RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7337
(233 letters)
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 30.9 bits (70), Expect = 0.050
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 90 CLLCEVQLVSNTFYIFPCGHTFHSHCIVQ 118
C +C + + + I PCGHTF CI +
Sbjct: 1 CPICLEEYLKDPV-ILPCGHTFCRSCIRK 28
>gnl|CDD|217756 pfam03839, Sec62, Translocation protein Sec62.
Length = 217
Score = 33.2 bits (76), Expect = 0.064
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 153 MIEKESKKEGGDGGGTEEKTKVN--DERVEK---KPKALEKE--EREVKMEGKEMKEEEE 205
+E E K D G E K+N D+ +EK KA E ++ E KE K++ +
Sbjct: 15 ALESEKYKANKDKGNPEIYNKINSQDKAIEKFKLLIKAQMAERVKKLHSQEKKEEKKKPK 74
Query: 206 DKDV 209
K V
Sbjct: 75 KKKV 78
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 30.4 bits (69), Expect = 0.083
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 88 DTCLLCEVQLVSN-TFYIFPCGHTFHSHCI 116
D C +C + + PCGH FH C+
Sbjct: 1 DECPICLDEFEPGEEVVVLPCGHVFHKECL 30
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 33.0 bits (76), Expect = 0.11
Identities = 16/60 (26%), Positives = 32/60 (53%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYLRVSGGKDKDS 228
+ + K +E+ EKK KA +++E + E ++ K+EEE ++ E+ + K K +
Sbjct: 418 KAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQA 477
Score = 30.7 bits (70), Expect = 0.63
Identities = 14/66 (21%), Positives = 39/66 (59%)
Query: 153 MIEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEK 212
I ++++K+ + ++K ++ E++ + ++++ E K E +E EEE++++ +K
Sbjct: 414 KIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKK 473
Query: 213 KRKRYL 218
K++ L
Sbjct: 474 KKQATL 479
Score = 29.1 bits (66), Expect = 2.1
Identities = 15/48 (31%), Positives = 29/48 (60%)
Query: 168 TEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRK 215
+K K E+ EKK + +KE+++ GK+ +EEEE++ +++ K
Sbjct: 408 ATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEK 455
Score = 29.1 bits (66), Expect = 2.1
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 4/53 (7%)
Query: 167 GTEEKTKVNDERVEKKPKALEKEERE----VKMEGKEMKEEEEDKDVVEKKRK 215
G+++ TK + VEK K E+E++E K+ +EEEE+K+ E++++
Sbjct: 404 GSKKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKE 456
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 29.8 bits (67), Expect = 0.13
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 88 DTCLLCEVQLVSNTFYIFPCGHTFHSHCIVQDLDPEQK 125
C +C L+ + + PCGH F CI++ L + K
Sbjct: 3 LECPICL-DLLRDPVVLTPCGHVFCRECILRYLKKKSK 39
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 29.7 bits (67), Expect = 0.15
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 104 IFPCGHTFHSHCIVQ 118
+ PCGH F CI +
Sbjct: 15 LLPCGHVFCRSCIDK 29
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 30.1 bits (68), Expect = 0.20
Identities = 14/43 (32%), Positives = 15/43 (34%), Gaps = 11/43 (25%)
Query: 80 RYHMIQNCDTCLL----CEVQLVSNTFYIFPCGHTFHSHCIVQ 118
R H C C C V CGH FH HCI +
Sbjct: 26 RNHFDGTCPECKSPGDDCPVVWG-------ECGHAFHLHCISR 61
>gnl|CDD|191696 pfam07168, Ureide_permease, Ureide permease. Heterocyclic nitrogen
compounds may serve as nitrogen sources or nitrogen
transport compounds in plants that are not able to fix
nitrogen. This family represents ureide permease, a
transporter of a wide spectrum of oxo derivatives of
heterocyclic nitrogen compounds, including allantoin,
uric acid and xanthine; it has 10 putative transmembrane
domains with a large cytosolic central domain containing
a 'Walker A' motif. Ureide permease is likely to
transport other purine degradation products when
nitrogen sources are low. Transport is dependent on
glucose and a proton gradient. The family is found in
bacteria, plants and yeast.
