RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17823
(92 letters)
>gnl|CDD|238100 cd00171, Sec7, Sec7 domain; Domain named after the S. cerevisiae
SEC7 gene product. The Sec7 domain is the central domain
of the guanine-nucleotide-exchange factors (GEFs) of the
ADP-ribosylation factor family of small GTPases (ARFs) .
It carries the exchange factor activity.
Length = 185
Score = 99 bits (250), Expect = 3e-28
Identities = 39/65 (60%), Positives = 50/65 (76%), Gaps = 3/65 (4%)
Query: 23 SVLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIFTN-- 80
VL FVDL DF+ L L +ALR+FL SFRLPGEAQKIDR++E F++RYC+ NP IF++
Sbjct: 65 LVLHEFVDLFDFSGLRLDEALRKFLQSFRLPGEAQKIDRLLEKFSERYCECNPGIFSSSA 124
Query: 81 -TAHT 84
A+T
Sbjct: 125 DAAYT 129
>gnl|CDD|216460 pfam01369, Sec7, Sec7 domain. The Sec7 domain is a
guanine-nucleotide-exchange-factor (GEF) for the
pfam00025 family.
Length = 188
Score = 96.5 bits (241), Expect = 8e-27
Identities = 34/59 (57%), Positives = 44/59 (74%)
Query: 24 VLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIFTNTA 82
VL+ +VDL DF L L +ALR FL SFRLPGEAQKIDR++E F++RY + NP+ +A
Sbjct: 69 VLKEYVDLFDFKGLPLDEALRLFLSSFRLPGEAQKIDRILEAFSERYYECNPSTVFKSA 127
>gnl|CDD|214569 smart00222, Sec7, Sec7 domain. Domain named after the S.
cerevisiae SEC7 gene product, which is required for
proper protein transport through the Golgi. The domain
facilitates guanine nucleotide exchange on the small
GTPases, ARFs (ADP ribosylation factors).
Length = 189
Score = 96.2 bits (240), Expect = 1e-26
Identities = 39/65 (60%), Positives = 48/65 (73%), Gaps = 4/65 (6%)
Query: 24 VLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIF----T 79
VL AFVDL DF+ L QALR+FL SFRLPGEAQKIDR++E F+ RYC+ NP +F
Sbjct: 69 VLHAFVDLFDFSAKDLDQALREFLESFRLPGEAQKIDRLLEAFSSRYCECNPGVFSKANA 128
Query: 80 NTAHT 84
+ A+T
Sbjct: 129 DAAYT 133
>gnl|CDD|227623 COG5307, COG5307, SEC7 domain proteins [General function prediction
only].
Length = 1024
Score = 82.1 bits (203), Expect = 7e-20
Identities = 30/62 (48%), Positives = 43/62 (69%)
Query: 23 SVLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIFTNTA 82
+VLR F+ L DF L + +ALR+ L SFRLPGEAQ+IDR++E F+ +Y NP F++
Sbjct: 332 AVLREFISLFDFKGLDIDEALRKLLQSFRLPGEAQQIDRILEAFSDKYYSDNPKKFSSKP 391
Query: 83 HT 84
+
Sbjct: 392 DS 393
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor
(ARF-GEF); Provisional.
Length = 1780
Score = 81.4 bits (201), Expect = 1e-19
Identities = 34/62 (54%), Positives = 45/62 (72%), Gaps = 2/62 (3%)
Query: 24 VLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIFT--NT 81
V+ A+VD DF + +A+R FL FRLPGEAQKIDR+ME FA+RYC+ NP F+ +T
Sbjct: 680 VMHAYVDSFDFQGMEFDEAIRAFLQGFRLPGEAQKIDRIMEKFAERYCKCNPKAFSSADT 739
Query: 82 AH 83
A+
Sbjct: 740 AY 741
>gnl|CDD|179262 PRK01250, PRK01250, inorganic pyrophosphatase; Provisional.
Length = 176
Score = 27.9 bits (63), Expect = 0.52
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 13 DDKTIAVTVPSVLRAFVDLHDFTDL--ILVQALRQF 46
D K IAV + + + D DL +L ++ F
Sbjct: 103 DAKIIAVPHDKLSPEYDHIKDVNDLPELLKAQIKHF 138
>gnl|CDD|216800 pfam01941, AdoMet_Synthase, S-adenosylmethionine synthetase (AdoMet
synthetase). This family consists of several
archaebacterial S-adenosylmethionine synthetase C(AdoMet
synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine
(AdoMet) occupies a central role in the metabolism of
all cells. The biological roles of AdoMet include acting
as the primary methyl group donor, as a precursor to the
polyamines, and as a progenitor of a 5'-deoxyadenosyl
radical. S-Adenosylmethionine synthetase catalyzes the
only known route of AdoMet biosynthesis. The synthetic
process occurs in a unique reaction in which the
complete triphosphate chain is displaced from ATP and a
sulfonium ion formed. MATs from various organisms
contain ~400-amino acid polypeptide chains.
