RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12939
(413 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 = 88.5 bits (220), Expect = 3e-19
Identities = 40/95 (42%), Positives = 48/95 (50%), Gaps = 13/95 (13%)
Query: 172 GITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYS 231
+ YP V+HWVW GWL KLG DFAG G VH+ G AA ++GPRIGRF
Sbjct: 132 TLVYPPVAHWVWGGGGWLYKLGVLDFAGGGVVHIVGGVAGLAAALVLGPRIGRFPR---P 188
Query: 232 SPPPGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
H++P V G+ LW F FGF
Sbjct: 189 VAIRPHNVP----LVV-LGTFILW-----FGWFGF 213
Score = 88.1 bits (219), Expect = 4e-19
Identities = 32/69 (46%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 340 GITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYS 399
+ YP V+HWVW GWL KLG DFAG G VH+ G AA ++GPRIGRF
Sbjct: 132 TLVYPPVAHWVWGGGGWLYKLGVLDFAGGGVVHIVGGVAGLAAALVLGPRIGRFPR---P 188
Query: 400 SPPPGHSLP 408
H++P
Sbjct: 189 VAIRPHNVP 197
Score = 79.2 bits (196), Expect = 4e-16
Identities = 33/89 (37%), Positives = 49/89 (55%), Gaps = 1/89 (1%)
Query: 69 WNFLFTVNAGLMGMVSVCAGANVFSMWSSLVIGLIAGPL-YVALRYLVIACGVDDPLDAS 127
L N L G+V++ G V + W +++IGL+AG L Y+A+ L +DDPLDA
Sbjct: 254 PTLLGACNGILAGLVAITPGCGVVTPWGAIIIGLVAGVLCYLAVSKLKKKLKIDDPLDAF 313
Query: 128 AVHFGGGLWGVMSEPLFRRGGLIYGITDD 156
AVH GG+WG+++ LF + T
Sbjct: 314 AVHGVGGIWGLIATGLFAAPKVGGVGTGG 342
Score = 54.2 bits (131), Expect = 5e-08
Identities = 33/111 (29%), Positives = 42/111 (37%), Gaps = 11/111 (9%)
Query: 188 WLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLPG----LL 243
KL D + AVH G IA G F + G L G L
Sbjct: 300 LKKKLKIDDPLDAFAVHGVGGIWGLIAT-------GLFAAPKVGGVGTGGLLGGNGKQLG 352
Query: 244 HNAVGAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAY 294
+G +I W+ +FI+ L LRV EE GLD+ +H E AY
Sbjct: 353 VQLIGIAAIIAWAFVVTFIILKILDKTIGLRVSEEEEKIGLDLAEHGEFAY 403
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 83.9 bits (208), Expect = 1e-17
Identities = 44/96 (45%), Positives = 54/96 (56%), Gaps = 13/96 (13%)
Query: 172 GITYPIVSHWVWSDEGWLNKLGYS-DFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRY 230
+ YP V+HWVW + GWL KLG DFAGS VH+F G AA ++GPRIGRF +
Sbjct: 124 TLVYPPVAHWVWGEGGWLAKLGVLVDFAGSTVVHIFGGYAGLAAALVLGPRIGRFTDKNE 183
Query: 231 SSPPPGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
+ P H+LP AV G+ LW F FGF
Sbjct: 184 AITP--HNLP----FAV-LGTFLLW-----FGWFGF 207
Score = 82.3 bits (204), Expect = 3e-17
Identities = 35/70 (50%), Positives = 44/70 (62%), Gaps = 3/70 (4%)
Query: 340 GITYPIVSHWVWSDEGWLNKLGYS-DFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRY 398
+ YP V+HWVW + GWL KLG DFAGS VH+F G AA ++GPRIGRF +
Sbjct: 124 TLVYPPVAHWVWGEGGWLAKLGVLVDFAGSTVVHIFGGYAGLAAALVLGPRIGRFTDKNE 183
Query: 399 SSPPPGHSLP 408
+ P H+LP
Sbjct: 184 AITP--HNLP 191
Score = 73.9 bits (182), Expect = 2e-14
Identities = 34/94 (36%), Positives = 49/94 (52%), Gaps = 10/94 (10%)
Query: 69 WNFLFTVNAGLMGMVSVCAGANVFSMWSSLVIGLIAGPL-YVALRYLVIACGVDDPLDAS 127
N L N L G+V++ A V + W +L+IGLIAG + + + L G+DDPLD
Sbjct: 249 PNMLGLANGALAGLVAITAACGVVTPWGALIIGLIAGVVSVLGYKKLKEKLGIDDPLDVF 308
