RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1864
(232 letters)
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 139 bits (352), Expect = 8e-39
Identities = 50/106 (47%), Positives = 68/106 (64%), Gaps = 3/106 (2%)
Query: 128 NLTYWSTISLTLSCPMNLKLYPLDRQSCSLKMASYGWTTDDLIFLWKEGDPVQVVKNL-- 185
++ Y I+LTL+CPM+L+ +P D Q+CSLK S+G+TT+D+ WKE VQV +L
Sbjct: 143 SVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAVQVDDSLFI 202
Query: 186 HLPRFTLEKFY-TDYCNSKTNTGAYSCLKVDLLFKREFSYYLIQIY 230
LP F L Y T YC S+TNTG Y CL + +R YYL+Q+Y
Sbjct: 203 SLPEFELLGVYGTRYCTSETNTGEYPCLTFSFVLRRRPLYYLLQLY 248
Score = 106 bits (267), Expect = 7e-27
Identities = 34/74 (45%), Positives = 47/74 (63%)
Query: 1 EYSVQLTFREQWLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNV 60
+Y+ + R++W DERL++N + L T +W+PD+FF NEK+ FH I M NV
Sbjct: 75 DYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNV 134
Query: 61 YIRIHPQGSVLYSI 74
+RIHP GSVLYS
Sbjct: 135 LVRIHPNGSVLYSP 148
Score = 50.9 bits (122), Expect = 1e-07
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 22/99 (22%)
Query: 54 NIIMPNVYIRIHPQGSVLYSISDLDNMRQCEVHMTVPQTPR--------------KNCCR 99
+ + +V +R G L S ++ RQ +H P + R
Sbjct: 364 HASLSSVEMRAKDGGRGLESPTE----RQRLLHSPPPAEGDLDLAGILEEVRIAHRFRKR 419
Query: 100 SWLAKFP----TRSKRIDVISRITFPLVFALFNLTYWST 134
+ R+K ID +SR+ FPL F LFN+ YW +
Sbjct: 420 DESEEVVRDWKFRAKVIDKLSRMAFPLAFLLFNIGYWMS 458
>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
binding domain. This family is the extracellular ligand
binding domain of these ion channels. This domain forms
a pentameric arrangement in the known structure.
Length = 215
Score = 98.1 bits (245), Expect = 3e-25
Identities = 54/228 (23%), Positives = 87/228 (38%), Gaps = 74/228 (32%)
Query: 1 EYSVQLTFREQWLDERLKYN--DYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMP 58
+ + + R+QW DERL ++ DY G I L L ++W PD+ N K H+I P
Sbjct: 46 DLTTNVWLRQQWTDERLAWDPEDYGG-ITSLRLPS-DKIWKPDIVLYN-KADGIHDITTP 102
Query: 59 NVYIRIHPQGSVLYSISDLDNMRQCEVHMTVPQTPRKNCCRSWLAKFPTRSKRIDVISRI 118
N +R++P G+VL+S
Sbjct: 103 NTNVRVYPDGTVLWSP-------------------------------------------- 118
Query: 119 TFPLVFALF---NLTYWSTISLTLSCPMNLKLYPLDRQSCSLKMASYGWTTDDLIFLWKE 175
P ++ +LTY+ P D+Q+CSLK S+ + +++ WK+
Sbjct: 119 --PAIYKSSCPMDLTYF---------PF-------DQQNCSLKFGSWTYNGEEVDLRWKD 160
Query: 176 GDPVQVVKNLHLPRFTLEKFYT-DYCNSKTN---TGAYSCLKVDLLFK 219
P + + + L FT + +K N G YS L D+ F
Sbjct: 161 DTPPILDEEIDLSDFTENGEWDIVDVPAKRNEYPYGCYSELYPDVTFY 208
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 38.4 bits (90), Expect = 0.001
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 110 KRIDVISRITFPLVFALFNLTYW 132
ID +SR FP+ F L L YW
Sbjct: 206 MVIDRLSRWIFPIAFVLGTLVYW 228
>gnl|CDD|135442 PRK05569, PRK05569, flavodoxin; Provisional.
