RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030915
(169 letters)
>gnl|CDD|235586 PRK05738, rplW, 50S ribosomal protein L23; Reviewed.
Length = 92
Score = 68.6 bits (169), Expect = 6e-16
Identities = 25/59 (42%), Positives = 37/59 (62%)
Query: 31 IALKTIPSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLK 89
+ P A+K EIK +E L+G +V+ V TLN++GK K+ G + + D+KKA VTL
Sbjct: 23 YVFEVAPDATKPEIKAAVEKLFGVKVESVNTLNVKGKTKRFGRRIGKRSDWKKAIVTLA 81
>gnl|CDD|223167 COG0089, RplW, Ribosomal protein L23 [Translation, ribosomal
structure and biogenesis].
Length = 94
Score = 60.3 bits (147), Expect = 1e-12
Identities = 30/54 (55%), Positives = 37/54 (68%), Gaps = 1/54 (1%)
Query: 37 PSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAK-PDYKKAYVTLK 89
P A+K EIK +E L+G +V+KV TLN +GK K+ G I DYKKAYVTLK
Sbjct: 30 PDATKPEIKAAVEELFGVKVEKVNTLNTKGKTKRAGVKRIGLRKDYKKAYVTLK 83
>gnl|CDD|144021 pfam00276, Ribosomal_L23, Ribosomal protein L23.
Length = 90
Score = 51.2 bits (123), Expect = 3e-09
Identities = 25/55 (45%), Positives = 34/55 (61%)
Query: 37 PSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNP 91
A+K EIK +E ++G +V+KV TL + GK K+ G L K YKKA VTL+
Sbjct: 28 KKANKTEIKDAVEHIFGVKVEKVNTLILPGKVKRNGQYLGRKKSYKKAIVTLEEG 82
>gnl|CDD|176971 CHL00030, rpl23, ribosomal protein L23.
Length = 93
Score = 44.5 bits (106), Expect = 9e-07
Identities = 16/52 (30%), Positives = 30/52 (57%)
Query: 39 ASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKN 90
++K EIK +E +G +V V + + KK++ G ++ K YK+ +TL+
Sbjct: 30 STKTEIKHWIELFFGVKVIAVNSHRLPRKKRRMGPIMGHKMHYKRMIITLQP 81
>gnl|CDD|237750 PRK14548, PRK14548, 50S ribosomal protein L23P; Provisional.
Length = 84
Score = 42.2 bits (100), Expect = 6e-06
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 26/81 (32%)
Query: 28 ITEIALKTI-----------PSASKIEIKRVLESLYGFEVDKVRTL-NMEGKKKKRGGLL 75
+TE A+ I A+K +IKR +E L+ +V+KV TL +G+
Sbjct: 10 VTEKAMNLIEKENKLTFIVDRRATKPDIKRAVEELFDVKVEKVNTLITPKGE-------- 61
Query: 76 IAKPDYKKAYVTLKNPLSLSE 96
KKAYV L E
Sbjct: 62 ------KKAYVKLAEEYDAEE 76
>gnl|CDD|132675 TIGR03636, L23_arch, archaeal ribosomal protein L23. This model
describes the archaeal ribosomal protein L23P and
rigorously excludes the bacterial counterpart L23. In
order to capture every known instance of archaeal L23P,
the trusted cutoff is set lower than a few of the
highest scoring eukaryotic cytosolic ribosomal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 77
Score = 41.8 bits (99), Expect = 6e-06
Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 13/59 (22%)
Query: 38 SASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNPLSLSE 96
A+K +IKR +E L+ +V+KV T LI KKAYV L + E
Sbjct: 24 KATKGDIKRAVEKLFDVKVEKVNT-------------LITPRGEKKAYVKLAEEYAAEE 69
>gnl|CDD|237035 PRK12280, rplW, 50S ribosomal protein L23; Reviewed.
Length = 158
Score = 40.1 bits (94), Expect = 1e-04
Identities = 32/89 (35%), Positives = 48/89 (53%), Gaps = 3/89 (3%)
Query: 37 PSASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNPLSLSE 96
A+KIEIK+ +E ++ +V KV N++ K K+ G YKKAYVTL S++
Sbjct: 31 RRANKIEIKKAVEFIFKVKVLKVNIFNVDKKPKRLGRFPGFTNSYKKAYVTLAEGYSIN- 89
Query: 97 DLFPIRVIQDEKERMRKEKESSIVEEGKK 125
LFP + E++ + KE E + KK
Sbjct: 90 -LFP-EESEKEQKEVSKETEEKEAIKAKK 116
>gnl|CDD|185507 PTZ00191, PTZ00191, 60S ribosomal protein L23a; Provisional.
Length = 145
Score = 32.7 bits (75), Expect = 0.038
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 39 ASKIEIKRVLESLYGFEVDKVRTLNMEGKKKK 70
A+K +IK+ +E LY +V KV TL KK
Sbjct: 93 ANKTQIKKAVEKLYDVKVVKVNTLITPDGLKK 124
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 30.6 bits (69), Expect = 0.49
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 39 ASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAK--PDYKKAYVTLKNPLSLSE 96
AS +EI LE L+ L+ + +K + + Y K YVT+ +P+ E
Sbjct: 1037 ASALEISNGLEKLFARLGHPYSPLSGDALRKITPQTIAEELLTHYTKGYVTITSPIPKEE 1096
Query: 97 DLF 99
DLF
Sbjct: 1097 DLF 1099
>gnl|CDD|212044 cd11474, SLC5sbd_CHT, Na(+)- and Cl(-)-dependent choline
cotransporter CHT and related proteins; solute-binding
domain. Na+/choline co-transport by CHT is Cl-
dependent. Human CHT (also called CHT1) is encoded by
the SLC5A7 gene, and is expressed in the central
nervous system. hCHT1-mediated choline uptake may be
the rate-limiting step in acetylcholine synthesis, and
essential for cholinergic transmission. Changes in this
choline uptake in cortical neurons may contribute to
Alzheimer's dementia. This subfamily belongs to the
solute carrier 5 (SLC5) transporter family.
