RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16482
(493 letters)
>gnl|CDD|218231 pfam04727, ELMO_CED12, ELMO/CED-12 family. This family represents
a conserved domain which is found in a number of
eukaryotic proteins including CED-12, ELMO I and ELMO
II. ELMO1 is a component of signalling pathways that
regulate phagocytosis and cell migration and is the
mammalian orthologue of the C. elegans gene, ced-12.
CED-12 is required for the engulfment of dying cells and
cell migration. In mammalian cells, ELMO1 interacts with
Dock180 as part of the CrkII/Dock180/Rac pathway
responsible for phagocytosis and cell migration. ELMO1
is ubiquitously expressed, although its expression is
highest in the spleen, an organ rich in immune cells.
ELMO1 has a PH domain and a polyproline sequence motif
at its C terminus which are not present in this
alignment.
Length = 170
Score = 197 bits (503), Expect = 4e-61
Identities = 71/170 (41%), Positives = 97/170 (57%), Gaps = 5/170 (2%)
Query: 303 QLKQEITLLARTQYDAENAEHEEKLLRLWQMLKPDVPLNSRVTKQWQTIGFQGDDPKTDF 362
+ L +T +D EN EH L LW+ L PD PL+SRV+++W+ +GFQGDDP TDF
Sbjct: 1 LTLNLLEKLRKTPFDLENPEHRRLLKTLWKALFPDEPLSSRVSEKWKDLGFQGDDPATDF 60
Query: 363 RGMGILGLDNLLHFASEYPTTAQHVLQHSLHP--QYGYAFAIVGINLTSLAYHLFQDDAA 420
RG G+LGL NLL+FA YP Q +L S H ++ Y FA+ IN+TS+ Y L +
Sbjct: 61 RGTGLLGLLNLLYFAENYPDEFQKLLLESSHRPAEHEYPFAVASINVTSMLYELLRIGKL 120
Query: 421 KTIVYNSCKSL---PSINVFHHFYCYLFYEFDRVWMESKPCVMDFSNVKT 467
Y + P++ F YC LF+ FDR W E + +MDF+ V
Sbjct: 121 DQEDYKNYGFPLFFPTLLAFEELYCALFHLFDRFWKEMRATIMDFNKVLE 170
>gnl|CDD|148383 pfam06747, CHCH, CHCH domain. we have identified a conserved motif
in the LOC118487 protein that we have called the CHCH
motif. Alignment of this protein with related members
showed the presence of three subgroups of proteins,
which are called the S (Small), N (N-terminal extended)
and C (C-terminal extended) subgroups. All three
sub-groups of proteins have in common that they contain
a predicted conserved [coiled coil 1]-[helix 1]-[coiled
coil 2]-[helix 2] domain (CHCH domain). Within each
helix of the CHCH domain, there are two cysteines
present in a C-X9-C motif. The N-group contains an
additional double helix domain, and each helix contains
the C-X9-C motif. This family contains a number of
characterized proteins: Cox19 protein - a nuclear gene
of Saccharomyces cerevisiae, codes for an 11-kDa protein
(Cox19p) required for expression of cytochrome oxidase.
Because cox19 mutants are able to synthesise the
mitochondrial and nuclear gene products of cytochrome
oxidase, Cox19p probably functions post-translationally
during assembly of the enzyme. Cox19p is present in the
cytoplasm and mitochondria, where it exists as a soluble
intermembrane protein. This dual location is similar to
what was previously reported for Cox17p, a low molecular
weight copper protein thought to be required for
maturation of the CuA centre of subunit 2 of cytochrome
oxidase. Cox19p have four conserved potential metal
ligands, these are three cysteines and one histidine.
Mrp10 - belongs to the class of yeast mitochondrial
ribosomal proteins that are essential for translation.
Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa
(NDUFA8) subunit. The CHCH domain was previously called
DUF657.
Length = 35
Score = 29.9 bits (68), Expect = 0.18
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 80 CFDEFQVYANCVDKSSTNFDLTPCRNTQAVFDKCMND 116
C +EF+ + C+ ++S CR F +C+
Sbjct: 1 CGEEFKAFLKCLKENSDELSK--CRKEFDAFRQCVKK 35
>gnl|CDD|219585 pfam07802, GCK, GCK domain. This domain is found in proteins
carrying other domains known to be involved in
intracellular signalling pathways (such as pfam00071)
indicating that it might also be involved in these
pathways. It has 4 highly conserved cysteine residues,
suggesting that it can bind zinc ions. Moreover, it is
found repeated in some members of this family ; this may
indicate that these domains are able to interact with
one another, raising the possibility that this domain
mediates heterodimerisation.
Length = 76
Score = 29.0 bits (65), Expect = 1.2
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 68 CALSFFRKVKESCFDEFQVYANCVD---KSSTNFDLTPCRNTQAVFDKCMND 116
C F K C + F + CV+ KS D+T C+ + KCM+
Sbjct: 3 CGFCLFMK-GGGCKEAFVAWEECVEEAEKSKEKDDVTKCKEARLTLKKCMDA 53
>gnl|CDD|112777 pfam03978, Borrelia_REV, Borrelia burgdorferi REV protein. This
family consists of several REV proteins from Borrelia
burgdorferi (Lyme disease spirochete). The function of
REV is unknown although it known that gene is induced
during the ingesting of host blood suggesting a role in
the metabolic activation of borreliae to adapt to
physiological stimuli.
