RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15677
(96 letters)
>gnl|CDD|238902 cd01921, cyclophilin_RRM, cyclophilin_RRM: cyclophilin-type
peptidylprolyl cis- trans isomerase domain occuring with
a C-terminal RNA recognition motif domain (RRM). This
subfamily of the cyclophilin domain family contains a
number of eukaryotic cyclophilins having the RRM domain
including the nuclear proteins: human hCyP-57,
Arabidopsis thaliana AtCYP59, Caenorhabditis elegans
CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241
protein has been shown to have a role in cell
morphogenesis.
Length = 166
Score = 122 bits (308), Expect = 4e-37
Identities = 54/96 (56%), Positives = 71/96 (73%), Gaps = 1/96 (1%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
+FIAQTGDPTG G GG S++ YG AR++E E P + HSK G VSMV+ G+ L GSQ
Sbjct: 45 DFIAQTGDPTGTGAGGESIYSQLYGRQARFFEPEILPLLKHSKKGTVSMVNAGDNLNGSQ 104
Query: 62 FFITLGPDLKSLN-EHCVFGEIAEGFDILLKLNNAI 96
F+ITLG +L L+ +H VFG++ EGFD+L K+N+AI
Sbjct: 105 FYITLGENLDYLDGKHTVFGQVVEGFDVLEKINDAI 140
>gnl|CDD|238908 cd01927, cyclophilin_WD40, cyclophilin_WD40: cyclophilin-type
peptidylprolyl cis- trans isomerases (cyclophilins)
having a WD40 domain. This group consists of several
hypothetical and putative eukaryotic and bacterial
proteins which have a cyclophilin domain and a WD40
domain. Function of the protein is not known.
Length = 148
Score = 79.8 bits (197), Expect = 1e-20
Identities = 37/94 (39%), Positives = 53/94 (56%), Gaps = 7/94 (7%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
F+ QTGDPTG GTGG S++G + +E E P + H +P +SM + G GSQ
Sbjct: 45 GFMIQTGDPTGDGTGGESIWG-------KEFEDEFSPSLKHDRPYTLSMANAGPNTNGSQ 97
Query: 62 FFITLGPDLKSLNEHCVFGEIAEGFDILLKLNNA 95
FFIT N+H VFG + +G D++ ++ N
Sbjct: 98 FFITTVATPWLDNKHTVFGRVVKGMDVVQRIENV 131
>gnl|CDD|215759 pfam00160, Pro_isomerase, Cyclophilin type peptidyl-prolyl
cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans
isomerases, also known as cyclophilins, share this
domain of about 109 amino acids. Cyclophilins have been
found in all organisms studied so far and catalyze
peptidyl-prolyl isomerisation during which the peptide
bond preceding proline (the peptidyl-prolyl bond) is
stabilised in the cis conformation. Mammalian
cyclophilin A (CypA) is a major cellular target for the
immunosuppressive drug cyclosporin A (CsA). Other roles
for cyclophilins may include chaperone and cell
signalling function.
Length = 144
Score = 77.3 bits (191), Expect = 1e-19
Identities = 38/95 (40%), Positives = 47/95 (49%), Gaps = 14/95 (14%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
F+ Q GDPTG GTGG R E K+ H K G +SM G GSQ
Sbjct: 47 GFMIQGGDPTGPGTGG-----------KRSIPDEFVSKLKH-KRGTLSMARSGPNSAGSQ 94
Query: 62 FFITLGPDLKSLN-EHCVFGEIAEGFDILLKLNNA 95
FFITLG D L+ + VFG + EG D++ K+
Sbjct: 95 FFITLG-DAPHLDGGYTVFGRVVEGMDVVEKIEKV 128
>gnl|CDD|238904 cd01923, cyclophilin_RING, cyclophilin_RING: cyclophilin-type
peptidylprolyl cis- trans isomerases (cyclophilins)
having a modified RING finger domain. This group
includes the nuclear proteins, Human hCyP-60 and
Caenorhabditis elegans MOG-6 which, compared to the
archetypal cyclophilin Human cyclophilin A exhibit
reduced peptidylprolyl cis- trans isomerase activity and
lack a residue important for cyclophilin binding. Human
hCyP-60 has been shown to physically interact with the
proteinase inhibitor peptide eglin c and; C. elegans
MOG-6 to physically interact with MEP-1, a nuclear zinc
finger protein. MOG-6 has been shown to function in
germline sex determination.