Length = 396
Score = 27.9 bits (63), Expect = 0.66
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 22/75 (29%)
Query: 11 FRDDKTIAVTVPSVLRAFVD--LHDFTD-LILVQALRQFLWSFRLPGEAQKIDRMMECFA 67
R+ I +TV + AFVD + D + + + L++++ E A
Sbjct: 201 LREGDKITLTVAA---AFVDRYVSDLDEYFEVKEELKEYV----------------EDLA 241
Query: 68 QRYCQLNPNIFTNTA 82
+Y +F NTA
Sbjct: 242 SKYTDREVEVFVNTA 256
>gnl|CDD|225917 COG3382, COG3382, Solo B3/4 domain (OB-fold DNA/RNA-binding) of
Phe-aaRS-beta [General function prediction only].
Length = 229
Score = 27.3 bits (61), Expect = 0.90
Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 7/51 (13%)
Query: 13 DDKTIAVTVPSVLRAFVDLHDFTDLILVQALRQFLWSF-------RLPGEA 56
+ + A++ +D +V+A R W F R EA
Sbjct: 36 LVDRLLLFEEEQADAYLTPETLSDEPVVKAWRDAYWRFGIKPTKTRPSAEA 86
>gnl|CDD|178513 PLN02925, PLN02925, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate
synthase.
Length = 733
Score = 27.0 bits (60), Expect = 1.3
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 6 SFSL----RFRDDKTIAVTVPSVLRAFVDLHDFTDLI 38
SF L R R+ KT V+ PS R DL + + I
Sbjct: 618 SFGLLQGCRMRNTKTEYVSCPSCGRTLFDLQEVSAEI 654
>gnl|CDD|177973 PLN02339, PLN02339, NAD+ synthase (glutamine-hydrolysing).
Length = 700
Score = 27.0 bits (60), Expect = 1.5
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 43 LRQFLWSFRLPGEAQKIDRMME 64
LRQFL++ R P + +KID ++E
Sbjct: 670 LRQFLYNTRWPYQFRKIDELVE 691
>gnl|CDD|220645 pfam10239, DUF2465, Protein of unknown function (DUF2465). FAM98A
and B proteins are found from worms to humans but their
function is unknown. This entry is of a family of
proteins that is rich in glycines.
Length = 318
Score = 25.6 bits (56), Expect = 4.4
Identities = 10/38 (26%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 46 FLWSFRLPGEAQKIDRMMECFAQRYCQLNPNIFTNTAH 83
F WS R K D+M + + L+ + AH
Sbjct: 222 FGWSDRA---KTKEDQMAAVYQPKRHSLDAGSTVDLAH 256
>gnl|CDD|225847 COG3310, COG3310, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 196
Score = 25.2 bits (55), Expect = 4.8
Identities = 7/30 (23%), Positives = 13/30 (43%)
Query: 16 TIAVTVPSVLRAFVDLHDFTDLILVQALRQ 45
T + P++L F D +D D+ +
Sbjct: 79 TTLLVHPTLLPDFDDFNDMLDIADAAIVEN 108
>gnl|CDD|217690 pfam03718, Glyco_hydro_49, Glycosyl hydrolase family 49. Family of
dextranase (EC 3.2.1.11) and isopullulanase (EC
3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic
bonds in dextran polymers.
Length = 566
Score = 25.6 bits (56), Expect = 4.9
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 2 PFAISFSLRFRDDKTIAVTVP 22
P + +F D T+ + VP
Sbjct: 117 PSSYNFEKSLVDAGTVRIKVP 137
>gnl|CDD|235394 PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1290
Score = 25.1 bits (56), Expect = 6.1
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 11/47 (23%)
Query: 12 RDDKTIAVTVPSVLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQK 58
RD KT+ P++ + +DL + A+ + L RLP A K
Sbjct: 609 RDVKTVKAKGPALDYSGIDLAE--------AVERVL---RLPTVASK 644
>gnl|CDD|185336 PRK15439, PRK15439, autoinducer 2 ABC transporter ATP-binding
protein LsrA; Provisional.
Length = 510
Score = 25.0 bits (55), Expect = 6.3
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 50 FRLPGEAQKIDRMMECFAQRYCQLNP 75
F LP + +M + A CQL+
Sbjct: 109 FGLPKRQASMQKMKQLLAALGCQLDL 134
>gnl|CDD|222893 PHA02587, 30, DNA ligase; Provisional.
