aquaporin 1, partial [Homo sapiens]

GenBank: BAG70216.1
LOCUS
BAG70216
269 aa
linear
PRI 02-SEP2008
DEFINITION aquaporin 1, partial [Homo sapiens].
FEATURES
Location/Qualifiers
source
1..269
/organism="Homo sapiens"
/db_xref="taxon:9606"
/clone="FLJ08105AAAF"
/note="Vector: pDONR201"
Protein
1..>269
/product="aquaporin 1"
Region
12..230
/region_name="MIP"
/note="Major intrinsic protein (MIP) superfamily.
Members
of the MIP superfamily function as membrane channels
that
selectively transport water, small neutral molecules,
and
ions out of and between cells. The channel proteins
share
a common fold: the N-terminal...; cd00333"
/db_xref="CDD:238204"
Site
order(56,74..76,188..189,192,195)
/site_type="other"
/note="amphipathic channel"
/db_xref="CDD:238204"
Site
order(76..78,192..194)
/site_type="other"
/note="Asn-Pro-Ala signature motifs"
/db_xref="CDD:238204"
CDS
1..269
/gene="AQP1"
/coded_by="AB451402.1:1..>807"
ORIGIN
1 masefkkklf wravvaefla ttlfvfisig salgfkypvg nnqtavqdnv kvslafglsi
61 atlaqsvghi sgahlnpavt lglllscqis ifralmyiia qcvgaivata ilsgitsslt
121 gnslgrndla dgvnsgqglg ieiigtlqlv lcvlattdrr rrdlggsapl aiglsvalgh
181 llaidytgcg inparsfgsa vithnfsnhw ifwvgpfigg alavliydfi laprssdltd
241 rvkvwtsgqv eeydldaddi nsrvemkpk

1.) Possible transmembrane helices

The sequence positions in brackets denominate the core region.
Only scores above 500 are considered significant.

Inside to outside helices :

6 found
from
to
score center
13 ( 17) 35 ( 33)
2078
25
55 ( 55) 75 ( 73)
1041
63
94 ( 96) 112 ( 112)
2086
104

138 ( 138) 154 ( 154)

164 ( 164) 184 ( 182)
210 ( 210) 227 ( 227)
Outside to inside
from
13 ( 13) 33 (
94 ( 97) 121 (
139 ( 139) 157 (
164 ( 164) 184 (
210 ( 210) 230 (

671
1463
2032

146
174
219

helices :
5 found
to
score center
33)
1876
23
115)
1648
106
155)
1212
147
182)
1368
174
230)
2402
220

2.) Table of correspondences

Here is shown, which of the inside->outside helices correspond to which of the outside->inside helices.

Helices shown in brackets are considered insignificant.

A "+"-symbol indicates a preference of this orientation.
A "++"-symbol indicates a strong preference of this orientation.

135594138164210-

inside->outside
(23) 2078 ++
(21) 1041 ++
(19) 2086 ++
(17) 671
(21) 1463 +
(18) 2032

35
75
112
154
184
227

| outside->inside
|
13- 33 (21) 1876
|
|
94- 121 (28) 1648
|
139- 157 (19) 1212 ++
|
164- 184 (21) 1368
|
210- 230 (21) 2402 ++

3.) Suggested models for transmembrane topology

These suggestions are purely speculative and should be used with extreme caution since they are based on the
assumption that all transmembrane helices have been found.
In most cases, the Correspondence Table shown above or the prediction plot that is also created should be used
for the topology assignment of unknown proteins.

2 possible models considered, only significant TM-segments used

*** the models differ in the number of TM-helices ! ***
-----> STRONGLY prefered model: N-terminus outside
6 strong transmembrane helices, total score : 8636
# from
to length score orientation
1
13
33 (21)
1876 o-i
2
55
75 (21)
1041 i-o
3
94 121 (28)
1648 o-i
4 138 154 (17)
671 i-o
5 164 184 (21)
1368 o-i
6 210 227 (18)
2032 i-o
------> alternative model
5 strong transmembrane helices, total score : 7797
# from
to length score orientation
1
13
35 (23)
2078 i-o
2
94 121 (28)
1648 o-i
3 138 154 (17)
671 i-o
4 164 184 (21)
1368 o-i
5 210 227 (18)
2032 i-o