RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 044901
(478 letters)
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 344 bits (886), Expect = e-115
Identities = 171/432 (39%), Positives = 235/432 (54%), Gaps = 25/432 (5%)
Query: 18 MNKGDNAWQLTAATLVGLQSIPGLVILYGSLVHKKWAINSAFMAFYAFAMVFVCWVGWAY 77
M+ GD AW L +A LV L PGL + YG LV KK +N+ +F AFA+V + W+ Y
Sbjct: 1 MDSGDTAWMLLSAALVLLM-TPGLALFYGGLVRKKNVLNTLMQSFVAFAIVTLLWIFVGY 59
Query: 78 RMSFGERLVNFLGKP-NVALDEKFLLGQAFLGYIPTATMVFFQGVFACITLILIAGALIG 136
++FG F+G L+ A IP FQ +FA IT LI+GA+
Sbjct: 60 SLAFGPDGNGFIGNLDQFFLNGLGFAAVAGGAGIPELVFFAFQMMFAAITPALISGAVAE 119
Query: 137 RMNFRAWMLFVPLWLTCSYTVAAFSIWCPNGWLAKLGIIDFAGGYVIHVSAGVAGFTASY 196
RM F A++LF LW T Y A +W GWLA LG +DFAGG V+H++AG A A+
Sbjct: 120 RMKFSAYLLFSVLWSTLVYPPVAHWVWGGGGWLALLGALDFAGGTVVHINAGFAALAAAL 179
Query: 197 WVGPRSDKDREKFPPNNIILMLAGAGLLWMGWSGFNGGGPFAISTDASLAILNTHVCTST 256
+G R PP+N+ L++ GA LLW GW GFN G A + A+LA +NT++ +
Sbjct: 180 VLGKRIGGKPVAIPPHNLPLVVLGAALLWFGWFGFNAGSALAANGVAALAFVNTNLAAAA 239
Query: 257 SLLTWLLLDTSFYGKPSVIGAVQGMITGLVCITPAAGVVQGWAALFMGLISGSVPWYTMM 316
L W+L++ GKPS++GA G + GLV ITPAAG V W AL +GLI+G + ++ +
Sbjct: 240 GALGWMLIEWLRNGKPSLLGAASGAVAGLVAITPAAGFVSPWGALIIGLIAGVICYFAVK 299
Query: 317 VLHNKIGLLRLVDDPMAVFHTHAVAGTLGGILTGFFAVPKLCRLFYMLPDWEKYIGLAYG 376
+L K+G VDD + VF H V G +G ILTG FA P + G G
Sbjct: 300 LLKKKLG----VDDALDVFGVHGVGGIVGAILTGIFAAPAV--------------GGGGG 341
Query: 377 LQNGRTSAGLRQMGVQLLGIAFVICLNIATTSIICWLIGLIVPLRLSKDELNIG-DEAVH 435
L G G Q+GVQLLG+ I T II ++ LI+ LR+S++E G D + H
Sbjct: 342 LFYG----GGVQLGVQLLGVLVTIVYAFVVTFIILKVLKLIIGLRVSEEEELEGLDISEH 397
Query: 436 GEKAFALVDDRE 447
GE A++ +
Sbjct: 398 GESAYSEEEATI 409
>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 = 335 bits (862), Expect = e-112
Identities = 153/424 (36%), Positives = 218/424 (51%), Gaps = 27/424 (6%)
Query: 23 NAWQLTAATLVGLQSIPGLVILYGSLVHKKWAINSAFMAFYAFAMVFVCWVGWAYRMSFG 82
AW L AA LV PG +LY LV K +N FA+ + W + Y ++FG
Sbjct: 1 TAWLLIAAALVFFM-QPGFALLYAGLVRSKNVLNIMMKNLLDFAIGSLLWWLFGYSLAFG 59
Query: 83 ERLVN--FLGKPNVALDEK-FLLGQAFLGYIPTATMVFFQGVFACITLILIAGALIGRMN 139
E F+G L + + G +P FQ +FA I +I+GA+ RM
Sbjct: 60 EDNPINGFIGTGGFGLKNFLYPGKISLAGTLPDLLFFLFQMMFAAIAATIISGAVAERMK 119
Query: 140 FRAWMLFVPLWLTCSYTVAAFSIWCPNGWLAKLGIIDFAGGYVIHVSAGVAGFTASYWVG 199
F A++LF LW T Y A +W GWL KLG++DFAGG V+H+ GVAG A+ +G
