RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8434
(114 letters)
>gnl|CDD|215997 pfam00566, RabGAP-TBC, Rab-GTPase-TBC domain. Identification of a
TBC domain in GYP6_YEAST and GYP7_YEAST, which are
GTPase activator proteins of yeast Ypt6 and Ypt7,
implies that these domains are GTPase activator proteins
of Rab-like small GTPases.
Length = 206
Score = 51.6 bits (124), Expect = 3e-09
Identities = 27/115 (23%), Positives = 43/115 (37%), Gaps = 5/115 (4%)
Query: 1 YSQVVLDVNRSLKRFPPGIPIEQRLALQDQLTLLILKVIHAYPRLRYYQGYHDVAITFLL 60
Q+ DV R+ P + Q QL ++ P + Y QG + +A LL
Sbjct: 39 EEQIEKDVPRTF----PHHFFFKNGEGQQQLRRILKAYSIYNPDVGYCQGMNFIAAPLLL 94
Query: 61 VVG-EMKAFRILEVLSNDHLSENMRDTMDETSYVLNYMFPLVNKRSSDLCEFLER 114
VV E +AF L L + + L L+ K +L + L++
Sbjct: 95 VVLDEEEAFWCFVSLLEYLLRDFFLPSFPGLQRDLYVFEELLKKHDPELYKHLQK 149
>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor
(ARF-GEF); Provisional.
Length = 1780
Score = 28.3 bits (63), Expect = 0.99
Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 7/76 (9%)
Query: 34 LILKVIHAYPRLRYYQGYH-DVAI-TFLL---VVGE-MKAFRILEVLSNDHLSENMRD-T 86
L LKV+HAY +QG D AI FL + GE K RI+E + + N + +
Sbjct: 676 LSLKVMHAYVDSFDFQGMEFDEAIRAFLQGFRLPGEAQKIDRIMEKFAERYCKCNPKAFS 735
Query: 87 MDETSYVLNYMFPLVN 102
+T+YVL Y ++N
Sbjct: 736 SADTAYVLAYSVIMLN 751
>gnl|CDD|216074 pfam00710, Asparaginase, Asparaginase.
Length = 318
Score = 27.9 bits (63), Expect = 1.0
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 85 DTMDETSYVLNYMFPLVNK 103
DT++ET+ L+ M ++K
Sbjct: 85 DTLEETASFLSLMLENLDK 103
>gnl|CDD|214418 MTH00071, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 322
Score = 27.7 bits (62), Expect = 1.2
Identities = 17/40 (42%), Positives = 21/40 (52%)
Query: 31 LTLLILKVIHAYPRLRYYQGYHDVAITFLLVVGEMKAFRI 70
L++L L V +YPR RY Q H V FL + M F I
Sbjct: 271 LSMLFLWVRASYPRFRYDQLMHLVWKNFLPITLAMTIFHI 310
>gnl|CDD|129591 TIGR00500, met_pdase_I, methionine aminopeptidase, type I.
Methionine aminopeptidase is a cobalt-binding enzyme.
Bacterial and organellar examples (type I) differ from
eukaroytic and archaeal (type II) examples in lacking a
region of approximately 60 amino acids between the 4th
and 5th cobalt-binding ligands. This model describes
type I. The role of this protein in general is to
produce the mature form of cytosolic proteins by
removing the N-terminal methionine [Protein fate,
Protein modification and repair].
Length = 247
Score = 27.7 bits (62), Expect = 1.3
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 10/57 (17%)
Query: 18 GIPIEQRLALQDQLTLLILKVIHAYPRLRYYQGYH-DVAITFLLVVGEMKAFRILEV 73
GIP ++ L D + + + Y GYH D A TFL+ +A ++LE
Sbjct: 77 GIPDKKVLKDGDIVNIDVGV---------IYDGYHGDTAKTFLVGKISPEAEKLLEC 124
>gnl|CDD|214873 smart00870, Asparaginase, Asparaginase, found in various plant,
animal and bacterial cells. Asparaginase catalyses the
deamination of asparagine to yield aspartic acid and an
ammonium ion, resulting in a depletion of free
circulatory asparagine in plasma. The enzyme is
effective in the treatment of human malignant lymphomas,
which have a diminished capacity to produce asparagine
synthetase: in order to survive, such cells absorb
asparagine from blood plasma..- if Asn levels have been
depleted by injection of asparaginase, the lymphoma
cells die.