Query: 128 AVHFGGGLWGVMSEPLF---------RRGGLIYG 152
VH GG+WG ++ +F GGL+ G
Sbjct: 309 PVHGVGGIWGGIAVGIFAAPYVPTSGIYGGLLGG 342
Score = 51.1 bits (123), Expect = 5e-07
Identities = 34/115 (29%), Positives = 40/115 (34%), Gaps = 18/115 (15%)
Query: 188 WLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLPGLLHN-- 245
KLG D VH G IA G F P GLL
Sbjct: 295 LKEKLGIDDPLDVFPVHGVGGIWGGIAV-------GIFAAPYV---PTSGIYGGLLGGGF 344
Query: 246 ------AVGAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAY 294
+G I ++ +FIL L L LRV EE GLD+ +H E AY
Sbjct: 345 KQLGVQLIGIAVILAYAFGVTFILGLLLGLTLGLRVSEEEEEVGLDVAEHGETAY 399
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 78.0 bits (193), Expect = 9e-16
Identities = 51/228 (22%), Positives = 74/228 (32%), Gaps = 80/228 (35%)
Query: 69 WNFLFTVNAGLMGMVSVCAGANVFSMWSSLVIGLIAGPL-YVALRYLVIACGVDDPLDAS 127
+ L + + G+V++ A S W +L+IGLIAG + Y A++ L GVDD LD
Sbjct: 255 PSLLGAASGAVAGLVAITPAAGFVSPWGALIIGLIAGVICYFAVKLLKKKLGVDDALDVF 314
Query: 128 AVHFGGGLWGVMSEPLFRRGGLIYGITDDAVKVTSTNKQTSPLPGITYPIVSHWVWSDEG 187
VH GG+ G + +F +P G G
Sbjct: 315 GVHGVGGIVGAILTGIF----------------------AAPAVGGGGG------LFYGG 346
Query: 188 WLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLPGLLHNAV 247
G ++A +FI ++ IG
Sbjct: 347 G--VQLGVQLLGVLVTIVYAFVVTFIILKVLKLIIG------------------------ 380
Query: 248 GAGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAYP 295
LRV EE+EGLDI++H E AY
Sbjct: 381 -------------------------LRVSEEEELEGLDISEHGESAYS 403
Score = 77.6 bits (192), Expect = 1e-15
Identities = 39/95 (41%), Positives = 50/95 (52%), Gaps = 15/95 (15%)
Query: 172 GITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYS 231
+ YP V+HWVW GWL LG DFAG VH+ AG + AA ++G RI G +
Sbjct: 135 TLVYPPVAHWVWGGGGWLALLGALDFAGGTVVHINAGFAALAAALVLGKRI---GGKPVA 191
Query: 232 SPPPGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
PP H+LP ++ +GA LW F FGF
Sbjct: 192 IPP--HNLPLVV---LGAA--LLW-----FGWFGF 214
Score = 75.7 bits (187), Expect = 5e-15
Identities = 31/72 (43%), Positives = 40/72 (55%), Gaps = 5/72 (6%)
Query: 340 GITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYS 399
+ YP V+HWVW GWL LG DFAG VH+ AG + AA ++G RI G +
Sbjct: 135 TLVYPPVAHWVWGGGGWLALLGALDFAGGTVVHINAGFAALAAALVLGKRI---GGKPVA 191
Query: 400 SPPPGHSLPVST 411
PP H+LP+
Sbjct: 192 IPP--HNLPLVV 201
>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 = 71.2 bits (175), Expect = 2e-13
Identities = 33/74 (44%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 338 LPGITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGR 397
L G YPI W W GWL+ LG+SDFAGSG VH+ + L+GPR G++G
Sbjct: 137 LTGFIYPIEGSWTWGG-GWLDDLGFSDFAGSGIVHMAGAAAALAGVLLLGPRKGKYGKNG 195
Query: 398 YSSPPPGHSLPVST 411
+P PG +LP++T
Sbjct: 196 EVNPIPGSNLPLAT 209
Score = 69.3 bits (170), Expect = 7e-13
Identities = 38/97 (39%), Positives = 48/97 (49%), Gaps = 11/97 (11%)
Query: 170 LPGITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGR 229
L G YPI W W GWL+ LG+SDFAGSG VH+ + L+GPR G++G
Sbjct: 137 LTGFIYPIEGSWTWGG-GWLDDLGFSDFAGSGIVHMAGAAAALAGVLLLGPRKGKYGKNG 195
Query: 230 YSSPPPGHSLPGLLHNAVGAGSIFLWSLTTSFILFGF 266
