RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037375
(183 letters)
>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 = 58.6 bits (142), Expect = 2e-10
Identities = 35/120 (29%), Positives = 61/120 (50%), Gaps = 2/120 (1%)
Query: 54 LPEASASLLIGLIVSALTNISNTETNIRYSFSFNELICSVATCLLMILFSWQKPFFSNFG 113
+PE+ ++ GL+V + S S+ L L F Q+ FF N G
Sbjct: 35 VPESVLLIVYGLLVGGIIKASPHIDPPTLDSSYFFLYLLPPIVLDAGYFMPQRNFFENLG 94
Query: 114 AIVTFAIFGTFLASMVTGILVYLGGVMFVM--YRLPFVECLMFGALISATDPITVLSIFQ 171
+I+ FA+ GT + + V G+ +Y ++ + ++ L+FG+LISA DP+ VL++F+
Sbjct: 95 SILIFAVVGTLINAFVIGLSLYGICLIGGFGSIDIGLLDNLLFGSLISAVDPVAVLAVFE 154
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 46.1 bits (110), Expect = 3e-06
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 5/63 (7%)
Query: 108 FFSNFGAIVTFAIFGTFLASMVTGILVYLGGVMFVMYRLPFVECLMFGALISATDPITVL 167
+ +I+ A+ + ++ G+L + ++ +P + GA++S TDP+ V
Sbjct: 83 LRRVWRSILVLALPLVLITALGIGLLAHW-----LLPGIPLAAAFLLGAILSPTDPVAVS 137
Query: 168 SIF 170
IF
Sbjct: 138 PIF 140
>gnl|CDD|216235 pfam00999, Na_H_Exchanger, Sodium/hydrogen exchanger family. Na/H
antiporters are key transporters in maintaining the pH
of actively metabolising cells. The molecular mechanisms
of antiport are unclear. These antiporters contain 10-12
transmembrane regions (M) at the amino-terminus and a
large cytoplasmic region at the carboxyl terminus. The
transmembrane regions M3-M12 share identity with other
members of the family. The M6 and M7 regions are highly
conserved. Thus, this is thought to be the region that
is involved in the transport of sodium and hydrogen
ions. The cytoplasmic region has little similarity
throughout the family.
Length = 370
Score = 38.3 bits (90), Expect = 0.001
Identities = 34/142 (23%), Positives = 66/142 (46%), Gaps = 17/142 (11%)
Query: 33 IMMLVLSFILGHVLRRHKFYYLPEASASLLIGLIVSALTNISNTETNIRYSFSFNELICS 92
+++L+L+ + G + RR LP +L G++ + + + E++
Sbjct: 2 VLLLLLALLAGLLARR---LGLPPVVGLILAGIL------LGPSGLGLVEPDLDLEVLAE 52
Query: 93 VATCLLMILFSW---QKPFFSNFGAIVTFAIFGTFLASMVTGILVYLGGVMFVMYRLPFV 149
+ LL+ L + N +I+ A+ G + ++ +L LGG +P +
Sbjct: 53 LGLPLLLFLAGLELDLRELRKNGKSILLLALLGVLIPFLLGLLLALLGG-----LGIPLL 107
Query: 150 ECLMFGALISATDPITVLSIFQ 171
E L+FGA +SAT P+ VL+I +
Sbjct: 108 EALLFGAALSATSPVVVLAILK 129
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. 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 bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 35.6 bits (82), Expect = 0.011
Identities = 32/144 (22%), Positives = 54/144 (37%), Gaps = 22/144 (15%)
Query: 33 IMMLVLSFILGHVLRRHKFYYLPEASASLLIGLIVSALTNISNTETNIRYSFSFNELICS 92
I+ LV+ V KF LP A +L GL++ + + E++
Sbjct: 3 IIELVMLATAVAV--TVKFIRLPYPIALILAGLLLGLAGLLPEVPLD-------REIVLF 53
Query: 93 VATCLLMILFSWQKP---FFSNFGAIVTFAIFGTFLASMVTGILVY--LGGVMFVMYRLP 147
+ L+ + NF I A + ++V G + LG +P
Sbjct: 54 LFLPPLLFEAAMNTDLRELRENFRPIALIAFLLVVVTTVVVGFSLNWILG--------IP 105
Query: 148 FVECLMFGALISATDPITVLSIFQ 171
L+ GA++S TD + VL F+
Sbjct: 106 LALALILGAVLSPTDAVAVLGTFK 129
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 34.1 bits (79), Expect = 0.027
Identities = 19/117 (16%), Positives = 47/117 (40%), Gaps = 18/117 (15%)
