RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14701
(136 letters)
>gnl|CDD|240161 cd05125, Mth938_2P1-like, Mth938_2P1-like domain. This model
contains sequences that are similar to 2P1, a partially
characterized nuclear protein, which is homologous to
E3-3 from rat and known to be alternatively spliced. Its
function is unknown. This family is part of the Mth938
family, for which structures, but no functional data are
available.
Length = 114
Score = 109 bits (274), Expect = 5e-32
Identities = 51/108 (47%), Positives = 64/108 (59%), Gaps = 6/108 (5%)
Query: 2 GFRLSNNSVVVGPLAVFNKCVFSWNILDDSDINMESLSLFLHLEPKLDVLIIGLGDFKFN 61
GFRL+NN V+ G A+ K VFSWN+ DI ESLSLF LEP+ ++L+IG G
Sbjct: 10 GFRLNNNKVI-GSGAILPKEVFSWNVSSFEDITEESLSLFELLEPRPEILVIGTGR---K 65
Query: 62 HTKLIP-VINEVRKH-CNVEVLPTERAIATFNFMVSEGRVAGAALVPP 107
L P + +K VEV+ T A ATFNF+ EGR AAL+PP
Sbjct: 66 SRPLSPELRKYFKKLGIAVEVVDTRNACATFNFLAEEGRRVAAALIPP 113
>gnl|CDD|218085 pfam04430, DUF498, Protein of unknown function (DUF498/DUF598).
This is a large family of uncharacterized proteins found
in all domains of life. The structure shows a novel fold
with three beta sheets. A dimeric form is found in the
crystal structure. It was suggested that the cleft in
between the two monomers might bing nucleic acid.
Length = 109
Score = 81.5 bits (202), Expect = 3e-21
Identities = 38/105 (36%), Positives = 54/105 (51%), Gaps = 5/105 (4%)
Query: 2 GFRLSNNSVVVGPLAVF-NKCVFSWNILDDSDINMESLSLFLHLEPKLDVLIIGLG-DFK 59
GFR+ N G L V + V+ W++ D++ E L+L L L P +VLIIG G +
Sbjct: 8 GFRI-NGVRYEGSLLVLPDGIVWDWDVGSFEDLSPEDLALLLALAPDPEVLIIGTGARLR 66
Query: 60 FNHTKLIPVINEVRKHCNVEVLPTERAIATFNFMVSEGRVAGAAL 104
F +L + + VEV+ T A T+N + SEGR AAL
Sbjct: 67 FLPPELREALRK--LGIGVEVMDTGAACRTYNVLASEGRRVAAAL 109
>gnl|CDD|238152 cd00248, Mth938-like, Mth938-like domain. The members of this
family include: Mth938, 2P1, Xcr35, Rpa2829, and several
uncharacterized sequences. Mth938 is a hypothetical
protein encoded by the Methanobacterium
thermoautotrophicum (Mth) genome. This protein
crystallizes as a dimer, although it is monomeric in
solution, with one disulfide bond in each monomer. 2P1
is a partially characterized nuclear protein which is
homologous to E3-3 from rat and known to be alternately
spliced. Xcr35 and Rpa2829 are hypothetical proteins of
unknown function from the Xanthomonas campestris and
Rhodopseudomonas palustris genomes, respectively, for
which the crystal structures have been determined.
Length = 109
Score = 67.3 bits (165), Expect = 1e-15
Identities = 36/105 (34%), Positives = 52/105 (49%), Gaps = 5/105 (4%)
Query: 2 GFRLSNNSVVVGPLAVFNKCVFSWNILDDSDINMESLSLFLHLEPKLDVLIIGLG-DFKF 60
GFR+ V GPL V V W+ SD++ E+L L + + D+L+IG G + F
Sbjct: 9 GFRI-AGQVYRGPLLVLPDGVVPWDGTSLSDLDPEALLPLLAED-RPDILLIGTGAEIAF 66
Query: 61 NHTKLIPVINEVRKHCNVEVLPTERAIATFNFMVSEGRVAGAALV 105
L + VEV+ T A T+N ++SEGR AAL+
Sbjct: 67 LPRALRAALRAAGI--GVEVMSTGAACRTYNVLLSEGRRVAAALI 109
>gnl|CDD|226260 COG3737, COG3737, Uncharacterized conserved protein [Function
unknown].
