RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16144
(122 letters)
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 32.0 bits (73), Expect = 0.024
Identities = 12/59 (20%), Positives = 29/59 (49%), Gaps = 1/59 (1%)
Query: 54 DDAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQI 112
D+A+ Y +A + + A + LA+ ++ +Y EA++ + ++ P K + +
Sbjct: 17 DEALEYYEKALELDPDNADAYY-NLAAAYYKLGKYEEALEDYEKALELDPDNAKAYYNL 74
>gnl|CDD|222112 pfam13414, TPR_11, TPR repeat.
Length = 69
Score = 28.4 bits (64), Expect = 0.31
Identities = 9/48 (18%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 74 LHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQIFEKAMVHLR 121
+ L + L ++ Y EAI+ + ++ P + + + A+ +L+
Sbjct: 5 ALKNLGNALFKLGDYDEAIEAYEKALELDPDNAEAY---YNLALAYLK 49
Score = 25.7 bits (57), Expect = 2.5
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 54 DDAVVQYTQACRIIGTSDLALHQKLASLLLRM-KRYAEAIDVSQTIMKAHP 103
D+A+ Y +A + + + LA L++ K Y EA++ + ++ P
Sbjct: 20 DEAIEAYEKALELD-PDNAEAYYNLALAYLKLGKDYEEALEDLEKALELDP 69
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 28.9 bits (65), Expect = 0.59
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 71 DLALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVH 109
D L LA L L K Y +AI QT++K P V
Sbjct: 769 DAVLRTALAELYLAQKDYDKAIKHYQTVVKKAPDNAVVL 807
Score = 28.5 bits (64), Expect = 0.88
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 53 PDDAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQI 112
+ A+ Y +A + +++A+ LA++L+ + EA + ++K P+ P H
Sbjct: 209 IELALAAYRKAIAL-RPNNIAVLLALATILIEAGEFEEAEKHADALLKKAPNSPLAH--- 264
Query: 113 FEKAMVHLR 121
+ KA+V +
Sbjct: 265 YLKALVDFQ 273
Score = 27.7 bits (62), Expect = 1.9
Identities = 10/54 (18%), Positives = 16/54 (29%), Gaps = 9/54 (16%)
Query: 78 LASLLLRMKRYAEAIDVSQTIMKAHPSYPKVH---------KQIFEKAMVHLRT 122
LLL + A+ + + P+ V FE+A H
Sbjct: 199 KGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALATILIEAGEFEEAEKHADA 252
Score = 27.4 bits (61), Expect = 2.6
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 53 PDDAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHP 103
PDDA+ Q + I +L LA L LR EA+ + + +P
Sbjct: 515 PDDAI-QRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNP 564
Score = 26.2 bits (58), Expect = 5.2
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 55 DAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHP 103
A+ Y +A + +S A+ KL LL AEA+ + +K HP
Sbjct: 721 AAIQAYRKALKRAPSSQNAI--KLHRALLASGNTAEAVKTLEAWLKTHP 767
Score = 26.2 bits (58), Expect = 5.7
Identities = 11/41 (26%), Positives = 19/41 (46%)
Query: 78 LASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQIFEKAMV 118
LA LLL KR A +++++ K HP + + +
Sbjct: 675 LAQLLLAAKRTESAKKIAKSLQKQHPKAALGFELEGDLYLR 715
>gnl|CDD|198111 smart01043, BTAD, Bacterial transcriptional activator domain.
Found in the DNRI/REDD/AFSR family of regulators. This
region of AFSR along with the C terminal region is
capable of independently directing actinorhodin
production. This family contains TPR repeats.
Length = 145
Score = 28.0 bits (63), Expect = 0.78
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 72 LALHQKLASLLLRMKRYAEAIDVSQTIMKAHP 103
L + LA LL + R+ EA+ + + ++ P
Sbjct: 61 LEALEALAEALLALGRHEEALALLERLLALDP 92
>gnl|CDD|222123 pfam13432, TPR_16, Tetratricopeptide repeat.
Length = 65
Score = 26.9 bits (60), Expect = 0.92
Identities = 14/54 (25%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 53 PDDAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYP 106
D+A+ A L LLR R AEA + + + A P P
Sbjct: 13 YDEALAALEAA-LARYPLAAEALLLLGEALLRQGRLAEAAALLRAALAADPDDP 65
Score = 25.3 bits (56), Expect = 3.1
Identities = 10/45 (22%), Positives = 15/45 (33%), Gaps = 3/45 (6%)
Query: 77 KLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQIFEKAMVHLR 121
LA LR Y EA+ + + +P + LR
Sbjct: 2 ALARAALRAGDYDEALAALEAALARYPLAAEAL---LLLGEALLR 43
>gnl|CDD|225344 COG2730, BglC, Endoglucanase [Carbohydrate transport and
metabolism].
