RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8288
(177 letters)
>gnl|CDD|193593 cd09979, LOTUS_3_Limkain_b1, The third LOTUS domain on Limkain
b1(LKAP). The third LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 72
Score = 33.6 bits (77), Expect = 0.006
Identities = 23/78 (29%), Positives = 36/78 (46%), Gaps = 14/78 (17%)
Query: 85 FSQRKIDTLLAKKKDLMKKFRDMLGDNGVFLFPTFINSAHYHYQIHYKFLNYGYVGLFNL 144
FS+ ID L ++ L+ F FI + H+H+ + +YGY L L
Sbjct: 4 FSREVIDLLKSQPSCLLP-------------FSRFIPAYHHHFGKQCRVSDYGYTKLIEL 50
Query: 145 LE-MPVTNVTVGLGSNKL 161
LE +P +G+GS +L
Sbjct: 51 LEAVPHVLQILGMGSKRL 68
>gnl|CDD|216494 pfam01425, Amidase, Amidase.
Length = 431
Score = 33.8 bits (78), Expect = 0.037
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 7/75 (9%)
Query: 100 LMKKFRDMLGDNGVFLFPTF------INSAHYHYQIHYKFLNY-GYVGLFNLLEMPVTNV 152
L ++F + + V L PT + A + Y L++ NL +P ++
Sbjct: 346 LRREFAGLFEELDVLLSPTTPTPAPRLGEAADSPTVLYNLLDFTANTVPANLAGLPAISL 405
Query: 153 TVGLGSNKLPVGFQV 167
G + LPVG Q+
Sbjct: 406 PAGFSEDGLPVGLQI 420
>gnl|CDD|180437 PRK06169, PRK06169, putative amidase; Provisional.
Length = 466
Score = 31.5 bits (72), Expect = 0.21
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 142 FNLLEMPVTNVTVGLGSNKLPVGFQV 167
FNL + P +V G + LPVG Q+
Sbjct: 410 FNLTQQPAASVPCGFTAAGLPVGLQI 435
>gnl|CDD|235698 PRK06102, PRK06102, hypothetical protein; Provisional.
Length = 452
Score = 30.0 bits (68), Expect = 0.69
Identities = 21/90 (23%), Positives = 34/90 (37%), Gaps = 19/90 (21%)
Query: 92 TLLAKKKDLMKKFRDMLGDNGVFLFPTFINSAH-------------YHYQIHYKFLNYGY 138
LL ++ L+ + LG + PT AH + + K L
Sbjct: 346 ALLEARERLIAQVTRELGGA-LLATPTV---AHVAPPLAPLEADDDLFFATNLKTLRNTM 401
Query: 139 VGLFNLLEMPVTNVTVGLGSNKLPVGFQVS 168
G N L+M ++ G G+ +PVG +S
Sbjct: 402 PG--NFLDMCGVSLPCGTGAAGMPVGLLLS 429
>gnl|CDD|223232 COG0154, GatA, Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit
and related amidases [Translation, ribosomal structure
and biogenesis].
Length = 475
Score = 29.2 bits (66), Expect = 1.4
Identities = 19/80 (23%), Positives = 30/80 (37%), Gaps = 7/80 (8%)
Query: 95 AKKKDLMKKFRDMLGDNGVFLFPTFINSAH---YHYQIHYKFLNYGYVG----LFNLLEM 147
A+K + + F + + V L PT A L + NL +
Sbjct: 367 AQKTLIRRAFDKLFEEVDVLLTPTTPTPAPKIGESESDGDDPLEMYLLDVFTVPANLAGL 426
Query: 148 PVTNVTVGLGSNKLPVGFQV 167
P +V G ++ LPVG Q+
Sbjct: 427 PAISVPAGFTADGLPVGLQL 446
>gnl|CDD|235686 PRK06061, PRK06061, amidase; Provisional.
Length = 483
Score = 28.9 bits (65), Expect = 1.7
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 11/39 (28%)
Query: 143 NLLEMPVTNVTVGLGSNKLPVGFQ-----------VSLA 170
N+L P NV G S+ LP+G Q +SLA
Sbjct: 423 NVLGWPSINVPAGFTSDGLPIGAQLMGPANSEPLLISLA 461
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 28.5 bits (64), Expect = 1.9
Identities = 16/80 (20%), Positives = 27/80 (33%), Gaps = 20/80 (25%)
Query: 45 LCFQVWSHSVTKEVLKWLMFSSKFTTTTVLYGVIKKAADCFSQRKIDTLLAKKKDLMKKF 104
+V + K+VL+ L+ + F D + TLLA D +
Sbjct: 856 FINRVDFKKLNKKVLEALIKAGAF--------------DSLGPNR-KTLLASLDDALDAV 900
Query: 105 R-----DMLGDNGVFLFPTF 119
+ LG N +F +
Sbjct: 901 SRKKKAEALGQNSLFGALSE 920
>gnl|CDD|233100 TIGR00713, hemL, glutamate-1-semialdehyde-2,1-aminomutase. This
enzyme, glutamate-1-semialdehyde-2,1-aminomutase
(glutamate-1-semialdehyde aminotransferase, GSA
aminotransferase), contains a pyridoxal phosphate
attached at a Lys residue at position 283 of the seed
alignment. It is in the family of class III
aminotransferases [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 423
Score = 28.4 bits (64), Expect = 2.0
Identities = 17/38 (44%), Positives = 22/38 (57%), Gaps = 9/38 (23%)
Query: 95 AKKKDL---MKKFRDMLGDNGVFLFPT-----FINSAH 124
AKK D K F +ML D GVFL P+ F+++AH
Sbjct: 368 AKKSDTELFAKFFHEML-DKGVFLPPSQFEACFLSAAH 404
>gnl|CDD|226151 COG3624, PhnG, Uncharacterized enzyme of phosphonate metabolism
[Inorganic ion transport and metabolism].
