RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12244
(257 letters)
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 208 bits (531), Expect = 3e-68
Identities = 78/158 (49%), Positives = 103/158 (65%), Gaps = 28/158 (17%)
Query: 29 RNFSIIAHVDHGKSTLADRLLEMTGTVLSSG-SSQVLDSLQVEQERGITVKAQTASLRYT 87
RNFSIIAH+DHGKSTLADRLLE+TGTV QVLDS+ +E+ERGIT+KAQ L Y
Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGITIKAQAVRLFYK 60
Query: 88 SILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA------------------- 128
+ DGEEYLLNLIDTPGHVDFS EV+RSLAAC+G +L++DA
Sbjct: 61 AK-DGEEYLLNLIDTPGHVDFSYEVSRSLAACEGALLVVDATQGVEAQTLANFYLALENN 119
Query: 129 -------NQVDLKNANPEACEEQLQTLFNIDKKSVLRI 159
N++DL A+P+ +++++ + +D + +
Sbjct: 120 LEIIPVINKIDLPAADPDRVKQEIEDVLGLDASEAILV 157
Score = 109 bits (275), Expect = 8e-30
Identities = 40/57 (70%), Positives = 46/57 (80%), Gaps = 1/57 (1%)
Query: 202 RNFSIIAHVDHGKSTLADRLLEMTGTVLSSG-SSQVLDSLQVEQERGITVKAQTASL 257
RNFSIIAH+DHGKSTLADRLLE+TGTV QVLDS+ +E+ERGIT+KAQ L
Sbjct: 1 RNFSIIAHIDHGKSTLADRLLELTGTVSEREMKEQVLDSMDLERERGITIKAQAVRL 57
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 210 bits (538), Expect = 2e-64
Identities = 77/163 (47%), Positives = 105/163 (64%), Gaps = 28/163 (17%)
Query: 24 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQVEQERGITVKAQTA 82
+ IRNFSIIAH+DHGKSTLADRL+E+TGT+ +QVLDS+ +E+ERGIT+KAQ
Sbjct: 3 DMKNIRNFSIIAHIDHGKSTLADRLIELTGTLSEREMKAQVLDSMDLERERGITIKAQAV 62
Query: 83 SLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA-------------- 128
L Y + DGE Y+LNLIDTPGHVDFS EV+RSLAAC+G +L++DA
Sbjct: 63 RLNYKA-KDGETYILNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLANVYL 121
Query: 129 ------------NQVDLKNANPEACEEQLQTLFNIDKKSVLRI 159
N++DL A+PE +++++ + ID + +
Sbjct: 122 ALENDLEIIPVLNKIDLPAADPERVKQEIEDVIGIDASDAVLV 164
Score = 115 bits (291), Expect = 2e-29
Identities = 39/62 (62%), Positives = 49/62 (79%), Gaps = 1/62 (1%)
Query: 197 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQVEQERGITVKAQTA 255
+ IRNFSIIAH+DHGKSTLADRL+E+TGT+ +QVLDS+ +E+ERGIT+KAQ
Sbjct: 3 DMKNIRNFSIIAHIDHGKSTLADRLIELTGTLSEREMKAQVLDSMDLERERGITIKAQAV 62
Query: 256 SL 257
L
Sbjct: 63 RL 64
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 200 bits (510), Expect = 2e-60
Identities = 78/167 (46%), Positives = 104/167 (62%), Gaps = 28/167 (16%)
Query: 20 YEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTV-LSSGSSQVLDSLQVEQERGITVK 78
P IRNFSIIAH+DHGKSTLADRLLE+TG + +QVLDS+ +E+ERGIT+K
Sbjct: 1 MTFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGITIK 60
Query: 79 AQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA---------- 128
AQ L Y + DGE Y+LNLIDTPGHVDFS EV+RSLAAC+G +L++DA
Sbjct: 61 AQAVRLNYKA-KDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLVVDASQGVEAQTLA 119
Query: 129 ----------------NQVDLKNANPEACEEQLQTLFNIDKKSVLRI 159
N++DL A+PE +++++ + ID + +
Sbjct: 120 NVYLALENNLEIIPVLNKIDLPAADPERVKQEIEDIIGIDASDAVLV 166
Score = 111 bits (279), Expect = 9e-28
Identities = 40/66 (60%), Positives = 48/66 (72%), Gaps = 1/66 (1%)
Query: 193 YEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTV-LSSGSSQVLDSLQVEQERGITVK 251
P IRNFSIIAH+DHGKSTLADRLLE+TG + +QVLDS+ +E+ERGIT+K
Sbjct: 1 MTFTPQKNIRNFSIIAHIDHGKSTLADRLLELTGGLSEREMRAQVLDSMDIERERGITIK 60
Query: 252 AQTASL 257
AQ L
Sbjct: 61 AQAVRL 66
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 185 bits (473), Expect = 4e-55
Identities = 77/161 (47%), Positives = 101/161 (62%), Gaps = 28/161 (17%)
Query: 26 ARIRNFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQVEQERGITVKAQTASL 84
IRNFSIIAH+DHGKSTLADRLLE TG + QVLDS+ +E+ERGIT+KAQ L
Sbjct: 1 KNIRNFSIIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKAQAVRL 60
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA---------------- 128
Y + DGE Y+LNLIDTPGHVDFS EV+RSLAAC+G +LL+DA
Sbjct: 61 NYKA-KDGETYVLNLIDTPGHVDFSYEVSRSLAACEGALLLVDAAQGIEAQTLANVYLAL 119
Query: 129 ----------NQVDLKNANPEACEEQLQTLFNIDKKSVLRI 159
N++DL +A+PE +++++ + +D +
Sbjct: 120 ENDLEIIPVINKIDLPSADPERVKKEIEEVIGLDASEAILA 160
Score = 97.0 bits (242), Expect = 5e-23
Identities = 38/56 (67%), Positives = 44/56 (78%), Gaps = 1/56 (1%)
Query: 199 ARIRNFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQVEQERGITVKAQ 253
IRNFSIIAH+DHGKSTLADRLLE TG + QVLDS+ +E+ERGIT+KAQ
Sbjct: 1 KNIRNFSIIAHIDHGKSTLADRLLEYTGAISEREMREQVLDSMDLERERGITIKAQ 56
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 139 bits (354), Expect = 2e-41
Identities = 48/106 (45%), Positives = 69/106 (65%), Gaps = 8/106 (7%)
Query: 27 RIRNFSIIAHVDHGKSTLADRLLEMTGTV--LSSGSSQVLDSLQVEQERGITVKAQTASL 84
R RN II HVDHGK+TL D LL +TG + S+ ++VLD L+ E+ERGIT+K S
Sbjct: 2 RHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSF 61
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
+ ++ L+N+IDTPGHVDF+ E+ R + G +L++DA +
Sbjct: 62 ------ETKKRLINIIDTPGHVDFTKEMIRGASQADGAILVVDAVE 101
Score = 82.5 bits (205), Expect = 2e-19
Identities = 31/60 (51%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 200 RIRNFSIIAHVDHGKSTLADRLLEMTGTV--LSSGSSQVLDSLQVEQERGITVKAQTASL 257
R RN II HVDHGK+TL D LL +TG + S+ ++VLD L+ E+ERGIT+K S
Sbjct: 2 RHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKEERERGITIKIAAVSF 61
>gnl|CDD|206672 cd01885, EF2, Elongation Factor 2 (EF2) in archaea and eukarya.
Translocation requires hydrolysis of a molecule of GTP
and is mediated by EF-G in bacteria and by eEF2 in
eukaryotes. The eukaryotic elongation factor eEF2 is a
GTPase involved in the translocation of the
peptidyl-tRNA from the A site to the P site on the
ribosome. The 95-kDa protein is highly conserved, with
60% amino acid sequence identity between the human and
yeast proteins. Two major mechanisms are known to
regulate protein elongation and both involve eEF2.
First, eEF2 can be modulated by reversible
phosphorylation. Increased levels of phosphorylated eEF2
reduce elongation rates presumably because
phosphorylated eEF2 fails to bind the ribosomes.
Treatment of mammalian cells with agents that raise the
cytoplasmic Ca2+ and cAMP levels reduce elongation rates
by activating the kinase responsible for phosphorylating
eEF2. In contrast, treatment of cells with insulin
increases elongation rates by promoting eEF2
dephosphorylation. Second, the protein can be
post-translationally modified by ADP-ribosylation.
Various bacterial toxins perform this reaction after
modification of a specific histidine residue to
diphthamide, but there is evidence for endogenous ADP
ribosylase activity. Similar to the bacterial toxins, it
is presumed that modification by the endogenous enzyme
also inhibits eEF2 activity.
Length = 218
Score = 137 bits (348), Expect = 4e-40
Identities = 52/105 (49%), Positives = 73/105 (69%), Gaps = 5/105 (4%)
Query: 29 RNFSIIAHVDHGKSTLADRLLEMTGTVL--SSGSSQVLDSLQVEQERGITVKAQTASLRY 86
RN IIAHVDHGK+TL+D LL G + +G ++ LD+ + EQERGIT+K+ SL +
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISLYF 60
Query: 87 T---SILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+DG +YL+NLID+PGHVDFS+EVT +L G ++++DA
Sbjct: 61 EYEEEKMDGNDYLINLIDSPGHVDFSSEVTAALRLTDGALVVVDA 105
Score = 75.0 bits (185), Expect = 2e-16
Identities = 30/58 (51%), Positives = 40/58 (68%), Gaps = 2/58 (3%)
Query: 202 RNFSIIAHVDHGKSTLADRLLEMTGTVL--SSGSSQVLDSLQVEQERGITVKAQTASL 257
RN IIAHVDHGK+TL+D LL G + +G ++ LD+ + EQERGIT+K+ SL
Sbjct: 1 RNICIIAHVDHGKTTLSDSLLASAGIISEKLAGKARYLDTREDEQERGITIKSSAISL 58
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 134 bits (340), Expect = 6e-36
Identities = 52/105 (49%), Positives = 73/105 (69%), Gaps = 6/105 (5%)
Query: 27 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS---SGSSQVLDSLQVEQERGITVKAQTAS 83
+IRN IIAH+DHGK+TL+D LL G ++S +G LD + EQ RGIT+KA S
Sbjct: 19 QIRNIGIIAHIDHGKTTLSDNLLAGAG-MISEELAGEQLALDFDEEEQARGITIKAANVS 77
Query: 84 LRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ + +G+EYL+NLIDTPGHVDF +VTR++ A G ++++DA
Sbjct: 78 MVHEY--EGKEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVDA 120
Score = 76.4 bits (189), Expect = 8e-16
Identities = 30/61 (49%), Positives = 40/61 (65%), Gaps = 4/61 (6%)
Query: 200 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS---SGSSQVLDSLQVEQERGITVKAQTAS 256
+IRN IIAH+DHGK+TL+D LL G ++S +G LD + EQ RGIT+KA S
Sbjct: 19 QIRNIGIIAHIDHGKTTLSDNLLAGAG-MISEELAGEQLALDFDEEEQARGITIKAANVS 77
Query: 257 L 257
+
Sbjct: 78 M 78
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 131 bits (332), Expect = 7e-35
Identities = 57/141 (40%), Positives = 81/141 (57%), Gaps = 19/141 (13%)
Query: 24 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKA 79
P+ RIRN I+AH+D GK+TL +R+L TG + G + +D ++ EQERGIT+ +
Sbjct: 6 PLERIRNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITS 65
Query: 80 QTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQVDLKNANPE 139
+L + +Y +NLIDTPGHVDF+ EV RSL G V+++DA E
Sbjct: 66 AATTLFWKG-----DYRINLIDTPGHVDFTIEVERSLRVLDGAVVVVDAV---------E 111
Query: 140 ACEEQLQTLFN-IDKKSVLRI 159
E Q +T++ DK V RI
Sbjct: 112 GVEPQTETVWRQADKYGVPRI 132
Score = 76.1 bits (188), Expect = 8e-16
Identities = 27/65 (41%), Positives = 41/65 (63%), Gaps = 4/65 (6%)
Query: 197 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKA 252
P+ RIRN I+AH+D GK+TL +R+L TG + G + +D ++ EQERGIT+ +
Sbjct: 6 PLERIRNIGIVAHIDAGKTTLTERILFYTGIISKIGEVHDGAATMDWMEQEQERGITITS 65
Query: 253 QTASL 257
+L
Sbjct: 66 AATTL 70
>gnl|CDD|206678 cd01891, TypA_BipA, Tyrosine phosphorylated protein A (TypA)/BipA
family belongs to ribosome-binding GTPases. BipA is a
protein belonging to the ribosome-binding family of
GTPases and is widely distributed in bacteria and
plants. BipA was originally described as a protein that
is induced in Salmonella typhimurium after exposure to
bactericidal/permeability-inducing protein (a cationic
antimicrobial protein produced by neutrophils), and has
since been identified in E. coli as well. The properties
thus far described for BipA are related to its role in
the process of pathogenesis by enteropathogenic E. coli.
It appears to be involved in the regulation of several
processes important for infection, including
rearrangements of the cytoskeleton of the host,
bacterial resistance to host defense peptides,
flagellum-mediated cell motility, and expression of K5
capsular genes. It has been proposed that BipA may
utilize a novel mechanism to regulate the expression of
target genes. In addition, BipA from enteropathogenic E.
coli has been shown to be phosphorylated on a tyrosine
residue, while BipA from Salmonella and from E. coli K12
strains is not phosphorylated under the conditions
assayed. The phosphorylation apparently modifies the
rate of nucleotide hydrolysis, with the phosphorylated
form showing greatly increased GTPase activity.
Length = 194
Score = 120 bits (302), Expect = 2e-33
Identities = 56/150 (37%), Positives = 82/150 (54%), Gaps = 34/150 (22%)
Query: 28 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSG--SSQVLDSLQVEQERGITVKAQTASLR 85
IRN +IIAHVDHGK+TL D LL+ +GT + +V+DS +E+ERGIT+ A+ ++
Sbjct: 2 IRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTAIT 61
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA----------------- 128
Y ++ +N+IDTPGH DF EV R L+ GV+LL+DA
Sbjct: 62 Y------KDTKINIIDTPGHADFGGEVERVLSMVDGVLLLVDASEGPMPQTRFVLKKALE 115
Query: 129 ---------NQVDLKNANPEACEEQLQTLF 149
N++D +A PE +++ LF
Sbjct: 116 AGLKPIVVINKIDRPDARPEEVVDEVFDLF 145
Score = 69.5 bits (171), Expect = 2e-14
Identities = 29/58 (50%), Positives = 41/58 (70%), Gaps = 2/58 (3%)
Query: 201 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSG--SSQVLDSLQVEQERGITVKAQTAS 256
IRN +IIAHVDHGK+TL D LL+ +GT + +V+DS +E+ERGIT+ A+ +
Sbjct: 2 IRNIAIIAHVDHGKTTLVDALLKQSGTFRENEEVGERVMDSNDLERERGITILAKNTA 59
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 114 bits (287), Expect = 2e-31
Identities = 51/132 (38%), Positives = 67/132 (50%), Gaps = 17/132 (12%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASLRYT 87
N +I HVDHGK+TL LL TG + G+ + LD+L+ E+ERGIT+K +
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEW- 59
Query: 88 SILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQVDLKNANPEACEEQLQT 147
+ +N IDTPGH DFS E R LA G +L++DAN E E Q +
Sbjct: 60 -----PKRRINFIDTPGHEDFSKETVRGLAQADGALLVVDAN---------EGVEPQTRE 105
Query: 148 LFNIDKKSVLRI 159
NI L I
Sbjct: 106 HLNIALAGGLPI 117
Score = 65.8 bits (161), Expect = 4e-13
Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASL 257
N +I HVDHGK+TL LL TG + G+ + LD+L+ E+ERGIT+K
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEF 57
>gnl|CDD|240409 PTZ00416, PTZ00416, elongation factor 2; Provisional.
