RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 017570
(369 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 = 267 bits (686), Expect = 6e-87
Identities = 111/315 (35%), Positives = 167/315 (53%), Gaps = 16/315 (5%)
Query: 27 AWQMTASTLVGIQSMPGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICWVLVCYRMAFGD 86
AW + A+ LV PG ++YA +V+ K +N L FA + W L Y +AFG+
Sbjct: 2 AWLLIAAALVFFM-QPGFALLYAGLVRSKNVLNIMMKNLLDFAIGSLLWWLFGYSLAFGE 60
Query: 87 QLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVYFQFTFAAITVI 146
P G G L ++ FQ FAAI
Sbjct: 61 DN-PINGFIGT--GGFGLKNFL---------YPGKISLAGTLPDLLFFLFQMMFAAIAAT 108
Query: 147 LLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWG-GGFLYQWGVIDYSGGYVIHVSSG 205
+++G+V RM A++ F LW Y A +WG GG+LY+ GV+D++GG V+H+ G
Sbjct: 109 IISGAVAERMKFSAYLLFSVLWTTLVYPPVAHWVWGGGGWLYKLGVLDFAGGGVVHIVGG 168
Query: 206 IAGLTAAYWVGPRLKSDKE--RFPPNNVLLMLAGAGLLWMGWSGFNGGAPYAAHIASSIA 263
+AGL AA +GPR+ P+NV L++ G +LW GW GFN G+ AA+ ++ A
Sbjct: 169 VAGLAAALVLGPRIGRFPRPVAIRPHNVPLVVLGTFILWFGWFGFNAGSALAANGTAAYA 228
Query: 264 ILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSWAAIVMGIL 323
+NTN+AAA L W +D + GKP+++GA G++ GLV ITPG G+V W AI++G++
Sbjct: 229 AVNTNLAAAAGGLTWLLIDWLKHGKPTLLGACNGILAGLVAITPGCGVVTPWGAIIIGLV 288
Query: 324 SGSIPWVTMMILHKK 338
+G + ++ + L KK
Sbjct: 289 AGVLCYLAVSKLKKK 303
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 244 bits (624), Expect = 2e-77
Identities = 113/319 (35%), Positives = 173/319 (54%), Gaps = 16/319 (5%)
Query: 21 LNKGDSAWQMTASTLVGIQSMPGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICWVLVCY 80
++ GD+AW + ++ LV + + PGL + Y +V+KK +N+ AFA V + W+ V Y
Sbjct: 1 MDSGDTAWMLLSAALVLLMT-PGLALFYGGLVRKKNVLNTLMQSFVAFAIVTLLWIFVGY 59
Query: 81 RMAFGDQLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVYFQFTF 140
+AFG F G + + V FQ F
Sbjct: 60 SLAFGPDGNGFIGNLDQFFL--------------NGLGFAAVAGGAGIPELVFFAFQMMF 105
Query: 141 AAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWG-GGFLYQWGVIDYSGGYV 199
AAIT L++G+V RM A++ F LW Y A +WG GG+L G +D++GG V
Sbjct: 106 AAITPALISGAVAERMKFSAYLLFSVLWSTLVYPPVAHWVWGGGGWLALLGALDFAGGTV 165
Query: 200 IHVSSGIAGLTAAYWVGPRLKSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGAPYAAHIA 259
+H+++G A L AA +G R+ PP+N+ L++ GA LLW GW GFN G+ AA+
Sbjct: 166 VHINAGFAALAAALVLGKRIGGKPVAIPPHNLPLVVLGAALLWFGWFGFNAGSALAANGV 225
Query: 260 SSIAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSWAAIV 319
+++A +NTN+AAA L W ++ + GKPS++GA G + GLV ITP AG V W A++
Sbjct: 226 AALAFVNTNLAAAAGALGWMLIEWLRNGKPSLLGAASGAVAGLVAITPAAGFVSPWGALI 285
Query: 320 MGILSGSIPWVTMMILHKK 338
+G+++G I + + +L KK
Sbjct: 286 IGLIAGVICYFAVKLLKKK 304
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 178 bits (453), Expect = 4e-52
Identities = 106/310 (34%), Positives = 167/310 (53%), Gaps = 17/310 (5%)
Query: 16 AVPDWLNKGDSAWQMTASTLVGIQSMPGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICW 75
A P +K D+A+ M + LV ++PG+ + Y +++ K ++ V FA V I W
Sbjct: 22 AAPAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILW 81
Query: 76 VLVCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVY 135
V+ Y +AFG+ F+G L V G Y V
Sbjct: 82 VVYGYSLAFGEG-NAFFG----NFNWLMLKNI-----ELTAVMGS------IYQYIH-VA 124