Length = 151
Score = 27.7 bits (62), Expect = 2.0
Identities = 11/24 (45%), Positives = 11/24 (45%)
Query: 142 FNLLEMPVTNVTVGLGSNKLPVGF 165
FNL E VT TV L VG
Sbjct: 60 FNLGEATVTRATVRLEDGTGTVGH 83
>gnl|CDD|235723 PRK06170, PRK06170, amidase; Provisional.
Length = 490
Score = 28.1 bits (63), Expect = 2.8
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 140 GLFNLLEMPVTNVTVGLGSNKLPVGFQV 167
GL L +P T + +GL + LPVG Q+
Sbjct: 434 GLATLPGLPATAIPIGLSATGLPVGVQI 461
>gnl|CDD|193595 cd09981, LOTUS_5_Limkain_b1, The fifth LOTUS domain on Limkain
b1(LKAP). The fifth LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 71
Score = 25.8 bits (57), Expect = 4.5
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 115 LFPTFINSAHYHYQIHYKFLNYGYVGLFNLLE 146
F FI S H+H+ K YG+ L L E
Sbjct: 21 PFTKFIPSYHHHFGRQCKLSYYGFTKLLELFE 52
>gnl|CDD|152490 pfam12055, DUF3536, Domain of unknown function (DUF3536). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and archaea. This domain is
typically between 274 to 285 amino acids in length.
This domain is found associated with pfam03065.
Length = 285
Score = 27.0 bits (60), Expect = 6.4
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 18 SLDWFRALLAGVFDMELKRLFI 39
+LDW R LA +F+ E +L
Sbjct: 12 ALDWLRDALAEIFEEEAGKLLK 33
>gnl|CDD|163564 TIGR03852, sucrose_gtfA, sucrose phosphorylase. In the forward
direction, this enzyme uses phosphate to cleave sucrose
into D-fructose + alpha-D-glucose 1-phosphate.
Characterized representatives from Streptococcus mutans
and Bifidobacterium adolescentis represent
well-separated branches of a molecular phylogenetic
tree. In S. mutans, the region including this gene has
been associated with neighboring transporter genes and
multiple sugar metabolism.
Length = 470
Score = 27.0 bits (60), Expect = 7.0
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 99 DLMKKFRDMLGDNGVFLFPTFINSAHYHYQIHYKFLNYGY 138
+L+ + RD+L G + P H HY I +K +GY
Sbjct: 211 ELLDEVRDILAPTGAEILPEI----HEHYTIQFKIAEHGY 246
>gnl|CDD|232778 TIGR00006, TIGR00006, 16S rRNA
(cytosine(1402)-N(4))-methyltransferase. This model
describes RsmH, a 16S rRNA methyltransferase.
Previously, this gene was designated MraW, known to be
essential in E. coli and widely conserved in bacteria
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 307
Score = 26.6 bits (59), Expect = 7.1
Identities = 13/69 (18%), Positives = 22/69 (31%), Gaps = 15/69 (21%)
Query: 66 SKFTTTTVLYGVIKKAADCFSQRKIDTLLAKK---------------KDLMKKFRDMLGD 110
TT L VI KA FS+ K + ++ ++ ++L
Sbjct: 171 KPIQTTKELAEVISKAVPGFSKYKSIHPATRVFQAIRIYVNDELEELEEALQFAPNLLAP 230
Query: 111 NGVFLFPTF 119
G +F
Sbjct: 231 GGRLSIISF 239
>gnl|CDD|235204 PRK04027, PRK04027, 30S ribosomal protein S7P; Reviewed.
Length = 195
Score = 26.4 bits (59), Expect = 7.4
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 70 TTTVLYGVIK--KAADCFSQRKIDTLL 94
TT + YG I KA D QR++D L
Sbjct: 116 TTRIKYGGISYPKAVDVSPQRRVDLAL 142
>gnl|CDD|220019 pfam08795, DUF1796, Putative papain-like cysteine peptidase
(DUF1796).
Length = 162
Score = 26.1 bits (58), Expect = 7.5
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 19 LDWFRALLAGVFDMELKRLFIYRMLTLCFQVWSHSVTKEVLKWLMFSSKFTTTTV 73
DW R+ L GV D+ +K F L + V + ++F ++ +
Sbjct: 29 FDWIRSSLDGVNDL-IKNDF-ADFLDPENLEERPFPPEPVARHILFRKQYGLFSH 81
>gnl|CDD|132012 TIGR02967, guan_deamin, guanine deaminase. This model describes
guanine deaminase, which hydrolyzes guanine to xanthine
and ammonia. Xanthine can then be converted to urate by
xanthine dehydrogenase, and urate subsequently degraded.
In some bacteria, the guanine deaminase gene is found
near the xdhABC genes for xanthine dehydrogenase.
Non-homologous forms of guanine deaminase also exist, as
well as distantly related forms outside the scope of
this model [Purines, pyrimidines, nucleosides, and
nucleotides, Other].
Length = 401
Score = 26.8 bits (60), Expect = 7.7
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 140 GLFNLLEMPVTNVTVGLGS 158
GLFNL + V VGLG+
Sbjct: 277 GLFNLKKALEHGVRVGLGT 295
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
0.329 0.140 0.424
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,889,453
Number of extensions: 817593
Number of successful extensions: 919
Number of sequences better than 10.0: 1
Number of HSP's gapped: 919
Number of HSP's successfully gapped: 37
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
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 (21.8 bits)
S2: 56 (25.5 bits)