Length = 836
Score = 114 bits (288), Expect = 5e-29
Identities = 51/108 (47%), Positives = 72/108 (66%), Gaps = 6/108 (5%)
Query: 27 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS--SGSSQVLDSLQVEQERGITVKAQTASL 84
+IRN S+IAHVDHGKSTL D L+ G + S +G ++ D+ EQERGIT+K+ SL
Sbjct: 18 QIRNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISL 77
Query: 85 RYTSILD----GEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
Y L+ + +L+NLID+PGHVDFS+EVT +L G ++++D
Sbjct: 78 YYEHDLEDGDDKQPFLINLIDSPGHVDFSSEVTAALRVTDGALVVVDC 125
Score = 70.5 bits (173), Expect = 8e-14
Identities = 31/60 (51%), Positives = 41/60 (68%), Gaps = 2/60 (3%)
Query: 200 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS--SGSSQVLDSLQVEQERGITVKAQTASL 257
+IRN S+IAHVDHGKSTL D L+ G + S +G ++ D+ EQERGIT+K+ SL
Sbjct: 18 QIRNMSVIAHVDHGKSTLTDSLVCKAGIISSKNAGDARFTDTRADEQERGITIKSTGISL 77
>gnl|CDD|177730 PLN00116, PLN00116, translation elongation factor EF-2 subunit;
Provisional.
Length = 843
Score = 114 bits (287), Expect = 8e-29
Identities = 52/112 (46%), Positives = 69/112 (61%), Gaps = 12/112 (10%)
Query: 28 IRNFSIIAHVDHGKSTLADRLLEMTGTVL--SSGSSQVLDSLQVEQERGITVKAQTASLR 85
IRN S+IAHVDHGKSTL D L+ G + +G ++ D+ E ERGIT+K+ SL
Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISLY 78
Query: 86 YT----------SILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLID 127
Y DG EYL+NLID+PGHVDFS+EVT +L G ++++D
Sbjct: 79 YEMTDESLKDFKGERDGNEYLINLIDSPGHVDFSSEVTAALRITDGALVVVD 130
Score = 67.4 bits (165), Expect = 7e-13
Identities = 29/59 (49%), Positives = 38/59 (64%), Gaps = 2/59 (3%)
Query: 201 IRNFSIIAHVDHGKSTLADRLLEMTGTVL--SSGSSQVLDSLQVEQERGITVKAQTASL 257
IRN S+IAHVDHGKSTL D L+ G + +G ++ D+ E ERGIT+K+ SL
Sbjct: 19 IRNMSVIAHVDHGKSTLTDSLVAAAGIIAQEVAGDVRMTDTRADEAERGITIKSTGISL 77
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 113 bits (285), Expect = 1e-28
Identities = 50/143 (34%), Positives = 80/143 (55%), Gaps = 20/143 (13%)
Query: 22 DIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 77
++P+ +IRN I+AH+D GK+TL +R+L TG + G + V D + EQERGIT+
Sbjct: 2 EMPLMQIRNIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITI 61
Query: 78 KAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQVDLKNAN 137
++ S + + + +NLIDTPGH+DF+ EV RSL G V++ DA
Sbjct: 62 ESAATSCDW------DNHRINLIDTPGHIDFTGEVERSLRVLDGAVVVFDAV-------- 107
Query: 138 PEACEEQLQTLFN-IDKKSVLRI 159
+ Q +T++ D+ + R+
Sbjct: 108 -TGVQPQTETVWRQADRYGIPRL 129
Score = 61.9 bits (151), Expect = 6e-11
Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 4/67 (5%)
Query: 195 DIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 250
++P+ +IRN I+AH+D GK+TL +R+L TG + G + V D + EQERGIT+
Sbjct: 2 EMPLMQIRNIGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITI 61
Query: 251 KAQTASL 257
++ S
Sbjct: 62 ESAATSC 68
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 111 bits (280), Expect = 5e-28
Identities = 49/105 (46%), Positives = 70/105 (66%), Gaps = 8/105 (7%)
Query: 28 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASLR 85
IRN +IIAHVDHGK+TL D LL+ +GT ++ + V+DS +E+ERGIT+ A+ ++R
Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIR 60
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
Y +N++DTPGH DF EV R L GV+LL+DA++
Sbjct: 61 Y------NGTKINIVDTPGHADFGGEVERVLGMVDGVLLLVDASE 99
Score = 66.9 bits (164), Expect = 1e-12
Identities = 29/59 (49%), Positives = 43/59 (72%), Gaps = 2/59 (3%)
Query: 201 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASL 257
IRN +IIAHVDHGK+TL D LL+ +GT ++ + V+DS +E+ERGIT+ A+ ++
Sbjct: 1 IRNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAI 59
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 111 bits (279), Expect = 7e-28
Identities = 48/104 (46%), Positives = 66/104 (63%), Gaps = 8/104 (7%)
Query: 28 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASLR 85
IRN +IIAHVDHGK+TL D LL+ +GT V+DS +E+ERGIT+ A+ ++
Sbjct: 5 IRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAVN 64
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
Y +N++DTPGH DF EV R L+ GV+LL+DA+
Sbjct: 65 Y------NGTRINIVDTPGHADFGGEVERVLSMVDGVLLLVDAS 102
Score = 67.6 bits (166), Expect = 5e-13
Identities = 29/59 (49%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 201 IRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTASL 257
IRN +IIAHVDHGK+TL D LL+ +GT V+DS +E+ERGIT+ A+ ++
Sbjct: 5 IRNIAIIAHVDHGKTTLVDALLKQSGTFREREEVAERVMDSNDLEKERGITILAKNTAV 63
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 109 bits (275), Expect = 2e-27
Identities = 49/104 (47%), Positives = 68/104 (65%), Gaps = 4/104 (3%)
Query: 27 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS--SGSSQVLDSLQVEQERGITVKAQTASL 84
IRN I+AH+DHGK+TL+D LL G + +G LD + EQERGIT+ A S+
Sbjct: 18 FIRNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSM 77
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ +G EYL+NLIDTPGHVDF +VTR++ A G ++++ A
Sbjct: 78 VHE--YEGNEYLINLIDTPGHVDFGGDVTRAMRAVDGAIVVVCA 119
Score = 59.1 bits (143), Expect = 4e-10
Identities = 28/60 (46%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 200 RIRNFSIIAHVDHGKSTLADRLLEMTGTVLS--SGSSQVLDSLQVEQERGITVKAQTASL 257
IRN I+AH+DHGK+TL+D LL G + +G LD + EQERGIT+ A S+
Sbjct: 18 FIRNIGIVAHIDHGKTTLSDNLLAGAGMISEELAGQQLYLDFDEQEQERGITINAANVSM 77
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 98.5 bits (246), Expect = 4e-25
Identities = 44/105 (41%), Positives = 62/105 (59%), Gaps = 6/105 (5%)
Query: 29 RNFSIIAHVDHGKSTLADRLLEMT-----GTVLSSGSSQVLDSLQVEQERGITVKAQTAS 83
RN I H+ HGK++L D L+E T L + D+ + EQERGI++K+ S
Sbjct: 1 RNVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPIS 60
Query: 84 LRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
L G+ YL+N+IDTPGHV+F +EV +L C GVVL++D
Sbjct: 61 LVLED-SKGKSYLINIIDTPGHVNFMDEVAAALRLCDGVVLVVDV 104
Score = 48.8 bits (117), Expect = 5e-07
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 202 RNFSIIAHVDHGKSTLADRLLEMT-----GTVLSSGSSQVLDSLQVEQERGITVKAQTAS 256
RN I H+ HGK++L D L+E T L + D+ + EQERGI++K+ S
Sbjct: 1 RNVCIAGHLHHGKTSLLDMLIEQTHKRTPSVKLGWKPLRYTDTRKDEQERGISIKSNPIS 60
Query: 257 L 257
L
Sbjct: 61 L 61
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 93.8 bits (234), Expect = 4e-23
Identities = 43/103 (41%), Positives = 65/103 (63%), Gaps = 10/103 (9%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASLR 85
N I+AHVD GK+TL + LL +G + GS + DS+++E++RGIT+ + AS +
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGITIFSAVASFQ 60
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ E+ +N+IDTPGH+DF EV RSL+ G +L+I A
Sbjct: 61 W------EDTKVNIIDTPGHMDFIAEVERSLSVLDGAILVISA 97
Score = 56.9 bits (138), Expect = 1e-09
Identities = 24/59 (40%), Positives = 37/59 (62%), Gaps = 4/59 (6%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASL 257
N I+AHVD GK+TL + LL +G + GS + DS+++E++RGIT+ + AS
Sbjct: 1 NIGILAHVDAGKTTLTESLLYTSGAIRELGSVDKGTTRTDSMELERQRGITIFSAVASF 59
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 96.4 bits (240), Expect = 1e-22
Identities = 46/155 (29%), Positives = 72/155 (46%), Gaps = 36/155 (23%)
Query: 23 IPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ----VLDSLQVEQERGITVK 78
+ R RN I AH+D GK+T +R+L TG + G +D ++ E+ERGIT+
Sbjct: 5 TDLNRFRNIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITIT 64
Query: 79 AQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA---------- 128
+ ++ + + + +N+IDTPGHVDF+ EV RSL G V ++DA
Sbjct: 65 SAATTVFW------KGHRINIIDTPGHVDFTVEVERSLRVLDGAVAVLDAVGGVQPQSET 118
Query: 129 ----------------NQVDLKNANPEACEEQLQT 147
N++D AN Q++
Sbjct: 119 VWRQANRYEVPRIAFVNKMDKTGANFLRVVNQIKQ 153
Score = 57.1 bits (138), Expect = 2e-09
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 4/59 (6%)
Query: 196 IPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ----VLDSLQVEQERGITV 250
+ R RN I AH+D GK+T +R+L TG + G +D ++ E+ERGIT+
Sbjct: 5 TDLNRFRNIGISAHIDAGKTTTTERILFYTGRIHKIGEVHDGAATMDWMEQEKERGITI 63
>gnl|CDD|104396 PRK10218, PRK10218, GTP-binding protein; Provisional.
Length = 607
Score = 95.5 bits (237), Expect = 2e-22
Identities = 47/106 (44%), Positives = 73/106 (68%), Gaps = 8/106 (7%)
Query: 25 IARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTA 82
I ++RN +IIAHVDHGK+TL D+LL+ +GT S +Q V+DS +E+ERGIT+ A+
Sbjct: 2 IEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNT 61
Query: 83 SLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
++++ +Y +N++DTPGH DF EV R ++ V+L++DA
Sbjct: 62 AIKWN------DYRINIVDTPGHADFGGEVERVMSMVDSVLLVVDA 101
Score = 62.4 bits (151), Expect = 4e-11
Identities = 31/62 (50%), Positives = 46/62 (74%), Gaps = 2/62 (3%)
Query: 198 IARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQ--VLDSLQVEQERGITVKAQTA 255
I ++RN +IIAHVDHGK+TL D+LL+ +GT S +Q V+DS +E+ERGIT+ A+
Sbjct: 2 IEKLRNIAIIAHVDHGKTTLVDKLLQQSGTFDSRAETQERVMDSNDLEKERGITILAKNT 61
Query: 256 SL 257
++
Sbjct: 62 AI 63
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 91.0 bits (227), Expect = 7e-22
Identities = 48/152 (31%), Positives = 73/152 (48%), Gaps = 36/152 (23%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASLR 85
N IIAH+D GK+T +R+L TG + G +D ++ E+ERGIT+ Q+A+
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITI--QSAA-- 56
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA----------------- 128
T+ +++ +N+IDTPGHVDF+ EV RSL G V + DA
Sbjct: 57 -TTC-FWKDHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVQPQTETVWRQADR 114
Query: 129 ---------NQVDLKNANPEACEEQLQTLFNI 151
N++D A+ EQ++
Sbjct: 115 YGVPRIAFVNKMDRTGADFYRVVEQIREKLGA 146
Score = 47.9 bits (115), Expect = 1e-06
Identities = 21/52 (40%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 250
N IIAH+D GK+T +R+L TG + G +D ++ E+ERGIT+
Sbjct: 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGEVHGGGATMDWMEQERERGITI 52
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 92.1 bits (230), Expect = 3e-21
Identities = 45/115 (39%), Positives = 64/115 (55%), Gaps = 14/115 (12%)
Query: 22 DIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 77
+ P+ R RN I+AH+D GK+T +R+L TG G + +D ++ EQERGIT+
Sbjct: 4 ETPLERYRNIGIMAHIDAGKTTTTERILFYTGVNHKIGEVHDGAATMDWMEQEQERGITI 63
Query: 78 K--AQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
A T + ++ +N+IDTPGHVDF+ EV RSL G V + DA
Sbjct: 64 TSAATTCFWK--------DHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVG 110
Score = 51.7 bits (125), Expect = 2e-07
Identities = 24/60 (40%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 195 DIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 250
+ P+ R RN I+AH+D GK+T +R+L TG G + +D ++ EQERGIT+
Sbjct: 4 ETPLERYRNIGIMAHIDAGKTTTTERILFYTGVNHKIGEVHDGAATMDWMEQEQERGITI 63
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 88.7 bits (221), Expect = 4e-20
Identities = 44/112 (39%), Positives = 64/112 (57%), Gaps = 16/112 (14%)
Query: 24 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTV-----LSSGSSQVLDSLQVEQERGITVK 78
P+ + RN I+AH+D GK+T +R+L TG + G++ +D ++ EQERGIT+
Sbjct: 4 PLEKTRNIGIMAHIDAGKTTTTERILYYTGKSHKIGEVHDGAAT-MDWMEQEQERGITIT 62
Query: 79 --AQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
A T + + +N+IDTPGHVDF+ EV RSL G V + DA
Sbjct: 63 SAATTCFWK--------GHRINIIDTPGHVDFTIEVERSLRVLDGAVAVFDA 106
Score = 49.1 bits (118), Expect = 9e-07
Identities = 23/59 (38%), Positives = 37/59 (62%), Gaps = 6/59 (10%)
Query: 197 PIARIRNFSIIAHVDHGKSTLADRLLEMTGTV-----LSSGSSQVLDSLQVEQERGITV 250
P+ + RN I+AH+D GK+T +R+L TG + G++ +D ++ EQERGIT+
Sbjct: 4 PLEKTRNIGIMAHIDAGKTTTTERILYYTGKSHKIGEVHDGAAT-MDWMEQEQERGITI 61
>gnl|CDD|226593 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 86.9 bits (216), Expect = 2e-19
Identities = 44/114 (38%), Positives = 68/114 (59%), Gaps = 18/114 (15%)
Query: 25 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQ--VLDSLQVEQERGIT 76
+AR R F+II+H D GK+TL ++LL + GTV S + D +++E++RGI+
Sbjct: 9 VARRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGIS 68
Query: 77 VKAQTASLRYTSIL--DGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
V +S++ D + L+NL+DTPGH DFS + R+L A V++IDA
Sbjct: 69 VT--------SSVMQFDYADCLVNLLDTPGHEDFSEDTYRTLTAVDSAVMVIDA 114
Score = 51.9 bits (125), Expect = 1e-07
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 8/61 (13%)
Query: 198 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQ--VLDSLQVEQERGIT 249
+AR R F+II+H D GK+TL ++LL + GTV S + D +++E++RGI+
Sbjct: 9 VARRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGKHAKSDWMEIEKQRGIS 68
Query: 250 V 250
V
Sbjct: 69 V 69
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 86.3 bits (215), Expect = 3e-19
Identities = 39/148 (26%), Positives = 64/148 (43%), Gaps = 36/148 (24%)
Query: 34 IAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASLRYTSI 89
+ H GK+TL + +L TG + G + +D + E+ERGI++ + + +
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGISITSAATTCEW--- 57
Query: 90 LDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA--------------------- 128
+ + +NLIDTPGHVDF+ EV R+L G V+++ A
Sbjct: 58 ---KGHKINLIDTPGHVDFTGEVERALRVLDGAVVVVCAVGGVEPQTETVWRQAEKYGVP 114
Query: 129 -----NQVDLKNANPEACEEQLQTLFNI 151
N++D A+ QLQ
Sbjct: 115 RIIFVNKMDRAGADFFRVLAQLQEKLGA 142
Score = 46.3 bits (111), Expect = 8e-06
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 207 IAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITV 250
+ H GK+TL + +L TG + G + +D + E+ERGI++
Sbjct: 1 VGHSGAGKTTLTEAILFYTGAIHRIGEVEDGTTTMDFMPEERERGISI 48
>gnl|CDD|206732 cd04169, RF3, Release Factor 3 (RF3) protein involved in the
terminal step of translocation in bacteria. Peptide
chain release factor 3 (RF3) is a protein involved in
the termination step of translation in bacteria.