Length = 159
Score = 75.5 bits (186), Expect = 7e-19
Identities = 35/94 (37%), Positives = 48/94 (51%), Gaps = 7/94 (7%)
Query: 1 ANFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
NF+ Q GDPTG G GG S++G + D E +P + H G++SM + G GS
Sbjct: 46 RNFMIQGGDPTGTGRGGESIWGKPFKD-------EFKPNLSHDGRGVLSMANSGPNTNGS 98
Query: 61 QFFITLGPDLKSLNEHCVFGEIAEGFDILLKLNN 94
QFFIT +H VFG + G + L + N
Sbjct: 99 QFFITYRSCKHLDGKHTVFGRVVGGLETLEAMEN 132
>gnl|CDD|238909 cd01928, Cyclophilin_PPIL3_like, Cyclophilin_PPIL3_like. Proteins
similar to Human cyclophilin-like peptidylprolyl cis-
trans isomerase (PPIL3). Members of this family lack a
key residue important for cyclosporin binding: the
tryptophan residue corresponding to W121 in human
hCyP-18a; most members have a histidine at this
position. The exact function of the protein is not
known.
Length = 153
Score = 73.2 bits (180), Expect = 4e-18
Identities = 36/94 (38%), Positives = 52/94 (55%), Gaps = 9/94 (9%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
F+ QTGDPTG G GG S++G + +E E + + H G+VSM + G GSQ
Sbjct: 48 GFMVQTGDPTGTGKGGESIWG-------KKFEDEFRETLKHDSRGVVSMANNGPNTNGSQ 100
Query: 62 FFITLGPDLKSLN-EHCVFGEIAEGFDILLKLNN 94
FFIT L+ ++ VFG++ +GF+ L L
Sbjct: 101 FFITYAK-QPHLDGKYTVFGKVIDGFETLDTLEK 133
>gnl|CDD|238906 cd01925, cyclophilin_CeCYP16-like, cyclophilin_CeCYP16-like:
cyclophilin-type peptidylprolyl cis- trans isomerase)
(PPIase) domain similar to Caenorhabditis elegans
cyclophilin 16. C. elegans CeCYP-16, compared to the
archetypal cyclophilin Human cyclophilin A has, a
reduced peptidylprolyl cis- trans isomerase activity, is
cyclosporin insensitive and shows an altered substrate
preference favoring, hydrophobic, acidic or amide amino
acids. Most members of this subfamily have a glutamate
residue in the active site at the position equivalent to
a tryptophan (W121 in Human cyclophilin A), which has
been shown to be important for cyclophilin binding.
Length = 171
Score = 73.9 bits (182), Expect = 4e-18
Identities = 38/96 (39%), Positives = 52/96 (54%), Gaps = 10/96 (10%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
FI Q GDPTG GTGG S++G + D E ++ ++ GLV M + G+ GSQ
Sbjct: 53 GFIIQGGDPTGTGTGGESIYGEPFKD-------EFHSRLRFNRRGLVGMANAGDDSNGSQ 105
Query: 62 FFITLGPDLKSLNEHCVFGEIAEGFDI--LLKLNNA 95
FF TL + N+H +FG++ G I LLKL
Sbjct: 106 FFFTLDKADELNNKHTLFGKV-TGDTIYNLLKLAEV 140
>gnl|CDD|238194 cd00317, cyclophilin, cyclophilin: cyclophilin-type peptidylprolyl
cis- trans isomerases. This family contains eukaryotic,
bacterial and archeal proteins which exhibit a
peptidylprolyl cis- trans isomerases activity (PPIase,
Rotamase) and in addition bind the immunosuppressive
drug cyclosporin (CsA). Immunosuppression in
vertebrates is believed to be the result of the
cyclophilin A-cyclosporin protein drug complex binding
to and inhibiting the protein-phosphatase calcineurin.
PPIase is an enzyme which accelerates protein folding by
catalyzing the cis-trans isomerization of the peptide
bonds preceding proline residues. Cyclophilins are a
diverse family in terms of function and have been
implicated in protein folding processes which depend on
catalytic /chaperone-like activities. This group
contains human cyclophilin 40, a co-chaperone of the
hsp90 chaperone system; human cyclophilin A, a
chaperone in the HIV-1 infectious process and; human
cyclophilin H, a component of the U4/U6 snRNP, whose
isomerization or chaperoning activities may play a role
in RNA splicing. .
