RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10916
(137 letters)
>gnl|CDD|223234 COG0156, BioF, 7-keto-8-aminopelargonate synthetase and related
enzymes [Coenzyme metabolism].
Length = 388
Score = 28.4 bits (64), Expect = 1.2
Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 17/68 (25%)
Query: 55 HGGQATLHSIRVLQPKQVRVDSQDDHDSTREFLWKRSSHIAHLVTEKLTSAARSLLQPIP 114
A L ++R+L+ + RE L + ++ + L +P
Sbjct: 277 AVAAAALAALRILE----------EGPERRERLQELAAF-------FRSLLKALGLVLLP 319
Query: 115 SNTPHIPL 122
S +P IP+
Sbjct: 320 SESPIIPV 327
>gnl|CDD|184752 PRK14573, PRK14573, bifunctional D-alanyl-alanine synthetase
A/UDP-N-acetylmuramate--L-alanine ligase; Provisional.
Length = 809
Score = 28.2 bits (63), Expect = 1.4
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 48 KINLRVMHGGQATLHSIRVLQPKQV-RVDSQDDHDS-----TREFLWKRSSHIAHLVTEK 101
K++L ++ GG++ H I +L K + + S + +D R+ LW+ S + + E
Sbjct: 451 KLSLGLVCGGKSCEHDISLLSAKNIAKYLSPEFYDVSYFLINRQGLWETVSSLETAIEED 510
>gnl|CDD|223460 COG0383, AMS1, Alpha-mannosidase [Carbohydrate transport and
metabolism].
Length = 943
Score = 27.4 bits (61), Expect = 3.2
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 1 MGSIVAILGHLMRM-RVYLKASIPTFQFGRGVK 32
+G G+L + ++Y A I FGRG
Sbjct: 120 LGYFPDTFGNLGQAPQLYENAGISAVAFGRGAA 152
>gnl|CDD|163191 TIGR03235, DNA_S_dndA, cysteine desulfurase DndA. This model
describes DndA, a protein related to IscS and part of a
larger family of cysteine desulfurases. It is encoded,
typically, divergently from a conserved, sparsely
distributed operon for sulfur modification of DNA. This
modification system is designated dnd, after the
phenotype of DNA degradation during electrophoresis. The
system is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndB is described
as a putative ATPase [DNA metabolism,
Restriction/modification].
Length = 353
Score = 27.1 bits (60), Expect = 3.6
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 11 LMRMRVYLKASIPTFQFGRGVKKELRSATATTAEMMG 47
++R R KA + FG G ++ LR T ++G
Sbjct: 211 VIRKRGKPKAPLKPIMFGGGQERGLRPGTLPVHLIVG 247
>gnl|CDD|114709 pfam06003, SMN, Survival motor neuron protein (SMN). This family
consists of several eukaryotic survival motor neuron
(SMN) proteins. The Survival of Motor Neurons (SMN)
protein, the product of the spinal muscular
atrophy-determining gene, is part of a large
macromolecular complex (SMN complex) that functions in
the assembly of spliceosomal small nuclear
ribonucleoproteins (snRNPs). The SMN complex functions
as a specificity factor essential for the efficient
assembly of Sm proteins on U snRNAs and likely protects
cells from illicit, and potentially deleterious,
non-specific binding of Sm proteins to RNAs.
Length = 264
Score = 26.9 bits (59), Expect = 4.0
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 112 PIPSNTPHIPLPPPPSRYPVYEEDNE 137
P P P IP PPP S P + ED+E
Sbjct: 203 PFPLGPPMIPPPPPMS--PDFGEDDE 226
>gnl|CDD|216194 pfam00922, Phosphoprotein, Vesiculovirus phosphoprotein.
Length = 283
Score = 26.8 bits (59), Expect = 4.0
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 97 LVTEKLTSAARSLLQPIPSNTPHIPLPPPPSR 128
++ E++T S + IPS+ P S
Sbjct: 163 IIKERMTPDVSSTSEHIPSSNTSPSTSEPVST 194
>gnl|CDD|179810 PRK04288, PRK04288, antiholin-like protein LrgB; Provisional.