Termination occurs when class I release factors (RF1 or
RF2) recognize the stop codon at the A-site of the
ribosome and activate the release of the nascent
polypeptide. The class II release factor RF3 then
initiates the release of the class I RF from the
ribosome. RF3 binds to the RF/ribosome complex in the
inactive (GDP-bound) state. GDP/GTP exchange occurs,
followed by the release of the class I RF. Subsequent
hydrolysis of GTP to GDP triggers the release of RF3
from the ribosome. RF3 also enhances the efficiency of
class I RFs at less preferred stop codons and at stop
codons in weak contexts.
Length = 268
Score = 83.4 bits (207), Expect = 5e-19
Identities = 40/110 (36%), Positives = 63/110 (57%), Gaps = 14/110 (12%)
Query: 27 RIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQ--VLDSLQVEQERGITVK 78
R R F+II+H D GK+TL ++LL + G V + S + D +++E++RGI+V
Sbjct: 1 RRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISVT 60
Query: 79 AQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ Y + ++NL+DTPGH DFS + R+L A V++IDA
Sbjct: 61 SSVMQFEY------KGCVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDA 104
Score = 48.7 bits (117), Expect = 7e-07
Identities = 22/59 (37%), Positives = 36/59 (61%), Gaps = 8/59 (13%)
Query: 200 RIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQ--VLDSLQVEQERGITV 250
R R F+II+H D GK+TL ++LL + G V + S + D +++E++RGI+V
Sbjct: 1 RRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGAVKARKSRKHATSDWMEIEKQRGISV 59
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 81.3 bits (202), Expect = 1e-17
Identities = 41/114 (35%), Positives = 67/114 (58%), Gaps = 18/114 (15%)
Query: 25 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQVLDS--LQVEQERGIT 76
+A+ R F+II+H D GK+TL ++LL + GTV S + S +++E++RGI+
Sbjct: 7 VAKRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGRHATSDWMEMEKQRGIS 66
Query: 77 VKAQTASLRYTSIL--DGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
V +S++ + L+NL+DTPGH DFS + R+L A +++IDA
Sbjct: 67 VT--------SSVMQFPYRDCLINLLDTPGHEDFSEDTYRTLTAVDSALMVIDA 112
Score = 48.6 bits (117), Expect = 1e-06
Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 8/61 (13%)
Query: 198 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQVLDS--LQVEQERGIT 249
+A+ R F+II+H D GK+TL ++LL + GTV S + S +++E++RGI+
Sbjct: 7 VAKRRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTVKGRKSGRHATSDWMEMEKQRGIS 66
Query: 250 V 250
V
Sbjct: 67 V 67
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 80.3 bits (198), Expect = 3e-17
Identities = 37/112 (33%), Positives = 63/112 (56%), Gaps = 14/112 (12%)
Query: 25 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQVLDS--LQVEQERGIT 76
+ + R F+II+H D GK+T+ +++L + G V GS + S +++E++RGI+
Sbjct: 8 VDKRRTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGIS 67
Query: 77 VKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ Y + L+NL+DTPGH DFS + R+L A +++IDA
Sbjct: 68 ITTSVMQFPY------RDCLVNLLDTPGHEDFSEDTYRTLTAVDNCLMVIDA 113
Score = 45.3 bits (107), Expect = 1e-05
Identities = 19/61 (31%), Positives = 37/61 (60%), Gaps = 8/61 (13%)
Query: 198 IARIRNFSIIAHVDHGKSTLADRLL------EMTGTVLSSGSSQVLDS--LQVEQERGIT 249
+ + R F+II+H D GK+T+ +++L + G V GS + S +++E++RGI+
Sbjct: 8 VDKRRTFAIISHPDAGKTTITEKVLLYGGAIQTAGAVKGRGSQRHAKSDWMEMEKQRGIS 67
Query: 250 V 250
+
Sbjct: 68 I 68
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 67.1 bits (165), Expect = 2e-13
Identities = 35/101 (34%), Positives = 45/101 (44%), Gaps = 33/101 (32%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGS---SQVLDSLQVEQE 72
N +I HVD GKSTL LL G V + S + VLD L+ E+E
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 73 RGITV-----KAQTASLRYTSILDGEEYLLNLIDTPGHVDF 108
RG+T+ K +T R+T +ID PGH DF
Sbjct: 61 RGVTIDVGLAKFETEKYRFT-----------IIDAPGHRDF 90
Score = 53.6 bits (130), Expect = 1e-08
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 17/65 (26%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGS---SQVLDSLQVEQE 245
N +I HVD GKSTL LL G V + S + VLD L+ E+E
Sbjct: 1 NLVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKYAWVLDKLKEERE 60
Query: 246 RGITV 250
RG+T+
Sbjct: 61 RGVTI 65
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 67.2 bits (165), Expect = 3e-13
Identities = 36/150 (24%), Positives = 64/150 (42%), Gaps = 36/150 (24%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASLR 85
N +++ H GK+TLA+ LL TG + G + V D E++R ++++ A L
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPLE 60
Query: 86 YTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA----------------- 128
+ + +NLIDTPG+ DF E +L A +++++A
Sbjct: 61 W------NGHKINLIDTPGYADFVGETLSALRAVDAALIVVEAQSGVEVGTEKVWEFLDD 114
Query: 129 ---------NQVDLKNANPEACEEQLQTLF 149
N++D A+ + L+ F
Sbjct: 115 AKLPRIIFINKMDRARADFDKTLAALREAF 144
Score = 36.4 bits (85), Expect = 0.008
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 4/59 (6%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGS----SQVLDSLQVEQERGITVKAQTASL 257
N +++ H GK+TLA+ LL TG + G + V D E++R ++++ A L
Sbjct: 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDPEEKKRKMSIETSVAPL 59
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 61.6 bits (150), Expect = 7e-12
Identities = 30/136 (22%), Positives = 49/136 (36%), Gaps = 34/136 (25%)
Query: 33 IIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDG 92
I+ + GKSTL +RLL ++ G T T + DG
Sbjct: 6 IVGDPNVGKSTLLNRLLGNKISITEYKP-------------GTTRNYVTTVIEE----DG 48
Query: 93 EEYLLNLIDTPGHVDFS-------NEVTRSLAACQGVVLLIDANQVDLKNANPEACEEQL 145
+ Y NL+DT G D+ V SL V+L++D E E+Q
Sbjct: 49 KTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVE---------EILEKQT 99
Query: 146 QTLFNI-DKKSVLRIW 160
+ + + + + +
Sbjct: 100 KEIIHHAESGVPIILV 115
Score = 37.4 bits (87), Expect = 0.002
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 3/50 (6%)
Query: 206 IIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSL--QVEQERGITVKAQ 253
I+ + GKSTL +RLL ++ + V +E G T K
Sbjct: 6 IVGDPNVGKSTLLNRLLGNKISITEYK-PGTTRNYVTTVIEEDGKTYKFN 54
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 64.2 bits (157), Expect = 8e-12
Identities = 39/119 (32%), Positives = 54/119 (45%), Gaps = 25/119 (21%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGS---SQVLDSLQVEQE 72
N I HVD GKSTL RLL G + L S + VLD + E+E
Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERE 68
Query: 73 RGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDF-SNEVTRSLAACQGVVLLIDANQ 130
RG+T+ + + ++Y +ID PGH DF N +T + A VL++DA
Sbjct: 69 RGVTIDVAHSK------FETDKYNFTIIDAPGHRDFVKNMITGASQADVA-VLVVDARD 120
Score = 45.4 bits (108), Expect = 1e-05
Identities = 24/72 (33%), Positives = 31/72 (43%), Gaps = 17/72 (23%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGS---SQVLDSLQVEQE 245
N I HVD GKSTL RLL G + L S + VLD + E+E
Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVLDKTKEERE 68
Query: 246 RGITVKAQTASL 257
RG+T+ +
Sbjct: 69 RGVTIDVAHSKF 80
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 64.2 bits (157), Expect = 9e-12
Identities = 33/96 (34%), Positives = 49/96 (51%), Gaps = 23/96 (23%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGSSQ---VLDSLQVEQE 72
N ++I HVDHGKSTL RLL TG + S + V+D L+ E+E
Sbjct: 8 NLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERE 67
Query: 73 RGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDF 108
RG+T+ A ++ + ++Y ++D PGH DF
Sbjct: 68 RGVTIDL--AHKKF----ETDKYYFTIVDCPGHRDF 97
Score = 51.5 bits (124), Expect = 1e-07
Identities = 25/65 (38%), Positives = 34/65 (52%), Gaps = 17/65 (26%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGSSQ---VLDSLQVEQE 245
N ++I HVDHGKSTL RLL TG + S + V+D L+ E+E
Sbjct: 8 NLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERE 67
Query: 246 RGITV 250
RG+T+
Sbjct: 68 RGVTI 72
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 59.1 bits (144), Expect = 1e-10
Identities = 38/118 (32%), Positives = 57/118 (48%), Gaps = 26/118 (22%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVL-----------SSGS-------SQVLDSLQVEQ 71
F VD GKSTL RLL + ++ SSG+ + ++D LQ E+
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAER 60
Query: 72 ERGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFS-NEVTRSLAACQGVVLLIDA 128
E+GIT+ A RY S +++ + DTPGH ++ N VT + +LL+DA
Sbjct: 61 EQGITI--DVAY-RYFS-TPKRKFI--IADTPGHEQYTRNMVT-GASTADLAILLVDA 111
Score = 43.3 bits (103), Expect = 3e-05
Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 18/66 (27%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVL-----------SSGS-------SQVLDSLQVEQ 244
F VD GKSTL RLL + ++ SSG+ + ++D LQ E+
Sbjct: 1 RFITCGSVDDGKSTLIGRLLYDSKSIFEDQLAALERSKSSGTQGEKLDLALLVDGLQAER 60
Query: 245 ERGITV 250
E+GIT+
Sbjct: 61 EQGITI 66
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 58.3 bits (141), Expect = 7e-10
Identities = 31/117 (26%), Positives = 49/117 (41%), Gaps = 23/117 (19%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGSSQ---VLDSLQVEQE 72
N + I HVDHGKST LL G + S + V+D L+ E+E
Sbjct: 9 NVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERE 68
Query: 73 RGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
RG+T+ + ++Y + ++D PGH DF + + VL++
Sbjct: 69 RGVTIDVAHWK------FETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVG 119
Score = 44.9 bits (106), Expect = 2e-05
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 17/65 (26%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTV--------------LSSGSSQ---VLDSLQVEQE 245
N + I HVDHGKST LL G + S + V+D L+ E+E
Sbjct: 9 NVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVMDRLKEERE 68
Query: 246 RGITV 250
RG+T+
Sbjct: 69 RGVTI 73
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 51.1 bits (123), Expect = 4e-09
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 158 RIWHRRCFSCADCHRSLDSTNLND 181
+ WH+ CF+CA C++ LDST L +
Sbjct: 19 KSWHKSCFTCAVCNKRLDSTTLAE 42
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 52.6 bits (127), Expect = 1e-08
Identities = 26/94 (27%), Positives = 40/94 (42%), Gaps = 16/94 (17%)
Query: 36 HVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEY 95
H+DHGK+TL L + D L E++RGIT+ L + + +
Sbjct: 7 HIDHGKTTLIKALTGIET-----------DRLPEEKKRGITI-----DLGFAYLDLPDGK 50
Query: 96 LLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
L ID PGH F + V+L++ A+
Sbjct: 51 RLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAAD 84
Score = 38.4 bits (90), Expect = 0.001
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 11/42 (26%)
Query: 209 HVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITV 250
H+DHGK+TL L + D L E++RGIT+
Sbjct: 7 HIDHGKTTLIKALTGIET-----------DRLPEEKKRGITI 37
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 54.2 bits (131), Expect = 2e-08
Identities = 35/118 (29%), Positives = 55/118 (46%), Gaps = 33/118 (27%)
Query: 36 HVDHGKSTLADRLLEMTGTV-------LSSGSSQ------------VLDSLQVEQERGIT 76
VD GKSTL RLL T + L S + ++D L+ E+E+GIT
Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73
Query: 77 VKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLA----ACQGVVLLIDANQ 130
+ + RY S + ++++ DTPGH + TR++A +LL+DA +
Sbjct: 74 IDV---AYRYFST-EKRKFII--ADTPGHEQY----TRNMATGASTADLAILLVDARK 121
Score = 39.2 bits (92), Expect = 0.001
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 19/61 (31%)
Query: 209 HVDHGKSTLADRLLEMTGTV-------LSSGSSQ------------VLDSLQVEQERGIT 249
VD GKSTL RLL T + L S + ++D L+ E+E+GIT
Sbjct: 14 SVDDGKSTLIGRLLYDTKAIYEDQLASLERDSKRKGTQGEKIDLALLVDGLEAEREQGIT 73
Query: 250 V 250
+
Sbjct: 74 I 74
>gnl|CDD|185474 PTZ00141, PTZ00141, elongation factor 1- alpha; Provisional.
Length = 446
Score = 51.7 bits (124), Expect = 1e-07
Identities = 33/101 (32%), Positives = 43/101 (42%), Gaps = 33/101 (32%)
Query: 30 NFSIIAHVDHGKSTLADRLL--------------EMTGTVLSSGS---SQVLDSLQVEQE 72
N +I HVD GKST L+ E + GS + VLD L+ E+E
Sbjct: 9 NLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 68
Query: 73 RGITV-----KAQTASLRYTSILDGEEYLLNLIDTPGHVDF 108
RGIT+ K +T +T +ID PGH DF
Sbjct: 69 RGITIDIALWKFETPKYYFT-----------IIDAPGHRDF 98
Score = 40.1 bits (94), Expect = 6e-04
Identities = 23/65 (35%), Positives = 30/65 (46%), Gaps = 17/65 (26%)
Query: 203 NFSIIAHVDHGKSTLADRLL--------------EMTGTVLSSGS---SQVLDSLQVEQE 245
N +I HVD GKST L+ E + GS + VLD L+ E+E
Sbjct: 9 NLVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERE 68
Query: 246 RGITV 250
RGIT+
Sbjct: 69 RGITI 73
>gnl|CDD|165621 PLN00043, PLN00043, elongation factor 1-alpha; Provisional.