Length = 488
Score = 25.1 bits (55), Expect = 6.9
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 10 RFRDDKTIAVTVPSVLRAFVDLH 32
R R DKT A T+ V F DL
Sbjct: 469 RIRIDKTEANTLEDV---FADLI 488
>gnl|CDD|218055 pfam04386, SspB, Stringent starvation protein B. Escherichia coli
stringent starvation protein B (SspB), is thought to
enhance the specificity of degradation of tmRNA-tagged
proteins by the ClpXP protease. The tmRNA tag, also
known as ssrA, is an 11-aa peptide added to the C
terminus of proteins stalled during translation, targets
proteins for degradation by ClpXP and ClpAP. SspB a
cytoplasmic protein that specifically binds to residues
1-4 and 7 of the tag. Binding of SspB enhances
degradation of tagged proteins by ClpX, and masks
sequence elements important for ClpA interactions,
inhibiting degradation by ClpA. However, more recent
work has cast doubt on the importance of SspB in
wild-type cells. SspB is encoded in an operon whose
synthesis is stimulated by carbon, amino acid, and
phosphate starvation. SspB may play a special role
during nutrient stress, for example by ensuring rapid
degradation of the products of stalled translation,
without causing a global increase in degradation of all
ClpXP substrates.
Length = 153
Score = 24.5 bits (54), Expect = 7.7
Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 4 AISFSLRFRDDKTIAVTVP-SVLRAFVD 30
SF+LRF + VP + + AF D
Sbjct: 75 GFSFNLRFG-GVPERLYVPFAAILAFYD 101
>gnl|CDD|213296 cd05930, A_NRPS, The adenylation domain of nonribosomal peptide
synthetases (NRPS). The adenylation (A) domain of NRPS
recognizes a specific amino acid or hydroxy acid and
activates it as an (amino) acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms a thioester
bond to the enzyme-bound cofactor phosphopantetheine of
a peptidyl carrier protein domain. NRPSs are large
multifunctional enzymes which synthesize many
therapeutically useful peptides in bacteria and fungi
via a template-directed, nucleic acid independent
nonribosomal mechanism. These natural products include
antibiotics, immunosuppressants, plant and animal
toxins, and enzyme inhibitors. NRPS has a distinct
modular structure in which each module is responsible
for the recognition, activation, and in some cases,
modification of a single amino acid residue of the final
peptide product. The modules can be subdivided into
domains that catalyze specific biochemical reactions.
Length = 445
Score = 24.7 bits (55), Expect = 7.7
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 12/62 (19%)
Query: 16 TIAVTVPSVLRAFVDLHDFTDLILVQALRQFLWSFRLPGEAQKIDRMMECFAQRYCQLNP 75
T+ VPS+LRA +D + L +LR + GEA + +R+ +L P
Sbjct: 186 TVLHLVPSLLRALLDALEPAAL---PSLRLVIVG----GEALPAE-----LVRRWRELFP 233
Query: 76 NI 77
Sbjct: 234 GA 235
>gnl|CDD|218655 pfam05608, DUF778, Protein of unknown function (DUF778). This
family consists of several eukaryotic proteins of
unknown function.
Length = 119
Score = 24.1 bits (53), Expect = 9.0
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 51 RLPGEAQKIDRMMECFAQRYCQLNPNIFTNTAHTH 85
G A+ D + + + N N+FTN H+
Sbjct: 54 PSAGTAETWDDALSKATREFRHRNYNLFTNNCHSF 88
>gnl|CDD|116198 pfam07579, DUF1548, Domain of Unknown Function (DUF1548). This
family appears to be found only in a small family of
Chlamydia proteins.
Length = 135
Score = 24.3 bits (53), Expect = 9.0
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 5/41 (12%)
Query: 39 LVQALRQFLW----SFRLPGEAQKIDRMMECFAQRYCQLNP 75
ALR +L + LP E + D + E F +LN
Sbjct: 83 QKAALRNYLLDDLTAINLP-ETEHADIVSELFYDDNYELNR 122
>gnl|CDD|214821 smart00797, AHS2, Allophanate hydrolase subunit 2. This domain
represents subunit 2 of allophanate hydrolase (AHS2).
Length = 280
Score = 24.4 bits (54), Expect = 9.9
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 7 FSLRFRDDKTIAVT 20
+LRF D IA+T
Sbjct: 38 PTLRFTADAVIALT 51
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
0.331 0.140 0.441
Gapped
Lambda K H
0.267 0.0845 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,757,619
Number of extensions: 389205
Number of successful extensions: 435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 25
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 53 (24.0 bits)