Length = 336
Score = 31.4 bits (71), Expect = 0.32
Identities = 12/61 (19%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKD-------VVEKKRKRYLRVS 221
+ K K+N + ++ E +M ++++ E D +VE +++R ++V
Sbjct: 154 DNKEKLNAFENYQSEFSISSLELMSRMNSEDLENGEADDAKAGTAEFLVELEKRRAIKVF 213
Query: 222 G 222
G
Sbjct: 214 G 214
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 31.3 bits (72), Expect = 0.41
Identities = 17/77 (22%), Positives = 45/77 (58%), Gaps = 8/77 (10%)
Query: 154 IEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEED------- 206
EKE ++ + E++ +E +++K + LEK E E++ + KE+++++++
Sbjct: 73 FEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEE 132
Query: 207 -KDVVEKKRKRYLRVSG 222
++++E++ + R+SG
Sbjct: 133 LEELIEEQLQELERISG 149
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.5 bits (71), Expect = 0.42
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 161 EGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEE 205
G DGG +EE+ + +E E+EE E + E +E +E EE
Sbjct: 856 GGSDGGDSEEEEEEEEEE--------EEEEEEEEEEEEEEEENEE 892
Score = 30.0 bits (67), Expect = 1.3
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 155 EKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKD 208
E + ++G DGGG + +E E+ E+EE E + E +E +EEEE+++
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEE-----EEEEEEEEEEEEEEEEEEENEE 892
Score = 28.4 bits (63), Expect = 3.5
Identities = 27/114 (23%), Positives = 44/114 (38%), Gaps = 17/114 (14%)
Query: 123 EQKAKLDSE-ETGSEAVNNYLSRECPYCGSHMIEKESKKEGGD--------GGGTEEKTK 173
E K + +SE E +E R+ G IE + G+ G TE +
Sbjct: 674 ETKGENESEGEIPAE-------RKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGT 726
Query: 174 VNDERVEKKPKALEKE-EREVKMEGKEMKEEEEDKDVVEKKRKRYLRVSGGKDK 226
++ +E + E E E E + EGK E E D+ E + + +D+
Sbjct: 727 EDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDE 780
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 31.2 bits (71), Expect = 0.47
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 7/74 (9%)
Query: 154 IEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKK 213
+E+E K+E E + K N + +EK + LE+ + +K E K +EEE+ +++EK
Sbjct: 96 LEREQKEE-------EVREKHNKKIIEKFGEDLEEVYKFMKGEAKVEEEEEKQMEILEKA 148
Query: 214 RKRYLRVSGGKDKD 227
K YL++ ++K
Sbjct: 149 LKSYLKIVKEENKS 162
>gnl|CDD|227627 COG5314, COG5314, Conjugal transfer/entry exclusion protein
[Intracellular trafficking and secretion].
Length = 252
Score = 30.6 bits (69), Expect = 0.55
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 53 IVDLKEDMSEATRSAEQVRNDIQACANRYHMIQN 86
+ +++ A RS EQV N IQ N+ QN
Sbjct: 39 PSNYAQNILTAVRSLEQVNNQIQQLQNQAQQYQN 72
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2
finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 29.0 bits (65), Expect = 0.58
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 107 CGHTFHSHCIVQDLDPEQ 124
C H FH HCI++ L E
Sbjct: 52 CKHNFHMHCILKWLATET 69
>gnl|CDD|143650 cd07934, RHD-n_NFkB2, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor kappa B2 (NF-kappa B2).
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the NF-kappa B2 family of
transcription factors, a class I member of the NF-kappa
B family. In class I NF-kappa Bs, the RHD domain
co-occurs with C-terminal ankyrin repeats. NF-kappa B2
is commonly referred to as p100 or p52 (proteolytically
processed form). NF-kappa B proteins are part of a
protein complex that acts as a transcription factor,
which is responsible for regulating a host of cellular
responses to a variety of stimuli. This complex tightly
regulates the expression of a large number of genes, and
is involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). NF-kappa B2 is involved in the alternative
NF-kappa B signaling pathway which is activated by few
agonists and plays an important role in secondary
lymphoid organogenesis, maturation of B-cells, and
adaptive humoral immunity. p100 may also act as an
I-kappa B due to its C-terminal ankyrin repeats.