Length = 447
Score = 49.3 bits (117), Expect = 7e-07
Identities = 35/116 (30%), Positives = 51/116 (43%), Gaps = 23/116 (19%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTV-----------------LSSGSSQVLDSLQVEQE 72
N +I HVD GKST L+ G + S + VLD L+ E+E
Sbjct: 9 NIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAERE 68
Query: 73 RGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
RGIT+ A ++ + +Y +ID PGH DF + + VL+ID+
Sbjct: 69 RGITI--DIALWKFETT----KYYCTVIDAPGHRDFIKNMITGTSQADCAVLIIDS 118
Score = 33.9 bits (77), Expect = 0.067
Identities = 22/65 (33%), Positives = 29/65 (44%), Gaps = 17/65 (26%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTV-----------------LSSGSSQVLDSLQVEQE 245
N +I HVD GKST L+ G + S + VLD L+ E+E
Sbjct: 9 NIVVIGHVDSGKSTTTGHLIYKLGGIDKRVIERFEKEAAEMNKRSFKYAWVLDKLKAERE 68
Query: 246 RGITV 250
RGIT+
Sbjct: 69 RGITI 73
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 48.7 bits (116), Expect = 1e-06
Identities = 27/101 (26%), Positives = 42/101 (41%), Gaps = 17/101 (16%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSI 89
+ HVDHGK+TL L + D L E++RG+T+ L +
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIAA-----------DRLPEEKKRGMTI-----DLGFAYF 45
Query: 90 LDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
+Y L ID PGH F + +L++DA++
Sbjct: 46 -PLPDYRLGFIDVPGHEKFISNAIAGGGGIDAALLVVDADE 85
Score = 31.8 bits (72), Expect = 0.37
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 11/48 (22%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITV 250
+ HVDHGK+TL L + D L E++RG+T+
Sbjct: 2 IIATAGHVDHGKTTLLKALTGIAA-----------DRLPEEKKRGMTI 38
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 48.2 bits (115), Expect = 2e-06
Identities = 30/96 (31%), Positives = 46/96 (47%), Gaps = 17/96 (17%)
Query: 35 AHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEE 94
H+DHGK+TL L TG V D L E++RGIT+ L + E+
Sbjct: 7 GHIDHGKTTLLKAL---TGGVT--------DRLPEEKKRGITID-----LGFYY-RKLED 49
Query: 95 YLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
++ ID PGH DF + + L +L++ A++
Sbjct: 50 GVMGFIDVPGHPDFISNLLAGLGGIDYALLVVAADE 85
Score = 30.4 bits (69), Expect = 0.98
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 11/44 (25%)
Query: 208 AHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 251
H+DHGK+TL L TG V D L E++RGIT+
Sbjct: 7 GHIDHGKTTLLKAL---TGG--------VTDRLPEEKKRGITID 39
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 47.4 bits (113), Expect = 3e-06
Identities = 35/113 (30%), Positives = 53/113 (46%), Gaps = 25/113 (22%)
Query: 37 VDHGKSTLADRLLEMTGTV-------LSSGS------------SQVLDSLQVEQERGITV 77
VD GKSTL RLL T + L S + ++D LQ E+E+GIT+
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
Query: 78 KAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
+ RY S D ++++ DTPGH ++ + + VLL+DA +
Sbjct: 69 DV---AYRYFST-DKRKFIV--ADTPGHEQYTRNMATGASTADLAVLLVDARK 115
Score = 32.7 bits (75), Expect = 0.15
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 19/60 (31%)
Query: 210 VDHGKSTLADRLLEMTGTV-------LSSGS------------SQVLDSLQVEQERGITV 250
VD GKSTL RLL T + L S + ++D LQ E+E+GIT+
Sbjct: 9 VDDGKSTLIGRLLHDTKQIYEDQLAALERDSKKHGTQGGEIDLALLVDGLQAEREQGITI 68
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 47.3 bits (112), Expect = 4e-06
Identities = 33/102 (32%), Positives = 48/102 (47%), Gaps = 14/102 (13%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV-----LDSLQVEQERGITVKAQTASL 84
N I HVDHGK+TL L T + S G S +D+ E+ RGIT+ TA++
Sbjct: 83 NIGTIGHVDHGKTTLTAAL---TMALASMGGSAPKKYDEIDAAPEERARGITI--NTATV 137
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLI 126
Y + E +D PGH D+ + A G +L++
Sbjct: 138 EYET----ENRHYAHVDCPGHADYVKNMITGAAQMDGAILVV 175
Score = 35.0 bits (80), Expect = 0.034
Identities = 22/57 (38%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV-----LDSLQVEQERGITVKAQT 254
N I HVDHGK+TL L T + S G S +D+ E+ RGIT+ T
Sbjct: 83 NIGTIGHVDHGKTTLTAAL---TMALASMGGSAPKKYDEIDAAPEERARGITINTAT 136
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 46.0 bits (110), Expect = 9e-06
Identities = 29/107 (27%), Positives = 43/107 (40%), Gaps = 37/107 (34%)
Query: 33 IIAHVDHGKSTLADRL----------LEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTA 82
I+ HVDHGK+TL D++ +T + G+ QV L V + GIT
Sbjct: 10 IMGHVDHGKTTLLDKIRKTNVAAGEAGGITQHI---GAYQVP--LDVIKIPGITF----- 59
Query: 83 SLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
IDTPGH F+ R + +L++ A+
Sbjct: 60 -----------------IDTPGHEAFTAMRARGASVTDIAILVVAAD 89
Score = 31.0 bits (71), Expect = 0.61
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 206 IIAHVDHGKSTLADRL 221
I+ HVDHGK+TL D++
Sbjct: 10 IMGHVDHGKTTLLDKI 25
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 44.0 bits (105), Expect = 1e-05
Identities = 28/100 (28%), Positives = 45/100 (45%), Gaps = 24/100 (24%)
Query: 33 IIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQE-RGIT--VKAQTASLRYTSI 89
++ HVDHGK+TL D++ + + V E GIT + A Y
Sbjct: 5 VMGHVDHGKTTLLDKIRK----------TNV-----AAGEAGGITQHIGA------YQVP 43
Query: 90 LDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
+D + + IDTPGH F+N R + +L++ A+
Sbjct: 44 IDVKIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAAD 83
Score = 30.5 bits (70), Expect = 0.46
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 206 IIAHVDHGKSTLADRL 221
++ HVDHGK+TL D++
Sbjct: 5 VMGHVDHGKTTLLDKI 20
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 45.4 bits (108), Expect = 1e-05
Identities = 31/104 (29%), Positives = 46/104 (44%), Gaps = 14/104 (13%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQV-----EQERGITVKAQTASL 84
N I HVDHGK+TL + T + G ++ Q+ E+ RGIT+ TA +
Sbjct: 14 NVGTIGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITI--NTAHV 68
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
Y Y +D PGH D+ + A G +L++ A
Sbjct: 69 EYE--TANRHY--AHVDCPGHADYVKNMITGAAQMDGAILVVAA 108
Score = 39.6 bits (93), Expect = 0.001
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 8/53 (15%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQV-----EQERGITV 250
N I HVDHGK+TL + T + G ++ Q+ E+ RGIT+
Sbjct: 14 NVGTIGHVDHGKTTLTAAI---TTVLAKKGGAEAKAYDQIDNAPEEKARGITI 63
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 44.8 bits (106), Expect = 2e-05
Identities = 32/102 (31%), Positives = 48/102 (47%), Gaps = 10/102 (9%)
Query: 30 NFSIIAHVDHGKSTLA---DRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRY 86
N I HVDHGK+TL +L G + Q+ D+ E+ RGIT+ TA + Y
Sbjct: 14 NIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-DNAPEEKARGITI--NTAHVEY 70
Query: 87 TSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ + Y +D PGH D+ + A G +L++ A
Sbjct: 71 ET--ENRHYA--HVDCPGHADYVKNMITGAAQMDGAILVVSA 108
Score = 34.4 bits (79), Expect = 0.054
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 203 NFSIIAHVDHGKSTLA---DRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKA 252
N I HVDHGK+TL +L G + Q+ D+ E+ RGIT+
Sbjct: 14 NIGTIGHVDHGKTTLTAAITTVLAKEGGAAARAYDQI-DNAPEEKARGITINT 65
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 43.2 bits (102), Expect = 2e-05
Identities = 25/130 (19%), Positives = 44/130 (33%), Gaps = 25/130 (19%)
Query: 33 IIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDG 92
++ GKS+L + LL + +V G T D
Sbjct: 2 VVGRGGVGKSSLLNALLG-------------GEVGEVSDVPGTTRDPDVYVKEL----DK 44
Query: 93 EEYLLNLIDTPGHVDFSNEVTRSLAA-----CQGVVLLIDANQVDLKNANPEACEEQLQT 147
+ L L+DTPG +F LA ++L++D+ + + +A L+
Sbjct: 45 GKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDS---TDRESEEDAKLLILRR 101
Query: 148 LFNIDKKSVL 157
L +L
Sbjct: 102 LRKEGIPIIL 111
>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein
(CRP). The second LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residu es,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 40.3 bits (94), Expect = 3e-05
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 160 WHRRCFSCADCHRSLDSTNLND 181
WH+ CF CA C +SL+ST L D
Sbjct: 21 WHKNCFRCAKCGKSLESTTLAD 42
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family. Mlp60A
exhibits only one LIM domain linked to a glycin-rich
region. Mlp84B and Mlp60A are muscle specific proteins
and have been implicated in muscle differentiation.
While Mlp84B transcripts are enriched at the terminal
ends of muscle fibers, Mlp60A transcripts are found
throughout the muscle fibers. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 40.2 bits (94), Expect = 3e-05
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 160 WHRRCFSCADCHRSLDSTN 178
WH+ CF C C++ LDSTN
Sbjct: 22 WHKMCFKCGMCNKLLDSTN 40
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 43.7 bits (103), Expect = 5e-05
Identities = 31/109 (28%), Positives = 46/109 (42%), Gaps = 24/109 (22%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV-----LDSLQVEQERGIT-----VKA 79
N I HVDHGK+TL +T + G ++ +D E+ RGIT V+
Sbjct: 63 NVGTIGHVDHGKTTLTA---AITKVLAEEGKAKAVAFDEIDKAPEEKARGITIATAHVEY 119
Query: 80 QTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+TA Y +D PGH D+ + A G +L++ A
Sbjct: 120 ETAKRHYAH-----------VDCPGHADYVKNMITGAAQMDGGILVVSA 157
Score = 33.6 bits (77), Expect = 0.079
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV-----LDSLQVEQERGITVKA 252
N I HVDHGK+TL +T + G ++ +D E+ RGIT+
Sbjct: 63 NVGTIGHVDHGKTTLTA---AITKVLAEEGKAKAVAFDEIDKAPEEKARGITIAT 114
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 42.4 bits (100), Expect = 6e-05
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 17/87 (19%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSS-GSSQVLDSLQVEQERGITV-------KAQT 81
N ++ HVD GK++LA LS S+ D QERGIT+ +
Sbjct: 2 NVGLLGHVDSGKTSLA--------KALSEIASTAAFDKNPQSQERGITLDLGFSSFEVDK 53
Query: 82 ASLRYTSILDG-EEYLLNLIDTPGHVD 107
+ E Y + L+D PGH
Sbjct: 54 PKHLEDNENPQIENYQITLVDCPGHAS 80
Score = 37.7 bits (88), Expect = 0.002
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 9/49 (18%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSS-GSSQVLDSLQVEQERGITV 250
N ++ HVD GK++LA LS S+ D QERGIT+
Sbjct: 2 NVGLLGHVDSGKTSLA--------KALSEIASTAAFDKNPQSQERGITL 42
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 39.2 bits (91), Expect = 8e-05
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 160 WHRRCFSCADCHRSLDSTNLND 181
WH+ CF CA C +SL+ST + D
Sbjct: 21 WHKTCFRCAICGKSLESTTVTD 42
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 43.0 bits (102), Expect = 8e-05
Identities = 38/115 (33%), Positives = 55/115 (47%), Gaps = 33/115 (28%)
Query: 37 VDHGKSTLADRLLEMTGTV-------LSSGSSQV------------LDSLQVEQERGITV 77
VD GKSTL RLL T + L + S + +D LQ E+E+GIT+
Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITI 95
Query: 78 KAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAA----CQGVVLLIDA 128
+ RY S + +++ + DTPGH + TR++A C +LLIDA
Sbjct: 96 D---VAYRYFST-EKRKFI--IADTPGH----EQYTRNMATGASTCDLAILLIDA 140
Score = 33.7 bits (78), Expect = 0.086
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 19/60 (31%)
Query: 210 VDHGKSTLADRLLEMTGTV-------LSSGSSQV------------LDSLQVEQERGITV 250
VD GKSTL RLL T + L + S + +D LQ E+E+GIT+
Sbjct: 36 VDDGKSTLIGRLLHDTKQIYEDQLASLHNDSKRHGTQGEKLDLALLVDGLQAEREQGITI 95
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 42.9 bits (102), Expect = 9e-05
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 26/90 (28%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGIT-----VK 78
N I HVDHGK+TL + VL+ G + Q+ E+ RGIT V+
Sbjct: 14 NVGTIGHVDHGKTTLTAAIT----KVLAKKGGGEAKAYDQIDNAPEEKARGITINTSHVE 69
Query: 79 AQTASLRYTSILDGEEYLLNLIDTPGHVDF 108
+TA+ Y +D PGH D+
Sbjct: 70 YETANRHYAH-----------VDCPGHADY 88
Score = 36.4 bits (85), Expect = 0.010
Identities = 19/54 (35%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGITV 250
N I HVDHGK+TL + VL+ G + Q+ E+ RGIT+
Sbjct: 14 NVGTIGHVDHGKTTLTAAIT----KVLAKKGGGEAKAYDQIDNAPEEKARGITI 63
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are identified
in a diverse group of proteins with wide variety of
biological functions, including gene expression
regulation, cell fate determination, cytoskeleton
organization, tumor formation and development. LIM
domains function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. They perform
their functions through interactions with other protein
partners. LIM domains are 50-60 amino acids in size and
share two characteristic highly conserved zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. The consensus
sequence of LIM domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 38.1 bits (89), Expect = 2e-04
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 158 RIWHRRCFSCADCHRSLD 175
+ WH CF C+ C + L
Sbjct: 19 KKWHPECFKCSVCGKPLG 36
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 41.3 bits (98), Expect = 2e-04
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 16/85 (18%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGITVKAQTAS 83
N I HVDHGK+TL + VL+ G ++ Q+ E+ RGIT+ TA
Sbjct: 14 NVGTIGHVDHGKTTLTAAIT----KVLAKKGGAEAKAYDQIDKAPEEKARGITI--NTAH 67
Query: 84 LRYTSILDGEEYLLNLIDTPGHVDF 108
+ Y + + Y +D PGH D+
Sbjct: 68 VEYET--EKRHY--AHVDCPGHADY 88
Score = 35.2 bits (82), Expect = 0.025
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGITV 250
N I HVDHGK+TL + VL+ G ++ Q+ E+ RGIT+
Sbjct: 14 NVGTIGHVDHGKTTLTAAIT----KVLAKKGGAEAKAYDQIDKAPEEKARGITI 63
>gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This
model describes archaeal and eukaryotic orthologs of
bacterial IF-2. Like IF-2, it helps convey the initiator
tRNA to the ribosome, although the initiator is
N-formyl-Met in bacteria and Met here. This protein is
not closely related to the subunits of eIF-2 of
eukaryotes, which is also involved in the initiation of
translation. The aIF-2 of Methanococcus jannaschii
contains a large intein interrupting a region of very
strongly conserved sequence very near the amino end; the
alignment generated by This model does not correctly
align the sequences from Methanococcus jannaschii and
Pyrococcus horikoshii in this region [Protein synthesis,
Translation factors].