Length = 464
Score = 28.6 bits (65), Expect = 1.4
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 72 GGLLIAKPDYKKAYVTL 88
GGL AKP + +TL
Sbjct: 83 GGLFFAKPMRRMGLLTL 99
>gnl|CDD|187737 cd09616, Peptidase_C12_UCH_L1_L3, Cysteine peptidase C12 containing
ubiquitin carboxyl-terminal hydrolase (UCH) families L1
and L3. This ubiquitin C-terminal hydrolase (UCH)
family includes UCH-L1 and UCH-L3, the two members
sharing around 53% sequence identity as well as
conserved catalytic residues. Both enzymes hydrolyze
carboxyl terminal esters and amides of ubiquitin (Ub).
UCH-L1, in dimeric form, has additional enzymatic
activity as a ubiquitin ligase. It is highly abundant in
the brain, constituting up to 2% of total protein, and
is expressed exclusively in neurons and testes. Abnormal
expression of UCH-L1 has been shown to correlate with
several forms of cancer, including several primary lung
tumors, lung tumor cell lines, and colorectal cancers.
Mutations in the UCH-L1 gene have been linked to
susceptibility to and protection from Parkinson's
disease (PD); dysfunction of the hydrolase activity can
lead to an accumulation of alpha-synuclein, which is
linked to Parkinson's disease (PD), while accumulation
of neurofibrillary tangles is linked to Alzheimer's
disease (AD). UCH-L3 hydrolyzes isopeptide bonds at the
C-terminal glycine of either Ub or Nedd8, a
ubiquitin-like protein. It can also interact with
Lys48-linked Ub dimers to protect them from degradation
while inhibiting its hydrolase activity at the same
time. Unlike UCH-L1, neither dimerization nor ligase
activity have been observed for UCH-L3. It has been
shown that levels of Nedd8 and the apoptotic protein p53
and Bax are elevated in UCH-L3 knockout mice upon
cryptorchid injury, possibly contributing to profound
germ cell loss via apoptosis.
Length = 222
Score = 26.8 bits (60), Expect = 5.1
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 22/69 (31%)
Query: 98 LFPIRVIQDEKERMRKEKESSIVEEGKKH-----WLDGKQVVK------------GNNNE 140
LFPI E RKE+E I E+G++ ++ KQ + NN +
Sbjct: 50 LFPI---TKAYEEFRKEEEEEIKEKGQEVSESVYFM--KQTIGNACGTIALIHAVANNED 104
Query: 141 RSNKKKGGF 149
R N +G F
Sbjct: 105 RINILEGSF 113
>gnl|CDD|237255 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 27.0 bits (60), Expect = 6.4
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 8/84 (9%)
Query: 43 EIKRVLESLYGFEVDKVRTLNMEGKKKKRGGLLIAKPDYKKAYVTLKNP-LSLSEDLFPI 101
I + SL D +R ME K + RG L + K L NP +SL E
Sbjct: 26 RINEIQASLASLSDDALREKGMELKSRVRGALEPIEQKKKDLEKKLDNPDISLEE----A 81
Query: 102 RVIQDEKERMRKEKE---SSIVEE 122
I +E + + KE E ++ +EE
Sbjct: 82 ESINEELDTLAKEYEEATAAALEE 105
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 26.8 bits (59), Expect = 6.9
Identities = 19/61 (31%), Positives = 25/61 (40%), Gaps = 17/61 (27%)
Query: 85 YVTLKNPLSLSEDLFPIRVIQDEKERMRKEKESSIVEEGKKHWLDGKQVVKGNNNERSNK 144
YV KNP EDL+P ++ D + R W+DGK N +R N
Sbjct: 345 YVPRKNPTKFQEDLYPPILMHDPERSSRN-------------WIDGKD----NKMKRINI 387
Query: 145 K 145
K
Sbjct: 388 K 388
>gnl|CDD|227391 COG5058, LAG1, Protein transporter of the TRAM (translocating
chain-associating membrane) superfamily, longevity
assurance factor [Intracellular trafficking and
secretion].
Length = 395
Score = 26.7 bits (59), Expect = 7.1
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 24/82 (29%)
Query: 22 PNTFQNITEIALKTIPS--------ASKIEIKRVLESLYGFEVDKVRTLNMEGKKKKRGG 73
+I +I L T+PS +SK+ KR ++ L GF K
Sbjct: 11 HRRSSSIGKIDLGTVPSLSTMPESISSKVPAKRRMKDLSGF-------------VAKDSW 57
Query: 74 LLIAKPDYKKAYVTLKNPLSLS 95
+ +P Y+ ++ PL L
Sbjct: 58 FSVREPSYRHVWIK---PLCLL 76
>gnl|CDD|182594 PRK10622, pheA, bifunctional chorismate mutase/prephenate
dehydratase; Provisional.
Length = 386
Score = 26.2 bits (58), Expect = 9.2
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 100 PIRVIQDEKERMRKEKESSIVEEGKKHWLDG 130
P+R + +R R + ++ GK H LD
Sbjct: 45 PVR----DIDRER-DLLERLITLGKAHHLDA 70
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
0.314 0.133 0.373
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,459,516
Number of extensions: 772974
Number of successful extensions: 577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 573
Number of HSP's successfully gapped: 31
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.9 bits)