RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1500
(80 letters)
>gnl|CDD|215807 pfam00230, MIP, Major intrinsic protein. MIP (Major Intrinsic
Protein) family proteins exhibit essentially two
distinct types of channel properties: (1) specific water
transport by the aquaporins, and (2) small neutral
solutes transport, such as glycerol by the glycerol
facilitators.
Length = 218
Score = 49.2 bits (118), Expect = 9e-09
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 1/71 (1%)
Query: 10 ALTPADFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIFGVCDGNKPHAKAP-AALAI 68
+T + +L + Q +E L F LV +F D + + A LAI
Sbjct: 104 GVTNGLQRAGGFANSLAPGVNAGQAFVVEIILTFQLVYTVFATTDDPRNGSLGHVAPLAI 163
Query: 69 GLTVALGHLAA 79
G V L HLA
Sbjct: 164 GFAVFLNHLAG 174
>gnl|CDD|238204 cd00333, MIP, 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 cytosolic portion
followed by six transmembrane helices, which might have
arisen through gene duplication. On the basis of
sequence similarity and functional characteristics, the
superfamily can be subdivided into two major groups:
water-selective channels called aquaporins (AQPs) and
glycerol uptake facilitators (GlpFs). AQPs are found in
all three kingdoms of life, while GlpFs have been
characterized only within microorganisms.
Length = 228
Score = 46.9 bits (112), Expect = 6e-08
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 9 QALTPADFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIFGVCD-GNKPHAKAPAALA 67
+ L + + T + ++ +EF F+LVLV+F D N P A LA
Sbjct: 107 EFLGANNIVAGIFGTYPSPGVSNGNAFFVEFIGTFILVLVVFATTDDPNGPPPGGLAPLA 166
Query: 68 IGLTVALGHLA 78
IGL VA LA
Sbjct: 167 IGLLVAAIGLA 177
>gnl|CDD|233156 TIGR00861, MIP, MIP family channel proteins. 1.A.8 The Major
Intrinsic Protein (MIP) FamilyThe MIP family is large
and diverse, possessing over 100 members that all form
transmembrane channels. These channel proteins function
in water, smallcarbohydrate (e.g., glycerol), urea, NH3,
CO2 and possibly ion transport by an energy independent
mechanism. They are found ubiquitously in bacteria,
archaeaand eukaryotes. The MIP family contains two major
groups of channels: aquaporins and glycerol
facilitators.The known aquaporins cluster loosely
together as do the known glycerol facilitators. MIP
family proteins are believed to form aqueous pores that
selectively allow passive transport of their solute(s)
across the membrane with minimal apparent recognition.
Aquaporins selectively transport water (but not
glycerol) while glycerol facilitators selectively
transport glycerol but not water. Some aquaporins can
transport NH3 and CO2. Glycerol facilitators function as
solute nonspecific channels, and may transport glycerol,
dihydroxyacetone, propanediol, urea and other small
neutral molecules in physiologically importantprocesses.
Some members of the family, including the yeast FPS
protein (TC #1.A.8.5.1) and tobacco NtTIPA may transport
both water and small solutes [Transport and binding
proteins, Unknown substrate].
Length = 216
Score = 43.1 bits (102), Expect = 2e-06
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 2/72 (2%)
Query: 10 ALTPADFQGNLGLTTLNKH-LTPVQGMGIEFFLGFVLVLVIFGVCDGNKPHAKAP-AALA 67
LT F GNL + ++ Q +EF +LVLVIF D + A LA
Sbjct: 99 GLTSGLFPGNLAVNGSASAGVSSGQAFFVEFIGTAILVLVIFATTDDRNRVPRGGFAPLA 158
Query: 68 IGLTVALGHLAA 79
IGL V L HL+
Sbjct: 159 IGLLVFLIHLSM 170
>gnl|CDD|223653 COG0580, GlpF, Glycerol uptake facilitator and related permeases
(Major Intrinsic Protein Family) [Carbohydrate transport
and metabolism].
Length = 241
Score = 36.4 bits (85), Expect = 4e-04
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 22 LTTLNKHLTPVQGMGIEFFLGFVLVLVIFGVCDGNKPHAKAPAALAIGLTVALGHLA 78
+T + Q IEF FVLVL I + D +A A LAIGL V L+
Sbjct: 126 FSTSPGGYSLGQAFLIEFVGTFVLVLGILALTDDGNANAGF-APLAIGLLVTAIGLS 181
>gnl|CDD|177778 PLN00184, PLN00184, aquaporin NIP1; Provisional.