Length = 590
Score = 41.7 bits (98), Expect = 2e-04
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 16/106 (15%)
Query: 32 SIIAHVDHGKSTLADRLL-------EMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASL 84
S++ HVDHGK+TL D++ E G G++++ + +E G +K L
Sbjct: 8 SVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDV-IEGICGDLLKKFKIRL 66
Query: 85 RYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
+ +L IDTPGH F+N R A +L++D N+
Sbjct: 67 KIPGLL--------FIDTPGHEAFTNLRKRGGALADLAILIVDINE 104
Score = 30.9 bits (70), Expect = 0.77
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 205 SIIAHVDHGKSTLADRL 221
S++ HVDHGK+TL D++
Sbjct: 8 SVLGHVDHGKTTLLDKI 24
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 41.2 bits (97), Expect = 3e-04
Identities = 33/121 (27%), Positives = 48/121 (39%), Gaps = 31/121 (25%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK---AQT----- 81
N ++ HVDHGK+TL L TG + S E +RGI+++ A
Sbjct: 6 NIGMVGHVDHGKTTLTKAL---TGVWTDTHSE--------ELKRGISIRLGYADAEIYKC 54
Query: 82 ----ASLRYTS-----ILDGEEYLL---NLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
YT+ E LL + +D PGH + A G +L+I AN
Sbjct: 55 PECDGPECYTTEPVCPNCGSETELLRRVSFVDAPGHETLMATMLSGAALMDGALLVIAAN 114
Query: 130 Q 130
+
Sbjct: 115 E 115
Score = 36.6 bits (85), Expect = 0.011
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 11/49 (22%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 251
N ++ HVDHGK+TL L TG + S E +RGI+++
Sbjct: 6 NIGMVGHVDHGKTTLTKAL---TGVWTDTHSE--------ELKRGISIR 43
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 40.6 bits (96), Expect = 3e-04
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 26/86 (30%)
Query: 34 IAHVDHGKSTLADRLLEMTGTVLSS-GSSQVLDSLQV-----EQERGIT-----VKAQTA 82
I HVDHGK+TL + VL+ G ++ ++ E+ RGIT V+ +TA
Sbjct: 8 IGHVDHGKTTLTAAIT----KVLAKKGGAKAKKYDEIDKAPEEKARGITINTAHVEYETA 63
Query: 83 SLRYTSILDGEEYLLNLIDTPGHVDF 108
+ Y +D PGH D+
Sbjct: 64 NRHYAH-----------VDCPGHADY 78
Score = 33.3 bits (77), Expect = 0.077
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 10/52 (19%)
Query: 207 IAHVDHGKSTLADRLLEMTGTVLSS-GSSQVLDSLQV-----EQERGITVKA 252
I HVDHGK+TL + VL+ G ++ ++ E+ RGIT+
Sbjct: 8 IGHVDHGKTTLTAAIT----KVLAKKGGAKAKKYDEIDKAPEEKARGITINT 55
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 41.5 bits (98), Expect = 3e-04
Identities = 37/108 (34%), Positives = 53/108 (49%), Gaps = 22/108 (20%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGITVKAQTAS 83
N I HVDHGK+TL + VL+ G +Q D + E+ERGIT+ TA
Sbjct: 14 NIGTIGHVDHGKTTLTAAI----TKVLAERGLNQAKDYDSIDAAPEEKERGITI--NTAH 67
Query: 84 LRYTSILDGEEYLLNLIDTPGHVDF-SNEVTRSLAACQ--GVVLLIDA 128
+ Y + + Y +D PGH D+ N +T A Q G +L++ A
Sbjct: 68 VEYET--EKRHYA--HVDCPGHADYVKNMIT---GAAQMDGAILVVAA 108
Score = 34.5 bits (80), Expect = 0.041
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 10/54 (18%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLS-SGSSQVLDSLQV-----EQERGITV 250
N I HVDHGK+TL + VL+ G +Q D + E+ERGIT+
Sbjct: 14 NIGTIGHVDHGKTTLTAAI----TKVLAERGLNQAKDYDSIDAAPEEKERGITI 63
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 41.3 bits (97), Expect = 3e-04
Identities = 32/141 (22%), Positives = 54/141 (38%), Gaps = 47/141 (33%)
Query: 32 SIIAHVDHGKSTLADRLLEMTGTVLSSGS-SQVLDSLQVEQERGITVKAQTASLRYTSIL 90
+I+ HVDHGK++L D + + +G +Q + + VE E G +
Sbjct: 91 TIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAYHVENEDGKMI------------- 137
Query: 91 DGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA---------------------- 128
+DTPGH F++ R VVL++ A
Sbjct: 138 -------TFLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPI 190
Query: 129 ----NQVDLKNANPEACEEQL 145
N++D ANP+ +++L
Sbjct: 191 IVAINKIDKPEANPDRVKQEL 211
Score = 29.7 bits (67), Expect = 1.5
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 205 SIIAHVDHGKSTLADRLLEMTGTVLSSGS-SQVLDSLQVEQERGITV 250
+I+ HVDHGK++L D + + +G +Q + + VE E G +
Sbjct: 91 TIMGHVDHGKTSLLDSIRKTKVAQGEAGGITQHIGAYHVENEDGKMI 137
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 37.7 bits (88), Expect = 3e-04
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 160 WHRRCFSCADCHRSLDSTN 178
WH CF CA C + L +
Sbjct: 22 WHPECFRCAVCGKPLGPGD 40
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein
2 (CRP2). The second LIM domain of Cysteine Rich
Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 37.4 bits (86), Expect = 3e-04
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 160 WHRRCFSCADCHRSLDSTNLND 181
WH+ CF CA C +SL+ST L +
Sbjct: 21 WHKNCFRCAKCGKSLESTTLTE 42
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 41.1 bits (97), Expect = 3e-04
Identities = 31/105 (29%), Positives = 47/105 (44%), Gaps = 16/105 (15%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV------LDSLQVEQERGITVKAQTAS 83
N I HVDHGK+TL + L++ +DS E+ RGIT+ TA
Sbjct: 14 NIGTIGHVDHGKTTLTAAI----TMTLAAKGGAKAKKYDEIDSAPEEKARGITIN--TAH 67
Query: 84 LRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA 128
+ Y + + Y +D PGH D+ + A G +L++ A
Sbjct: 68 VEYET--ENRHY--AHVDCPGHADYVKNMITGAAQMDGAILVVSA 108
Score = 34.2 bits (79), Expect = 0.062
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV------LDSLQVEQERGITV 250
N I HVDHGK+TL + L++ +DS E+ RGIT+
Sbjct: 14 NIGTIGHVDHGKTTLTAAI----TMTLAAKGGAKAKKYDEIDSAPEEKARGITI 63
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 36.2 bits (84), Expect = 9e-04
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 158 RIWHRRCFSCADCHRSLDSTN 178
++WH CF CA C + L
Sbjct: 21 KVWHPECFKCATCGKPLSGDT 41
>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein
(TLP). The LIM domain of thymus LIM protein (TLP) like
proteins: This family includes the LIM domains of TLP
and CRIP (Cysteine-Rich Intestinal Protein). TLP is the
distant member of the CRP family of proteins. TLP has
two isomers (TLP-A and TLP-B) and sharing approximately
30% with each of the three other CRPs. Like CRP1, CRP2
and CRP3/MLP, TLP has two LIM domains, connected by a
flexible linker region. Unlike the CRPs, TLP lacks the
nuclear targeting signal (K/R-K/R-Y-G-P-K) and is
localized solely in the cytoplasm. TLP is specifically
expressed in the thymus in a subset of cortical
epithelial cells. TLP has a role in development of
normal thymus and in controlling the development and
differentiation of thymic epithelial cells. CRIP is a
short LIM protein with only one LIM domain. CRIP gene is
developmentally regulated and can be induced by
glucocorticoid hormones during the first three postnatal
weeks. The domain shows close sequence homology to LIM
domain of thymus LIM protein. However, unlike the TLP
proteins which have two LIM domains, the members of this
family have only one LIM domain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 36.2 bits (84), Expect = 9e-04
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 149 FNIDKKSVLRIWHRRCFSCADCHRSLDSTNLNDGLAKP 186
F K S+ R WH+ C C C ++L ++ KP
Sbjct: 10 FAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKP 47
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains ,but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 35.8 bits (83), Expect = 0.001
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 141 CEEQLQTLFNIDKKSVL-RIWHRRCFSCADCHRSLDSTN 178
C +T++ +K + L +IWH+ CF C C +L+ N
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKN 39
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 39.2 bits (92), Expect = 0.001
Identities = 33/121 (27%), Positives = 47/121 (38%), Gaps = 31/121 (25%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK---AQT----- 81
N ++ HVDHGK+TL L +G S E +RGIT+K A
Sbjct: 12 NIGMVGHVDHGKTTLTKAL---SGVWTDRHSE--------ELKRGITIKLGYADAKIYKC 60
Query: 82 ----ASLRYTS-----ILDGEEYLL---NLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
YT+ E L+ + +D PGH + A G +L+I AN
Sbjct: 61 PECYRPECYTTEPKCPNCGAETELVRRVSFVDAPGHETLMATMLSGAALMDGALLVIAAN 120
Query: 130 Q 130
+
Sbjct: 121 E 121
Score = 34.2 bits (79), Expect = 0.060
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 251
N ++ HVDHGK+TL L +G S E +RGIT+K
Sbjct: 12 NIGMVGHVDHGKTTLTKAL---SGVWTDRHSE--------ELKRGITIK 49
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Is l2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 35.4 bits (82), Expect = 0.002
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 151 IDKKSVLRI-----WHRRCFSCADCHRSLDST 177
I + +LR+ WH C CA+C + LD T
Sbjct: 8 IHDQYILRVAPDLEWHAACLKCAECGQYLDET 39
>gnl|CDD|235194 PRK04000, PRK04000, translation initiation factor IF-2 subunit
gamma; Validated.
Length = 411
Score = 38.3 bits (90), Expect = 0.002
Identities = 36/127 (28%), Positives = 51/127 (40%), Gaps = 43/127 (33%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK---AQTASLRY 86
N ++ HVDHGK+TL L TG S E +RGIT++ A A++R
Sbjct: 11 NIGMVGHVDHGKTTLVQAL---TGVWTDRHSE--------ELKRGITIRLGYAD-ATIRK 58
Query: 87 TSILDGEEYL------------------LNLIDTPGHVDFSNEV---TR-SLAAC-QGVV 123
+ E ++ +D PGH E T S AA G +
Sbjct: 59 CPDCEEPEAYTTEPKCPNCGSETELLRRVSFVDAPGH-----ETLMATMLSGAALMDGAI 113
Query: 124 LLIDANQ 130
L+I AN+
Sbjct: 114 LVIAANE 120
Score = 35.2 bits (82), Expect = 0.025
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 11/49 (22%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 251
N ++ HVDHGK+TL L TG S E +RGIT++
Sbjct: 11 NIGMVGHVDHGKTTLVQAL---TGVWTDRHSE--------ELKRGITIR 48
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 34.7 bits (80), Expect = 0.003
Identities = 17/42 (40%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 136 ANPEACEEQLQTLFNIDKKSVL---RIWHRRCFSCADCHRSL 174
AN CEE + D K + R WH CF C C RSL
Sbjct: 2 ANT--CEE-CKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSL 40
>gnl|CDD|182508 PRK10512, PRK10512, selenocysteinyl-tRNA-specific translation
factor; Provisional.
Length = 614
Score = 37.7 bits (88), Expect = 0.004
Identities = 31/87 (35%), Positives = 37/87 (42%), Gaps = 35/87 (40%)
Query: 33 IIA---HVDHGKSTL--------ADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQT 81
IIA HVDHGK+TL ADRL E E++RG+T+
Sbjct: 2 IIATAGHVDHGKTTLLQAITGVNADRLPE-------------------EKKRGMTIDLGY 42
Query: 82 ASLRYTSILDGEEYLLNLIDTPGHVDF 108
A Y DG +L ID PGH F
Sbjct: 43 A---YWPQPDGR--VLGFIDVPGHEKF 64
Score = 30.8 bits (70), Expect = 0.82
Identities = 16/29 (55%), Positives = 17/29 (58%), Gaps = 11/29 (37%)
Query: 206 IIA---HVDHGKSTL--------ADRLLE 223
IIA HVDHGK+TL ADRL E
Sbjct: 2 IIATAGHVDHGKTTLLQAITGVNADRLPE 30
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The third LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 34.2 bits (79), Expect = 0.004
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 160 WHRRCFSCADCHRSLDSTNLND 181
WH +CF+C+ CHR + S +
Sbjct: 20 WHLKCFTCSRCHREISSELSDA 41
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 37.9 bits (88), Expect = 0.005
Identities = 35/142 (24%), Positives = 56/142 (39%), Gaps = 42/142 (29%)
Query: 32 SIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILD 91
+I+ HVDHGK+TL D+ + + +Q ++ GIT K + +
Sbjct: 248 TILGHVDHGKTTLLDK-------IRKTQIAQ-------KEAGGITQKIGAYEVEF--EYK 291
Query: 92 GEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDA----------------------- 128
E + +DTPGH FS+ +R +L+I A
Sbjct: 292 DENQKIVFLDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQAANVPII 351
Query: 129 ---NQVDLKNANPEACEEQLQT 147
N++D NAN E ++QL
Sbjct: 352 VAINKIDKANANTERIKQQLAK 373
Score = 29.8 bits (67), Expect = 1.4
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 205 SIIAHVDHGKSTLADRL 221
+I+ HVDHGK+TL D++
Sbjct: 248 TILGHVDHGKTTLLDKI 264
>gnl|CDD|235195 PRK04004, PRK04004, translation initiation factor IF-2; Validated.
Length = 586
Score = 37.1 bits (87), Expect = 0.008
Identities = 36/113 (31%), Positives = 56/113 (49%), Gaps = 32/113 (28%)
Query: 32 SIIAHVDHGKSTLADRLLEMTGTVLSS----------GSSQV-LDSLQVEQERGITVKAQ 80
++ HVDHGK+TL D++ GT +++ G+++V +D +E+ G K
Sbjct: 10 VVLGHVDHGKTTLLDKI---RGTAVAAKEAGGITQHIGATEVPIDV--IEKIAGPLKKPL 64
Query: 81 TASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTR--SLA--ACQGVVLLIDAN 129
L + G LL IDTPGH F+N R +LA A +L++D N
Sbjct: 65 PIKL----KIPG---LL-FIDTPGHEAFTNLRKRGGALADIA----ILVVDIN 105
Score = 30.9 bits (71), Expect = 0.76
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 205 SIIAHVDHGKSTLADR 220
++ HVDHGK+TL D+
Sbjct: 10 VVLGHVDHGKTTLLDK 25
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 36.1 bits (84), Expect = 0.015
Identities = 32/117 (27%), Positives = 52/117 (44%), Gaps = 33/117 (28%)
Query: 37 VDHGKSTLADRLLEMTGTV-------LSSGSSQV------------LDSLQVEQERGITV 77
VD GKSTL RLL + + L S +V +D L E+E+GIT+
Sbjct: 33 VDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQGITI 92
Query: 78 KAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLA----ACQGVVLLIDANQ 130
+ RY + +++ + DTPGH + TR++ ++L+DA +
Sbjct: 93 D---VAYRYFAT-PKRKFI--VADTPGHEQY----TRNMVTGASTADLAIILVDARK 139
Score = 29.1 bits (66), Expect = 2.6
Identities = 20/60 (33%), Positives = 27/60 (45%), Gaps = 19/60 (31%)
Query: 210 VDHGKSTLADRLLEMTGTV-------LSSGSSQV------------LDSLQVEQERGITV 250
VD GKSTL RLL + + L S +V +D L E+E+GIT+
Sbjct: 33 VDDGKSTLIGRLLYDSKMIFEDQLAALERDSKKVGTQGDEIDLALLVDGLAAEREQGITI 92
>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL)-like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 32.4 bits (74), Expect = 0.017
Identities = 10/26 (38%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 159 IWHRRCFSCADCHRSL--DSTNLNDG 182
I+H+ CF C DC++ L D+ ++G
Sbjct: 20 IYHKNCFRCKDCNKQLKVDNYQSHEG 45
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 32.4 bits (74), Expect = 0.019
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH +C C DC L
Sbjct: 19 RTWHAKCLKCNDCGAQL 35
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 32.4 bits (74), Expect = 0.021
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 160 WHRRCFSCADCHRSL 174
WHR CF+C +C +SL
Sbjct: 20 WHRECFTCTNCSKSL 34
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 32.1 bits (73), Expect = 0.022
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 158 RIWHRRCFSCADCHRSLD 175
+ +H CF+C CHRSLD
Sbjct: 18 KAYHPHCFTCVVCHRSLD 35
>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule
interacting with CasL) like family. The LIM domain of
Mical (molecule interacting with CasL) like family:
Known members of this family includes LIM domain
containing proteins; Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2) and
Ltd-1. The members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth and mobility. Eplin has
also found to be tumor suppressor. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs.. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 32.2 bits (74), Expect = 0.023
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 158 RIWHRRCFSCADCHRSLDSTN 178
+++H+ CF C+ C+++L N
Sbjct: 19 KLFHKSCFRCSHCNKTLRLGN 39
>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function. The
first Lim domain of a LIM domain containing protein: The
functions of the proteins are unknown. The members of
this family contain two copies of LIM domain. The LIM
domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 58
Score = 32.2 bits (74), Expect = 0.026
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 160 WHRRCFSCADCH 171
WHR CF C C
Sbjct: 24 WHRECFVCTTCG 35
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a role
in development of normal thymus and in controlling the
development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 31.9 bits (72), Expect = 0.028
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 6/43 (13%)
Query: 155 SVLRIWHRRCFSCADCHRSLDSTNLNDGLAKPDSKATPYEDIP 197
S+ R WHR C C C ++L + G A+ D +PY +P
Sbjct: 16 SLGRNWHRPCLRCQRCKKTLTA----GGHAEHD--GSPYCHVP 52
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 33.9 bits (78), Expect = 0.033
Identities = 15/47 (31%), Positives = 24/47 (51%)
Query: 83 SLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
S R +LDGEE LN++DT G D++ + +G +L+
Sbjct: 36 SYRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSIT 82
>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM
domains protein 3 (FHL3). The fourth LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 32.0 bits (73), Expect = 0.033
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH+ CF C+ C SL
Sbjct: 22 RQWHQPCFKCSRCSVSL 38
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. .