Length = 185
Score = 30.3 bits (68), Expect = 0.62
Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 170 EKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYLRVSGG 223
EK K R K E EERE++ E KE+K + D +V K YLR S G
Sbjct: 115 EKLKRQKLRNTGPYKLTEAEERELEQEAKELK-KVMDLSIVRLKFTAYLRDSNG 167
>gnl|CDD|152034 pfam11598, COMP, Cartilage oligomeric matrix protein. This
family of proteins represents the five-stranded
coiled-coil domain of cartilage oligomeric matrix
protein (COMP). This region has a binding site between
two internal rings formed by Leu37 and Thr40.
Length = 45
Score = 27.7 bits (62), Expect = 0.63
Identities = 9/38 (23%), Positives = 19/38 (50%)
Query: 41 AICASLEQYNQHIVDLKEDMSEATRSAEQVRNDIQACA 78
+ L + Q + +L+ED+ + + +RN I+ C
Sbjct: 5 QLARQLSELTQLLQELREDLRQQVKETAFLRNTIEECQ 42
>gnl|CDD|177033 CHL00104, rpl33, ribosomal protein L33.
Length = 66
Score = 28.4 bits (64), Expect = 0.68
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 146 CPYCGSHMIEKESKK 160
CPYC H I KE KK
Sbjct: 52 CPYCYKHTIHKEIKK 66
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 28.6 bits (64), Expect = 0.85
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 88 DTCLLCEVQLVSN---TFYIFPCGHTFHSHCIVQDLDPEQKAKLDSEE 132
TC C+ + C H FH HCI + LD + LD +
Sbjct: 32 GTCPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQT 79
>gnl|CDD|224359 COG1442, RfaJ, Lipopolysaccharide biosynthesis proteins,
LPS:glycosyltransferases [Cell envelope biogenesis,
outer membrane].
Length = 325
Score = 30.0 bits (68), Expect = 0.88
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 14/51 (27%)
Query: 103 YIFPCGHTFHS------------HCIVQDLDPEQKAKLD--SEETGSEAVN 139
Y+ P G + +S H +V L+ E K KL+ +E S V
Sbjct: 13 YLIPAGVSIYSLLEHNRKIFYKFHILVDGLNEEDKKKLNETAEPFKSFIVL 63
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 30.4 bits (68), Expect = 0.91
Identities = 13/37 (35%), Positives = 28/37 (75%), Gaps = 1/37 (2%)
Query: 180 EKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKR 216
+K+ +A+EK +RE + + +E +E E++K+ E++R+R
Sbjct: 579 KKREEAVEKAKREAEQKAREEREREKEKE-KERERER 614
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 29.9 bits (67), Expect = 1.1
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 154 IEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKK 213
KE K E G E++ +++ +K+ E ++R+ K E KE + +E + EKK
Sbjct: 94 PAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKK 153
Query: 214 RK 215
+
Sbjct: 154 VE 155
Score = 27.2 bits (60), Expect = 8.7
Identities = 15/59 (25%), Positives = 28/59 (47%)
Query: 158 SKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKR 216
KE + G EE+ + + EKK K + +E + KE +E+ EK++++
Sbjct: 94 PAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEK 152
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 29.7 bits (67), Expect = 1.2
Identities = 14/47 (29%), Positives = 29/47 (61%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRK 215
E + +V DE E++ + ++EE + + +E+ EEEE ++ +K +K
Sbjct: 30 EVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKK 76
Score = 29.4 bits (66), Expect = 1.6
Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 153 MIEKESKKEGGDGGGTEEKTKVNDERVEKKPK----ALEKEEREVKMEGKEMKEEEEDKD 208
+EKE +KE D EEK + +E + K E+E+ E K + K++KE + +
Sbjct: 26 WVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWE 85
Query: 209 VVEKKRKRYLR 219
++ K + + R
Sbjct: 86 LLNKTKPIWTR 96
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 29.6 bits (66), Expect = 1.5
Identities = 15/56 (26%), Positives = 20/56 (35%), Gaps = 24/56 (42%)
Query: 106 PCGHTFHSHCIVQDLDPEQKAKLDSEETGSEAVNNYLSRE--CPYCGSHMIEKESK 159
PCGH H HC+ N+L R+ CP C +I +S
Sbjct: 317 PCGHILHLHCL----------------------KNWLERQQTCPICRRPVIFDQSS 350
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.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 = 397
Score = 29.6 bits (66), Expect = 1.5
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 17/68 (25%)
Query: 88 DTCLLCEVQLVSNTFY----IFPCGHTFHSHCIVQDLD----------PEQKAKLDSEET 133
DT L C + F+ + C HTF S CI + L +Q++KL S
Sbjct: 24 DTSLRC---HICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQESKLRSNWL 80
Query: 134 GSEAVNNY 141
SE V ++
Sbjct: 81 VSEIVESF 88
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 29.5 bits (67), Expect = 1.5
Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYL-RVSG 222
EE E ++KK + LEK+E+E+ + K + E+EE+ + + +++ L R+SG
Sbjct: 89 EETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISG 143
>gnl|CDD|200540 cd11279, Sema_RON, The Sema domain, a protein interacting module,
of RON Receptor Tyrosine Kinase. RON receptor tyrosine
kinase is a Macrophage-stimulating protein (MSP)
receptor. Upon binding of MSP, RON is activated via
autophosphorylation within its kinase catalytic domain,
resulting in a wide range of effects, including
proliferation, tubular morphogenesis, angiogenesis,
cellular motility and invasiveness. By interacting with
downstream signaling molecules, it regulates macrophage
migration, phagocytosis, and nitric oxide production.