Length = 296
Score = 28.4 bits (63), Expect = 0.27
Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 32 VQGMGIEFFLGFVLVLVIFGVCDGNKPHAKAPAALAIGLTVALGHLAA 79
+Q +EF + F L+ +I GV N+ + A LAIG TV L L A
Sbjct: 178 LQAFVMEFIVTFYLMFIISGVATDNRAIGEL-AGLAIGSTVLLNVLIA 224
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 27.3 bits (61), Expect = 0.62
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 5 FSNSQ----ALTPADFQGNLGLTTLNKHLTPVQG 34
+N Q A+TPA+ +LGLT++ H +QG
Sbjct: 122 LANKQDLKGAMTPAEISESLGLTSIRDHTWHIQG 155
>gnl|CDD|235453 PRK05420, PRK05420, aquaporin Z; Provisional.
Length = 231
Score = 26.9 bits (60), Expect = 1.0
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 37 IEFFLGFVLVLVIFGVCDGNKPHAKAPAALAIGLTVALGHL 77
E L +LVI G D P AP A+ + LT L HL
Sbjct: 137 CEVVLTAFFLLVILGATDKRAPAGFAPIAIGLALT--LIHL 175
>gnl|CDD|187745 cd09223, Photo_RC, D1, D2 subunits of photosystem II (PSII); M, L
subunits of bacterial photosynthetic reaction center.
This protein superfamily contains the D1, D2 subunits of
the photosystem II (PS II) and the M, L subunits of the
bacterial photosynthetic reaction center (RC). These
four proteins are highly homologous and share a common
fold. PS II is a multi-subunit protein found in the
photosynthetic membranes of plants, algae, and
cyanobacteria. It utilizes light-induced electron
transfer and water-splitting reactions to produce
protons, electrons, and molecular oxygen. The protons
generated are instrumental in ATP formation. Bacterial
photosynthetic reaction center (RC) complex is found in
photosynthetic bacteria, such as purple bacteria and
other proteobacteria species. It couples light-induced
electron transfer to proton pumping across the membrane
by reactions of a quinone molecule (QB) that binds two
electrons and two protons at the active site. Protons
are translocated from the bacterial cytoplasm to the
periplasmic space, generating an electrochemical
gradient of protons (the protonmotive force) that can be
used to power reactions such as the synthesis of ATP.
Length = 199
Score = 26.6 bits (59), Expect = 1.3
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 15 DFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIFG 51
D+ N N H P +G+ F G L+ + G
Sbjct: 96 DWVNNFQYEHNNWHYNPFHMLGVAFVFGGALLCAMHG 132
>gnl|CDD|220620 pfam10183, ESSS, ESSS subunit of NADH:ubiquinone oxidoreductase
(complex I). This subunit is part of the mitochondrial
NADH:ubiquinone oxidoreductase (complex I). It carries
mitochondrial import sequences.
Length = 101
Score = 25.9 bits (57), Expect = 1.4
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 32 VQGMGIEFFLGFVLVLVIFGVCDGNKP 58
+ + F+ GF L LVI GV KP
Sbjct: 55 WEDWELPFYFGFFLTLVILGVGLNYKP 81
>gnl|CDD|240230 PTZ00016, PTZ00016, aquaglyceroporin; Provisional.
Length = 294
Score = 25.9 bits (57), Expect = 2.3
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 38 EFFLGFVLVLVIFGVCDGNKPHAKAPAALAIGLTV 72
E L +L+LVI + D N A +A+GL V
Sbjct: 190 ELILTAILLLVILAITDPNNCPAFNYLPVAVGLLV 224
>gnl|CDD|215133 PLN02241, PLN02241, glucose-1-phosphate adenylyltransferase.
Length = 436
Score = 25.6 bits (57), Expect = 3.0
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 23 TTLNKHLTPV--QGMGIEFFLGFVLVL 47
+LN+HL+ G G F GFV VL
Sbjct: 62 ASLNRHLSRAYNFGNGGNFGDGFVEVL 88
>gnl|CDD|215734 pfam00124, Photo_RC, Photosynthetic reaction centre protein.