Length = 146
Score = 71.9 bits (177), Expect = 1e-17
Identities = 34/94 (36%), Positives = 45/94 (47%), Gaps = 8/94 (8%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQ 61
F+ Q GDPTG G GGS + E P H + G +SM + G GSQ
Sbjct: 45 GFMIQGGDPTGTGGGGS--------GPGYKFPDENFPLKYHHRRGTLSMANAGPNTNGSQ 96
Query: 62 FFITLGPDLKSLNEHCVFGEIAEGFDILLKLNNA 95
FFIT P +H VFG++ EG D++ K+
Sbjct: 97 FFITTAPTPHLDGKHTVFGKVVEGMDVVDKIERG 130
>gnl|CDD|238903 cd01922, cyclophilin_SpCYP2_like, cyclophilin_SpCYP2_like:
cyclophilin 2-like peptidylprolyl cis- trans isomerase
(PPIase) domain similar to Schizosaccharomyces pombe
cyp-2. These proteins bind their respective SNW
chromatin binding protein in autologous systems, in a
CsA independent manner indicating interaction with a
surface outside the PPIase active site. SNW proteins
play a basic and broad range role in signaling.
Length = 146
Score = 71.8 bits (176), Expect = 1e-17
Identities = 33/93 (35%), Positives = 54/93 (58%), Gaps = 7/93 (7%)
Query: 1 ANFIAQTGDPTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
+F+ Q GDPTG G GG+S++G + +E E P++ H+ G++SM + G GS
Sbjct: 44 KDFMIQGGDPTGTGRGGASIYG-------KKFEDEIHPELKHTGAGILSMANAGPNTNGS 96
Query: 61 QFFITLGPDLKSLNEHCVFGEIAEGFDILLKLN 93
QFFITL P +H +FG +++G ++ +
Sbjct: 97 QFFITLAPTPWLDGKHTIFGRVSKGMKVIENMV 129
>gnl|CDD|238907 cd01926, cyclophilin_ABH_like, cyclophilin_ABH_like: Cyclophilin
A, B and H-like cyclophilin-type peptidylprolyl cis-
trans isomerase (PPIase) domain. This family represents
the archetypal cystolic cyclophilin similar to human
cyclophilins A, B and H. PPIase is an enzyme which
accelerates protein folding by catalyzing the cis-trans
isomerization of the peptide bonds preceding proline
residues. These enzymes have been implicated in protein
folding processes which depend on catalytic
/chaperone-like activities. As cyclophilins, Human
hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae
Cpr1 and C. elegans Cyp-3, are inhibited by the
immunosuppressive drug cyclopsporin A (CsA). CsA binds
to the PPIase active site. Cyp-3. S. cerevisiae Cpr1
interacts with the Rpd3 - Sin3 complex and in addition
is a component of the Set3 complex. S. cerevisiae Cpr1
has also been shown to have a role in Zpr1p nuclear
transport. Human cyclophilin H associates with the
[U4/U6.U5] tri-snRNP particles of the splicesome.
Length = 164
Score = 68.8 bits (169), Expect = 3e-16
Identities = 39/98 (39%), Positives = 53/98 (54%), Gaps = 17/98 (17%)
Query: 2 NFIAQTGDPT-GVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
+F+ Q GD T G GTGG S++G + D K+ H+ PGL+SM + G GS
Sbjct: 61 DFMIQGGDFTRGNGTGGKSIYGEKFPDENF--------KLKHTGPGLLSMANAGPNTNGS 112
Query: 61 QFFITLGP----DLKSLNEHCVFGEIAEGFDILLKLNN 94
QFFIT D K H VFG++ EG D++ K+ N
Sbjct: 113 QFFITTVKTPWLDGK----HVVFGKVVEGMDVVKKIEN 146
>gnl|CDD|223725 COG0652, PpiB, Peptidyl-prolyl cis-trans isomerase (rotamase) -
cyclophilin family [Posttranslational modification,
protein turnover, chaperones].