Length = 127
Score = 51.3 bits (123), Expect = 3e-09
Identities = 31/107 (28%), Positives = 46/107 (42%), Gaps = 6/107 (5%)
Query: 2 GFRLSNNSVVVGPLAVFNKCVFSWNILDDSDINMESLSLFLHLEPKLDVLIIGLGDFKFN 61
GFR + G L V V W + SD+ E L P +++L+IG G
Sbjct: 25 GFRF-ADMSHRGSLLVLPDGVCDWEVATLSDLTPEDFERVLAEAPDVEILLIGTGA---R 80
Query: 62 HTKLIPVINEV--RKHCNVEVLPTERAIATFNFMVSEGRVAGAALVP 106
P + +VE + T A+ T+N ++SEGR AAL+
Sbjct: 81 LRFPPPKLRAALKAAGISVEPMSTGAAVRTYNVLLSEGRRVAAALIA 127
>gnl|CDD|240187 cd05560, Xcc1710_like, Xcc1710_like family, specific to
proteobacteria. Xcc1710 is a hypothetical protein from
Xanthomonas campestris pv. campestris str. ATCC 33913,
similar to Mth938, a hypothetical protein encoded by the
Methanobacterium thermoautotrophicum (Mth) genome. Their
three-dimensional structures have been determined, but
their functions are unknown.
Length = 109
Score = 39.1 bits (92), Expect = 7e-05
Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 9/98 (9%)
Query: 9 SVVVGPLAVFNKCVFSWNILDDSDINMESLSLFLHLEPKLDVLIIGLGD-FKFNHTKLIP 67
S++V P ++ + W + D+ L L+P +V+++G G+ +F L+
Sbjct: 20 SLIVTP----DELITDWPVARFEDLTAAHFEALLALQP--EVILLGTGERQRFPPPALLA 73
Query: 68 VINEVRKHCNVEVLPTERAIATFNFMVSEGRVAGAALV 105
+ + + VEV+ T+ A T+N ++ EGR AAL+
Sbjct: 74 PL--LARGIGVEVMDTQAACRTYNILMGEGRRVVAALL 109
>gnl|CDD|240162 cd05126, Mth938, Mth938 domain. Mth938 is a hypothetical protein
encoded by the Methanobacterium thermoautotrophicum
(Mth) genome. This protein crystallizes as a dimer,
although it is monomeric in solution, with one disulfide
bond in each monomer. The function of the protein has
not been determined.
Length = 117
Score = 32.3 bits (74), Expect = 0.027
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 44 LEPKLDVLIIGLGDFKFNHTKLIPVINEVRKHCNVEVLP--TERAIATFNFMVSEGRVAG 101
LE ++V++IG G K+ P E + VEVL TE A+ +N + +GR
Sbjct: 55 LEEGVEVIVIGTGQSGA--LKVPPETVEKLEKRGVEVLVLPTEEAVKRYNELAGKGRRVL 112
Query: 102 AAL 104
A +
Sbjct: 113 AVI 115
>gnl|CDD|237054 PRK12316, PRK12316, peptide synthase; Provisional.
Length = 5163
Score = 31.9 bits (72), Expect = 0.095
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 94 VSEGRVAGAALVPPVRISFTEEDIQATKHQNRDV 127
+G +G + PV+ F E+ I +H N+ +
Sbjct: 1092 ADQGPASGEVALAPVQRWFFEQAIPQRQHWNQSL 1125
Score = 27.6 bits (61), Expect = 2.3
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 92 FMVSEGRVAGAALVPPVRISFTEEDIQATKHQNRDV 127
V +G V+G L+ P++ F EE + H N+ +
Sbjct: 3628 VAVDQGPVSGETLLLPIQQQFFEEPVPERHHWNQSL 3663
>gnl|CDD|224421 COG1504, COG1504, Uncharacterized conserved protein [Function
unknown].
Length = 121
Score = 29.0 bits (65), Expect = 0.48
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 10/67 (14%)
Query: 44 LEPKLDVLIIGLGDFKFNHTKLIPVINEVR-----KHCNVEVLPTERAIATFNFMVSEGR 98
LE +V+++G G + + E R K C V LPT AI +N + + R
Sbjct: 58 LEEGPEVIVVGTGQSGM-----LELSEEAREFFRKKGCEVIELPTPEAIKRYNELRGKKR 112
Query: 99 VAGAALV 105
VA V
Sbjct: 113 VAAIIHV 119
>gnl|CDD|176868 cd07826, SRPBCC_CalC_Aha1-like_9, Putative hydrophobic
ligand-binding SRPBCC domain of an uncharacterized
subgroup of CalC- and Aha1-like proteins. SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a
functionally uncharacterized subgroup of CalC- and
Aha1-like proteins. This group shows similarity to the
SRPBCC domains of Micromonospora echinospora CalC (a
protein which confers resistance to enediynes) and human
Aha1 (one of several co-chaperones which regulate the
dimeric chaperone Hsp90), and belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket and they bind diverse ligands.