Length = 232
Score = 26.6 bits (59), Expect = 4.4
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 8/43 (18%)
Query: 1 MGSIVAILGHLMRMRVYLKASIPTFQFGRGVKKELRSATATTA 43
+GS+ ++L +YL A + Q V + ATTA
Sbjct: 102 VGSVCSVLI------IYLVAKL--IQLDNAVMASMLPQAATTA 136
>gnl|CDD|239493 cd03399, Band_7_flotillin, Band_7_flotillin: a subgroup of the band
7 domain of flotillin (reggie) like proteins. This
subgroup contains proteins similar to stomatin,
prohibitin, flotillin, HlfK/C and podicin. These two
proteins are lipid raft-associated. Individual proteins
of this band 7 domain family may cluster to form
membrane microdomains which may in turn recruit
multiprotein complexes. Microdomains formed from
flotillin proteins may in addition be dynamic units with
their own regulatory functions. Flotillins have been
implicated in signal transduction, vesicle trafficking,
cytoskeleton rearrangement and, interact with a variety
of proteins. Flotillins may play a role in the
progression of prion disease, in the pathogenesis of
neurodegenerative diseases such as Parkinson's and
Alzheimer's disease and, in cancer invasion and
metastasis.
Length = 128
Score = 26.0 bits (58), Expect = 5.3
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 71 QVRVDSQDDHDST--REFLWKRSSHIAHLVTEKLTSAARSLL 110
QV+V ++ +T FL K I LV E L R+++
Sbjct: 31 QVKVGGTEEAIATAAERFLGKSEEEIEELVKEVLEGHLRAVV 72
>gnl|CDD|185104 PRK15182, PRK15182, Vi polysaccharide biosynthesis protein TviB;
Provisional.
Length = 425
Score = 26.6 bits (58), Expect = 5.3
Identities = 13/49 (26%), Positives = 27/49 (55%)
Query: 31 VKKELRSATATTAEMMGKINLRVMHGGQATLHSIRVLQPKQVRVDSQDD 79
+KK +TA AE++ ++ +++ G SI+V + +V ++Q D
Sbjct: 168 IKKITSGSTAQIAELIDEVYQQIISAGTYKAESIKVAEAAKVIENTQRD 216
>gnl|CDD|220828 pfam10630, DUF2476, Protein of unknown function (DUF2476). This is
a family of proteins of unknown function. The family is
rich in proline residues.
Length = 255
Score = 26.0 bits (56), Expect = 6.7
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 108 SLLQPIPSNTPHIPLPPPPSRYP 130
S+L+P+P +P PLPP PS P
Sbjct: 216 SMLKPLPD-SPLQPLPPSPSPNP 237
>gnl|CDD|240134 cd04864, LigD_Pol_like_1, LigD_Pol_like_1: Polymerase (Pol) domain
of mostly bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD, subgroup 1. 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. 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 Pol domains of PaeLigD and Mycobacterium
tuberculosis (Mt)LigD are stimulated by manganese, are
error-prone, and prefer adding rNTPs to dNTPs in vitro;
however PaeLigD and MtLigD belong to other subgroups,
proteins in this subgroup await functional
characterization.
