RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3809
(112 letters)
>gnl|CDD|204202 pfam09336, Vps4_C, Vps4 C terminal oligomerisation domain. This
domain is found at the C terminal of ATPase proteins
involved in vacuolar sorting. It forms an alpha helix
structure and is required for oligomerisation.
Length = 62
Score = 92.7 bits (231), Expect = 2e-26
Identities = 34/62 (54%), Positives = 46/62 (74%)
Query: 48 LLTPCSPSTPGAVEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMED 107
LTPCSP PGA+EM +MD+ DKLLEPP++M +K+L T+KPTV+ DD+ K +F +
Sbjct: 1 KLTPCSPGDPGAIEMTWMDIEEDKLLEPPLTMKDFIKALATTKPTVSKDDLEKHEEFTNE 60
Query: 108 FG 109
FG
Sbjct: 61 FG 62
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 34.9 bits (80), Expect = 0.004
Identities = 21/107 (19%), Positives = 42/107 (39%), Gaps = 31/107 (28%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
Y+GADI V R+A M +R + G + + ++
Sbjct: 656 YTGADIEAVCREAAMAALR---------ESIGSPAKEKLEVGEEEFLK------------ 694
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQ 110
+ V M H L++L+ KP+V+ +DM++ + ++ +
Sbjct: 695 ----------DLKVEMRHFLEALKKVKPSVSKEDMLRYERLAKELKR 731
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 29.4 bits (66), Expect = 0.35
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 4 YSGADISIVVRDALMQPVR 22
YSGADI+ +VR+A ++ +R
Sbjct: 446 YSGADIAALVREAALEALR 464
>gnl|CDD|213633 TIGR01504, glyox_carbo_lig, glyoxylate carboligase. Glyoxylate
carboligase, also called tartronate-semialdehyde
synthase, releases CO2 while synthesizing a single
molecule of tartronate semialdehyde from two molecules
of glyoxylate. It is a thiamine pyrophosphate-dependent
enzyme, closely related in sequence to the large subunit
of acetolactate synthase. In the D-glycerate pathway,
part of allantoin degradation in the Enterobacteriaceae,
tartronate semialdehyde is converted to D-glycerate and
then 3-phosphoglycerate, a product of glycolysis and
entry point in the general metabolism.
Length = 588
Score = 26.5 bits (58), Expect = 3.6
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 7 ADISIVVRDALMQPVRLVQSATHFVRTSGPSPV 39
+ +++ VR+A + P R++Q A H +R+ P PV
Sbjct: 126 SKMAVTVREAALVP-RVLQQAFHLMRSGRPGPV 157
>gnl|CDD|218986 pfam06317, Arena_RNA_pol, Arenavirus RNA polymerase. This family
consists of several Arenavirus RNA polymerase proteins
(EC:2.7.7.48).
Length = 2206
Score = 26.5 bits (59), Expect = 3.8
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 12 VVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNF 64
V D + P L S + SG + +++ +LL S G+VE++
Sbjct: 1900 VWSDFEIGPAYLNSS---QLIASGLTNRKNFESLSELLDLVSNLEVGSVELSI 1949
Score = 26.1 bits (58), Expect = 4.5
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 69 SDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMED 107
S +LLE V M+H+L S+ + P + ++ L FM D
Sbjct: 1720 SVRLLEDKVGMNHVLHSIRRNYPKLFEE---HLLPFMSD 1755
>gnl|CDD|236057 PRK07578, PRK07578, short chain dehydrogenase; Provisional.
Length = 199
Score = 25.9 bits (58), Expect = 4.4
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 7 ADISIVVRDALMQPVRLVQSATHFVRTSG 35
D ++ ++ LM V LV H++ G
Sbjct: 77 EDFNVGLQSKLMGQVNLVLIGQHYLNDGG 105
>gnl|CDD|226469 COG3960, COG3960, Glyoxylate carboligase [General function
prediction only].
Length = 592
Score = 26.0 bits (57), Expect = 4.6
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 10 SIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVD----------DLLTPCSPSTPGA 59
++ VR+ + P R++Q A H +R+ P PV D D+ P P A
Sbjct: 130 AVTVREPALVP-RVLQQAFHLMRSGRPGPVLIDLPFDVQVAEIEFDPDMYEPLPVYKPAA 188
Query: 60 VEM 62
+
Sbjct: 189 TRV 191
>gnl|CDD|226234 COG3711, BglG, Transcriptional antiterminator [Transcription].
Length = 491
Score = 25.9 bits (57), Expect = 5.1
Identities = 10/40 (25%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 72 LLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQE 111
LL +S+H + L SK T+ +D+ +R + +
Sbjct: 96 LLSELLSLHELADELFVSKSTII-NDLKDVRLKLLLYDLT 134
>gnl|CDD|219469 pfam07569, Hira, TUP1-like enhancer of split. The Hira proteins
are found in a range of eukaryotes and are implicated
in the assembly of repressive chromatin. These proteins
also contain pfam00400.
Length = 214
Score = 25.7 bits (57), Expect = 5.7
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 66 DVPSDKLLEPPVSMHHILKSLETSKPTV 93
+V + K + PPVS+ +L S TS P +
Sbjct: 38 NVKTKKAILPPVSLAPLLDSSSTSGPNI 65
>gnl|CDD|213331 cd05129, RasGAP_RAP6, Ras-GTPase Activating Domain of
Rab5-activating protein 6. Rab5-activating protein 6
(RAP6) is an endosomal protein with a role in the
regulation of receptor-mediated endocytosis. RAP6
contains a Vps9 domain, which is involved in the
activation of Rab5, and a Ras GAP domain (RGD). Rab5 is
a small GTPase required for the control of the endocytic
route, and its activity is regulated by guanine
nucleotide exchange factor, such as Rabex5, and GAPs,
such as RN-tre. Human Rap6 protein is localized on the
plasma membrane and on the endosome. RAP6 binds to Rab5
and Ras through the Vps9 and RGD domains, respectively.
Length = 365
Score = 25.8 bits (57), Expect = 6.8
Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 27/111 (24%)
Query: 5 SGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDP--------------SKTVDDLLT 50
S A IS V R LMQ +++Q + DP S +D ++
Sbjct: 246 SDAPISEVARHNLMQVAQILQVLAL----TEFESPDPRLKELLSKFDKDCVSAFLDVVIV 301
Query: 51 PCSPSTPGAVEMNFMDVPSDKLLEPPVSMHHI------LKSLETSKPTVND 95
+ TP ++ +L ++ + L+S++T D
Sbjct: 302 GRAVETPPPSSSALLEGSRTAVL---ITESDLATLVEFLRSVKTGDEEKED 349
>gnl|CDD|149046 pfam07764, Omega_Repress, Omega Transcriptional Repressor. The
omega transcriptional repressor regulates expression of
involved in copy number control and stable maintenance
of plasmids. The omega protein belongs to the structural
superfamily of MetJ/Arc repressors featuring a
ribbon-helix-helix DNA-binding motif with the
beta-ribbon located in and recognising the major groove
of operator DNA.
Length = 71
Score = 24.6 bits (53), Expect = 6.8
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 66 DVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLR 102
D+ DK + +HHI+K +ET+K N +++
Sbjct: 23 DIMGDKTVRVRADLHHIIK-IETAKNGGNVKEVMDQA 58
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
0.315 0.132 0.381
Gapped
Lambda K H
0.267 0.0758 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,585,581
Number of extensions: 461609
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 448
Number of HSP's successfully gapped: 23
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 41 (21.6 bits)
S2: 53 (24.1 bits)