Length = 158
Score = 66.1 bits (162), Expect = 3e-15
Identities = 34/98 (34%), Positives = 47/98 (47%), Gaps = 15/98 (15%)
Query: 2 NFIAQTGDPTG-VGTGGSSVFGLAYGDHARYYEAETQPKIPH-SKPGLVSMVHCGE-GLL 58
F+ Q GDPTG GTGG ++ E K G +SM G+
Sbjct: 47 GFMIQGGDPTGGDGTGGPGPP----------FKDENFALNGDRHKRGTLSMARAGDPNSN 96
Query: 59 GSQFFITLGPDLKSLNE-HCVFGEIAEGFDILLKLNNA 95
GSQFFIT+ D L+ + VFG++ EG D++ K+ N
Sbjct: 97 GSQFFITVV-DNPFLDGKYTVFGQVVEGMDVVDKIKNG 133
>gnl|CDD|240249 PTZ00060, PTZ00060, cyclophilin; Provisional.
Length = 183
Score = 62.9 bits (153), Expect = 9e-14
Identities = 34/89 (38%), Positives = 48/89 (53%), Gaps = 9/89 (10%)
Query: 2 NFIAQTGDPT-GVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
F+ Q GD T GTGG S++G + D K+ H +PGL+SM + G GS
Sbjct: 77 QFMCQGGDITNHNGTGGESIYGRKFTDE--------NFKLKHDQPGLLSMANAGPNTNGS 128
Query: 61 QFFITLGPDLKSLNEHCVFGEIAEGFDIL 89
QFFIT P +H VFG++ EG +++
Sbjct: 129 QFFITTVPCPWLDGKHVVFGKVIEGMEVV 157
>gnl|CDD|178694 PLN03149, PLN03149, peptidyl-prolyl isomerase H (cyclophilin H);
Provisional.
Length = 186
Score = 46.8 bits (111), Expect = 1e-07
Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 10/95 (10%)
Query: 2 NFIAQTGD-PTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
+F+ Q GD G GTG S++G + D + A+ H+ PGL+SM + G G
Sbjct: 79 DFMIQGGDFLKGDGTGCVSIYGSKFEDEN--FIAK------HTGPGLLSMANSGPNTNGC 130
Query: 61 QFFITLGPDLKSLNEHCVFGEI-AEGFDILLKLNN 94
QFFIT N+H VFG + +G ++ K+ N
Sbjct: 131 QFFITCAKCDWLDNKHVVFGRVLGDGLLVVRKIEN 165
>gnl|CDD|140248 PTZ00221, PTZ00221, cyclophilin; Provisional.
Length = 249
Score = 38.3 bits (89), Expect = 2e-04
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 39 KIPHSKPGLVSMVHCGEGLLGSQFFITLGPDLKSLN-EHCVFGEIAEGFDILLKL 92
+ H++ GL++M+ G GS F ITLGP SL+ + VFG+ + +L KL
Sbjct: 143 RHRHTERGLLTMISEGPHTSGSVFGITLGPS-PSLDFKQVVFGKAVDDLSLLEKL 196
>gnl|CDD|235658 PRK05972, ligD, ATP-dependent DNA ligase; Reviewed.
Length = 860
Score = 35.7 bits (83), Expect = 0.001
Identities = 17/37 (45%), Positives = 21/37 (56%)
Query: 27 DHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQFF 63
D ARYYEA +PH K VS+V +G+ G FF
Sbjct: 591 DLARYYEAVADWMLPHLKGRPVSLVRAPDGIGGELFF 627
>gnl|CDD|238905 cd01924, cyclophilin_TLP40_like, cyclophilin_TLP40_like:
cyclophilin-type peptidylprolyl cis- trans isomerases
(cyclophilins) similar ot the Spinach thylakoid lumen
protein TLP40. Compared to the archetypal cyclophilin
Human cyclophilin A, these proteins have similar
peptidylprolyl cis- trans isomerase activity and reduced
affinity for cyclosporin A. Spinach TLP40 has been shown
to have a dual function as a folding catalyst and
regulator of dephosphorylation.