Sbjct: 120 FSAYLLFSVLWTTLVYPPVAHWVWGGGGWLYKLGVLDFAGGGVVHIVGGVAGLAAALVLG 179
Query: 200 PRSDKD--REKFPPNNIILMLAGAGLLWMGWSGFNGGGPFAISTDASLAILNTHVCTSTS 257
PR + P+N+ L++ G +LW GW GFN G A + A+ A +NT++ +
Sbjct: 180 PRIGRFPRPVAIRPHNVPLVVLGTFILWFGWFGFNAGSALAANGTAAYAAVNTNLAAAAG 239
Query: 258 LLTWLLLDTSFYGKPSVIGAVQGMITGLVCITPAAGVVQGWAALFMGLISGSVPWYTMMV 317
LTWLL+D +GKP+++GA G++ GLV ITP GVV W A+ +GL++G + + +
Sbjct: 240 GLTWLLIDWLKHGKPTLLGACNGILAGLVAITPGCGVVTPWGAIIIGLVAGVLCYLAVSK 299
Query: 318 LHNKIGLLRLVDDPMAVFHTHAVAGTLGGILTGFFAVPKLCRLFYMLPDWEKYIGLAYGL 377
L K+ +DDP+ F H V G G I TG FA PK+
Sbjct: 300 LKKKLK----IDDPLDAFAVHGVGGIWGLIATGLFAAPKVG----------------GVG 339
Query: 378 QNGRTSAGLRQMGVQLLGIAFVICLNIATTSIICWLIGLIVPLRLSKDELNIG-DEAVHG 436
G +Q+GVQL+GIA +I T II ++ + LR+S++E IG D A HG
Sbjct: 340 TGGLLGGNGKQLGVQLIGIAAIIAWAFVVTFIILKILDKTIGLRVSEEEEKIGLDLAEHG 399
Query: 437 EKAF 440
E A+
Sbjct: 400 EFAY 403
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 236 bits (604), Expect = 5e-73
Identities = 159/429 (37%), Positives = 225/429 (52%), Gaps = 25/429 (5%)
Query: 13 ANPEWMNKGDNAWQLTAATLVGLQSIPGLVILYGSLVHKKWAINSAFMAFYAFAMVFVCW 72
A P +K DNA+ + LV +IPG+ + YG L+ K ++ FA+V + W
Sbjct: 22 AAPAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILW 81
Query: 73 VGWAYRMSFGERLVNFLGKPNVALDEKFLLGQAFLGYIPTATMVFFQGVFACITLILIAG 132
V + Y ++FGE F + L K + A +G I V FQG FACIT+ LI G
Sbjct: 82 VVYGYSLAFGEGNAFFGNFNWLML--KNIELTAVMGSIYQYIHVAFQGSFACITVGLIVG 139
Query: 133 ALIGRMNFRAWMLFVPLWLTCSYTVAAFSIWCPNGWLAKLGIIDFAGGYVIHVSAGVAGF 192
AL R+ F A ++FV +WLT SY A +W G LA G +DFAGG V+H++A VAG
Sbjct: 140 ALAERIRFSAVLIFVVVWLTLSYIPIAHMVW-GGGLLASDGALDFAGGTVVHINAAVAGL 198
Query: 193 TASYWVGPRSDKDREKFPPNNIILMLAGAGLLWMGWSGFNGGGPFAISTDASLAILNTHV 252
+Y +G R +E F P+N+ ++ G +L++GW GFN G A + A+LA +NT V
Sbjct: 199 VGAYLLGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGAANEIAALAFVNTVV 258
Query: 253 CTSTSLLTWLLLDTSFYGKPSVIGAVQGMITGLVCITPAAGVVQGWAALFMGLISGSVPW 312
T+ ++L W+ + + GKPS++GA G I GLV +TPA G V AL +G+++G
Sbjct: 259 ATAAAILGWVFGEWALRGKPSLLGACSGAIAGLVGVTPACGYVGVGGALIIGVVAGLAGL 318
Query: 313 YTMMVLHNKIGLLRLVDDPMAVFHTHAVAGTLGGILTGFFAVPKLCRLFYMLPDWEKYIG 372
+ + +L LR VDDP VF H V G +G ILTG FA L +G
Sbjct: 319 WGVTMLKR---WLR-VDDPCDVFGVHGVCGIVGCILTGIFAASSL-----------GGVG 363
Query: 373 LAYGLQNGRTSAGLRQMGVQLLGIAFVICLNIATTSIICWLIGLIVPLRLSKDELNIG-D 431
A G+ G Q+ VQL IA I + I L L V LR+ +++ G D