Length = 323
Score = 27.5 bits (62), Expect = 1.3
Identities = 6/14 (42%), Positives = 10/14 (71%)
Query: 85 DTMDETSYVLNYMF 98
DT++ET+Y L+
Sbjct: 88 DTLEETAYFLSLTL 101
>gnl|CDD|237588 PRK14022, PRK14022,
UDP-N-acetylmuramoylalanyl-D-glutamate--L-lysine ligase;
Provisional.
Length = 481
Score = 27.7 bits (62), Expect = 1.5
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 65 MKAFRILEVLSNDHLSENMRDTMDETSYVLNYMFPLVNKRSSD 107
+ +L++L DH N R+ +D+ Y NY + S D
Sbjct: 1 ITIETLLDILKKDH---NFREIIDQDHYHYNYSGVQFDDISYD 40
>gnl|CDD|223330 COG0252, AnsB, L-asparaginase/archaeal Glu-tRNAGln amidotransferase
subunit D [Amino acid transport and metabolism /
Translation, ribosomal structure and biogenesis].
Length = 351
Score = 27.3 bits (61), Expect = 2.0
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 7/30 (23%)
Query: 85 DTMDETSYVLNYMF----PLV---NKRSSD 107
DTM+ET++ L+ P+V R +D
Sbjct: 111 DTMEETAFFLSLTLNTPKPVVLTGAMRPAD 140
>gnl|CDD|151323 pfam10874, DUF2746, Protein of unknown function (DUF2746). This
family of proteins has no known function.
Length = 57
Score = 25.6 bits (56), Expect = 2.6
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 70 ILEVLSNDHLSENMRDTMDETSYVLNYMFPLVNKRSSDLCEFL 112
I E + N H NMRD +DE + F V + L E L
Sbjct: 1 IHEQVQNTH-DTNMRDDLDELVETVREGFKEVRRDIGGLREEL 42
>gnl|CDD|176181 cd05278, FDH_like, Formaldehyde dehydrogenases. Formaldehyde
dehydrogenase (FDH) is a member of the
zinc-dependent/medium chain alcohol dehydrogenase
family. Formaldehyde dehydrogenase (aka ADH3) may be
the ancestral form of alcohol dehydrogenase, which
evolved to detoxify formaldehyde. This CD contains
glutathione dependant FDH, glutathione independent FDH,
and related alcohol dehydrogenases. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. Unlike typical FDH, Pseudomonas
putida aldehyde-dismutating FDH (PFDH) is
glutathione-independent. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 347
Score = 26.9 bits (60), Expect = 2.8
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 5 VLDVNRSLKRFPPGIPIEQRLALQDQLT 32
V + +L + P G+P E L L D L
Sbjct: 127 VPYADMNLAKIPDGLPDEDALMLSDILP 154
>gnl|CDD|99744 cd06451, AGAT_like, Alanine-glyoxylate aminotransferase (AGAT)
family. This family belongs to pyridoxal phosphate
(PLP)-dependent aspartate aminotransferase superfamily
(fold I). The major groups in this CD correspond to
alanine-glyoxylate aminotransferase (AGAT),
serine-glyoxylate aminotransferase (SGAT), and
3-hydroxykynurenine transaminase (HKT). AGAT is a
homodimeric protein, which catalyses the transamination
of glyoxylate to glycine, and SGAT converts serine and
glyoxylate to hydroxypyruvate and glycine. HKT
catalyzes the PLP-dependent transamination of
3-hydroxykynurenine, a potentially toxic metabolite of
the kynurenine pathway.