Length = 407
Score = 28.2 bits (63), Expect = 1.2
Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 3/56 (5%)
Query: 5 SVDTMQIIQTIAEWHFLLYLLPWRWEPLSAGLRKKQYISSATNIYNLFPDDAVVQY 60
+ T + I F +P + L A Y+ T + L D + +
Sbjct: 72 NFITEEDFDQIKSAGFNAVRIPIGYWALQATDGDNPYLIGLTQLKIL---DEAINW 124
>gnl|CDD|188247 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of
this protein family are the product of one of seven
genes regularly clustered in operons to encode the
proteins of the tol-pal system, which is critical for
maintaining the integrity of the bacterial outer
membrane. The gene for this periplasmic protein has been
designated orf2 and ybgF. All members of the seed
alignment were from unique tol-pal gene regions from
completed bacterial genomes. The architecture of this
protein is a signal sequence, a low-complexity region
usually rich in Asn and Gln, a well-conserved region
with tandem repeats that resemble the tetratricopeptide
(TPR) repeat, involved in protein-protein interaction.
Length = 117
Score = 27.2 bits (61), Expect = 1.3
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 77 KLASLLLRMKRYAEAIDVSQTIMKAHPSYPKV 108
A L+L+ YA+AI Q +K +P
Sbjct: 5 DAALLVLKAGDYADAIQAFQAFLKKYPKSTYA 36
>gnl|CDD|222121 pfam13428, TPR_14, Tetratricopeptide repeat.
Length = 44
Score = 25.6 bits (56), Expect = 1.7
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 72 LALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVHKQ 111
A LA LL + EA+ + + + P P+
Sbjct: 1 PAALLALARALLALGDLDEALALLRRALALDPDDPEALLL 40
>gnl|CDD|221956 pfam13174, TPR_6, Tetratricopeptide repeat.
Length = 33
Score = 25.1 bits (56), Expect = 2.2
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 77 KLASLLLRMKRYAEAIDVSQTIMKAHP 103
KLA L++ EA + + ++K +P
Sbjct: 5 KLALAYLKLGDTDEAKEALERLLKRYP 31
>gnl|CDD|184954 PRK14992, PRK14992, tetrathionate reductase subunit C;
Provisional.
Length = 335
Score = 27.1 bits (60), Expect = 2.3
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 13 QTIAEWHFLLYLLPWRWEPLSA 34
QT WHF + PW W P A
Sbjct: 73 QTARVWHFYAWPTPWSWMPWGA 94
>gnl|CDD|191994 pfam08311, Mad3_BUB1_I, Mad3/BUB1 homology region 1. Proteins
containing this domain are checkpoint proteins involved
in cell division. This region has been shown to be
essential for the binding of the binding of BUB1 and
MAD3 to CDC20p.
Length = 124
Score = 26.4 bits (59), Expect = 2.4
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 54 DDAVVQYTQACRI-IGTSDLALHQKLASLLLRMKRYAEAIDVSQ 96
+ + IGT +++ ASLL ++ +A +V Q
Sbjct: 78 SEPRDIFQYLYSKGIGTKLALFYEEWASLLESRGKFKKADEVFQ 121
>gnl|CDD|223119 COG0041, PurE, Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase
[Nucleotide transport and metabolism].
Length = 162
Score = 26.1 bits (58), Expect = 4.0
Identities = 7/25 (28%), Positives = 10/25 (40%)
Query: 63 ACRIIGTSDLALHQKLASLLLRMKR 87
A +I+ D L +KLA
Sbjct: 126 AAQILAIKDPELAEKLAEFREAQTE 150
>gnl|CDD|227044 COG4700, COG4700, Uncharacterized protein conserved in bacteria
containing a divergent form of TPR repeats [Function
unknown].
Length = 251
Score = 25.6 bits (56), Expect = 6.5
Identities = 14/55 (25%), Positives = 25/55 (45%)
Query: 55 DAVVQYTQACRIIGTSDLALHQKLASLLLRMKRYAEAIDVSQTIMKAHPSYPKVH 109
+AV Y QA I D A+ LA ++ +A A + +M+ +P++
Sbjct: 107 EAVPHYQQALSGIFAHDAAMLLGLAQAQFAIQEFAAAQQTLEDLMEYNPAFRSPD 161
>gnl|CDD|221837 pfam12895, Apc3, Anaphase-promoting complex, cyclosome, subunit
3. Apc3, otherwise known as Cdc27, is one of the
subunits of the anaphase-promoting complex or
cyclosome. The anaphase-promoting complex is a
multiprotein subunit E3 ubiquitin ligase complex that
controls segregation of chromosomes and exit from
mitosis in eukaryotes. The protein members of this
family contain TPR repeats just as those of Apc7 do,
and it appears that these TPR units bind the C-termini
of the APC co-activators CDH1 and CDC20.