Sbjct: 364 YAEGVTMG------HQVLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLD 417
Query: 432 EAVHGEKAF 440
HGE A+
Sbjct: 418 VNSHGENAY 426
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 234 bits (599), Expect = 2e-72
Identities = 151/425 (35%), Positives = 216/425 (50%), Gaps = 34/425 (8%)
Query: 24 AWQLTAATLVGLQSIPGLVILYGSLVHKKWAINSAFMAFYAFAMVFVCWVGWAYRMSFGE 83
A+ L AA LV PG +L LV K +N + F A+ + + G+ Y ++FG+
Sbjct: 1 AFILLAAALVIF-MQPGFALLESGLVRSKNVLNILYKNFQDVAIGVLAYWGFGYSLAFGK 59
Query: 84 RLV--NFLGKPNVALDEKFLLGQAFLGYIPTATMVFFQGVFACITLILIAGALIGRMNFR 141
R F+G V+ G +P FQ +FA + +++GA+ R+ F
Sbjct: 60 RYGFSGFIGNLGVSAAG------IQWGTLPDGLFFLFQMMFAATAITIVSGAVAERIKFS 113
Query: 142 AWMLFVPLWLTCSYTVAAFSIWCPNGWLAKLG-IIDFAGGYVIHVSAGVAGFTASYWVGP 200
A++LF L T Y A +W GWLAKLG ++DFAG V+H+ G AG A+ +GP
Sbjct: 114 AYLLFSALLGTLVYPPVAHWVWGEGGWLAKLGVLVDFAGSTVVHIFGGYAGLAAALVLGP 173
Query: 201 RSDK---DREKFPPNNIILMLAGAGLLWMGWSGFNGGGPFAIS-TDASLAILNTHVCTST 256
R + E P+N+ + G LLW GW GFN G + ++A +NT++ +
Sbjct: 174 RIGRFTDKNEAITPHNLPFAVLGTFLLWFGWFGFNAGSALTANGRARAIAAVNTNLAAAG 233
Query: 257 SLLTWLLLDTSFYGKPSVIGAVQGMITGLVCITPAAGVVQGWAALFMGLISGSVPWYTMM 316
LT LL+ GKP+++G G + GLV IT A GVV W AL +GLI+G V
Sbjct: 234 GGLTALLISRLKTGKPNMLGLANGALAGLVAITAACGVVTPWGALIIGLIAGVVSVLGYK 293
Query: 317 VLHNKIGLLRLVDDPMAVFHTHAVAGTLGGILTGFFAVPKLCRLFYMLPDWEKYIGLAYG 376
L K+G +DDP+ VF H V G GGI G FA P +P Y GL G
Sbjct: 294 KLKEKLG----IDDPLDVFPVHGVGGIWGGIAVGIFAAPY-------VPTSGIYGGLLGG 342
Query: 377 LQNGRTSAGLRQMGVQLLGIAFVICLNIATTSIICWLIGLIVPLRLSKDELNIG-DEAVH 435
G +Q+GVQL+GIA ++ T I+ L+GL + LR+S++E +G D A H
Sbjct: 343 --------GFKQLGVQLIGIAVILAYAFGVTFILGLLLGLTLGLRVSEEEEEVGLDVAEH 394
Query: 436 GEKAF 440
GE A+
Sbjct: 395 GETAY 399
>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 (263), Expect = 1e-24
Identities = 87/321 (27%), Positives = 137/321 (42%), Gaps = 49/321 (15%)
Query: 117 FFQGVFACITLILIAGALIGRMNFRAWMLFVPLWLTCSYTVAAFSIWCPNGWLAKLGIID 176
FFQ VF + +++GA+ RM ++LF + Y + W GWL LG D
Sbjct: 104 FFQVVFVATAMSIVSGAVAERMKLWPFLLFAVVLTGFIYPIEGSWTW-GGGWLDDLGFSD 162
Query: 177 FAGGYVIHVSAGVAGFTASYWVGPRSDKDREK-----FPPNNIILMLAGAGLLWMGWSGF 231
FAG ++H++ A +GPR K + P +N+ L G +LWMGW GF
Sbjct: 163 FAGSGIVHMAGAAAALAGVLLLGPRKGKYGKNGEVNPIPGSNLPLATLGTFILWMGWFGF 222
Query: 232 NGGGPFAIST-----DASLAILNTHVCTSTSLLTWLLLDTSFYGKPSVIGAVQGMITGLV 286
NGG A+S + NT+ + + LLL +GK + + G + GLV