RON has been implicated in cancers of the breast, colon,
pancreas and ovaries because both splice variants and
receptor overexpression have been identified in these
tumors. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as ligand recognition and
binding model. RON is composed of an alpha-beta
heterodimer. The extracellular alpha chain is disulfide
linked to the beta chain, which contains an
extracellular ligand-binding region with a Sema domain,
a PSI domain and four IPT repeats, a transmembrane
segment, and an intracellular catalytic tyrosine kinase
domain. The Sema domain of RON may be necessary for
receptor dimerization and activation.
Length = 493
Score = 29.4 bits (66), Expect = 1.6
Identities = 23/106 (21%), Positives = 36/106 (33%), Gaps = 27/106 (25%)
Query: 70 VRNDIQACANRYHMIQN----------CDTCLLCEVQ-------------LVSNTF--YI 104
RN + ++QN C C LC LV + ++
Sbjct: 45 TRNHLHVLNPELKLLQNLVTGPTGSPGCQICALCPPGPPGPSPEDTDNKVLVLDPEEPWL 104
Query: 105 FPCGHTFHSHCIVQDLDPEQKA-KLDSEETGSEAVNNYLSRECPYC 149
+ CG + H C + +L+ A + S A N S +CP C
Sbjct: 105 YSCGSSLHGRCFLHELESRGSAVHIASTACLFSANANKPS-DCPDC 149
>gnl|CDD|110400 pfam01396, zf-C4_Topoisom, Topoisomerase DNA binding C4 zinc
finger.
Length = 39
Score = 26.5 bits (59), Expect = 1.6
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 144 RECPYCGSHMIEKESKK 160
+CP CG ++ K K
Sbjct: 2 GKCPKCGGDLVLKRGKF 18
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 26.3 bits (58), Expect = 1.9
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 90 CLLCEVQLVSNTFYIFPCGHTFHSHCIVQ 118
C +C + + I PCGH F S CI+
Sbjct: 1 CPICL-EEPKDPVTILPCGHLFCSKCILS 28
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 28.5 bits (64), Expect = 2.2
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 153 MIEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEK 212
E E + VE++ K +K+++EVK E KE K+++++K V K
Sbjct: 123 GPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKE-KKDKKEKMVEPK 181
Query: 213 KRKR 216
K+
Sbjct: 182 GSKK 185
Score = 27.4 bits (61), Expect = 5.9
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 167 GTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYLRVSGGKDK 226
G+E +T + K K E EE E K K+ K+E K+ EKK K+ V K
Sbjct: 129 GSESETSEKETT-AKVEKEAEVEEEEKK--EKKKKKEV-KKEKKEKKDKKEKMVEPKGSK 184
Query: 227 DSR 229
+
Sbjct: 185 KKK 187
>gnl|CDD|112998 pfam04208, MtrA, Tetrahydromethanopterin S-methyltransferase,
subunit A. The N5-methyltetrahydromethanopterin:
coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is
a membrane-associated, corrinoid-containing protein that
uses a transmethylation reaction to drive an
energy-conserving sodium ion pump.
