ATSLL 268
A +L+
Sbjct: 533 ALALV 537
>gnl|CDD|219650 pfam07934, OGG_N, 8-oxoguanine DNA glycosylase, N-terminal domain.
The presence of 8-oxoguanine residues in DNA can give
rise to G-C to T-A transversion mutations. This enzyme
is found in archaeal, bacterial and eukaryotic species,
and is specifically responsible for the process which
leads to the removal of 8-oxoguanine residues. It has
DNA glycosylase activity (EC:3.2.2.23) and DNA lyase
activity (EC:4.2.99.18). The region featured in this
family is the N-terminal domain, which is organised into
a single copy of a TBP-like fold. The domain contributes
residues to the 8-oxoguanine binding pocket.
Length = 113
Score = 27.6 bits (62), Expect = 6.1
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 407 TSIICVIINKVIPLRMTEEQLL---IGDDAVHGEEAYALW 443
TS VI +V+ L+ E+ L +G + + G++A
Sbjct: 29 TSYTGVIGGRVVELKQDEDDLEYRFLGKEDLKGKDAEEFL 68
>gnl|CDD|213711 TIGR02453, TIGR02453, TIGR02453 family protein. Members of this
family are widely (though sparsely) distributed
bacterial proteins about 230 residues in length. All
members have a motif RxxRDxRFxxx[DN]KxxY. The function
of this protein family is unknown. In several fungi,
this model identifies a conserved region of a longer
protein. Therefore, it may be incorrect to speculate
that all members share a common function.
Length = 217
Score = 28.1 bits (63), Expect = 7.4
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 1/39 (2%)
Query: 173 WGGGFLFHWGVMDYSGGYVIHLSSGIAGFTAAYWVGPRS 211
G + H G + G+ IHL F GP +
Sbjct: 82 HLGALISHKGKDLEAPGFYIHLQPD-GCFAGGGLWGPEA 119
>gnl|CDD|205286 pfam13105, DUF3959, Protein of unknown function (DUF3959). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 260 amino acids in length.
Length = 242
Score = 27.9 bits (62), Expect = 8.9
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 118 PFYPMASMVWFQCVFAAITLVILAGSVLGRMNIKAWMAFVPLWL---TFSYTVGAFSLWG 174
PF + ++W Q I S+L I A +A +P L T+ T G +LWG
Sbjct: 53 PFITLLLVIWHQ--------DITTSSLLANAKIAACIALIPCILRFRTYGITFGLLALWG 104
Query: 175 G 175
Sbjct: 105 A 105
>gnl|CDD|224971 COG2060, KdpA, K+-transporting ATPase, A chain [Inorganic ion
transport and metabolism].
Length = 560
Score = 28.4 bits (64), Expect = 9.5
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 7 PDWLNKGDNAWQMISATLVGLQSVPGLVILYGSIVKKK---WAVNSAFMALYAFAAVVIC 63
P L N +M+S L+ LV +G +V + A+ +A L+ VV
Sbjct: 250 PTALT---NLVEMLSILLIPA----ALVFAFGRMVGDRKQGRAILAAMFVLFIAGVVVAM 302
Query: 64 WA 65
WA
Sbjct: 303 WA 304
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
0.325 0.139 0.459
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: 23,957,352
Number of extensions: 2414931
Number of successful extensions: 3458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3392
Number of HSP's successfully gapped: 153
Length of query: 452
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 352
Effective length of database: 6,502,202
Effective search space: 2288775104
Effective search space used: 2288775104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 61 (27.2 bits)