Sbjct: 223 NGGSQLALSDVADANAVARIFANTNAAAAGGAIAALLLTKLLFGKADLTMVLNGALAGLV 282
Query: 287 CITPAAGVVQGWAALFMGLISGSVPWYTMMVLHNKIGLLRL-VDDPMAVFHTHAVAGTLG 345
IT AA +G + G ++V+ + + L +L +DDP+ H VAG
Sbjct: 283 AITAEPLTPSPLAATLIGAVGG------VIVVFSIVLLDKLKIDDPVGAISVHGVAGIW- 335
Query: 346 GILTGFFAVPKLCRLFYMLPDWEKYIGLAYGLQNGRTSAGLRQMGVQLLGIAFVICLNIA 405
G VP + NG S G QL+G A +
Sbjct: 336 ----GTLVVP---------------------ITNGDAS-----FGAQLIGAATIFAWVFV 365
Query: 406 TTSIICWLIGLIVPLRLSKDE 426
T+ I+ +++ + +R+S++E
Sbjct: 366 TSLIVWFILKATMGIRVSEEE 386
>gnl|CDD|220674 pfam10282, Lactonase, Lactonase, 7-bladed beta-propeller. This
entry contains bacterial 6-phosphogluconolactonases
(6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse
6-phosphogluconolactone to 6-phosphogluconate. The entry
also contains the fungal muconate lactonising enzyme
carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and
muconate cycloisomerase (EC:5.5.1.1), which convert
cis,cis-muconates to muconolactones and vice versa as
part of the microbial beta-ketoadipate pathway.
Structures of proteins in this family have revealed a
7-bladed beta-propeller fold.
Length = 344
Score = 30.3 bits (69), Expect = 2.1
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 3/46 (6%)
Query: 154 SYTVAAFSIWCPNGWLAKLGIIDFAGGYVIHVSAGVAG---FTASY 196
V+AF I G L L + G H+S G F A+Y
Sbjct: 60 DGGVSAFRIDPDTGKLTLLNQVPTGGASPCHLSVDPDGRFLFVANY 105
>gnl|CDD|215077 PLN00148, PLN00148, potassium transporter; Provisional.
Length = 785
Score = 29.8 bits (67), Expect = 3.5
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 19/90 (21%)
Query: 19 NKGDNAWQLTAATLVGLQSIPGLVILYGSLVHKKWAINSAFM----AFYAFAMVFVCWVG 74
NK W L +G+ +PG+ ++Y L AI S F+ AF+ +VFVC
Sbjct: 509 NKVSLKWLLGLGPSLGIVRVPGIGLIYSELATGVPAIFSHFVTNLPAFHK-VLVFVC--- 564
Query: 75 WAYRMSFGERLVNFLGKPNVALDEKFLLGQ 104
V + P V+ +E+FL+G+
Sbjct: 565 -----------VKSVPVPYVSPEERFLIGR 583
>gnl|CDD|132035 TIGR02990, ectoine_eutA, ectoine utilization protein EutA. Members
of this protein family are EutA, a predicted
arylmalonate decarboxylase found in a conserved ectoine
utilization operon of species that include Sinorhizobium
meliloti 1021 (where it is known to be induced by
ectoine), Mesorhizobium loti and Silicibacter pomeroyi.
It is missing from two other species with the other
ectoine transport and utilization genes: Pseudomonas
putida and Agrobacterium tumefaciens.