Length = 176
Score = 28.2 bits (63), Expect = 2.8
Identities = 15/37 (40%), Positives = 22/37 (59%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEE 205
+E TK E V K P A E+E +++E + +EEEE
Sbjct: 138 DEITKKVRECVSKDPGAFEEEPLVIEIEEEGEEEEEE 174
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 2.9
Identities = 19/61 (31%), Positives = 28/61 (45%)
Query: 156 KESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRK 215
+E+KK D E K E +K + +KE E K + K EEE+K E+ +K
Sbjct: 1678 EEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKK 1737
Query: 216 R 216
Sbjct: 1738 E 1738
Score = 29.0 bits (64), Expect = 3.0
Identities = 16/61 (26%), Positives = 30/61 (49%)
Query: 156 KESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRK 215
+E+KK E E E+K +A EK++ E K + K++ E+K ++ +K
Sbjct: 1339 EEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKK 1398
Query: 216 R 216
+
Sbjct: 1399 K 1399
Score = 28.6 bits (63), Expect = 3.8
Identities = 14/61 (22%), Positives = 28/61 (45%)
Query: 156 KESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRK 215
+E KK + + E +KK + +K E + K + +K+E E+ E+ +K
Sbjct: 1650 EELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK 1709
Query: 216 R 216
+
Sbjct: 1710 K 1710
Score = 28.6 bits (63), Expect = 4.0
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 155 EKESKKEGGDGGGTEEKTKV-----NDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDV 209
E E K EE K + +KK + L+K E E K++ +E K+E E+
Sbjct: 1685 EDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEE--- 1741
Query: 210 VEKKRKRYLRVSGGKDK 226
+KK+ + + K
Sbjct: 1742 -DKKKAEEAKKDEEEKK 1757
Score = 27.4 bits (60), Expect = 7.5
Identities = 17/65 (26%), Positives = 26/65 (40%)
Query: 155 EKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKR 214
+E+KK D EE K ++ + ++ E K E + KE EE K E K+
Sbjct: 1664 AEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKK 1723
Query: 215 KRYLR 219
Sbjct: 1724 AEEEN 1728
Score = 27.4 bits (60), Expect = 8.5
Identities = 18/61 (29%), Positives = 24/61 (39%)
Query: 155 EKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKR 214
E + K + E K + E + A E E E K E E K+EE K K+
Sbjct: 1326 EAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKK 1385
Query: 215 K 215
K
Sbjct: 1386 K 1386
>gnl|CDD|223436 COG0359, RplI, Ribosomal protein L9 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 27.6 bits (62), Expect = 3.5
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 172 TKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKR 214
TK N + +E + LEK+ E E + +KE+ E K V +
Sbjct: 40 TKGNLKLLEARRAKLEKKAAEELAEAEALKEKLEGKTVEIAVK 82
>gnl|CDD|179867 PRK04598, tatA, twin arginine translocase protein A; Provisional.
Length = 81
Score = 26.7 bits (59), Expect = 3.8
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 162 GGDGGGT----------EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEE 203
G D G EE K N + + +PK LE+ + E E K+ KE+
Sbjct: 29 GSDLGSAVKGFKKAMSEEESAKANKKDADFEPKNLEQAKTEAAAEKKKDKEQ 80
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 28.3 bits (64), Expect = 4.2
Identities = 15/47 (31%), Positives = 30/47 (63%), Gaps = 9/47 (19%)
Query: 176 DERVEKKPKALEKEERE------VKMEGKEMKEEEEDKDVVEKKRKR 216
++V+++ +EK +RE +K KE+ E+++DKD VE+ R++
Sbjct: 215 RKKVKEQ---MEKSQREYYLREQLKAIQKELGEDDDDKDEVEELREK 258
>gnl|CDD|130181 TIGR01111, mtrA, N5-methyltetrahydromethanopterin:coenzyme M
methyltransferase subunit A. This model describes
N5-methyltetrahydromethanopterin: coenzyme M
methyltransferase subunit A in methanogenic archaea.