Length = 54
Score = 31.6 bits (72), Expect = 0.036
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH CF CA C++ L
Sbjct: 20 RYWHETCFRCAKCYKPL 36
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 31.5 bits (72), Expect = 0.042
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH CF+C C SL
Sbjct: 22 RQWHSDCFNCGKCSVSL 38
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 33.3 bits (77), Expect = 0.057
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 27/107 (25%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGIT-VKAQTASLRYTS 88
+++ GKSTL + LL +VL + G+T A LRY
Sbjct: 2 LLAVVGEFSAGKSTLLNALLG----------EEVLPT-------GVTPTTAVITVLRY-G 43
Query: 89 ILDGEEYLLNLIDTPG---HVDFSNEVTRS-LAACQGVVLLIDANQV 131
+L G + L+DTPG ++ E+T S L V+ ++ A+Q
Sbjct: 44 LLKG----VVLVDTPGLNSTIEHHTEITESFLPRADAVIFVLSADQP 86
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family: The
Enigma LIM domain family is comprised of three members:
Enigma, ENH, and Cypher (mouse)/ZASP (human). These
subfamily members contain a single PDZ domain at the
N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and the
second LIM domain interacts with the receptor tyrosine
kinase Ret and the adaptor protein APS. Thus Enigma is
implicated in signal transduction processes, such as
mitogenic activity, insulin related actin organization,
and glucose metabolism. The second member, ENH protein,
was first identified in rat brain. It has been shown
that ENH interacts with protein kinase D1 (PKD1) via its
LIM domains and forms a complex with PKD1 and the
alpha1C subunit of cardiac L-type voltage-gated calcium
channel in rat neonatal cardiomyocytes. The N-terminal
PDZ domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 31.3 bits (71), Expect = 0.061
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 160 WHRRCFSCADCHRSLD 175
WH CF CA CH +L+
Sbjct: 22 WHDTCFVCAVCHVNLE 37
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 31.1 bits (71), Expect = 0.063
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 139 EACEEQLQTLFNIDKKSVL---RIWHRRCFSCADCHR 172
E C E F D+K V ++H +CF CA C +
Sbjct: 2 ERCREG----FEPDEKIVNSNGELYHEQCFVCAQCFQ 34
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first LIM
domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. Human Lmx1a
can be found in pancreas, skeletal muscle, adipose
tissue, developing brain, mammary glands, and pituitary.
The functions of Lmx1a in the developing nervous system
were revealed by studies of mutant mouse. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within pancreatic
cells, the Lmx1a protein interacts synergistically with
the bHLH transcription factor E47 to activate the
insulin gene enhancer/promoter. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 30.9 bits (70), Expect = 0.078
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 10/43 (23%)
Query: 139 EACEEQLQTLFNIDKKSVLRI----WHRRCFSCADCHRSLDST 177
E C +Q F +LR+ WH RC CA C L++T
Sbjct: 2 EGCNRVIQDRF------LLRVNDSLWHERCLQCASCKEPLETT 38
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. Studies using mutant mice have
revealed roles for Lhx7 and Lhx8 in the development of
cholinergic neurons in the telencephalon and in basal
forebrain development. Mice lacking alleles of the
LIM-homeobox gene Lhx7 or Lhx8 display dramatically
reduced number of forebrain cholinergic neurons. In
addition, Lhx7 mutation affects male and female mice
differently, with females appearing more affected than
males. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 30.7 bits (69), Expect = 0.089
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 160 WHRRCFSCADCHRSLDS 176
WH RC SC+ C SL
Sbjct: 22 WHVRCLSCSVCRTSLGR 38
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The third
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle 1
and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 30.5 bits (69), Expect = 0.098
Identities = 9/17 (52%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 160 WH--RRCFSCADCHRSL 174
WH +CF CA C +SL
Sbjct: 24 WHATEKCFCCAQCKKSL 40
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function not
only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the arrangement
of the myofibrillar/cytoskeletal network. It is evident
that CRP1, CRP2, and CRP3/MLP are involved in promoting
protein assembly along the actin-based cytoskeleton.
Although members of the CRP family share common binding
partners, they are also capable of recognizing different
and specific targets. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 30.3 bits (68), Expect = 0.12
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 158 RIWHRRCFSCADCHRSLDSTNL 179
R +H+ CF C C ++LDST +
Sbjct: 19 RSFHKSCFLCMVCRKNLDSTTV 40
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 30.1 bits (68), Expect = 0.13
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH CF+CA C SL
Sbjct: 22 RHWHNDCFNCAGCRTSL 38
>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4. The first LIM
domain of Lhx4. Lhx4 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 30.3 bits (68), Expect = 0.13
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH C CADC L
Sbjct: 19 RHWHSSCLKCADCQMQL 35
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first LIM
domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3b is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 30.3 bits (68), Expect = 0.14
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 154 KSVLRIWHRRCFSCADCHRSL 174
K + R WH +C C+DC L
Sbjct: 18 KVLDRHWHSKCLKCSDCQTQL 38
>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM
(abLIM) proteins. The third LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 30.0 bits (68), Expect = 0.14
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 8/38 (21%)
Query: 140 ACEEQL---QTLFNIDKKSVLRIWHRRCFSCADCHRSL 174
C +++ Q L +DK+ WH CF C +C + L
Sbjct: 3 GCGQEIKNGQALLALDKQ-----WHVWCFKCKECGKVL 35
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 31.8 bits (73), Expect = 0.15
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 13/68 (19%)
Query: 97 LNLIDTPGHVD------FSNEVTRSLAA-CQGVVLLIDANQVDLKNANPEACEEQLQTLF 149
+ LIDTPG + E R +A V+L++D++ P E +L L
Sbjct: 48 VVLIDTPGLDEEGGLGRERVEEARQVADRADLVLLVVDSDL------TPVEEEAKLGLLR 101
Query: 150 NIDKKSVL 157
K +L
Sbjct: 102 ERGKPVLL 109
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 30.0 bits (68), Expect = 0.15
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 158 RIWHRRCFSCADCHR 172
++H CF+C DC +
Sbjct: 18 DVYHLDCFTCHDCGK 32
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation
initiation factor that consists of alpha, beta, and
gamma subunits. The GTP-bound gamma subunit also binds
initiator methionyl-tRNA and delivers it to the 40S
ribosomal subunit. Following hydrolysis of GTP to GDP,
eIF2:GDP is released from the ribosome. The gamma
subunit has no intrinsic GTPase activity, but is
stimulated by the GTPase activating protein (GAP) eIF5,
and GDP/GTP exchange is stimulated by the guanine
nucleotide exchange factor (GEF) eIF2B. eIF2B is a
heteropentamer, and the epsilon chain binds eIF2. Both
eIF5 and eIF2B-epsilon are known to bind strongly to
eIF2-beta, but have also been shown to bind directly to
eIF2-gamma. It is possible that eIF2-beta serves simply
as a high-affinity docking site for eIF5 and
eIF2B-epsilon, or that eIF2-beta serves a regulatory
role. eIF2-gamma is found only in eukaryotes and
archaea. It is closely related to SelB, the
selenocysteine-specific elongation factor from
eubacteria. The translational factor components of the
ternary complex, IF2 in eubacteria and eIF2 in
eukaryotes are not the same protein (despite their
unfortunately similar names). Both factors are GTPases;
however, eubacterial IF-2 is a single polypeptide,
while eIF2 is heterotrimeric. eIF2-gamma is a member of
the same family as eubacterial IF2, but the two
proteins are only distantly related. This family
includes translation initiation, elongation, and
release factors.
Length = 197
Score = 32.2 bits (74), Expect = 0.16
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 11/49 (22%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 78
N I HV HGK+TL L SG V E +R IT+K
Sbjct: 2 NIGTIGHVAHGKTTLVKAL---------SGVWTVRHK--EELKRNITIK 39
Score = 32.2 bits (74), Expect = 0.16
Identities = 18/49 (36%), Positives = 21/49 (42%), Gaps = 11/49 (22%)
Query: 203 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 251
N I HV HGK+TL L SG V E +R IT+K
Sbjct: 2 NIGTIGHVAHGKTTLVKAL---------SGVWTVRHK--EELKRNITIK 39
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 29.9 bits (67), Expect = 0.16
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 141 CEEQLQTLFNIDKKSVL-RIWHRRCFSCADCHRSL 174
C +T++ +K S L + WHR C C C + L
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKIL 35
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3
(CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. CRP3/MLP interacts with
cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 29.7 bits (66), Expect = 0.19
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 158 RIWHRRCFSCADCHRSLDSTNL 179
R +H+ CF C C ++LDST +
Sbjct: 20 RSFHKTCFICMACRKALDSTTV 41
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 32.5 bits (75), Expect = 0.19
Identities = 35/135 (25%), Positives = 53/135 (39%), Gaps = 37/135 (27%)
Query: 9 EAAKPDSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQ 68
E PD + E+ +I +II + GKS+L + +L G +V+
Sbjct: 162 ELLPPDEEEEEEEETDPIKI---AIIGRPNVGKSSLINAIL---------GEERVI---- 205
Query: 69 VEQERGITVKAQTASLRYTSILDGEEYLLNLIDTPG----------HVDFSNEVTRSLAA 118
V G T + DG +Y+ LIDT G +S V R+L A
Sbjct: 206 VSDIAGTTRDSIDIEFER----DGRKYV--LIDTAGIRRKGKITESVEKYS--VARTLKA 257
Query: 119 ---CQGVVLLIDANQ 130
V+L+IDA +
Sbjct: 258 IERADVVLLVIDATE 272
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2
(CRP2). The first LIM domain of Cysteine Rich Protein 2
(CRP2): The CRP family members include CRP1, CRP2,
CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation, and
involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network. CRP2 specifically
binds to protein inhibitor of activated STAT-1 (PIAS1)
and a novel human protein designed CRP2BP (for CRP2
binding partner). PIAS1 specifically inhibits the STAT-1
pathway and CRP2BP is homologous to members of the
histone acetyltransferase family raising the possibility
that CRP2 is a modulator of cytokine-controlled pathways
or is functionally active in the transcriptional
regulatory network. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 29.6 bits (66), Expect = 0.20
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 158 RIWHRRCFSCADCHRSLDSTNL 179
R +H+ CF C C ++LDST +
Sbjct: 20 RSFHKCCFLCMVCRKNLDSTTV 41
>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like
family. The first LIM domain of Enigma-like family: The
Enigma LIM domain family is comprised of three members:
Enigma, ENH, and Cypher (mouse)/ZASP (human). These
subfamily members contain a single PDZ domain at the
N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and the
second LIM domain interacts with the receptor tyrosine
kinase Ret and the adaptor protein APS. Thus Enigma is
implicated in signal transduction processes, such as
mitogenic activity, insulin related actin organization,
and glucose metabolism. The second member, ENH protein,
was first identified in rat brain. It has been shown
that ENH interacts with protein kinase D1 (PKD1) via its
LIM domains and forms a complex with PKD1 and the
alpha1C subunit of cardiac L-type voltage-gated calcium
channel in rat neonatal cardiomyocytes. The N-terminal
PDZ domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 29.6 bits (67), Expect = 0.21
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH F+C+ CH SL
Sbjct: 18 RSWHPEEFTCSHCHCSL 34
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1
(CRP1). The first LIM domain of Cysteine Rich Protein 1
(CRP1): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and
CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 29.6 bits (66), Expect = 0.21
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 158 RIWHRRCFSCADCHRSLDSTNL 179
R +H+ CF C C ++LDST +
Sbjct: 21 RSFHKSCFLCMVCKKNLDSTTV 42
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 29.6 bits (67), Expect = 0.21
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH+ CF C C + L
Sbjct: 20 WHKECFVCTGCKKQL 34
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 29.6 bits (67), Expect = 0.21
Identities = 7/17 (41%), Positives = 8/17 (47%)
Query: 160 WHRRCFSCADCHRSLDS 176
WH CF C C + L
Sbjct: 21 WHIHCFKCYKCDKKLSC 37
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 29.8 bits (67), Expect = 0.22
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 140 ACEEQLQTLFNIDKKSVL---RIWHRRCFSCADCHRSL 174
CEE + ID K + + WH CF C+ C SL
Sbjct: 4 QCEE-CSKIIGIDSKDLSYKDKHWHEACFLCSKCKISL 40
>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin. The
third LIM domain of Leupaxin: Leupaxin is a cytoskeleton
adaptor protein, which is preferentially expressed in
hematopoietic cells. Leupaxin belongs to the paxillin
focal adhesion protein family. Same as other members of
the family, it has four leucine-rich LD-motifs in the
N-terminus and four LIM domains in the C-terminus. It
may function in cell type-specific signaling by
associating with interaction partners PYK2, FAK, PEP and
p95PKL. When expressed in human leukocytic cells,
leupaxin significantly suppressed integrin-mediated cell
adhesion to fibronectin and the tyrosine phosphorylation
of paxillin. These findings indicate that leupaxin may
negatively regulate the functions of paxillin during
integrin signaling. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 29.4 bits (66), Expect = 0.22
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 159 IWHRRCFSCADCHRS 173
+WH CF C+DC +
Sbjct: 19 VWHPECFVCSDCLKP 33
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Lhx1 is required for regulating
the vertebrate head organizer, the nervous system, and
female reproductive tract development. During
embryogenesis in the mouse, Lhx1 is expressed early in
mesodermal tissue, then later during urogenital, kidney,
liver, and nervous system development. In the adult,
expression is restricted to the kidney and brain. A
mouse embryos with Lhx1 gene knockout cannot grow normal
anterior head structures, kidneys, and gonads, but with
normally developed trunk and tail morphology. In the
developing nervous system, Lhx1 is required to direct
the trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 29.3 bits (66), Expect = 0.22
Identities = 10/21 (47%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 155 SVL-RIWHRRCFSCADCHRSL 174
+VL R WH +C C DC L
Sbjct: 15 NVLDRAWHAKCVQCCDCKCPL 35
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 29.2 bits (66), Expect = 0.24
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 160 WHRRCFSCADCHRS 173
WH CF C +CH+
Sbjct: 20 WHPECFVCRECHKP 33
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 31.7 bits (73), Expect = 0.25
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 40 GKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNL 99
GKST + L GT L + + + +K A L +G + L +
Sbjct: 16 GKSTFINTLF---GTKLYPSKYPPAPGEHITK--TVEIKISKAEL----EENGVKLKLTV 66
Query: 100 IDTPGHVDFSN 110
IDTPG D N
Sbjct: 67 IDTPGFGDNIN 77
>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like
family. The first LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 58
Score = 29.5 bits (67), Expect = 0.27
Identities = 6/14 (42%), Positives = 7/14 (50%)
Query: 158 RIWHRRCFSCADCH 171
WH CF C C+
Sbjct: 24 ACWHPGCFVCETCN 37
>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1. The Lim domain of DA1:
DA1 contains one copy of LIM domain and a domain of
unknown function. DA1 is predicted as an ubiquitin
receptor, which sets final seed and organ size by
restricting the period of cell proliferation. The LIM
domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 53
Score = 29.1 bits (66), Expect = 0.28
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 158 RIWHRRCFSCADCHR 172
+WH CF C C +
Sbjct: 19 AVWHPECFRCHACRK 33
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain , the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 54
Score = 29.2 bits (66), Expect = 0.29
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 156 VLRIWHRRCFSCADCHRSLDS 176
V R WH C C +C LDS
Sbjct: 17 VDRQWHASCLKCCECRLPLDS 37
>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9. The first LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 54
Score = 29.2 bits (65), Expect = 0.29
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 5/29 (17%)
Query: 148 LFNIDKKSVLRIWHRRCFSCADCHRSLDS 176
L +DK+ WH RC C +C +L+S
Sbjct: 14 LLAVDKQ-----WHLRCLKCCECKLALES 37
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 29.5 bits (66), Expect = 0.30
Identities = 9/17 (52%), Positives = 9/17 (52%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH CF C C SL
Sbjct: 24 RHWHESCFHCFQCKNSL 40
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 29.2 bits (65), Expect = 0.30
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 160 WHRRCFSCADCHRSLDSTNLNDGLAKPDSK 189
WH CF CA CH +L+ KP K
Sbjct: 22 WHDTCFICAVCHVNLEGQPFYSKKDKPLCK 51
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 29.3 bits (66), Expect = 0.30
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 159 IWHRRCFSCADC 170
+WH CF C+ C
Sbjct: 25 LWHPACFRCSTC 36
>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 28.9 bits (65), Expect = 0.32
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 158 RIWHRRCFSCADCHRSLDS 176
+++HR CF C +C +L
Sbjct: 19 KLYHRNCFRCKECSSTLLP 37
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain shows
close sequence homology to LIM domain of thymus LIM
protein. However, unlike the TLP proteins which have two
LIM domains, the members of this family have only one
LIM domain. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 29.1 bits (65), Expect = 0.33
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 6/38 (15%)
Query: 160 WHRRCFSCADCHRSLDSTNLNDGLAKPDSKATPYEDIP 197
WHR C C C ++L A+ D K PY + P
Sbjct: 21 WHRPCLKCEKCGKTLTP----GSHAEHDGK--PYCNHP 52
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family.
