RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14648
(154 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 = 75.6 bits (186), Expect = 1e-16
Identities = 38/139 (27%), Positives = 78/139 (56%), Gaps = 4/139 (2%)
Query: 2 VKYLARTY---SKTLVFLITGLAIFSFRHRVEPALVIWSLILCLVGRACNIFPLAILVNR 58
+KY + S+TL+F+ G+++ + H A V+ +L C++ R + L+ + N
Sbjct: 288 IKYFMKMLSSLSETLIFIFLGVSLVTENHEWNWAFVVATLSFCVIYRVLGVRTLSWITNE 347
Query: 59 FREHQITRRMMFIMWFSGLRGAISYALSLHL-EFSDETRHVIITSTLIIVLVTTLVFGGS 117
FR +I + +++++GLRGA+++AL+L L E + + +T+TL++V T + GG+
Sbjct: 348 FRPVEIPYKDQLVIFYAGLRGAVAFALALLLDEKIFPYKFLFVTTTLVVVFFTVIFQGGT 407
Query: 118 TMPLMKILQTSSNQKIGRR 136
PL+++L+ +
Sbjct: 408 IKPLVEVLKVKKGCISKTK 426
>gnl|CDD|223104 COG0025, NhaP, NhaP-type Na+/H+ and K+/H+ antiporters [Inorganic
ion transport and metabolism].
Length = 429
Score = 55.8 bits (135), Expect = 6e-10
Identities = 31/139 (22%), Positives = 59/139 (42%), Gaps = 3/139 (2%)
Query: 10 SKTLVFLITGLAI-FSFRHRVEPALVIWSLILCLVGRACNIFPLAILVNRFREHQITRRM 68
L+F++ G + S + ++ +L+ L+ R +F N + R
Sbjct: 287 LNGLLFVLLGAQLPLSLLLALGLLGLLVALVAVLLARPLWVFLSLKGSNLKLRDPLPWRE 346
Query: 69 MFIMWFSGLRGAIS--YALSLHLEFSDETRHVIITSTLIIVLVTTLVFGGSTMPLMKILQ 126
+ ++G RG +S AL + LE R +I+ +++L + LV G + PL K L+
Sbjct: 347 RLFLSWAGPRGVVSLALALLIPLELPGPARELILFIVFLVILFSLLVQGLTLPPLAKKLE 406
Query: 127 TSSNQKIGRRRRGRKGKTA 145
S + + G + A
Sbjct: 407 VSEESALAKEILGARRAQA 425
>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 = 38.2 bits (89), Expect = 8e-04
Identities = 37/145 (25%), Positives = 62/145 (42%), Gaps = 15/145 (10%)
Query: 13 LVFLITGLAIF--SFRHRVEPALVIWSLILCLVGRACNIFPLAILVNRFREHQITRRMMF 70
L+FL+ GL + PA+++ SL + V R +F + + FR ++ R +F
Sbjct: 280 LMFLVLGLLVTPSQLLPIAIPAILL-SLWMIFVARPLAVF---LGLIPFRFNR--REKLF 333
Query: 71 IMWFSGLRGAISYALS-LHLEFSDETRHVIITSTLIIVLVTTLVFGGSTMPLMKILQTSS 129
+ W GLRGA+ L+ + E + +VLV+ L+ G + K L+
Sbjct: 334 VSW-VGLRGAVPIILAIFPMMAGLENARLFFNVAFFVVLVSLLIQGSTLPWAAKKLKV-- 390
Query: 130 NQKIGRRRRGRKGKTAISLSKTKEW 154
I R G K + + T W
Sbjct: 391 ---IVPPRGGPVSKVGLDIHPTANW 412
>gnl|CDD|235410 PRK05326, PRK05326, potassium/proton antiporter; Reviewed.
Length = 562
Score = 35.9 bits (84), Expect = 0.005
Identities = 35/118 (29%), Positives = 56/118 (47%), Gaps = 23/118 (19%)
Query: 14 VFLITGLAIF--SFRHRVEPALVIWSLILCLVGRACNIFPLA--ILVNRFREHQITRRMM 69
+FL+ GL + PAL++ +L L LV R PLA + + FR + R +
Sbjct: 283 MFLVLGLLVTPSRLLDIALPALLL-ALFLILVAR-----PLAVFLSLLPFRFN--LREKL 334
Query: 70 FIMWFSGLRGAIS-----YALSLHLEFSDETRHVIITSTLIIVLVTTLVFGGSTMPLM 122
FI W GLRGA+ + + L + +V+ +VLV+ L+ G+T+P
Sbjct: 335 FISW-VGLRGAVPIVLATFPMMAGLPNAQLIFNVV----FFVVLVSLLL-QGTTLPWA 386
>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 = 32.6 bits (75), Expect = 0.069
Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 8/115 (6%)
Query: 2 VKYLARTYSKTLVFLITGLAI-FSFRHRVEPALVIWSLILCLVGRACNIFPLAILVNRFR 60
++ L F+ GL++ S LV+ L+ L+G+ +F LA L+
Sbjct: 257 LEPFGYGLFLPLFFVSVGLSLDLSSLLLSLLLLVLLLLVAILLGKLLGVFLLARLLG--- 313
Query: 61 EHQITRRMMFIMWFSGL-RGAISYALSLHLEFSDETRHVIITSTLIIVLVTTLVF 114
++ R I+ F GL RGA+S AL+ + T + +VL+TTL+
Sbjct: 314 ---LSLREALIVGFGGLQRGAVSLALAAIGLQLGLIDRELYTLLVAVVLLTTLLK 365
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 30.0 bits (68), Expect = 0.38
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 1/74 (1%)
Query: 53 AILVNRFREHQITRRMMFIMWFSGLRGAISYALSLHLEFSDETRHVIITSTLIIVLVTTL 112
+++ N E + M F S L I + E + ++ T+ +++ +
Sbjct: 128 SLISNDASEVAVNDLMAFFKRISSLNKVIILTANPK-ELDESVLTILRTAATMLIRLEVK 186
Query: 113 VFGGSTMPLMKILQ 126
VFGG KI++
Sbjct: 187 VFGGDLKNSAKIVK 200
>gnl|CDD|220240 pfam09435, DUF2015, Fungal protein of unknown function (DUF2015).