Length = 142
Score = 28.0 bits (63), Expect = 1.0
Identities = 17/50 (34%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 79 EVLPTERAIATFNFMVSEGRVAGAALVPPVRISFTEEDIQATKHQNRDVY 128
EV P ER + T F EG G AL ++FTE T+ Y
Sbjct: 69 EVTPPERIVQTEEF---EGLPDGVAL---ETVTFTELG-GRTRLTATSRY 111
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 28.4 bits (64), Expect = 1.2
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 17/73 (23%)
Query: 62 HTKLIPVINEVRKHCNVEVLPTERAIATFNFMVSEGRVAGAALVPPVRIS---FTE---- 114
HT +P+ R N E L + RAI+ F+++ G VP R++ F E
Sbjct: 270 HTDNVPLSGTGRFRDNWE-LSSARAISVVKFLIALG-------VPADRLAAAGFGEFQPL 321
Query: 115 --EDIQATKHQNR 125
D + +NR
Sbjct: 322 DPGDTPEARARNR 334
>gnl|CDD|188048 TIGR00417, speE, spermidine synthase. the SpeE subunit of
spermidine synthase catalysesthe reaction (putrescine +
S-adenosylmethioninamine = spermidine +
5'-methylthioadenosine) and is involved in polyamine
biosynthesis and in the biosynthesis of spermidine from
arganine. The region between residues 77 and 120 of the
seed alignment is thought to be involved in binding to
decarboxylated SAM [Central intermediary metabolism,
Polyamine biosynthesis].
Length = 271
Score = 27.8 bits (62), Expect = 1.6
Identities = 18/45 (40%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 35 MESLSLFLHLEPKLDVLIIGLGDFKFNHTKLIPVINEVRKHCNVE 79
+ + LF H PK VL+IG GD V+ EV KH +VE
Sbjct: 62 ITHVPLFTHPNPK-HVLVIGGGDGG--------VLREVLKHKSVE 97
>gnl|CDD|215767 pfam00171, Aldedh, Aldehyde dehydrogenase family. This family of
dehydrogenases act on aldehyde substrates. Members use
NADP as a cofactor. The family includes the following
members: The prototypical members are the aldehyde
dehydrogenases EC:1.2.1.3. Succinate-semialdehyde
dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase
EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28.
Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27.
Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9.
Delta-1-pyrroline-5-carboxylate dehydrogenase EC:
1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10.
Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This
family also includes omega crystallin, an eye lens
protein from squid and octopus that has little aldehyde
dehydrogenase activity.
Length = 459
Score = 27.9 bits (63), Expect = 2.0
Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 90 FNFMVSEGRVAGAALV--PPVR-ISFT 113
N + G G ALV P V +SFT
Sbjct: 186 LNVVTGSGSEVGDALVEHPDVDKVSFT 212
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 27.7 bits (62), Expect = 2.3
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 55 LGDFKFNHTKLIPVINEVRKHCNVEVL 81
+GD F H+ ++ +IN V N+ V+
Sbjct: 452 IGDSTFFHSGILALINAVYNKANILVV 478
>gnl|CDD|182862 PRK10953, cysJ, sulfite reductase subunit alpha; Provisional.
Length = 600
Score = 27.4 bits (61), Expect = 2.8
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 44 LEPKLDVLIIGLGDFKFNHT---KLIPVINEVRKHCNVEVLPTERAIATFNFMVS 95
L KL+V ++ GD+KF KL+ V+ + E P E A+A F+ S
Sbjct: 87 LAAKLNVNLVNAGDYKFKQIAQEKLLIVVTSTQG----EGEPPEEAVALHKFLFS 137
>gnl|CDD|215551 PLN03050, PLN03050, pyridoxine (pyridoxamine) 5'-phosphate oxidase;
Provisional.
Length = 246
Score = 27.1 bits (60), Expect = 2.8
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 94 VSEGRVAGAALVPPVRISFTEEDIQATKHQNR 125
V EG V+G + P V +S T + A K + R
Sbjct: 183 VDEGDVSGTGMRPDVLVSLTAPKLSAKKFEGR 214
>gnl|CDD|143415 cd07097, ALDH_KGSADH-YcbD, Bacillus subtilis NADP+-dependent
alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like.
Kinetic studies of the Bacillus subtilis ALDH-like ycbD
protein, which is involved in d-glucarate/d-galactarate
utilization, reveal that it is a NADP+-dependent,
alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH).
KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent
conversion of KGSA to alpha-ketoglutarate.
Interestingly, the NADP+-dependent, tetrameric,
2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an
enzyme involved in the catabolic pathway for D-arabinose
in Sulfolobus solfataricus, also clusters in this group.