Length = 176
Score = 33.6 bits (77), Expect = 0.006
Identities = 31/120 (25%), Positives = 44/120 (36%), Gaps = 33/120 (27%)
Query: 3 FIAQTGDPTGVGTG---------------------GSSVFGLAYGDHARYYEAETQPKIP 41
F+ QTGDP G G V+G + RY + QP +P
Sbjct: 46 FVVQTGDPQGKNPGFPDPETGKSRTIPLEIKPEGQKQPVYGKTLEEAGRY---DEQPVLP 102
Query: 42 HSKPGLVSMVHCGEGLLG--SQFFITLG-PDLKSLN------EHCVFGEIAEGFDILLKL 92
+ G ++M SQFF L +L + VFG + +G DIL +L
Sbjct: 103 FNAFGAIAMARTEFDPNSASSQFFFLLKDNELTPSRNNVLDGRYAVFGYVTDGLDILREL 162
>gnl|CDD|240132 cd04862, PaeLigD_Pol_like, PaeLigD_Pol_like: Polymerase (Pol)
domain of bacterial LigD proteins similar to
Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain
belongs to the archaeal/eukaryal primase (AEP)
superfamily. In prokaryotes, LigD along with Ku is
required for non-homologous end joining (NHEJ)-mediated
repair of DNA double-strand breaks (DSB). NHEJ-mediated
DNA DSB repair is error-prone. PaeLigD is monomeric,
containing an N-terminal phosphoesterase module, a
central polymerase (Pol) domain, and a C-terminal
ATP-dependent ligase domain. It has been suggested that
LigD Pol contributes to NHEJ-mediated DNA DSB repair in
vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The PaeLigD Pol domain in vitro, in a
manganese-dependent fashion, catalyzes templated
extensions of 5'-overhang duplex DNA, and nontemplated
single-nucleotide additions to blunt-end duplex DNA; it
preferentially adds single ribonucleotides at blunt DNA
ends. PaeLigD Pol adds a correctly paired rNTP to the
DNA primer termini more rapidly than it does a
correctly paired dNTP; it has higher infidelity as an
RNA polymerase than it does as a DNA polymerase, which
is in keeping with the mutagenic property of
NHEJ-mediated DNA DSB repair.
Length = 227
Score = 30.7 bits (70), Expect = 0.064
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 26 GDHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQFF 63
D ARYY A +PH +S+V C +G+ G FF
Sbjct: 2 LDLARYYAAVAPWMLPHLAGRPLSLVRCPDGIGGECFF 39
>gnl|CDD|238901 cd01920, cyclophilin_EcCYP_like, cyclophilin_EcCYP_like:
cyclophilin-type A-like peptidylprolyl cis- trans
isomerase (PPIase) domain similar to the cytosolic E.
coli cyclophilin A and Streptomyces antibioticus
SanCyp18. Compared to the archetypal cyclophilin Human
cyclophilin A, these have reduced affinity for
cyclosporin A. E. coli cyclophilin A has a similar
peptidylprolyl cis- trans isomerase activity to the
human cyclophilin A. Most members of this subfamily
contain a phenylalanine residue at the position
equivalent to Human cyclophilin W121, where a tyrptophan
has been shown to be important for cyclophilin binding.
Length = 155
Score = 28.9 bits (65), Expect = 0.25
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 60 SQFFITLGPDLKSLNE------HCVFGEIAEGFDILLKLNN 94
SQFFI L D SL+ + VFGE+ EG D++ K+
Sbjct: 94 SQFFINL-KDNASLDYQNEQWGYTVFGEVTEGMDVVDKIAG 133
>gnl|CDD|225823 COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA
replication, recombination, and repair].
Length = 299
Score = 27.4 bits (61), Expect = 1.2
Identities = 15/37 (40%), Positives = 19/37 (51%)
Query: 27 DHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQFF 63
D ARYY A +P VS+V C +G+ G FF
Sbjct: 28 DLARYYAAVADRMLPFLAGRPVSLVRCPDGIGGEAFF 64
>gnl|CDD|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D. Members of this protein
family are DNA ligases involved in the repair of DNA
double-stranded breaks by non-homologous end joining
(NHEJ). The system of the bacterial Ku protein
(TIGR02772) plus this DNA ligase is seen in about 20 %
of bacterial genomes to date and at least one archaeon
(Archeoglobus fulgidus). This model describes a central
and a C-terminal domain. These two domains may be
permuted, as in genus Mycobacterium, or divided into
tandem ORFs, and therefore not be identified by This
model. An additional N-terminal 3'-phosphoesterase (PE)
domain present in some but not all examples of this
ligase is not included in the seed alignment for this
model; This model models only the central ATP-dependent
ligase domain and the C-terminal polymerase domain. Most
examples of genes for this ligase are adjacent to the
gene for Ku [DNA metabolism, DNA replication,
recombination, and repair].