This is a fungal family of uncharacterized proteins.
Length = 124
Score = 26.5 bits (59), Expect = 3.3
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 2 VKYLARTYSKTLVFLITGLAIFSFRHRVEPAL 33
+ YL YS L L+ G A++ RHR P L
Sbjct: 1 MAYLL--YSLVLSVLVCGTALYLTRHRWLPLL 30
>gnl|CDD|225143 COG2234, Iap, Predicted aminopeptidases [General function
prediction only].
Length = 435
Score = 26.8 bits (59), Expect = 5.0
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 53 AILVN---RFREHQITRRMMFIMWFS---GLRGAISYALSLHLEFSDETRHVIIT 101
A L+ + + R + F+ + + GL G+ +Y L + + VI
Sbjct: 234 AALLELARVLKGNPPKRTVRFVAFGAEESGLLGSEAYVKRLSKDLDKKIALVINL 288
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 317
Score = 26.4 bits (59), Expect = 6.8
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 85 LSLHLEFSDETRHVI 99
+SLH ++ ET H+I
Sbjct: 203 VSLHAPYTPETHHLI 217
>gnl|CDD|225146 COG2237, COG2237, Predicted membrane protein [Function unknown].
Length = 364
Score = 26.5 bits (59), Expect = 7.2
Identities = 34/159 (21%), Positives = 59/159 (37%), Gaps = 22/159 (13%)
Query: 2 VKYLART---YSKT------LVFLITGL-AIFSFRHRVEPALVIWSLI-LCLVGRACNIF 50
+YL +T YS+T LV L+ G+ A+ + + + I ++ L ++ + +
Sbjct: 146 KRYLKKTDPEYSRTVLGPPGLVLLLYGILALANILYPAGAVIGILLIVGLYMLYKGFGLD 205
Query: 51 PL-AILVNRFREHQITRRMMFIMWF-SGLRGAISYALSLHLEFSDETRHVIITSTLIIVL 108
L A L+ R RE R+ FI + +GL + A SL + + L I
Sbjct: 206 DLVAELLERVREALYEGRVSFITYVVAGLLLILGGASSLTI-----ALSSSAGALLAIST 260
Query: 109 VTTLVFGGSTMPLMKILQTSSNQKIGRRRRGRKGKTAIS 147
ST + T+ G K +
Sbjct: 261 FILY----STWWFTLAILTTMVGIFFDLIIGGKVRIEYL 295
>gnl|CDD|240646 cd12169, PGDH_like_1, Putative D-3-Phosphoglycerate Dehydrogenases.
Phosphoglycerate dehydrogenases (PGDHs) catalyze the
initial step in the biosynthesis of L-serine from
D-3-phosphoglycerate. PGDHs come in 3 distinct
structural forms, with this first group being related to
2-hydroxy acid dehydrogenases, sharing structural
similarity to formate and glycerate dehydrogenases of
the D-specific 2-hydroxyacid dehydrogenase superfamily,
which also include groups such as L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase.
Despite often low sequence identity, these proteins
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann fold NAD+ binding
form. The NAD+ binding domain is inserted within the
linear sequence of the mostly N-terminal catalytic
domain, which has a similar domain structure to the
internal NAD binding domain. Structurally, these domains
are connected by extended alpha helices and create a
cleft in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. Many, not all,
members of this family are dimeric.
Length = 308
Score = 26.3 bits (59), Expect = 7.2
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 85 LSLHLEFSDETRHVI 99
+SLHL SD TR ++
Sbjct: 201 VSLHLVLSDRTRGLV 215
>gnl|CDD|211319 cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia
coli YciH. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. The function of non-eukaryotic family
members is unclear. Escherichia coli YciH is a
non-essential protein and was reported to be able to
perform some of the functions of IF3 in prokaryotic
initiation.
Length = 76
Score = 24.7 bits (55), Expect = 8.7
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 132 KIGRRRRGRKGKTAI 146
++ +RGR GKT
Sbjct: 4 RVRLEKRGRGGKTVT 18
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 0.140 0.419
Gapped
Lambda K H
0.267 0.0816 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,809,159
Number of extensions: 719846
Number of successful extensions: 1170
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1160
Number of HSP's successfully gapped: 82
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 55 (24.8 bits)