Length = 160
Score = 29.8 bits (67), Expect = 1.7
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 301 YRQLKQEITLLARTQYDAENAEHEEKLLRL 330
++ K++I L D NAE EEKLL L
Sbjct: 49 FKNYKEKINELKEDLKDVGNAELEEKLLNL 78
>gnl|CDD|223550 COG0474, MgtA, Cation transport ATPase [Inorganic ion transport and
metabolism].
Length = 917
Score = 30.4 bits (69), Expect = 2.5
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 5/82 (6%)
Query: 251 MAVERKLHGNGLMMSVKGSVDTILLVKKINPTVHV---SFVKAISRCIEHIW--GYRQLK 305
M+V K ++ VKG+ + IL K + ++ + ++ + G R L
Sbjct: 455 MSVIVKTDEGKYILFVKGAPEVILERCKSIGELEPLTEEGLRTLEEAVKELASEGLRVLA 514
Query: 306 QEITLLARTQYDAENAEHEEKL 327
L R + D E E E L
Sbjct: 515 VAYKKLDRAEKDDEVDEIESDL 536
>gnl|CDD|217189 pfam02696, UPF0061, Uncharacterized ACR, YdiU/UPF0061 family.
Length = 487
Score = 29.9 bits (67), Expect = 3.1
Identities = 20/80 (25%), Positives = 28/80 (35%), Gaps = 9/80 (11%)
Query: 296 EHIWGYRQLKQEITLL--ARTQYDAENAEH---EEKLLRLWQMLKPDVPLNSRVTKQWQT 350
E Q +Q LL Y E + +E + + V +++ QWQ
Sbjct: 190 ERFHYRHQTEQIAQLLDHVIVTYYPEVSGSNSDDEDKYIAF--FRVVVERVAKLVAQWQA 247
Query: 351 IGFQGDDPKTDFRGMGILGL 370
GF TD M I GL
Sbjct: 248 AGFAHGVLNTD--NMSITGL 265
>gnl|CDD|225467 COG2915, COG2915, Uncharacterized protein involved in purine
metabolism [General function prediction only].
Length = 207
Score = 28.9 bits (65), Expect = 4.4
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 217 YGENHGARRSLGVEYSLSH---SRRYELQELIKF-LNKMAVERKLHGNGLMMS 265
YG H LG+E LS S R EL ++ L+ MA+ERKL + +
Sbjct: 54 YG-GHERNLKLGLETLLSVLNASSRGLNAELTRYALSLMALERKLSKDKDALD 105
>gnl|CDD|237351 PRK13326, PRK13326, pantothenate kinase; Reviewed.
Length = 262
Score = 28.6 bits (64), Expect = 6.6
Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 6/92 (6%)
Query: 402 IVGINLTSLAYHLFQDDAAKTIVYNSCKSLPSINVFHHFYCYLF-YEFDRVWMESKPCVM 460
I+ I TS+++ L++D+ + K S + + F F ++ ++V++ S V+
Sbjct: 10 IIDIGNTSISFALYKDNKMQIFCKLKTKLDLSFDELYSFLKEKFDFKVNQVFVSSVVPVI 69
Query: 461 DFSNVKTKFENNIRSLLSNSSVLLKTDLSIDI 492
D N I SL + + DL+ D+
Sbjct: 70 D-----KVLINVIFSLYKVKPLFIGFDLNYDL 96
>gnl|CDD|240530 cd13125, MATE_like_10, Uncharacterized subfamily of the multidrug
and toxic compound extrusion (MATE) proteins. This
family might function as a translocase for
lipopolysaccharides, such as O-antigen. The integral
membrane proteins from the MATE family are involved in
exporting metabolites across the cell membrane and are
responsible for multidrug resistance (MDR) in many
bacteria and animals. A number of family members are
involved in the synthesis of peptidoglycan components in
bacteria.
Length = 409
Score = 28.7 bits (65), Expect = 7.9
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 174 AFTVIMFYYLRPVW----YSVYFSYVRPLFKWIL 203
A ++ Y LR + +S F R LF W L
Sbjct: 301 AIGALLIYLLRDLIIQILFSEEFLPARELFLWQL 334
>gnl|CDD|192107 pfam08638, Med14, Mediator complex subunit MED14. Saccharomyces
cerevisiae RGR1 mediator complex subunit affects
chromatin structure, transcriptional regulation of
diverse genes and sporulation, required for glucose
repression, HO repression, RME1 repression and
sporulation. This subunit is also found in higher
eukaryotes and Med14 is the agreed unified nomenclature
for this subunit. Med14 is found in the tail region of
Mediator.
Length = 195
Score = 28.0 bits (63), Expect = 9.2
Identities = 11/46 (23%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 285 VSFVKAISRCIEHIWGYRQLKQEITLLARTQYDAENAEHEEKLLRL 330
+ ++R + Y +L Q I LLA E+ E + ++L
Sbjct: 3 IPLSLLLNRLAQQ--SYNELTQLIELLASGDTSEEDVEKKVRILNF 46
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
0.323 0.137 0.425
Gapped
Lambda K H
0.267 0.0673 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,110,212
Number of extensions: 2420976
Number of successful extensions: 1735
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1731
Number of HSP's successfully gapped: 16
Length of query: 493
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 392
Effective length of database: 6,457,848
Effective search space: 2531476416
Effective search space used: 2531476416
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 (22.0 bits)
S2: 61 (27.4 bits)