Length = 141
Score = 34.0 bits (78), Expect = 0.021
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 144 NLKLYPLDRQSCSLKMASYGWTTDDLIFLWKE 175
KL P + + C L SYGW + + LWK+
Sbjct: 75 QFKLTPNENKKCIL-FGSYGWDNGEFMKLWKD 105
>gnl|CDD|236376 PRK09084, PRK09084, aspartate kinase III; Validated.
Length = 448
Score = 31.7 bits (73), Expect = 0.28
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 157 LKMASYGWTTDDLIFLWKEGDPVQVVKNLH 186
++M YG ++ +L FL E D QVV+ LH
Sbjct: 413 IRMICYGASSHNLCFLVPESDAEQVVQALH 442
>gnl|CDD|153189 cd04917, ACT_AKiii-LysC-EC_2, ACT domains located C-terminal to the
catalytic domain of the lysine-sensitive aspartokinase
isoenzyme AKIII. This CD includes the second of two ACT
domains located C-terminal to the catalytic domain of
the lysine-sensitive aspartokinase isoenzyme AKIII, a
monofunctional class enzyme found in bacteria
(Escherichia coli (EC) LysC). Aspartokinase is the first
enzyme in the aspartate metabolic pathway and catalyzes
the conversion of aspartate and ATP to aspartylphosphate
and ADP. The E. coli AKIII (LysC) binds two feedback
allosteric inhibitor lysine molecules at the dimer
interface located between the ACT1 domain of two
subunits. The second ACT domain (ACT2), this CD, is not
involved in the binding of heterotrophic effectors.
Members of this CD belong to the superfamily of ACT
regulatory domains.
Length = 64
Score = 29.1 bits (66), Expect = 0.32
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 157 LKMASYGWTTDDLIFLWKEGDPVQVVKNLH 186
++M YG + +L FL KE D +VV+ LH
Sbjct: 30 VRMICYGASNHNLCFLVKEEDKDEVVQRLH 59
>gnl|CDD|237780 PRK14659, acpS, 4'-phosphopantetheinyl transferase; Provisional.
Length = 122
Score = 27.0 bits (60), Expect = 5.0
Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 8 FREQWLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNVYIRIHPQ 67
F E+ +++ LKY + R ++ A R + + G I M ++ +
Sbjct: 31 FSEKEIEDSLKYTSQEARARHF----AKRFAAKEAYVKALGTGFGRGIKMKDISVYNDLY 86
Query: 68 GSVLYSIS 75
G ++S
Sbjct: 87 GKPQITVS 94
>gnl|CDD|173174 PRK14711, ureE, urease accessory protein UreE; Provisional.
Length = 191
Score = 27.3 bits (60), Expect = 6.5
Identities = 11/21 (52%), Positives = 12/21 (57%)
Query: 167 DDLIFLWKEGDPVQVVKNLHL 187
D I LW EGD VV +HL
Sbjct: 62 DGDILLWNEGDKCAVVARVHL 82
>gnl|CDD|237937 PRK15304, PRK15304, putative fimbrial outer membrane usher protein;
Provisional.
Length = 801
Score = 27.0 bits (60), Expect = 9.9
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 67 QGSVLYSISDLDNMRQCEVHMTVPQTPRKN 96
LY+ D D R C +H T+P+ K
Sbjct: 762 DIPALYAKDD-DMNRLCRIHYTLPEDQDKE 790
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
0.325 0.139 0.449
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,848,683
Number of extensions: 1071825
Number of successful extensions: 1111
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1108
Number of HSP's successfully gapped: 21
Length of query: 232
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 138
Effective length of database: 6,768,326
Effective search space: 934028988
Effective search space used: 934028988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.6 bits)