The second LIM domain of Lhx3-Lhx4 family: Lhx3 and
Lhx4 belong to the LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the development
of specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription.Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 56
Score = 28.9 bits (65), Expect = 0.34
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 159 IWHRRCFSCADCHRSLDS 176
++H CF+C C R L++
Sbjct: 21 VYHLECFACFMCKRQLET 38
>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein
(LASP)-like proteins. The LIM domain of LIM and SH3
Protein (LASP) like proteins: This family contains two
types of LIM containing proteins; LASP and N-RAP. LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their LIM,
nebulin-like, and SH3 domains, but differ significantly
at their linker regions. Both proteins are ubiquitously
expressed and involved in cytoskeletal architecture,
especially in the organization of focal adhesions.
LASP-1 and LASP-2, are important during early embryo-
and fetogenesis and are highly expressed in the central
nervous system of the adult. However, only LASP-1 seems
to participate significantly in neuronal differentiation
and plays an important functional role in migration and
proliferation of certain cancer cells while the role of
LASP-2 is more structural. The expression of LASP-1 in
breast tumors is increased significantly. N-RAP is a
muscle-specific protein concentrated at myotendinous
junctions in skeletal muscle and intercalated disks in
cardiac muscle. LIM domain is found at the N-terminus of
N-RAP and the C-terminal of N-RAP contains a region with
multiple of nebulin repeats. N-RAP functions as a
scaffolding protein that organizes alpha-actinin and
actin into symmetrical I-Z-I structures in developing
myofibrils. Nebulin repeat is known as actin binding
domain. The N-RAP is hypothesized to form antiparallel
dimerization via its LIM domain. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 28.8 bits (64), Expect = 0.35
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 158 RIWHRRCFSCADCHRSLDSTNLNDGLAKP 186
+ WH+ CF C C +L+ N KP
Sbjct: 19 KTWHKACFHCEVCKMTLNMNNYKGYQKKP 47
>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM
domains protein 1 (FHL1). The third LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 28.6 bits (64), Expect = 0.41
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH CF C+ C + L
Sbjct: 20 WHSECFVCSSCSKKL 34
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Although Lhx2 and
Lhx9 are highly homologous, they seems to play
regulatory roles in different organs. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. Lhx9 is expressed in several regions of the
developing mouse brain, the spinal cord, the pancreas,
in limb mesenchyme, and in the urogenital region. Lhx9
plays critical roles in gonad development. Homozygous
mice lacking functional Lhx9 alleles exhibit numerous
urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
are phenotypically female, even those that are
genotypically male. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 59
Score = 28.8 bits (65), Expect = 0.41
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 159 IWHRRCFSCADCHRSL 174
++H CF+CA C++ L
Sbjct: 25 VFHLNCFTCATCNKPL 40
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 29.0 bits (65), Expect = 0.42
Identities = 6/14 (42%), Positives = 12/14 (85%)
Query: 159 IWHRRCFSCADCHR 172
+WH+ CF+C++C +
Sbjct: 21 VWHKDCFTCSNCKQ 34
>gnl|CDD|227583 COG5258, GTPBP1, GTPase [General function prediction only].
Length = 527
Score = 31.7 bits (72), Expect = 0.44
Identities = 32/125 (25%), Positives = 46/125 (36%), Gaps = 21/125 (16%)
Query: 6 YSTEAAKPDSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV-- 63
Y E E + + + HVDHGKSTL L+ TG L G
Sbjct: 101 YVAEVLVRRKTEEAPEHVLVG------VAGHVDHGKSTLVGVLV--TGR-LDDGDGATRS 151
Query: 64 -LDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGV 122
LD + E ERG++ SLR DG+ ++ L + E + +
Sbjct: 152 YLDVQKHEVERGLS---ADISLRVYGFDDGK--VVRLKNP----LDEAEKAAVVKRADKL 202
Query: 123 VLLID 127
V +D
Sbjct: 203 VSFVD 207
Score = 29.4 bits (66), Expect = 2.1
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 187 DSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQV---LDSLQVE 243
E + + + HVDHGKSTL L+ TG L G LD + E
Sbjct: 109 RKTEEAPEHVLVG------VAGHVDHGKSTLVGVLV--TGR-LDDGDGATRSYLDVQKHE 159
Query: 244 QERGIT 249
ERG++
Sbjct: 160 VERGLS 165
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 28.8 bits (65), Expect = 0.46
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 161 HRRCFSCADCHRSL 174
HR CF C+ C +L
Sbjct: 22 HRSCFKCSYCGTTL 35
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 28.4 bits (64), Expect = 0.48
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 153 KKSVLRI----WHRRCFSCADCHRSL 174
K VLR+ +H +CF+C C L
Sbjct: 9 KGEVLRVQDKYFHIKCFTCKVCGCDL 34
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 30.5 bits (70), Expect = 0.50
Identities = 32/111 (28%), Positives = 47/111 (42%), Gaps = 30/111 (27%)
Query: 31 FSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSIL 90
+II + GKS+L + LL G +V+ V G T + Y
Sbjct: 5 IAIIGRPNVGKSSLLNALL---------GEERVI----VSDIAGTTRDSIDVPFEY---- 47
Query: 91 DGEEYLLNLIDTPG-----HVDFSNE---VTRSLAA---CQGVVLLIDANQ 130
DG++Y LIDT G V E V R+L A V+L++DA++
Sbjct: 48 DGQKYT--LIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASE 96
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 30.5 bits (69), Expect = 0.50
Identities = 21/98 (21%), Positives = 37/98 (37%), Gaps = 11/98 (11%)
Query: 33 IIAHVDHGKSTLADRLLE-MTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILD 91
+I V GK+T L + + SS G + T ++ + SI
Sbjct: 15 VIGPVGAGKTTFVRALSDKPLVITEADASS----------VSGKGKRPTTVAMDFGSIEL 64
Query: 92 GEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLLIDAN 129
E+ ++L TPG F G ++L+D++
Sbjct: 65 DEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSS 102
>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2. The first LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In animals, Lhx2
plays important roles in eye, cerebral cortex, limb, the
olfactory organs, and erythrocyte development. Lhx2 gene
knockout mice exhibit impaired patterning of the
cortical hem and the telencephalon of the developing
brain, and a lack of development in olfactory
structures. The Lhx2 protein has been shown to bind to
the mouse M71 olfactory receptor promoter. Similar to
other LIM domains, this domain family is 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 64
Score = 28.8 bits (64), Expect = 0.52
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 5/29 (17%)
Query: 148 LFNIDKKSVLRIWHRRCFSCADCHRSLDS 176
L +DK+ WH RC C +C +L+S
Sbjct: 24 LLAVDKQ-----WHMRCLKCCECKLNLES 47
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first LIM
domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3a is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 28.6 bits (64), Expect = 0.52
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 158 RIWHRRCFSCADCHRSL 174
+ WH +C C DC L
Sbjct: 22 KPWHSKCLKCVDCQAQL 38
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 28.5 bits (64), Expect = 0.53
Identities = 11/36 (30%), Positives = 14/36 (38%), Gaps = 2/36 (5%)
Query: 140 ACEEQLQTLFNIDKKSVLRIWHRRCFSCADCHRSLD 175
C E + F + K R WH C C C L+
Sbjct: 3 GCGEPITDRFLL--KVSGRSWHVSCLRCCVCQTPLE 36
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 30.4 bits (69), Expect = 0.59
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 4/77 (5%)
Query: 76 TVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSL-AACQGVVLLIDANQVDLK 134
TV + ++ + L L+D PGH +++ L A+ + +V ++D+ K
Sbjct: 28 TVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDS-ATFQK 86
Query: 135 NANPEACEEQLQTLFNI 151
N A E L +
Sbjct: 87 NIRDVA--EFLYDILTD 101
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only
protein 4). The second LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 28.2 bits (63), Expect = 0.69
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 158 RIWHRRCFSCADCHRSL 174
++H +CF+C+ CH L
Sbjct: 20 NVYHLKCFTCSTCHNQL 36
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, altering the rate of actin depolymerization.
LIMK activity is activated by phosphorylation of a
threonine residue within the activation loop of the
kinase by p21-activated kinases 1 and 4 and by Rho
kinase. LIMKs can function in both cytoplasm and
nucleus. Both LIMK1 and LIMK2 can act in the nucleus to
suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2
is expressed in all tissues. While LIMK1 localizes
mainly at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 27.9 bits (62), Expect = 0.70
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 141 CEEQLQTLFNIDKKSVLRIWHRRCFSCADCHRSLDSTN 178
C ++Q F+ + V WH CF C+ C L TN
Sbjct: 4 CGGRIQDSFHY--RVVQEAWHNSCFQCSVCQDLL--TN 37
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 29.6 bits (66), Expect = 0.74
Identities = 25/94 (26%), Positives = 31/94 (32%), Gaps = 5/94 (5%)
Query: 40 GKSTLADRLLEMTG-TVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLN 98
GKSTLA +L E G V+S + L E + G ILD
Sbjct: 11 GKSTLAKKLAEKLGIPVISLDDLLREEGL-AELDDGELDDIDIDLELLEEILDELAKQEW 69
Query: 99 LIDTPGHVDFSNEVTRSLAACQGVVLLIDANQVD 132
+ID V S R A V L +
Sbjct: 70 VID---GVRESTLELRLEEADLVVFLDLPLPACR 100
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 28.2 bits (63), Expect = 0.75
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 158 RIWHRRCFSCADC 170
+ WH +CF C +C
Sbjct: 20 QQWHEKCFCCCEC 32
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. The second member, ENH protein, was
first identified in rat brain. It has been shown that
ENH interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 27.8 bits (62), Expect = 0.78
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 2/25 (8%)
Query: 160 WHRRCFSCADCHRSL--DSTNLNDG 182
WH CF CA C + + ++ DG
Sbjct: 20 WHVSCFVCAACKQPIGNSLFHMEDG 44
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are polypeptides
of 30-65kDa with three characteristic GTPase motifs
(G-1, G-3 and G-4) that are similar to those of the Ras
family. The G-4 motif is strictly conserved with a
unique septin consensus of AKAD. Most septins are
thought to have at least one coiled-coil region, which
in some cases is necessary for intermolecular
interactions that allow septins to polymerise to form
rod-shaped complexes. In turn, these are arranged into
tandem arrays to form filaments. They are
multifunctional proteins, with roles in cytokinesis,
sporulation, germ cell development, exocytosis and
apoptosis.
Length = 280
Score = 30.3 bits (69), Expect = 0.79
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 9/71 (12%)
Query: 40 GKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNL 99
GK+TL + L T L + + + ++ + +KA T + DG + L +
Sbjct: 16 GKTTLINTLFL---TDLIP--ERGIPGPSEKIKKTVEIKATTVEIEE----DGVKLNLTV 66
Query: 100 IDTPGHVDFSN 110
IDTPG D +
Sbjct: 67 IDTPGFGDAID 77
>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM
domains protein (FHL). The second LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 28.0 bits (63), Expect = 0.80
Identities = 6/11 (54%), Positives = 10/11 (90%)
Query: 160 WHRRCFSCADC 170
WH +CF+C++C
Sbjct: 22 WHEKCFTCSEC 32
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. The consensus sequence of LIM domain
has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 28.2 bits (63), Expect = 0.80
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 158 RIWHRRCFSCADCHRSLDSTN 178
+++HR CF CA C L +
Sbjct: 23 KVYHRTCFKCARCGVQLTPGS 43
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 27.7 bits (62), Expect = 0.92
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH CF C C++ L
Sbjct: 20 WHPDCFRCEICNKEL 34
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 74
Score = 28.3 bits (63), Expect = 0.94
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH CF C +C SL
Sbjct: 42 WHADCFRCCECGASL 56
>gnl|CDD|239032 cd02114, bact_SorA_Moco, sulfite:cytochrome c oxidoreductase
subunit A (SorA), molybdopterin binding domain. SorA is
involved in oxidation of sulfur compounds during
chemolithothrophic growth. Together with SorB, a small
c-type heme containing subunit, it forms a hetrodimer.
It is a member of the sulfite oxidase (SO) family of
molybdopterin binding domains. This molybdopterin
cofactor (Moco) binding domain is found in a variety of
oxidoreductases, main members of this family are nitrate
reductase (NR) and sulfite oxidase (SO). Common features
of all known members of this family are that they
contain one single pterin cofactor and part of the
coordination of the metal (Mo) is a cysteine ligand of
the protein and that they catalyze the transfer of an
oxygen to or from a lone pair of electrons on the
substrate.
Length = 367
Score = 30.2 bits (68), Expect = 1.0
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 180 NDGLAKPDSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS 233
N A P PI R + S I +++G L + G GS
Sbjct: 236 NADAGVEPGTA-PDRTAPINRFKVRSFITSLENGAIVAPAGELALRGIAFDGGS 288
Score = 29.4 bits (66), Expect = 1.7
Identities = 11/44 (25%), Positives = 16/44 (36%)
Query: 17 ATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGS 60
P PI R + S I +++G L + G GS
Sbjct: 245 TAPDRTAPINRFKVRSFITSLENGAIVAPAGELALRGIAFDGGS 288
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 30.4 bits (70), Expect = 1.0
Identities = 39/135 (28%), Positives = 54/135 (40%), Gaps = 46/135 (34%)
Query: 13 PDSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQE 72
P+ + ED PI +II + GKS+L + LL G +V+ V
Sbjct: 162 PEEEEEDEEDEPI----KIAIIGRPNVGKSSLINALL---------GEERVI----VSDI 204
Query: 73 RGITVKAQTASLR---YTSI-LDGEEYLLNLIDTPG-----HVD-----FSNEVTRSLAA 118
G T R T DG++Y L IDT G V +S V R+L A
Sbjct: 205 AGTT--------RDSIDTPFERDGQKYTL--IDTAGIRRKGKVTEGVEKYS--VIRTLKA 252
Query: 119 ---CQGVVLLIDANQ 130
V+L+IDA +
Sbjct: 253 IERADVVLLVIDATE 267
>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH). The
second LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 27.8 bits (62), Expect = 1.1
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 158 RIWHRRCFSCADCHRSLDST 177
++H CF+C C R L ST
Sbjct: 20 HVYHLACFACDACKRQL-ST 38
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first LIM
domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. In mouse, Lmx1b
functions in the developing limbs and eyes, the kidneys,
the brain, and in cranial mesenchyme. The disruption of
Lmx1b gene results kidney and limb defects. In the
brain, Lmx1b is important for generation of
mesencephalic dopamine neurons and the differentiation
of serotonergic neurons. In the mouse eye, Lmx1b
regulates anterior segment (cornea, iris, ciliary body,
trabecular meshwork, and lens) development. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 27.3 bits (61), Expect = 1.1
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 151 IDKKSVLRI----WHRRCFSCADCHRSL 174
I + +LR+ WH C C+ C + L
Sbjct: 8 ISDRYLLRVNERSWHEECLQCSVCQQPL 35
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase
). The first LIM domain of LIMK (LIM domain Kinase ):
LIMK protein family is comprised of two members LIMK1
and LIMK2. LIMK contains two LIM domains, a PDZ domain
and a kinase domain. LIMK is involved in the regulation
of actin polymerization and microtubule disassembly.