Query: 136 FQFTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWGGGFLYQWGVIDYS 195
FQ +FA ITV L+ G++ R+ A + FV +WL SY A +WGGG L G +D++
Sbjct: 125 FQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASDGALDFA 184
Query: 196 GGYVIHVSSGIAGLTAAYWVGPRLKSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGAPYA 255
GG V+H+++ +AGL AY +G R+ KE F P+N+ ++ G +L++GW GFN G+ A
Sbjct: 185 GGTVVHINAAVAGLVGAYLLGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGA 244
Query: 256 AHIASSIAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSW 315
A+ +++A +NT VA A ++L W + GKPS++GA G + GLV +TP G V
Sbjct: 245 ANEIAALAFVNTVVATAAAILGWVFGEWALRGKPSLLGACSGAIAGLVGVTPACGYVGVG 304
Query: 316 AAIVMGILSG 325
A+++G+++G
Sbjct: 305 GALIIGVVAG 314
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 162 bits (411), Expect = 4e-46
Identities = 87/306 (28%), Positives = 141/306 (46%), Gaps = 29/306 (9%)
Query: 30 MTASTLVGIQSMPGLLIIYASIVKKKWAVNSAFMVLYAFAAVLICWVLVCYRMAFGD--Q 87
+ + + I PG ++ + +V+ K +N + A ++ + Y +AFG
Sbjct: 3 ILLAAALVIFMQPGFALLESGLVRSKNVLNILYKNFQDVAIGVLAYWGFGYSLAFGKRYG 62
Query: 88 LLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVTTEPFYAMATLVYFQFTFAAITVIL 147
F G V + FQ FAA + +
Sbjct: 63 FSGFIG--------------------NLGVSAAGIQWGTLPDGL-FFLFQMMFAATAITI 101
Query: 148 LAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWG-GGFLYQWGV-IDYSGGYVIHVSSG 205
++G+V R+ A++ F L Y A +WG GG+L + GV +D++G V+H+ G
Sbjct: 102 VSGAVAERIKFSAYLLFSALLGTLVYPPVAHWVWGEGGWLAKLGVLVDFAGSTVVHIFGG 161
Query: 206 IAGLTAAYWVGPRL---KSDKERFPPNNVLLMLAGAGLLWMGWSGFNGGAPYAA-HIASS 261
AGL AA +GPR+ E P+N+ + G LLW GW GFN G+ A A +
Sbjct: 162 YAGLAAALVLGPRIGRFTDKNEAITPHNLPFAVLGTFLLWFGWFGFNAGSALTANGRARA 221
Query: 262 IAILNTNVAAATSLLVWTCLDVIFFGKPSVIGAVQGMMTGLVCITPGAGLVQSWAAIVMG 321
IA +NTN+AAA L + + GKP+++G G + GLV IT G+V W A+++G
Sbjct: 222 IAAVNTNLAAAGGGLTALLISRLKTGKPNMLGLANGALAGLVAITAACGVVTPWGALIIG 281
Query: 322 ILSGSI 327
+++G +
Sbjct: 282 LIAGVV 287
>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 = 105 bits (264), Expect = 2e-25
Identities = 78/284 (27%), Positives = 126/284 (44%), Gaps = 21/284 (7%)
Query: 64 VLYAFAAVLICWVLVCYRMAFGDQLLPFWGKGAPALGQKYLVGRARVPESTHEVDGKTVT 123
L+A A I ++LV Y + + + G LG L V + +G
Sbjct: 44 ALFAIAC--IMYLLVGYNIMYPGGGIFLGG----ILGSFLLGADNPVGDLIAGFEG---- 93
Query: 124 TEPFYAMATLVYFQFTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGAFSLWGG 183
+ Y+ + +FQ F A + +++G+V RM + ++ F + F Y + WGG
Sbjct: 94 -DADYSSGSDFFFQVVFVATAMSIVSGAVAERMKLWPFLLFAVVLTGFIYPIEGSWTWGG 152
Query: 184 GFLYQWGVIDYSGGYVIHVSSGIAGLTAAYWVGPRL---KSDKE--RFPPNNVLLMLAGA 238
G+L G D++G ++H++ A L +GPR + E P +N+ L G
Sbjct: 153 GWLDDLGFSDFAGSGIVHMAGAAAALAGVLLLGPRKGKYGKNGEVNPIPGSNLPLATLGT 212
Query: 239 GLLWMGWSGFNGGAPYAAHIASSIA-----ILNTNVAAATSLLVWTCLDVIFFGKPSVIG 293
+LWMGW GFNGG+ A + NTN AAA + L + FGK +
Sbjct: 213 FILWMGWFGFNGGSQLALSDVADANAVARIFANTNAAAAGGAIAALLLTKLLFGKADLTM 272
Query: 294 AVQGMMTGLVCITPGAGLVQSWAAIVMGILSGSIPWVTMMILHK 337
+ G + GLV IT AA ++G + G I ++++L K
Sbjct: 273 VLNGALAGLVAITAEPLTPSPLAATLIGAVGGVIVVFSIVLLDK 316
>gnl|CDD|237913 PRK15119, PRK15119, undecaprenyl-phosphate
alpha-N-acetylglucosaminyl 1-phosphate transferase;
Provisional.