Length = 228
Score = 25.9 bits (57), Expect = 7.0
Identities = 24/107 (22%), Positives = 38/107 (35%), Gaps = 16/107 (14%)
Query: 3 SIVAILGHLMRMRVYLKASIPTFQFGRGVKKELRSATATTAEMMGKINLR--VMHGGQAT 60
S L H M L S + +R+A E++ ++ L V G
Sbjct: 92 SRADDLEHPDLMVFDLDPSADDIE-------AVRTAALAVRELLDELGLPSFVKTTGSRG 144
Query: 61 LHSIRVLQPKQVRVDSQDDHDSTREFLWKRSSHIAHLVTEKLTSAAR 107
H V +D + D D R F + + +A + LT+ AR
Sbjct: 145 FHV-------VVPLDGRGDFDDVRAFAAEAADALAKRDPDLLTTEAR 184
>gnl|CDD|133151 cd05484, retropepsin_like_LTR_2, Retropepsins_like_LTR,
pepsin-like aspartate proteases. Retropepsin of
retrotransposons with long terminal repeats are
pepsin-like aspartate proteases. While fungal and
mammalian pepsins are bilobal proteins with
structurally related N- and C-termini, retropepsins are
half as long as their fungal and mammalian
counterparts. The monomers are structurally related to
one lobe of the pepsin molecule and retropepsins
function as homodimers. The active site aspartate
occurs within a motif (Asp-Thr/Ser-Gly), as it does in
pepsin. Retroviral aspartyl protease is synthesized as
part of the POL polyprotein that contains an aspartyl
protease, a reverse transcriptase, RNase H, and an
integrase. The POL polyprotein undergoes specific
enzymatic cleavage to yield the mature proteins. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where
catalytic residues have been identified. This group of
aspartate peptidases is classified by MEROPS as the
peptidase family A2 (retropepsin family, clan AA),
subfamily A2A.
Length = 91
Score = 25.2 bits (56), Expect = 7.3
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 31 VKKELRSATATTAEMMGKINLRVMHGGQA 59
KK LR+AT T ++G+I + V +GG+
Sbjct: 41 TKKRLRTATGTKLSVLGQILVTVKYGGKT 69
>gnl|CDD|227657 COG5354, COG5354, Uncharacterized protein, contains Trp-Asp (WD)
repeat [General function prediction only].
Length = 561
Score = 26.0 bits (57), Expect = 7.6
Identities = 9/41 (21%), Positives = 14/41 (34%), Gaps = 3/41 (7%)
Query: 81 DSTREFLW---KRSSHIAHLVTEKLTSAARSLLQPIPSNTP 118
+F +A+ EKL A + IP N+
Sbjct: 174 VGILDFSISPEGNHDELAYWTPEKLNKPAMVRILSIPKNSV 214
>gnl|CDD|219970 pfam08689, Med5, Mediator complex subunit Med5. The mediator
complex is required for the expression of nearly all RNA
pol II dependent genes in Saccharomyces cerevisiae.
Deletion of the MED5 gene leads to increased
transcription of nuclear genes encoding components of
the oxidative phosphorylation machinery, and decreased
transcription of mitochondrial genes encoding components
of the same machinery. There is no orthologue from
pombe, and this subunit appears to be fungal specific.
Length = 977
Score = 26.3 bits (58), Expect = 7.7
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 74 VDSQDDHDSTREFLWKRSSHIAHLVTEKLTSAARSLLQPIPSNTPHIPLPPPPS 127
V S+D +S R+ L + +++ + +TS R+ L IPS T L PS
Sbjct: 198 VLSKDLSESLRKKLGQ--AYLPLCNSPSITSPQRNRLDAIPSPTTFNKLGEDPS 249
>gnl|CDD|236431 PRK09250, PRK09250, fructose-bisphosphate aldolase; Provisional.
Length = 348
Score = 26.0 bits (58), Expect = 7.8
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 98 VTEKLTSAARSLLQ---PIPSNTPHIPLPPPPSRYPVYEEDN 136
+ L A SLL IP + H+P P R +Y + N
Sbjct: 4 IAMLLGKDADSLLSHRCKIPKDQLHLPGPDFVDRVMIYSDRN 45
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 0.132 0.386
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,870,741
Number of extensions: 572186
Number of successful extensions: 680
Number of sequences better than 10.0: 1
Number of HSP's gapped: 677
Number of HSP's successfully gapped: 25
Length of query: 137
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 50
Effective length of database: 7,078,804
Effective search space: 353940200
Effective search space used: 353940200
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 (21.8 bits)
S2: 54 (24.8 bits)