This methyltranferase is a membrane-associated enzyme
complex that uses methyl-transfer reaction to drive
sodium-ion pump. Archaea have evolved energy-yielding
pathways marked by one-carbon biochemistry featuring
novel cofactors and enzymes. This transferase (encoded
by subunit A) is involved in the transfer of 'methyl'
group from N5-methyltetrahydromethanopterin to coenzyme
M. In an accompanying reaction, methane is produced by
two-electron reduction of methyl-coenzyme M by another
enzyme, methyl-coenzyme M reductase [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 238
Score = 27.9 bits (62), Expect = 4.2
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 172 TKVNDERVEKKPKALEKEEREVKMEGKEMKEEEE 205
T E K P A +++ +++E + +EEE
Sbjct: 145 TSKVKECASKDPGAFDEDPMIIELEEEGGEEEEG 178
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.1 bits (63), Expect = 4.4
Identities = 13/58 (22%), Positives = 36/58 (62%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYLRVSGGKDK 226
E + + ++E+K + LE+ E+K E +E++E+ ++ +++K + Y+++S ++
Sbjct: 247 LESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEYIKLSEFYEE 304
>gnl|CDD|181661 PRK09124, PRK09124, pyruvate dehydrogenase; Provisional.
Length = 574
Score = 28.0 bits (63), Expect = 4.5
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 11/53 (20%)
Query: 81 YHMIQNCDTCLLCEVQLVSNTFYIFPCGHTFHSHCIVQ-DLDPEQ---KAKLD 129
YH + NCDT L+ FY P I+Q D++P ++ +D
Sbjct: 260 YHAMMNCDTLLMLGTDFPYRQFY--PTDAK-----IIQIDINPGSLGRRSPVD 305
>gnl|CDD|240520 cd13156, KOW_RPL6, KOW motif of Ribosomal Protein L6. RPL6
contains KOW motif that has an extra ribosomal role as
an oncogenic. KOW domain is known as an RNA-binding
motif that is shared so far among some families of
ribosomal proteins, the essential bacterial
transcriptional elongation factor NusG, the eukaryotic
chromatin elongation factor Spt5, the higher eukaryotic
KIN17 proteins and Mtr4. .
Length = 152
Score = 27.5 bits (62), Expect = 4.5
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 172 TKVNDE----RVEKKPKALEKEEREVKMEGKEMKEE-EEDKDVVEK------KRKRYLR 219
K+ND + +KK K E E E K + + EE +ED+ V+ K+ L+
Sbjct: 74 PKLNDAYFKRKKKKKKKKKEGEFFEEKKKKYVVSEERKEDQKAVDAALLAAIKKVPLLK 132
>gnl|CDD|191249 pfam05279, Asp-B-Hydro_N, Aspartyl beta-hydroxylase N-terminal
region. This family includes the N-terminal regions of
the junctin, junctate and aspartyl beta-hydroxylase
proteins. Junctate is an integral ER/SR membrane calcium
binding protein, which comes from an alternatively
spliced form of the same gene that generates aspartyl
beta-hydroxylase and junctin. Aspartyl beta-hydroxylase
catalyzes the post-translational hydroxylation of
aspartic acid or asparagine residues contained within
epidermal growth factor (EGF) domains of proteins.
Length = 240
Score = 27.6 bits (61), Expect = 4.8
Identities = 14/61 (22%), Positives = 21/61 (34%)
Query: 155 EKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKR 214
+K E D + E E E + K + KE E+E++D E
Sbjct: 135 DKFLLAEDSDDRQETLEAGKVHEETEDSYHVEETASEQYKQDMKEKASEQENEDSKEPVE 194
Query: 215 K 215
K
Sbjct: 195 K 195
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 27.3 bits (61), Expect = 4.8
Identities = 12/40 (30%), Positives = 24/40 (60%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKD 208
++K K E +EK K E++++ + K K++++DKD
Sbjct: 61 KKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKD 100
>gnl|CDD|226549 COG4063, MtrA, Tetrahydromethanopterin S-methyltransferase, subunit
A [Coenzyme metabolism].
Length = 238
Score = 27.4 bits (61), Expect = 5.1
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 169 EEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEE 205
+E T +E VEK P A E+E +++E + +EEEE
Sbjct: 141 DEITAKVEECVEKDPGAYEEEPMVIEVEEEGEEEEEE 177
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 27.0 bits (61), Expect = 5.3
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 172 TKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVV 210
TK N +++E + LE + E E + + E+ E V
Sbjct: 40 TKGNLKQLEARRAELEAKAAEELAEAEALAEKLEGLTVT 78
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 28.0 bits (62), Expect = 5.4
Identities = 10/50 (20%), Positives = 24/50 (48%)
Query: 168 TEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRY 217
++ ND+ ++ + ++E E ++ +E K + + KK+K Y
Sbjct: 800 KPKEKGPNDKEIKIESPSVETEGERCTIKQREEKGIDAPAILNVKKKKPY 849
>gnl|CDD|115907 pfam07282, OrfB_Zn_ribbon, Putative transposase DNA-binding domain.