Length = 365
Score = 30.0 bits (68), Expect = 2.2
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 142 AITVILLAGSVLGRMNIRA-WMAFVPLWLMFSYTVGAFSLWG 182
A +I LA ++L + + + FVP W+M + AF L+G
Sbjct: 294 AFVLITLAAALLASIGVLGEYSHFVPEWVMLVLFLLAFFLYG 335
>gnl|CDD|237328 PRK13274, mdoG, glucan biosynthesis protein G; Provisional.
Length = 516
Score = 29.5 bits (67), Expect = 3.0
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 205 GIAGLTAAYWVGPRLKSDKERFPPN----NVLLMLAGAG-LLW 242
GIA LT+ + GP S + F P + LL+ G G LW
Sbjct: 253 GIAPLTSMFLFGPNQPSPADDFRPEVHDSDGLLIHTGNGEWLW 295
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 29.5 bits (67), Expect = 3.5
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 282 DVIFFGKPSVIGAVQGMMTG 301
++I +P++I A GM+ G
Sbjct: 488 EIIESDEPAIILATSGMLNG 507
>gnl|CDD|215604 PLN03151, PLN03151, cation/calcium exchanger; Provisional.
Length = 650
Score = 29.3 bits (66), Expect = 3.7
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 4/45 (8%)
Query: 133 LVYFQFTFAAITVILLAGSVLGRMNIRAWMAFVPLWLMFSYTVGA 177
L +F FT ++ VIL+ G V + +AFV +++++++ V A
Sbjct: 249 LCFFLFTLVSLLVILMVGKV----TVGGAIAFVSIYVVYAFLVAA 289
>gnl|CDD|237009 PRK11883, PRK11883, protoporphyrinogen oxidase; Reviewed.
Length = 451
Score = 29.0 bits (66), Expect = 4.8
Identities = 8/17 (47%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 198 YVIHVSSGIAGLTAAYW 214
I + GI GL+AAY
Sbjct: 3 VAI-IGGGITGLSAAYR 18
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 28.9 bits (65), Expect = 5.3
Identities = 12/66 (18%), Positives = 21/66 (31%), Gaps = 11/66 (16%)
Query: 127 FYAMATLVYFQFTFAAITVILLAGSVLGRMNIRAW-----------MAFVPLWLMFSYTV 175
+ T + FQ F I V V R +A +PL+++
Sbjct: 396 LFLFLTNMTFQNVFPVINVFTAELPVFLRETRSGLYRVSAYFLAKTIAELPLFIILPALF 455
Query: 176 GAFSLW 181
+ + W
Sbjct: 456 TSITYW 461
>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
This model represents the alpha chain of all three
varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
nitrogenase [Central intermediary metabolism, Nitrogen
fixation].
Length = 443
Score = 28.6 bits (64), Expect = 5.8
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 199 VIHVSSGIAGLTAAYWVGPRLKSDKERFPPNNV 231
+IH+S G G T W R SD E +
Sbjct: 52 MIHISHGPVGCTYYTWGTKRYPSDNENGVGAFL 84
>gnl|CDD|219089 pfam06570, DUF1129, Protein of unknown function (DUF1129). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 206
Score = 27.6 bits (62), Expect = 8.4
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 194 YSGGYVIHVSSGIAGLTAAY---WVGPRLKSDKERFPPNNVLLMLAGAGLLWMGW 245
YSG + ++S + GL Y ++ LK +R P LL+L A ++WM
Sbjct: 109 YSGITTLLLTSLVGGLAMYYMYRYLYRYLKDKSKRPPWWKSLLILVLAVVVWMAV 163
>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 = 28.2 bits (63), Expect = 9.0
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 312 VQSWAAIVMGILSGSIPWVTMMILHKKCSLLQQVSFTFLKLFYFLTIASFVK 363
VQS ++ IL S+ + + HK + + + L + Y L + +K
Sbjct: 5 VQSPYEFILWILLASLAKIGFHLTHKVIRAVPE---SVLLIVYGLLVGGIIK 53
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 0.138 0.451
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,492,934
Number of extensions: 1947166
Number of successful extensions: 3063
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3024
Number of HSP's successfully gapped: 128
Length of query: 369
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 271
Effective length of database: 6,590,910
Effective search space: 1786136610
Effective search space used: 1786136610
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: 60 (26.8 bits)