+P PG +LP G+ LW FGF
Sbjct: 196 EVNPIPGSNLP-----LATLGTFILW-----MGWFGF 222
Score = 45.0 bits (107), Expect = 5e-05
Identities = 34/107 (31%), Positives = 45/107 (42%), Gaps = 18/107 (16%)
Query: 189 LNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSSPPPGHSLPGLLHNAVG 248
L+KL D G+ +VH AG + G + NG S +G
Sbjct: 314 LDKLKIDDPVGAISVHGVAG--------IWGTLVVPITNGDAS----------FGAQLIG 355
Query: 249 AGSIFLWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAYP 295
A +IF W TS I++ L +RV EE EGLDI + AYP
Sbjct: 356 AATIFAWVFVTSLIVWFILKATMGIRVSEEEEYEGLDIAECGMEAYP 402
Score = 42.7 bits (101), Expect = 2e-04
Identities = 21/68 (30%), Positives = 36/68 (52%)
Query: 76 NAGLMGMVSVCAGANVFSMWSSLVIGLIAGPLYVALRYLVIACGVDDPLDASAVHFGGGL 135
N L G+V++ A S ++ +IG + G + V L+ +DDP+ A +VH G+
Sbjct: 275 NGALAGLVAITAEPLTPSPLAATLIGAVGGVIVVFSIVLLDKLKIDDPVGAISVHGVAGI 334
Query: 136 WGVMSEPL 143
WG + P+
Sbjct: 335 WGTLVVPI 342
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 43.2 bits (102), Expect = 2e-04
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 6/69 (8%)
Query: 341 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 400
++Y ++H VW G L G DFAG VH+ A + AYL+G R+G G+ +
Sbjct: 160 LSYIPIAHMVWGG-GLLASDGALDFAGGTVVHINAAVAGLVGAYLLGKRVGF---GKEAF 215
Query: 401 PPPGHSLPV 409
P H+LP+
Sbjct: 216 KP--HNLPM 222
Score = 43.2 bits (102), Expect = 2e-04
Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 173 ITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTCSFIAAYLMGPRIGRFGNGRYSS 232
++Y ++H VW G L G DFAG VH+ A + AYL+G R+G G+ +
Sbjct: 160 LSYIPIAHMVWGG-GLLASDGALDFAGGTVVHINAAVAGLVGAYLLGKRVGF---GKEAF 215
Query: 233 PPPGHSLP 240
P H+LP
Sbjct: 216 KP--HNLP 221
Score = 39.7 bits (93), Expect = 0.002
Identities = 18/41 (43%), Positives = 23/41 (56%)
Query: 254 LWSLTTSFILFGFLYLINMLRVPSTEEIEGLDITKHNEIAY 294
+WS +FI + L LRVP +E EGLD+ H E AY
Sbjct: 386 VWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAY 426
>gnl|CDD|233668 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase. This
model represents an O-methyltransferase believed to act
at two points in the ubiquinone biosynthetic pathway in
bacteria (UbiG) and fungi (COQ3). A separate methylase
(MenG/UbiE) catalyzes the single C-methylation step. The
most commonly used names for genes in this family do not
indicate whether this gene is an O-methyl, or C-methyl
transferase [Biosynthesis of cofactors, prosthetic
groups, and carriers, Menaquinone and ubiquinone].
Length = 224
Score = 31.9 bits (73), Expect = 0.39
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 132 GGGLWGVMSEPLFRRGGLIYGI--TDDAVKVTSTNKQTSPLPGITY 175
GGGL +SEPL R G + GI +++ ++V + + PL I Y
Sbjct: 55 GGGL---LSEPLARLGANVTGIDASEENIEVAKLHAKKDPLLKIEY 97
>gnl|CDD|115810 pfam07180, DUF1401, Protein of unknown function (DUF1401). This
family consists of several hypothetical bacterial
proteins of around 135 residues in length. Members of
this family appear to be found exclusively in the
Enterobacteria Escherichia coli, Citrobacter rodentium
and Salmonella typhi. The function of this family is
unknown.