This putative domain is found at the C-terminus of a
large number of transposase proteins. This domain
contains four conserved cysteines suggestive of a zinc
binding domain. Given the need for transposases to bind
DNA as well as the large number of DNA-binding zinc
fingers we hypothesise this domain is DNA-binding.
Length = 69
Score = 25.6 bits (57), Expect = 5.7
Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 3/40 (7%)
Query: 123 EQKAKLDSEETGSEAVN-NYLSRECPYCGSHMIEKESKKE 161
E KAK VN Y S+ C CG E S +
Sbjct: 9 EYKAKEYGIPV--VYVNPAYTSKTCSVCGHKNKESLSGRT 46
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 27.7 bits (62), Expect = 6.0
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 178 RVEKKPKALEKEEREV----KMEGKEMKEEEEDKDVVEKKRKR 216
+K+ EKEE+E K K K+EE+ K +EK K
Sbjct: 547 LDDKEELQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLEKA 589
>gnl|CDD|235848 PRK06664, fliD, flagellar hook-associated protein FliD; Validated.
Length = 661
Score = 27.4 bits (61), Expect = 6.9
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 7/46 (15%)
Query: 167 GTEEKTKVNDERVEKKPKALEKEEREVK-----MEG--KEMKEEEE 205
G +E+ N++++E+ K LE +ER++K M+ K+MKE+
Sbjct: 604 GLDERIADNNKKIEEYEKKLESKERKLKGKYLTMDQTVKKMKEQSN 649
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 27.3 bits (61), Expect = 7.0
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 178 RVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEK 212
R + EE E + E +E +EEE ++ E+
Sbjct: 338 RCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPEE 372
>gnl|CDD|220438 pfam09845, DUF2072, Zn-ribbon containing protein (DUF2072). This
archaeal protein has no known function.
Length = 121
Score = 26.7 bits (59), Expect = 7.0
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 146 CPYCGSHMIEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEE 205
CP CG E K D EK + +E+E E +E K+ +E+ E
Sbjct: 22 CPSCGGKKFLYV----------RERKRPKPDVPEEKPVEEIERETDEELLEVKQDREQGE 71
Query: 206 DKDVVEKKR 214
+ + +E R
Sbjct: 72 EGERIESVR 80
>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 27.5 bits (62), Expect = 7.5
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 173 KVNDERVEKKPKALEKEEREV---KMEGKEMKEEEEDKDVVE--KKRK 215
K+ +V KP A E E + EG + + EED V++ KKRK
Sbjct: 118 KIEKGKVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKELKKRK 165
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 27.3 bits (61), Expect = 7.7
Identities = 16/80 (20%), Positives = 32/80 (40%), Gaps = 14/80 (17%)
Query: 154 IEKESKKEGGDGGGTEEKTKVND--------ERVEKKPKALEK------EEREVKMEGKE 199
+ KE +K D E + + + ++++ + LE+ + EG
Sbjct: 11 LAKELRKLTEDEKLAEAEEEKAEYDALKEEIDKLDAEIDRLEELLDELEAKPAASGEGGG 70
Query: 200 MKEEEEDKDVVEKKRKRYLR 219
+EEEE+ + + YLR
Sbjct: 71 GEEEEEEAKAEAAEFRAYLR 90
>gnl|CDD|217752 pfam03833, PolC_DP2, DNA polymerase II large subunit DP2.
Length = 852
Score = 27.4 bits (61), Expect = 7.9
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 195 MEGKEMKEEEEDKDVVEKKRKRYLR 219
+ KE KE+ E+K V K ++L+
Sbjct: 269 SKKKEDKEDTEEKVAVSKPSDKFLK 293
>gnl|CDD|165190 PHA02852, PHA02852, putative virion structural protein;
Provisional.