Length = 257
Score = 24.9 bits (55), Expect = 4.6
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 15 DFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIFG 51
D+ N N H P +GI F G L+L + G
Sbjct: 134 DWTSNFSYRYGNFHYNPFHMLGIAFLFGSALLLAMHG 170
>gnl|CDD|165748 PLN00182, PLN00182, putative aquaporin NIP4; Provisional.
Length = 283
Score = 24.9 bits (54), Expect = 4.9
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 30 TPVQGMGIEFFLGFVLVLVIFGVCDGNKPHAKAPAALAIGLTVALGHLAA 79
+ Q + E + F+L+ VI GV ++ + A +A+G+T+ L A
Sbjct: 157 SSGQALVAEIIISFLLMFVISGVATDSRAVGEL-AGIAVGMTIILNVFVA 205
>gnl|CDD|130225 TIGR01157, pufL, photosynthetic reaction center L subunit. This
model describes the photosynthetic reaction center L
subunit in non-oxygenic photosynthetic bacteria.
Reaction center is an integral membrane pigment-protein
that carries out light-driven electron transfer
reactions. At the core of reaction center is a
collection light-harvesting cofactors and closely
associated polypeptides. The core protein complex is
made of L, M and H subunits. The common cofactors
include bacterichlorophyll, bacteriopheophytins,
ubiquinone and no-heme ferrous iron. The net result of
electron tranfer reactions is the establishment of
proton electrochemical gradient and production of
reducing equivalents in form of NADH. Ultimately the
process results in the reduction of C02 to
carbohydrates(C6H12O6) In non-oxygenic organisms, the
electron donor is some organic acid and not water. Much
of our current functional understanding of
photosynthesis comes from the structural determination,
spectroscopic studies and mutational analysis on the
reaction center of Rhodobacter sphaeroides [Energy
metabolism, Electron transport, Energy metabolism,
Photosynthesis].
Length = 239
Score = 24.8 bits (54), Expect = 5.5
Identities = 13/40 (32%), Positives = 16/40 (40%)
Query: 12 TPADFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIFG 51
T D+ N G N H P + I FF L L + G
Sbjct: 119 THLDWVSNTGYQYGNFHYNPAHMIAISFFFTNALALALHG 158
>gnl|CDD|226999 COG4652, COG4652, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 657
Score = 24.7 bits (54), Expect = 5.7
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 3/46 (6%)
Query: 7 NSQALTP--ADFQGNLGLTTLNKHLTPVQGMGIEFFLGFVLVLVIF 50
LTP + F LT ++ GI+ GF L+ +IF
Sbjct: 156 TPLILTPLASLFLPFFYLTIFDRIKNLRAA-GIKLLAGFTLLWIIF 200
>gnl|CDD|215237 PLN02433, PLN02433, uroporphyrinogen decarboxylase.
Length = 345
Score = 24.9 bits (55), Expect = 5.8
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 29 LTPVQGMGIEF 39
LTP+ MGI F
Sbjct: 71 LTPLPAMGIPF 81
>gnl|CDD|185117 PRK15195, PRK15195, fimbrial chaperone protein FimC; Provisional.
Length = 229
Score = 24.8 bits (54), Expect = 6.3
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 6 SNSQALTPADFQGNLGLTTLNKH--LTPVQ 33
NSQ P+ QG L T+N + +TP +
Sbjct: 196 VNSQIPLPSGVQGKLKFQTVNDYGAVTPAR 225
>gnl|CDD|145544 pfam02461, AMO, Ammonia monooxygenase. Ammonia monooxygenase plays
a key role in the nitrogen cycle and degrades a wide
range of hydrocarbons and halogenated hydrocarbons.
Length = 245
Score = 24.3 bits (53), Expect = 8.7
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 22 LTTLNKHLTPVQGMGIEFFLGFVLVLVIF 50
L T K + PV FF GFV +LV F
Sbjct: 204 LRTFGKDVVPVAA----FFSGFVSMLVYF 228
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 0.426
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,131,971
Number of extensions: 339997
Number of successful extensions: 584
Number of sequences better than 10.0: 1
Number of HSP's gapped: 577
Number of HSP's successfully gapped: 44
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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 (21.6 bits)
S2: 53 (24.1 bits)