Length = 239
Score = 29.5 bits (66), Expect = 3.7
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 253 CTSTSLLTWLLLDTSFYGKPSVIGAVQGMITGLVCITPAAGVVQGWAALFMGLISGSVPW 312
CTS S++ G V A+ G +TP++ V G AAL + IS P+
Sbjct: 79 CTSASVVI---------GDDEVTRAINAAKPGTPVVTPSSAAVDGLAALGVRRISLLTPY 129
>gnl|CDD|220685 pfam10311, Ilm1, Increased loss of mitochondrial DNA protein 1.
This is a family of proteins of approximately 200
residues that are conserved in fungi. Ilm1 is part of
the peroxisome, a complex that is the sole site of
beta-oxidation in Saccharomyces cerevisiae and known to
be required for optimal growth in the presence of fatty
acid. Ilm1 may participate in the control of the C16/C18
ratio since it interacts strongly with Mga2p, a
transcription factor that controls expression of Ole1,
the sole fatty acyl desaturase in S. cerevisiae
responsible for conversion of the saturated fatty acids
stearate (C18) and palmitate (C16) to oleate and
palmitoleate, respectively.
Length = 143
Score = 28.0 bits (63), Expect = 5.7
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 10/90 (11%)
Query: 88 FLGKPNVALDEKF--LLGQAFLGYIPTATMVFFQGVFACITLILIAGALIGRM-----NF 140
L P V L+ F LLGQA +P + + ++++ AL + N
Sbjct: 21 LLKNPEVILESGFVFLLGQAM--QLPALRLSRPSPLLGLLSILFALLALSDLIPLLANNL 78
Query: 141 RAWMLFVPLWLTCSYTVAAFS-IWCPNGWL 169
+ VPL L + + A+S + + +L
Sbjct: 79 EYFESIVPLRLILFFALTAYSYLSKSSLYL 108
>gnl|CDD|238141 cd00229, SGNH_hydrolase, SGNH_hydrolase, or GDSL_hydrolase, is a
diverse family of lipases and esterases. The tertiary
fold of the enzyme is substantially different from that
of the alpha/beta hydrolase family and unique among all
known hydrolases; its active site closely resembles the
typical Ser-His-Asp(Glu) triad from other serine
hydrolases, but may lack the carboxlic acid.
Length = 187
Score = 28.1 bits (62), Expect = 7.0
Identities = 12/69 (17%), Positives = 27/69 (39%), Gaps = 1/69 (1%)
Query: 154 SYTVAAFSIWCPNGWLAKLGIIDFAGGYVIHV-SAGVAGFTASYWVGPRSDKDREKFPPN 212
S T + + L ++ AGG + V + GV+G T + + +
Sbjct: 7 SITAGYGASSGSTFYSLLLYLLLLAGGPGVEVINLGVSGATTADALRRLGLRLALLKDKP 66
Query: 213 NIILMLAGA 221
+++++ G
Sbjct: 67 DLVIIELGT 75
>gnl|CDD|218361 pfam04983, RNA_pol_Rpb1_3, RNA polymerase Rpb1, domain 3. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 3, represents the pore domain. The 3' end
of RNA is positioned close to this domain. The pore
delimited by this domain is thought to act as a channel
through which nucleotides enter the active site and/or
where the 3' end of the RNA may be extruded during
back-tracking.
Length = 158
Score = 28.0 bits (63), Expect = 7.5
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 269 YGKPSVIGAVQGMITGLVCIT 289
GKP +IG Q M+ GL +T
Sbjct: 7 NGKP-IIGPSQDMVLGLYLLT 26
>gnl|CDD|225070 COG2159, COG2159, Predicted metal-dependent hydrolase of the
TIM-barrel fold [General function prediction only].
Length = 293
Score = 28.2 bits (63), Expect = 9.6
Identities = 14/49 (28%), Positives = 15/49 (30%), Gaps = 2/49 (4%)
Query: 182 VIHVSAGVAGFTASYWVGPRSDKDR--EKFPPNNIILMLAGAGLLWMGW 228
VIH AG G D KFP I+L G W
Sbjct: 161 VIHTGAGPGGAGLEKGHSDPLYLDDVARKFPELKIVLGHMGEDYPWELE 209
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 0.141 0.461
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,500,809
Number of extensions: 2605507
Number of successful extensions: 3568
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3516
Number of HSP's successfully gapped: 120
Length of query: 478
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 377
Effective length of database: 6,457,848
Effective search space: 2434608696
Effective search space used: 2434608696
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: 61 (27.2 bits)