Length = 356
Score = 26.5 bits (59), Expect = 3.4
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 69 RILEVLSN---DHLSENMRDTMDETSYVLNYMF 98
R+L+ ++ H S MDE L Y+F
Sbjct: 13 RVLKAMNRPMLGHRSPEFLALMDEILEGLRYVF 45
>gnl|CDD|178745 PLN03206, PLN03206, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1307
Score = 26.7 bits (59), Expect = 3.9
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 49 QGYHDVAITFLLVVGEMKAFRILEVLSND--HLSENM---RDTMDETSYVL 94
+ +T V+G++ A ++EV + LSE RD +ETS+ L
Sbjct: 944 EKLAAAGVT-AEVIGQVTASPLIEVKVDGATCLSEKTASLRDMWEETSFQL 993
>gnl|CDD|153078 cd07931, eukaryotic_phosphagen_kinases, Phosphagen (guanidino)
kinases mostly found in eukaryotes. Phosphagen
(guanidino) kinases are enzymes that transphosphorylate
a high energy phosphoguanidino compound, like
phosphocreatine (PCr) in the case of creatine kinase
(CK) or phosphoarginine in the case of arginine kinase,
which is used as an energy-storage and -transport
metabolite, to ADP, thereby creating ATP. The substrate
binding site is located in the cleft between the N and
C-terminal domains, but most of the catalytic residues
are found in the larger C-terminal domain. In higher
eukaryotes, CK exists in tissue-specific (muscle,
brain), as well as compartment-specific (mitochondrial
and cytosolic) isoforms. They are either coupled to
glycolysis (cytosolic form) or oxidative phosphorylation
(mitochondrial form). Besides CK and AK, the most
studied members of this family are also other phosphagen
kinases with different substrate specificities, like
glycocyamine kinase (GK), lombricine kinase (LK),
taurocyamine kinase (TK) and hypotaurocyamine kinase
(HTK).
Length = 338
Score = 25.7 bits (57), Expect = 5.5
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 8 VNRSLK--RFPPGIPIEQRLALQDQL 31
V R+L PPG+ EQR ++ +
Sbjct: 108 VARNLDGFPLPPGMTKEQRRQIERLM 133
>gnl|CDD|234571 PRK00011, glyA, serine hydroxymethyltransferase; Reviewed.
Length = 416
Score = 25.8 bits (58), Expect = 6.5
Identities = 9/16 (56%), Positives = 9/16 (56%), Gaps = 2/16 (12%)
Query: 42 YPRLRYYQG--YHDVA 55
YP RYY G Y DV
Sbjct: 57 YPGKRYYGGCEYVDVV 72
>gnl|CDD|177192 MTH00134, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 324
Score = 25.7 bits (57), Expect = 7.0
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 31 LTLLILKVIHAYPRLRYYQGYHDVAITFL 59
L+++ L V +YPR RY Q H V FL
Sbjct: 272 LSVVFLWVRASYPRFRYDQLMHLVWKNFL 300
>gnl|CDD|237273 PRK13018, PRK13018, cell division protein FtsZ; Provisional.
Length = 378
Score = 25.4 bits (56), Expect = 7.5
Identities = 9/28 (32%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 4 VVLDVNRSLKRFPPGIPIEQRLALQDQL 31
+V+D NR L P +PI ++ D++
Sbjct: 179 IVIDNNR-LLDIVPNLPIADAFSVADEV 205
>gnl|CDD|199208 cd08964, L-asparaginase_II, Type II (periplasmic) bacterial
L-asparaginase. Asparaginases (amidohydrolases, E.C.
3.5.1.1) are enzymes that catalyze the hydrolysis of
asparagine to aspartic acid and ammonia. In bacteria,
there are two classes of amidohydrolases. This model
represents type II L-asparaginases, which tend to be
highly specific for asparagine and localized to the
periplasm. They are potent antileukemic agents and have
been used in the treatment of acute lymphoblastic
leukemia (ALL), but not without severe side effects.
Tumor cells appear to have a heightened dependence on
exogenous L-aspartate, and depleting their surroundings
of L-aspartate may starve cancerous ALL cells. Type II
L-asparaginase acts as a tetramer, which is actually a
dimer of two tightly bound dimers. A conserved
threonine residue is thought to supply the nucleophile
hydroxy-group that attacks the amide bond. Many
bacterial L-asparaginases have both L-asparagine and
L-glutamine hydrolysis activities, to a different
degree, and some of them are annotated as
asparaginase/glutaminase.
Length = 319
Score = 25.5 bits (57), Expect = 8.0
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 85 DTMDETSYVLN 95
DT++ET+Y L+
Sbjct: 89 DTLEETAYFLD 99
>gnl|CDD|177166 MTH00104, ND1, NADH dehydrogenase subunit 1; Provisional.
Length = 318
Score = 25.4 bits (56), Expect = 9.3
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 31 LTLLILKVIHAYPRLRYYQGYH 52
LT+L L + +YPR RY Q H
Sbjct: 266 LTILFLWIRASYPRFRYDQLMH 287
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
0.326 0.142 0.407
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,826,818
Number of extensions: 510432
Number of successful extensions: 557
Number of sequences better than 10.0: 1
Number of HSP's gapped: 555
Number of HSP's successfully gapped: 34
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)