Length = 552
Score = 26.9 bits (60), Expect = 1.7
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 27 DHARYYEAETQPKIPHSKPGLVSMVHCGEGLLGSQFF 63
D A YY +P K +S++ C +G+ G FF
Sbjct: 299 DLAVYYAEVGDWMLPFLKGRPLSLIRCPDGIGGECFF 335
>gnl|CDD|222164 pfam13480, Acetyltransf_6, Acetyltransferase (GNAT) domain. This
family contains proteins with N-acetyltransferase
functions.
Length = 144
Score = 26.1 bits (58), Expect = 2.5
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 18 SSVFGLAYGDHARYYEAETQPKIPHSKPGLVSMVHC 53
++V GL G YY P+ PGL+ +
Sbjct: 86 AAVLGLRDGGRLYYYLGGYDPEFARLSPGLLLLWEL 121
>gnl|CDD|182734 PRK10791, PRK10791, peptidyl-prolyl cis-trans isomerase B (rotamase
B); Provisional.
Length = 164
Score = 26.0 bits (57), Expect = 3.1
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 10/42 (23%)
Query: 60 SQFFITLGPDLKSLN---------EHCVFGEIAEGFDILLKL 92
+QFFI + D LN +CVF E+ EG D++ K+
Sbjct: 96 AQFFINVV-DNDFLNFSGESLQGWGYCVFAEVVEGMDVVDKI 136
>gnl|CDD|132852 cd07213, Pat17_PNPLA8_PNPLA9_like1, Patatin-like phospholipase.
Patatin is a storage protein of the potato tuber that
shows Phospholipase A2 activity (PLA2; EC 3.1.1.4).
Patatin catalyzes the nonspecific hydrolysis of
phospholipids, glycolipids, sulfolipids, and mono- and
diacylglycerols, thereby showing lipid acyl hydrolase
activity. The active site includes an oxyanion hole
with a conserved GGxR motif; it is found in almost all
the members of this family. The catalytic dyad is
formed by a serine and an aspartate. Patatin belongs to
the alpha-beta hydrolase family which is identified by
a characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Members of this family
have been found also in vertebrates. This family
includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9
(iPLA2-beta) like phospholipases from human as well as
the Pat17 isozyme from Solanum cardiophyllum.
Length = 288
Score = 25.7 bits (57), Expect = 4.0
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 4/55 (7%)
Query: 2 NFIAQTGDPTGVGTGGSSVFGLAYGDH----ARYYEAETQPKIPHSKPGLVSMVH 52
+F+ Q G G GLA G + YE S G + +
Sbjct: 30 SFLDQIDLFAGTSAGSLIALGLALGYSPRQVLKLYEEVGLKVFSKSSAGGGAGNN 84
>gnl|CDD|226148 COG3621, COG3621, Patatin [General function prediction only].
Length = 394
Score = 25.6 bits (56), Expect = 5.4
Identities = 10/38 (26%), Positives = 12/38 (31%), Gaps = 4/38 (10%)
Query: 11 TGVGTGGSSVFGLAYGDHAR----YYEAETQPKIPHSK 44
G GG GLA G R + A+ P
Sbjct: 47 GGTSIGGILALGLALGKSPRELKQLFSAQQAQIFPEEM 84
>gnl|CDD|233046 TIGR00603, rad25, DNA repair helicase rad25. All proteins in this
family for which functions are known are DNA-DNA
helicases used for the initiation of nucleotide excision
repair and transacription as part of the TFIIH
complex.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 = 732
Score = 25.1 bits (55), Expect = 6.6
Identities = 11/36 (30%), Positives = 13/36 (36%), Gaps = 1/36 (2%)
Query: 10 PTGVGTGGSSVFGLAYGDHARYYEAETQPKIPHSKP 45
G S+ L+ GD Y E P I SK
Sbjct: 690 SGKAVRRGGSLSSLSGGDDMAYMEYRK-PAIKKSKK 724
>gnl|CDD|233274 TIGR01110, mdcA, malonate decarboxylase, alpha subunit. This model
describes malonate decarboxylase alpha subunit, from
both the water-soluble form as found in Klebsiella
pneumoniae and the form couple to sodium ion pumping in
Malonomonas rubra. Malonate decarboxylase Na+ pump is
the paradigm of the family of Na+ transport
decarboxylases. Essentially, it couples the energy
derived from decarboxylation of a carboxylic acid
substrate to move Na+ ion across the bilayer. Functional
malonate decarboylase is a multi subunit protein. The
alpha subunit enzymatically performs the transfer of
malonate (substrate) to an acyl carrier protein subunit
for subsequent decarboxylation, hence the name:
acetyl-S-acyl carrier protein:malonate carrier
protein-SH transferase [Transport and binding proteins,
Cations and iron carrying compounds, Energy metabolism,
Other].