Length = 153
Score = 26.5 bits (58), Expect = 8.1
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 83 MIQNCDTCLLCEVQLVSNTFYIF 105
+IQNC+ EV L+ N +IF
Sbjct: 10 IIQNCNAVFSNEVNLLYNEKFIF 32
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 27.1 bits (60), Expect = 8.3
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 154 IEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEE 203
I+K +K + EE + E E++ L+KEE E +M ++ K+
Sbjct: 133 IQKNKEKSTREQEELEEALEFEKEEEEQRRLLLQKEEEEQQMNKRKNKQA 182
>gnl|CDD|200493 cd11356, AmyAc_Sucrose_phosphorylase-like_1, Alpha amylase
catalytic domain found in sucrose phosphorylase-like
proteins (also called sucrose glucosyltransferase,
disaccharide glucosyltransferase, and sucrose-phosphate
alpha-D glucosyltransferase). Sucrose phosphorylase is
a bacterial enzyme that catalyzes the phosphorolysis of
sucrose to yield glucose-1-phosphate and fructose.
These enzymes do not have the conserved calcium ion
present in other alpha amylase family enzymes. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2
Asp residues (GH31). The family members are quite
extensive and include: alpha amylase,
maltosyltransferase, cyclodextrin glycotransferase,
maltogenic amylase, neopullulanase, isoamylase,
1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 458
Score = 27.1 bits (61), Expect = 8.5
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 7 IKTALEFLDE--SDLISIEDILPFF---SD--FTCMD 36
++T +FL E D IS ILPFF SD F+ +D
Sbjct: 23 LQTLHKFLKEHLKDTISGVHILPFFPYSSDDGFSVID 59
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 27.0 bits (60), Expect = 8.6
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 155 EKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEEREVKMEGKEMKEEEEDK 207
+ ES EG + E + R ++K KA +E+ K +E KEE++ K
Sbjct: 254 DDESAWEGFES---EYEPINKPVRPKRKTKAQRNKEKRRKELEREAKEEKQLK 303
>gnl|CDD|234747 PRK00398, rpoP, DNA-directed RNA polymerase subunit P; Provisional.
Length = 46
Score = 24.9 bits (55), Expect = 8.7
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 145 ECPYCGSHMIEKESKK 160
CPYCG ++ KE
Sbjct: 23 RCPYCGYRILFKERPP 38
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 27.1 bits (60), Expect = 8.9
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 154 IEKESKKEGGDGGGTEEKTKVNDERVEKKPKALEKEE--REVKMEGKEMKEEEEDKD 208
++ +KK G T+ + + E+K K E E+ +E E KE ++++E K
Sbjct: 378 LQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERKK 434
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 27.1 bits (61), Expect = 9.0
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 9/60 (15%)
Query: 169 EEKTKVND---------ERVEKKPKALEKEEREVKMEGKEMKEEEEDKDVVEKKRKRYLR 219
E+K K+N+ +E+K + E +E + +E++E++E E K
Sbjct: 513 EDKEKLNELIASLEELERELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAE 572
>gnl|CDD|227499 COG5171, YRB1, Ran GTPase-activating protein (Ran-binding protein)
[Intracellular trafficking and secretion].
Length = 211
Score = 26.9 bits (59), Expect = 9.6
Identities = 21/103 (20%), Positives = 37/103 (35%), Gaps = 9/103 (8%)
Query: 128 LDSEETGSEAVNNYLSRECPYCGSHMIEKESKKEGGDGGGTEEKTKVNDERVEKKPKALE 187
+ E +A E ++ K G GG E+K + + P+ E
Sbjct: 1 MSVERKKKQAKIEKEENEQKERSLDVVSKGDAFGDGKAGGEEKKVQQSPFLENAVPEGDE 60
Query: 188 KEERE---------VKMEGKEMKEEEEDKDVVEKKRKRYLRVS 221
+ E V+++ +K EED+ V+ K R + R
Sbjct: 61 GKGPESPNIHFEPVVELQRVHLKTNEEDETVLFKARAKLFRFD 103
>gnl|CDD|219131 pfam06676, DUF1178, Protein of unknown function (DUF1178). This
family consists of several hypothetical bacterial
proteins of around 150 residues in length. The function
of this family is unknown.
Length = 145
Score = 26.4 bits (59), Expect = 9.9
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 145 ECPYCGSHMIEK 156
CP CGS +EK
Sbjct: 34 SCPVCGSTEVEK 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
0.314 0.131 0.378
Gapped
Lambda K H
0.267 0.0812 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,369,622
Number of extensions: 1044323
Number of successful extensions: 2711
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2421
Number of HSP's successfully gapped: 331
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.6 bits)