Length = 150
Score = 30.1 bits (67), Expect = 1.4
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 9/67 (13%)
Query: 319 NHNTDARVKVTSTNKQTSPLPGITYPIVSHWVWSDEGWLNKLGYSDFAGSGAVHLFAGTC 378
N + + + N PL Y IV+HW E W+ + +D A A + A
Sbjct: 5 NKHDACFIPDSVKNYAGEPL----YIIVAHWCKLQEKWIQR---NDIA--EAFGINARRA 55
Query: 379 SFIAAYL 385
SFI AY+
Sbjct: 56 SFIIAYI 62
>gnl|CDD|218784 pfam05861, PhnI, Bacterial phosphonate metabolism protein (PhnI).
This family consists of several Proteobacterial
phosphonate metabolism protein (PhnI) sequences.
Bacteria that use phosphonates as a phosphorus source
must be able to break the stable carbon-phosphorus bond.
In Escherichia coli phosphonates are broken down by a
C-P lyase that has a broad substrate specificity. The
genes for phosphonate uptake and degradation in E. coli
are organised in an operon of 14 genes, named phnC to
phnP. Three gene products (PhnC, PhnD and PhnE) comprise
a binding protein-dependent phosphonate transporter,
which also transports phosphate, phosphite, and certain
phosphate esters such as phosphoserine; two gene
products (PhnF and PhnO) may have a role in gene
regulation; and nine gene products (PhnG, PhnH, PhnI,
PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably
comprise a membrane-associated C-P lyase enzyme complex.
Length = 356
Score = 30.3 bits (69), Expect = 1.9
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 185 DEGWLNKLGYSDFAGSGAVHLFAG 208
DEG+L L YS G G H F G
Sbjct: 202 DEGFLLALAYSTQRGYGRNHPFVG 225
Score = 30.3 bits (69), Expect = 1.9
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 353 DEGWLNKLGYSDFAGSGAVHLFAG 376
DEG+L L YS G G H F G
Sbjct: 202 DEGFLLALAYSTQRGYGRNHPFVG 225
>gnl|CDD|226153 COG3626, PhnI, Uncharacterized enzyme of phosphonate metabolism
[Inorganic ion transport and metabolism].
Length = 367
Score = 29.7 bits (67), Expect = 3.3
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 185 DEGWLNKLGYSDFAGSGAVHLFAG 208
DEG+L L YS G G H FAG
Sbjct: 202 DEGFLLALAYSTQRGYGRNHPFAG 225
Score = 29.7 bits (67), Expect = 3.3
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 353 DEGWLNKLGYSDFAGSGAVHLFAG 376
DEG+L L YS G G H FAG
Sbjct: 202 DEGFLLALAYSTQRGYGRNHPFAG 225
>gnl|CDD|173866 cd08501, PBP2_Lpqw, The substrate-binding domain of mycobacterial
lipoprotein Lpqw contains type 2 periplasmic binding
fold. LpqW is one of key players in synthesis and
transport of the unique components of the mycobacterial
cell wall which is a complex structure rich in two
related lipoglycans, the phosphatidylinositol mannosides
(PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly
conserved lipoprotein that transport intermediates from
a pathway for mature PIMs production into a pathway for
LAMs biosynthesis, thus controlling the relative
abundance of these two essential components of cell
wall. LpqW is thought to have been adapted by the
cell-wall biosynthesis machinery of mycobacteria and
other closely related pathogens, evolving to play an
important role in PIMs/LAMs biosynthesis. Most of
periplasmic binding proteins are comprised of only two
globular subdomains corresponding to domains I and III
of the LpqW protein. The structural topology of these
domains is most similar to that of the type 2
periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 486
Score = 28.5 bits (64), Expect = 7.1
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 316 DVLNHNTDARVKVTSTNKQTSPLPGITYPIVSHWVWSD 353
DV N + V+VTS + QT +TY I WSD
Sbjct: 45 DVPNPDYVGSVEVTSDDPQT-----VTYTINPEAQWSD 77
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 0.141 0.465
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,844,237
Number of extensions: 2150434
Number of successful extensions: 1992
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1975
Number of HSP's successfully gapped: 53
Length of query: 413
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 314
Effective length of database: 6,546,556
Effective search space: 2055618584
Effective search space used: 2055618584
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 (21.9 bits)
S2: 60 (26.8 bits)