Query: 30 LLQIMMLVLSFILGHVLRRHKF------YYLPEASASLLIGLIVSALTNISNTETNIRYS 83
LL +++++L+ +L ++LR YL ++L+ L++ AL + + R
Sbjct: 1 LLDLLLILLALLLAYLLRFGSRGIPDIESYLALLLLAVLLFLLIFALFGL---YRSWRRR 57
Query: 84 FSFNELICSVATC-----LLMILFSWQKPFFSNFGAIVTFAIFGTFLASMVTGILVY 135
E++ + L++ L + F +G + + + +L+
Sbjct: 58 SRLREMLLRILLAWTLTFLILALLA----FLLKYGTEFSRLWLLLWFLLALALLLLG 110
>gnl|CDD|233148 TIGR00844, c_cpa1, na(+)/h(+) antiporter. 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
fungal members of this family [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 810
Score = 32.2 bits (73), Expect = 0.14
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 128 MVTGILVYLGGVMFVMYRLPFVECLMFGALISATDPITVLSIFQGTCA 175
M +G LV V ++ L F L+ GA I+ATDP+ S+ GT A
Sbjct: 110 MTSGWLVIALFVWILVPGLNFPASLLMGACITATDPVLAQSVVSGTFA 157
>gnl|CDD|214457 MTH00205, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 448
Score = 31.9 bits (73), Expect = 0.17
Identities = 28/114 (24%), Positives = 47/114 (41%), Gaps = 13/114 (11%)
Query: 33 IMMLVLSFILGHVLRRHKFYYLPEASASLLIGLIVSA--LTNISNTETNIRYSFSFNEL- 89
+ V S ++ + + K + S LLIGL S+ +N + I SFSF+ L
Sbjct: 2 SIFGVFSLLIILFVLKFKDWSF--FSNLLLIGLFFSSFFFSNSFLMTSFISSSFSFDSLS 59
Query: 90 ----ICSVATCLLMILFSWQ----KPFFSNFGAIVTFAIFGTFLASMVTGILVY 135
+ S LLM+L S++ F V + L+ V +L++
Sbjct: 60 LPLIMLSFWISLLMVLASYKVFKSNKNSKLFTVSVIMLLLILILSFSVDNLLLF 113
>gnl|CDD|184389 PRK13912, PRK13912, nuclease NucT; Provisional.
Length = 177
Score = 31.3 bits (71), Expect = 0.18
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 33 IMMLVLSFILGHVLRRHKFYYLPEASASLLIGLIVSALTNISNTETNIR---YSFSFNEL 89
+ + +L LG + + Y+LP L L+ ISN ++I+ YSF+ ++
Sbjct: 6 VGVFLLVGCLGVLQAKSSLYFLPYEQKDALNKLVSL----ISNARSSIKIAIYSFTHKDI 61
Query: 90 I 90
Sbjct: 62 A 62
>gnl|CDD|235410 PRK05326, PRK05326, potassium/proton antiporter; Reviewed.
Length = 562
Score = 29.4 bits (67), Expect = 0.98
Identities = 23/95 (24%), Positives = 44/95 (46%), Gaps = 15/95 (15%)
Query: 84 FSFNELICSVATCLLMILFS------WQKPFFSNFGAIVTFAIFGTFLASMVTGILVYLG 137
+ L+ ++A L +ILF W F G ++ A G + + +TG+ +
Sbjct: 56 YPLAYLVGNLA--LAVILFDGGLRTRWSS-FRPALGPALSLATLGVLITAGLTGLFAHW- 111
Query: 138 GVMFVMYRLPFVECLMFGALISATDPITVLSIFQG 172
+ L ++E L+ GA++ +TD V S+ +G
Sbjct: 112 -----LLGLDWLEGLLLGAIVGSTDAAAVFSLLRG 141
>gnl|CDD|139571 PRK13434, PRK13434, F0F1 ATP synthase subunit delta; Provisional.
Length = 184
Score = 28.0 bits (62), Expect = 2.0
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 14 PHGSPAKEQQAAGVGILLQIMMLVLSFILGHVLRRHKFYYLPEASASLLIGL 65
P SP +++Q + +I + L+F LG +L + +F YLPE + L
Sbjct: 48 PTVSPEEKEQTLAKNLRGKISDITLNF-LGVLLNKGRFIYLPEIQKDFTVEL 98
>gnl|CDD|114930 pfam06238, Borrelia_lipo_2, Borrelia burgdorferi BBR25
lipoprotein. This family consists of a number of
lipoproteins from the Lyme disease spirochete Borrelia
burgdorferi.
Length = 111
Score = 26.9 bits (59), Expect = 3.0
Identities = 14/33 (42%), Positives = 26/33 (78%), Gaps = 5/33 (15%)
Query: 63 IGL---IVSALTNISNTETNIRYSF--SFNELI 90
IGL ++S+LTNI+ T+TNI +++ +F+++I
Sbjct: 6 IGLGLNLLSSLTNIAKTDTNIDHNYINTFSKVI 38
>gnl|CDD|237114 PRK12488, PRK12488, acetate permease; Provisional.