Length = 543
Score = 25.2 bits (55), Expect = 7.0
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 40 IPHSKPGLVSMVHCGEGLLGSQFFITLGPDL 70
IP + G V VH G LG + +I PD+
Sbjct: 286 IPAIESGWVESVHSFGGELGMEDYIEARPDV 316
>gnl|CDD|238617 cd01292, metallo-dependent_hydrolases, Superfamily of
metallo-dependent hydrolases (also called amidohydrolase
superfamily) is a large group of proteins that show
conservation in their 3-dimensional fold (TIM barrel)
and in details of their active site. The vast majority
of the members have a conserved metal binding site,
involving four histidines and one aspartic acid residue.
In the common reaction mechanism, the metal ion (or
ions) deprotonate a water molecule for a nucleophilic
attack on the substrate. The family includes urease
alpha, adenosine deaminase, phosphotriesterase
dihydroorotases, allantoinases, hydantoinases, AMP-,
adenine and cytosine deaminases, imidazolonepropionase,
aryldialkylphosphatase, chlorohydrolases,
formylmethanofuran dehydrogenases and others.
Length = 275
Score = 25.0 bits (54), Expect = 7.2
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 5/54 (9%)
Query: 44 KPGLVSMVHCGEGLLGSQFFITL----GPDLKSLNEHCVFGEIAEGFDILLKLN 93
K GL ++H GE ++ L + + H + E ++L +
Sbjct: 144 KLGLPVVIHAGELPDPTRALEDLVALLRLGGRVVIGHVSHLD-PELLELLKEAG 196
>gnl|CDD|131967 TIGR02921, PEP_integral, PEP-CTERM family integral membrane
protein. Members of this protein family, found in three
different species so far, have a PEP-CTERM sequence at
the carboxyl-terminus (see model TIGR02595), but are
unusual among PEP-CTERM proteins in having multiple
predicted transmembrane segments. The function is
unknown. It is proposed that a member of the EpsH
family, to be designated exosortase (see TIGR02602),
recognizes and cleaves PEP-CTERM proteins in a manner
analogous to the cleavage of LPXTG proteins by sortase
(see Haft, et al., 2006).
Length = 952
Score = 25.0 bits (54), Expect = 8.0
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 32 YEAETQPKIPHSKPGLVSMVHCGEGLLGS 60
YE E K+ ++ + +VH GE L G+
Sbjct: 740 YELEKNFKLKAAQMAPLWLVHLGETLAGA 768
>gnl|CDD|211782 TIGR03064, sortase_srtB, sortase, SrtB family. Members of this
transpeptidase family are, in most cases, designated
sortase B, product of the srtB gene. This protein shows
only distant similarity to the sortase A family, for
which there may be several members in a single
bacterial genome. Typical SrtB substrate motifs include
NAKTN, NPKSS, etc, and otherwise resemble the LPXTG
sorting signals recognized by sortase A proteins [Cell
envelope, Other, Protein fate, Protein and peptide
secretion and trafficking].
Length = 232
Score = 24.6 bits (54), Expect = 8.4
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 71 KSLNEHCVFGEIAEGFDILLKLNNAI 96
KS+ + GE+ + F+ LL +N+ I
Sbjct: 44 KSMAKQSEEGEVRKQFEDLLAINSDI 69
>gnl|CDD|221240 pfam11814, DUF3335, Peptidase_C39 like family.
Length = 208
Score = 24.5 bits (54), Expect = 9.7
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 14 GTGGSSVFGLAYGDHARYYEAE 35
G GG S GLA H R +E E
Sbjct: 50 GHGGCSPHGLALAAHRRGFEVE 71
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
0.319 0.141 0.428
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,893,745
Number of extensions: 393420
Number of successful extensions: 320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 301
Number of HSP's successfully gapped: 36
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)