This CD shows a distant phylogenetic relationship to the
Azospirillum brasilense KGSADH-II (-III) group.
Length = 473
Score = 27.2 bits (61), Expect = 3.3
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 90 FNFMVSEGRVAGAALV--PPVR-ISFT 113
FN ++ G G ALV P V +SFT
Sbjct: 195 FNLVMGSGSEVGQALVEHPDVDAVSFT 221
>gnl|CDD|216573 pfam01564, Spermine_synth, Spermine/spermidine synthase. Spermine
and spermidine are polyamines. This family includes
spermidine synthase that catalyzes the fifth (last) step
in the biosynthesis of spermidine from arginine, and
spermine synthase.
Length = 240
Score = 26.5 bits (59), Expect = 5.1
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 9/40 (22%)
Query: 40 LFLHLEPKLDVLIIGLGDFKFNHTKLIPVINEVRKHCNVE 79
L H PK VLIIG GD + EV KH +VE
Sbjct: 70 LCSHPNPK-KVLIIGGGDGG--------ALREVVKHPSVE 100
>gnl|CDD|223498 COG0421, SpeE, Spermidine synthase [Amino acid transport and
metabolism].
Length = 282
Score = 26.2 bits (58), Expect = 5.8
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 4/31 (12%)
Query: 30 DSDINMESLSL---FLHLEPKLDVLIIGLGD 57
D I E L+ H PK VLIIG GD
Sbjct: 58 DEFIYHEMLAHVPLLAHPNPK-RVLIIGGGD 87
>gnl|CDD|206247 pfam14077, WD40_alt, Alternative WD40 repeat motif. WD repeats are
short subdomains of about 40 amino acids and fold into 4
antiparallel beta hairpins. This domain here has been
detected on the C-terminus of WD repeat-containing
protein 18 during target selection by the Joint Center
for Structural Genomics.
Length = 48
Score = 24.4 bits (53), Expect = 6.7
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 94 VSEGRVAGAALVPPVRISFTEEDIQATKHQNRDVYKLDIKI 134
V+E V G VR+S EE+++ + N+D++ +I
Sbjct: 4 VTEKSVLGDQEQLRVRVSELEEEVRTLRKINKDLFDFSTRI 44
>gnl|CDD|226469 COG3960, COG3960, Glyoxylate carboligase [General function
prediction only].
Length = 592
Score = 26.4 bits (58), Expect = 6.9
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 51 LIIGLGD-FKFNHTKLIPVINEVRKHCNVEVLPTE--RAIATFNFMVSEGRVAGAAL 104
++ G+G+ + HT + V E RK +V++ PT+ R +VS+ A AAL
Sbjct: 273 MVFGIGNRWANRHTGSVEVYTEGRKFIHVDIEPTQIGRVFCPDLGIVSD---AKAAL 326
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 25.8 bits (57), Expect = 9.1
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 72 VRKHCNVEVLPTERAIATFNFMVSEGRVAGAALVPP 107
+R+ +++ L E IA + E A LV P
Sbjct: 171 IRRDPDIKWLRREADIAQLAELQKELLKAAWDLVKP 206
>gnl|CDD|197766 smart00509, TFS2N, Domain in the N-terminus of transcription
elongation factor S-II (and elsewhere).
Length = 75
Score = 24.6 bits (54), Expect = 9.6
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 62 HTKLIPVINEVRKHCNVEV 80
T++ +N +RKH N E+
Sbjct: 40 ETRIGKKVNGLRKHKNEEI 58
>gnl|CDD|220670 pfam10274, ParcG, Parkin co-regulated protein. This family of
proteins is transcribed anti-sense along the DNA to the
Parkin gene product and the two appear to be transcribed
under the same promoter. The protein has predicted
alpha-helical and beta-sheet domains which suggest its
function is in the ubiquitin/proteasome system.
Mutations in parkin are the genetic cause of early-onset
and autosomal recessive juvenile parkinsonism.
Length = 183
Score = 25.3 bits (56), Expect = 9.6
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 19/61 (31%)
Query: 61 NHTKLIPVINEVRKHCNVEVLPTERAIATFN------------FMVSEGRVAGAALVPPV 108
K++PV+ ++ +LP + A+ T + +V + G ALVP
Sbjct: 70 GGEKILPVLPQL-------ILPLKAALNTRDPEVFCVALKVLQQLVKSSPLIGEALVPYY 122
Query: 109 R 109
R
Sbjct: 123 R 123
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
0.324 0.141 0.415
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,939,456
Number of extensions: 621940
Number of successful extensions: 524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 521
Number of HSP's successfully gapped: 34
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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: 41 (22.0 bits)
S2: 54 (24.6 bits)