Length = 549
Score = 27.8 bits (62), Expect = 4.0
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 125 LASMVTGILVYLGGVMFVMYRLPFVECLMFGALISATDPITVLSIF 170
+A++ G+L + G+MF + F+ L+ S P+ LS+F
Sbjct: 407 IATLGIGLLAVVLGLMFESQNIAFLSGLVLAIAASVNFPVLFLSMF 452
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 27.8 bits (62), Expect = 4.4
Identities = 23/93 (24%), Positives = 41/93 (44%), Gaps = 15/93 (16%)
Query: 86 FNELICSVATCLLMILF------SWQKPFFSNFGAIVTFAIFGTFLASMVTGILVYLGGV 139
F ++ ++A L +ILF F G ++ A G + S +TG+
Sbjct: 59 FAYMVGNLA--LAIILFDGGFGTQLSS-FRVAAGPALSLATLGVLITSGLTGVAAAY--- 112
Query: 140 MFVMYRLPFVECLMFGALISATDPITVLSIFQG 172
+ L ++E L+ GA++ +TD V S+ G
Sbjct: 113 ---LLNLDWLEGLLIGAIVGSTDAAAVFSLLGG 142
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 27.3 bits (61), Expect = 5.1
Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 3/98 (3%)
Query: 39 SFILGHVLRRHKFYYLPEASASLLIGLIVSALTNISNTETNIRYSFSFNELICSVATCLL 98
+ ++ R H P S +G I + + S + N+ ++ + N + V LL
Sbjct: 32 AIMMVAFYR-HAGRMWPGILLSCSLGNIAANILLFSTSSLNLTWT-TINLVEAVVGAVLL 89
Query: 99 MILFSWQKPFFSNFGAIVTFAIFGTFLASMVTGILVYL 136
L W P N + A+ + ++ G+LV L
Sbjct: 90 RKLLPWYNPLQ-NLADWLRLALGSAIVPPLLGGVLVVL 126
>gnl|CDD|184004 PRK13365, PRK13365, protocatechuate 4,5-dioxygenase subunit beta;
Provisional.
Length = 279
Score = 27.2 bits (60), Expect = 5.3
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 23 QAAGVGILLQIMMLVLSFILGHVLRR-HKFYYLPEASA 59
+ G + QIM L + LG +R+ H+ YYL +A
Sbjct: 232 RLGGAESVEQIMWLAMRGALGGPIRKLHQNYYLMTTTA 269
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 27.3 bits (61), Expect = 5.7
Identities = 21/131 (16%), Positives = 49/131 (37%), Gaps = 22/131 (16%)
Query: 10 PANDPHGSPAKEQQAAGVGILLQIMMLVLSFILGHVLRRHKFYYLPEASASLLIGLIVSA 69
P P+ + + + +L+ + ++ KF+ L L+G++V A
Sbjct: 378 PDKRPNAVKWRPKIQGSWSRDYLVAILICALATAIAIQLDKFFDLANIVMLFLLGVLVVA 437
Query: 70 LTNISNTETNIRYSFSFNELICSVATCLLMILF------SWQKPFFSNFGAIVTFAIFGT 123
+ T + + ++ + L+ F ++ S+ +VTFA+
Sbjct: 438 VL------TGRWPAV-----LAALLSVLVFNYFFTEPRYTFA---VSDPQYLVTFAVM-- 481
Query: 124 FLASMVTGILV 134
+++TG L
Sbjct: 482 LAVALLTGNLT 492
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and
TFIID) that are involved in accurate initiation of
transcription by RNA polymerase II in eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs to
show the relationship between TAF orthologs and
paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 26.9 bits (60), Expect = 6.2
Identities = 24/97 (24%), Positives = 41/97 (42%), Gaps = 17/97 (17%)
Query: 30 LLQIMMLVLSFILGHVLRRHKF----YYLPEASASLLIGLIVSALTNISNTETNIRYSFS 85
L Q++ VL+ ++ L + L + +A LL I ++S S
Sbjct: 256 LHQLIPSVLTCLVAKQLCSRPPDDNHWALRDYAARLL-AQICR------------KFSTS 302
Query: 86 FNELICSVATCLLMILFSWQKPFFSNFGAIVTFAIFG 122
+N L + LL L +KP +++GAIV + G
Sbjct: 303 YNTLQPRITRTLLKALLDPKKPLTTHYGAIVGLSALG 339
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 27.3 bits (61), Expect = 6.4
Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 17/93 (18%)
Query: 56 EASASLLIGLIVSALTNISNTET--NIRYSFSFNELICSVATCLLMILFSWQKPFFSNFG 113
E + L GL+ S ++ IS T ++ +F S M+
Sbjct: 163 ETTLDLSFGLLQSVISLISFTGILWSLSGGLAFTIGGFSFGIPGYMVW------------ 210
Query: 114 AIVTFAIFGTFLASMVTGILVYLGGVMFVMYRL 146
A++ +AI + L ++ L+ + F +L
Sbjct: 211 AVIIYAISASLLTHLIGRPLI---RLNFERQKL 240
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
0.331 0.143 0.428
Gapped
Lambda K H
0.267 0.0755 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,353,500
Number of extensions: 893322
Number of successful extensions: 2149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2080
Number of HSP's successfully gapped: 327
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 56 (25.3 bits)