Length = 80
Score = 24.9 bits (55), Expect = 6.6
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 59 QYTQACRIIGTSDLALHQKLASL----LLRMKRYAEAIDV 94
QY +A ++ L L LL++ +Y EAI V
Sbjct: 37 QYKRAYELLRKLKLDNSSGCRYLLAQCLLKLGKYDEAIAV 76
>gnl|CDD|129779 TIGR00696, wecG_tagA_cpsF, bacterial polymer biosynthesis proteins,
WecB/TagA/CpsF family. The WecG member of this
superfamily, believed to be
UDP-N-acetyl-D-mannosaminuronic acid transferase, plays
a role in enterobacterial common antigen (eca) synthesis
in Escherichia coli. Another family member, the Bacillus
subtilis TagA protein, is involved in the biosynthesis
of the cell wall polymer poly(glycerol phosphate). The
third family member, CpsF, CMP-N-acetylneuraminic acid
synthetase has a role in the capsular polysaccharide
biosynthesis pathway [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 177
Score = 25.5 bits (56), Expect = 7.9
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 17 EWHFLLYLLPWRW 29
EW + L + PWRW
Sbjct: 156 EWLYRLRMEPWRW 168
>gnl|CDD|225428 COG2873, MET17, O-acetylhomoserine sulfhydrylase [Amino acid
transport and metabolism].
Length = 426
Score = 25.7 bits (57), Expect = 8.0
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 17/63 (26%)
Query: 60 YTQACRIIGTSDL----------ALHQKLASLLLRMKRYAE-AIDVSQTIMKAHP----- 103
+ R+ DL L Q L +L LRM+R+ E A+ V++ ++ HP
Sbjct: 259 FIIKARVQLLRDLGATLSPFNAFLLLQGLETLSLRMERHCENALKVAEF-LENHPKVAWV 317
Query: 104 SYP 106
+YP
Sbjct: 318 NYP 320
>gnl|CDD|233616 TIGR01881, cas_Cmr5, CRISPR type III-B/RAMP module-associated
protein Cmr5. CRISPR is a term for Clustered, Regularly
Interspaced Short Palidromic Repeats. A number of
protein families appear only in association with these
repeats and are designated Cas (CRISPR-Associated)
proteins. This model family, represented by TM1791.1 of
Thermotoga maritima, is found in both archaeal and
bacterial species as part of the 6-gene CRISPR RAMP
module [Mobile and extrachromosomal element functions,
Other].
Length = 127
Score = 25.1 bits (55), Expect = 8.0
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 13/62 (20%)
Query: 32 LSAGLRKKQYISSATNIYNLFPDDAVVQYTQACRIIGTSDLALHQKLA-SLLLRMKRYAE 90
+ L++++ + N + SD + + A L +KR AE
Sbjct: 75 ILYWLKERELVDKFKNALKELMEK------------DYSDSRIATEEALRYLNWLKRLAE 122
Query: 91 AI 92
A+
Sbjct: 123 AL 124
>gnl|CDD|202730 pfam03704, BTAD, Bacterial transcriptional activator domain. Found
in the DNRI/REDD/AFSR family of regulators. This region
of AFSR along with the C terminal region is capable of
independently directing actinorhodin production. This
family contains TPR repeats.
Length = 146
Score = 25.3 bits (56), Expect = 8.7
Identities = 8/32 (25%), Positives = 15/32 (46%)
Query: 72 LALHQKLASLLLRMKRYAEAIDVSQTIMKAHP 103
L + LR+ R+ EA+ + ++ HP
Sbjct: 62 LRALEARIEADLRLGRHREALAELRALVALHP 93
>gnl|CDD|219099 pfam06595, BDV_P24, Borna disease virus P24 protein. This family
consists of several Borna disease virus (BDV) P24
proteins. The function of this family is unknown.
Length = 201
Score = 25.4 bits (55), Expect = 9.3
Identities = 12/62 (19%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 60 YTQACRIIGTSDLALHQKLASLLLRMKRYAEAID---------VSQTIMKAHPSYPKVHK 110
++ + RI+G + L + + +++ MK E +D S ++ +HP+ P+++
Sbjct: 127 HSDSIRILGENIKILDRSMKTMMETMKLMMEKVDLLYASTAVGTSAPMLPSHPAPPRIYP 186
Query: 111 QI 112
+
Sbjct: 187 SL 188
>gnl|CDD|132417 TIGR03374, ABALDH, 1-pyrroline dehydrogenase. Members of this
protein family are 1-pyrroline dehydrogenase (1.5.1.35),
also called gamma-aminobutyraldehyde dehydrogenase. This
enzyme can follow putrescine transaminase (EC 2.6.1.82)
for a two-step conversion of putrescine to
gamma-aminobutyric acid (GABA). The member from
Escherichia coli is characterized as a homotetramer that
binds one NADH per momomer. This enzyme belongs to the
medium-chain aldehyde dehydrogenases, and is quite
similar in sequence to the betaine aldehyde
dehydrogenase (EC 1.2.1.8) family.
Length = 472
Score = 25.3 bits (55), Expect = 9.9
Identities = 10/30 (33%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 7 DTMQIIQTIAEWHFLLYLLPWRWEP-LSAG 35
D + ++ +IA W++ L + W+ P L+AG
Sbjct: 136 DPLGVVASIAPWNYPLMMAAWKLAPALAAG 165
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 0.133 0.401
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,035,413
Number of extensions: 506517
Number of successful extensions: 708
Number of sequences better than 10.0: 1
Number of HSP's gapped: 707
Number of HSP's successfully gapped: 42
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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: 40 (21.6 bits)
S2: 53 (24.2 bits)