LIMK influences architecture of the actin cytoskeleton
by regulating the activity of the cofilin family
proteins cofilin1, cofilin2, and destrin. The mechanism
of the activation is to phosphorylates cofilin on serine
3 and inactivates its actin-severing activity, and
altering the rate of actin depolymerisation. LIMKs can
function in both cytoplasm and nucleus and are expressed
in all tissues. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 53
Score = 27.5 bits (61), Expect = 1.1
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 160 WHRRCFSCADCHRSLDS 176
WH CF C+ C SL +
Sbjct: 21 WHCDCFRCSVCSDSLSN 37
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM domains
at the C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also been shown that ENH
interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line. ENH
is expressed in multiple tissues, such as skeletal
muscle, heart, bone, and brain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 27.3 bits (60), Expect = 1.2
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 158 RIWHRRCFSCADCHRSLDST--NLNDG 182
+ WH CF C CH + + +L DG
Sbjct: 18 QTWHVSCFVCVACHNPIRNNVFHLEDG 44
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 29.7 bits (67), Expect = 1.3
Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 30/125 (24%)
Query: 32 SIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILD 91
+I+ + GKSTL ++L ++ S KAQT R + I
Sbjct: 4 AILGRPNVGKSTLLNQLHGQKISITSP-------------------KAQTTRNRISGIHT 44
Query: 92 GEEYLLNLIDTPG-HVD-------FSNEVTRSLAACQGVVLLIDANQVDLKNANPEACEE 143
+ IDTPG H E ++ ++ ++D++Q N + E
Sbjct: 45 TGASQIIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQ---WNGDGEFVLT 101
Query: 144 QLQTL 148
+LQ L
Sbjct: 102 KLQNL 106
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 30.1 bits (69), Expect = 1.3
Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 37/131 (28%)
Query: 13 PDSKATPYEDIPIARIRNFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQE 72
P+ + E+ +I +II + GKSTL + LL G +V+ V
Sbjct: 160 PEEEEEEEEEDGPIKI---AIIGRPNVGKSTLVNALL---------GEERVI----VSDI 203
Query: 73 RGITVKAQTASLRYTSILDGEEYLLNLIDTPG-----HVD-----FSNEVTRSLAA---C 119
G T + +G++Y LIDT G V +S V R+L A
Sbjct: 204 AGTTRDSIDIPFER----NGKKYT--LIDTAGIRRKGKVTEGVEKYS--VLRTLKAIERA 255
Query: 120 QGVVLLIDANQ 130
V+L++DA +
Sbjct: 256 DVVLLVLDATE 266
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 64
Score = 27.4 bits (61), Expect = 1.3
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH CF+C C +L
Sbjct: 29 WHDYCFNCKKCSLNL 43
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 30.0 bits (68), Expect = 1.3
Identities = 30/81 (37%), Positives = 36/81 (44%), Gaps = 21/81 (25%)
Query: 180 NDGLAKPD------SKATPYEDIPIAR---IRNFSIIAHVDHGKSTLADRLLEMTGTVLS 230
+DGLAK D K TP I+R I N I HV HGKST+ L
Sbjct: 5 DDGLAKQDLSKLDLDKLTPLTPEVISRQATI-NIGTIGHVAHGKSTVVKAL--------- 54
Query: 231 SGSSQVLDSLQVEQERGITVK 251
SG V + E+ R IT+K
Sbjct: 55 SGVKTV--RFKREKVRNITIK 73
Score = 28.8 bits (65), Expect = 3.2
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 11/49 (22%)
Query: 30 NFSIIAHVDHGKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVK 78
N I HV HGKST+ L SG V + E+ R IT+K
Sbjct: 36 NIGTIGHVAHGKSTVVKAL---------SGVKTV--RFKREKVRNITIK 73
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 29.9 bits (68), Expect = 1.4
Identities = 27/128 (21%), Positives = 45/128 (35%), Gaps = 32/128 (25%)
Query: 40 GKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNL 99
GKSTL + L+ G +S S K QT R I+ + +
Sbjct: 18 GKSTLLNALV---GQKISIVSP----------------KPQTTRNRIRGIVTTDNAQIIF 58
Query: 100 IDTPG-HVD-------FSNEVTRSLAACQGVVLLIDANQVDLKNANPEACEEQLQTLFNI 151
+DTPG H + +L ++ ++DA++ P E L+ L
Sbjct: 59 VDTPGIHKPKHALGELMNKAARSALKDVDLILFVVDADE----GWGPGD-EFILEQLKKT 113
Query: 152 DKKSVLRI 159
+L +
Sbjct: 114 KTPVILVV 121
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 30.0 bits (68), Expect = 1.4
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 12/73 (16%)
Query: 40 GKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNL 99
GK+T + L + ++D +++ R + L+ + + LNL
Sbjct: 35 GKTTFINTLF----------GTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNL 84
Query: 100 --IDTPGHVDFSN 110
IDTPG DF +
Sbjct: 85 TVIDTPGFGDFID 97
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 27.4 bits (61), Expect = 1.5
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 159 IWHRRCFSCADCHRSL 174
++H CF+C C R+L
Sbjct: 21 LYHTNCFTCCSCGRTL 36
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 27.3 bits (60), Expect = 1.5
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH F+C CH SL
Sbjct: 18 RSWHPEEFTCHYCHTSL 34
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 57
Score = 27.4 bits (61), Expect = 1.5
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 160 WH--RRCFSCADCHRSL 174
WH CF C++C +SL
Sbjct: 22 WHATEECFCCSNCKKSL 38
>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM
domains protein 2 (FHL2). The fourth LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 58
Score = 27.3 bits (60), Expect = 1.5
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 158 RIWHRRCFSCADCHRSL 174
R WH CF+C C SL
Sbjct: 22 RQWHNDCFNCKKCSLSL 38
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 29.8 bits (68), Expect = 1.5
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 33 IIAHVDHGKSTLADRL 48
I+ HVDHGK++L D +
Sbjct: 254 IMGHVDHGKTSLLDAI 269
Score = 29.8 bits (68), Expect = 1.5
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 206 IIAHVDHGKSTLADRL 221
I+ HVDHGK++L D +
Sbjct: 254 IMGHVDHGKTSLLDAI 269
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga GTPase-Activating
Proteins. The second LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 27.1 bits (60), Expect = 1.6
Identities = 8/31 (25%), Positives = 12/31 (38%), Gaps = 4/31 (12%)
Query: 150 NIDKKSVLRI----WHRRCFSCADCHRSLDS 176
ID ++L + CF C C R +
Sbjct: 7 KIDDTAILLSSDEAYCSDCFRCRRCSRDITD 37
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated in
roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 27.1 bits (60), Expect = 1.6
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH +CF CA C L
Sbjct: 26 WHPQCFQCASCQELL 40
>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM
domains protein 2 (FHL2). The third LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 27.3 bits (60), Expect = 1.6
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 160 WHRRCFSCADCHRSL 174
WH+ CF C C + L
Sbjct: 20 WHKECFVCTGCKKQL 34
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 29.1 bits (66), Expect = 1.6
Identities = 18/49 (36%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 120 QGVVLLIDANQVDLKNANPEA-CEEQLQTLFNIDKKSVLRIWHRRCFSC 167
+G LLI AN+ DL A E+ E L L +I R WH C
Sbjct: 99 KGAPLLILANKQDLPGALTESELIELLG-LESIKG----RRWH--IQPC 140
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH)
family. The third LIM domain of the Enigma Homolog
(ENH) family: ENH was initially identified in rat brain.
Same as enigma, it contains three LIM domains at the
C-terminus and a PDZ domain at N-terminus. ENH is
implicated in signal transduction processes involving
protein kinases. It has also been shown that ENH
interacts with protein kinase D1 (PKD1) via its LIM
domains and forms a complex with PKD1 and the alpha1C
subunit of cardiac L-type voltage-gated calcium channel
in rat neonatal cardiomyocytes. The N-terminal PDZ
domain interacts with alpha-actinin at the Z-line. ENH
is expressed in multiple tissues, such as skeletal
muscle, heart, bone, and brain. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 26.9 bits (59), Expect = 1.9
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 160 WHRRCFSCADCHRSLDSTNLNDGLAKPDSK 189
WH CF C+ C SL+ KP K
Sbjct: 22 WHDTCFVCSVCCESLEGQTFFSKKDKPLCK 51
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein
SF3. The first Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 63
Score = 27.0 bits (60), Expect = 2.0
Identities = 12/42 (28%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 140 ACEEQLQTLFNIDKKSV-LRIWHRRCFSCADCHRSLDSTNLN 180
AC+ +T++ +D+ S ++H+ CF C+ C +L +N +
Sbjct: 7 ACD---KTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYS 45
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as the
pituitary gland and the pancreas. Lhx6 functions in the
brain and nervous system. It is expressed at high
levels in several regions of the embryonic mouse CNS,
including the telencephalon and hypothalamus, and the
first branchial arch. Lhx6 is proposed to have a role in
patterning of the mandible and maxilla, and in signaling
during odontogenesis. In brain sections, knockdown of
Lhx6 gene blocks the normal migration of neurons to the
cortex. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 26.5 bits (58), Expect = 2.3
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 159 IWHRRCFSCADCHRSLDSTN 178
IWH RC C+ C SL N
Sbjct: 20 IWHVRCLECSVCRTSLRQHN 39
>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma. The third
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 26.5 bits (58), Expect = 2.4
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 160 WHRRCFSCADCHRSLDSTNLNDGLAKPDSKATPY 193
WH CF CA C +L+ KP K+ +
Sbjct: 22 WHDTCFVCAICQINLEGKTFYSKKDKPLCKSHAF 55
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 26.6 bits (59), Expect = 2.4
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 161 HRRCFSCADCHRSL 174
H CF CADC +L
Sbjct: 21 HPECFVCADCGLNL 34
>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin. The second
LIM domain of Zyxin: Zyxin exhibits three copies of the
LIM domain, an extensive proline-rich domain and a
nuclear export signal. Localized at sites of
cellsubstratum adhesion in fibroblasts, Zyxin interacts
with alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors o r
scaffolds to support the assembly of multimeric protein.
Length = 60
Score = 26.8 bits (59), Expect = 2.6
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 154 KSVLRIWHRRCFSCADCHRSLDST 177
K+ + +H +CF+C C L+
Sbjct: 14 KATGKSYHPQCFTCVVCKCPLEGE 37
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as the
pituitary gland and the pancreas. Mouse Lmx1a is
expressed in multiple tissues, including the roof plate
of the neural tube, the developing brain, the otic
vesicles, the notochord, and the pancreas. In mouse,
mutations in Lmx1a result in failure of the roof plate
to develop. Lmx1a may act upstream of other roof plate
markers such as MafB, Gdf7, Bmp6, and Bmp7. Further
characterization of these mice reveals numerous defects
including disorganized cerebellum, hippocampus, and
cortex; altered pigmentation; female sterility, skeletal
defects, and behavioral abnormalities. In the mouse,
Lmx1b functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for generation
of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 55
Score = 26.6 bits (59), Expect = 2.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 159 IWHRRCFSCADCHRSL 174
++H RCF C C R L
Sbjct: 21 VYHLRCFCCCVCERQL 36
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 28.2 bits (63), Expect = 2.9
Identities = 43/161 (26%), Positives = 73/161 (45%), Gaps = 26/161 (16%)
Query: 40 GKSTLADRLL--EMTGTVLSSGSSQVLDSLQVEQERGIT-----VKAQTASLR-----YT 87
GK+T+ RL E TV + G + + + +G+T V Q LR YT
Sbjct: 15 GKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQE-KLRPLWKSYT 73
Query: 88 SILDGEEYLLNLIDTPGHVDFSNE---VTRSLAACQGVVLLIDANQVDLKNANPEACEEQ 144
DG ++++ +D + E +T+ + QGV +L+ AN+ DL NA P + +
Sbjct: 74 RCTDGIVFVVDSVDVERMEEAKTELHKITK-FSENQGVPVLVLANKQDLPNALPVS---E 129
Query: 145 LQTLFNIDKKSVLRIWHRRCFSCADCHRSLDSTNLNDGLAK 185
++ L + + S WH + +CA + L +GL K
Sbjct: 130 VEKLLALHELSSSTPWHVQP-ACA-----IIGEGLQEGLEK 164
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 26.4 bits (58), Expect = 3.3
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 158 RIWHRRCFSCADCHRSL 174
R +H CF C C RSL
Sbjct: 24 RHYHEHCFRCFRCDRSL 40
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.8 bits (62), Expect = 3.4
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 40 GKSTLADRLLEMTGTVLSS 58
GK+TLA L E G VL
Sbjct: 10 GKTTLAKELAERLGDVLRD 28
Score = 27.8 bits (62), Expect = 3.4
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 213 GKSTLADRLLEMTGTVLSS 231
GK+TLA L E G VL
Sbjct: 10 GKTTLAKELAERLGDVLRD 28
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only
protein 2). The second LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 26.1 bits (57), Expect = 3.9
Identities = 7/33 (21%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 140 ACEEQLQTLFNIDKKSVLRIWHRRCFSCADCHR 172
+C+++++ + + + +++H CF CA C +
Sbjct: 3 SCDKRIRA-YEMTMRVKDKVYHLECFKCAACQK 34
>gnl|CDD|219490 pfam07627, PSCyt3, Protein of unknown function (DUF1588). A region
of similarity shared by several Rhodopirellula baltica
cytochrome-like proteins that are predicted to be
secreted. These proteins also match pfam07626 and
pfam07624.
Length = 102
Score = 26.7 bits (60), Expect = 5.4
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 161 HRRCFSCADCHRSLDS 176
HR +CA CHR +D
Sbjct: 66 HRENPACASCHRKIDP 81
>gnl|CDD|237833 PRK14845, PRK14845, translation initiation factor IF-2;
Provisional.
Length = 1049
Score = 27.9 bits (62), Expect = 5.8
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 97 LNLIDTPGHVDFSNEVTRSLAACQGVVLLIDANQ 130
L IDTPGH F++ R + VL++D N+
Sbjct: 528 LLFIDTPGHEAFTSLRKRGGSLADLAVLVVDINE 561
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 27.1 bits (61), Expect = 5.9
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 90 LDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVL 124
+DGE Y L+++DT G +FS + + G +L
Sbjct: 42 VDGETYTLDILDTAGQEEFSAMRDQYIRNGDGFIL 76
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 25.7 bits (56), Expect = 6.1
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 158 RIWHRRCFSCADCHRSL 174
++H CF C+ C R L
Sbjct: 20 SVYHIECFRCSVCSRQL 36
>gnl|CDD|237827 PRK14832, PRK14832, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 253
Score = 27.7 bits (61), Expect = 6.9
Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 24/89 (26%)
Query: 66 SLQVEQERGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSLAACQGVVLL 125
SLQ E ER +T ++ +T ++ NE+TR AC+ V
Sbjct: 120 SLQTEMERSMTETLNNQAIHFTVAVN--------------YGSRNEITR---ACRQV--- 159
Query: 126 IDANQVDLKNANPEACEEQL--QTLFNID 152
A V + +A EQL Q L+ D
Sbjct: 160 --AELVQQGKLSADAVNEQLVEQHLYTAD 186
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears to
be involved in plant resistance to bacteria.
Length = 211
Score = 27.2 bits (61), Expect = 6.9
Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 16/66 (24%)
Query: 71 QERGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFS-------NEVTRSLA-ACQG- 121
+ +G+T Q S DG +N+IDTPG D S E+ R L A G
Sbjct: 31 RAQGVTKTCQLVS----RTWDGRI--INVIDTPGLFDLSVSNDFISKEIIRCLLLAEPGP 84
Query: 122 -VVLLI 126
VLL+
Sbjct: 85 HAVLLV 90
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 26.5 bits (59), Expect = 7.6
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 11/77 (14%)
Query: 90 LDGEEYLLNLIDTPG---------HVDFSNEVTRSLAACQGVVLLIDANQVDLKNANPEA 140
+ G + L+DTPG V+ N ++ ++L++DA+ + + E
Sbjct: 41 VLGLGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDAS--EGLTEDDEE 98
Query: 141 CEEQLQTLFNIDKKSVL 157
E+L+ L VL
Sbjct: 99 ILEELEKLPKKPIILVL 115
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 26.7 bits (60), Expect = 8.6
Identities = 23/99 (23%), Positives = 36/99 (36%), Gaps = 27/99 (27%)
Query: 40 GKSTLADRLLEMTGTVLSSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNL 99
GKSTL + L+ G +S S K QT R I ++ +
Sbjct: 15 GKSTLLNALV---GQKISIVSP----------------KPQTTRNRIRGIYTDDDAQIIF 55
Query: 100 IDTPG-HVDFS-------NEVTRSLAACQGVVLLIDANQ 130
+DTPG H +L V+ ++DA++
Sbjct: 56 VDTPGIHKPKKKLGERMVKAAWSALKDVDLVLFVVDASE 94
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 27.0 bits (59), Expect = 9.6
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 57 SSGSSQVLDSLQVEQERGITVKAQTASLRYTSILDGEEYLLNLIDTPGHVDFSNEVTRSL 116
+SG S +L+ + E+ +T K QT T I+ ++ + L DTPG + + +++
Sbjct: 62 NSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPKGSLEKAM 121
Query: 117 AAC 119
C
Sbjct: 122 VRC 124
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
0.315 0.130 0.363
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,521,898
Number of extensions: 1151416
Number of successful extensions: 1678
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1521
Number of HSP's successfully gapped: 270
Length of query: 257
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 162
Effective length of database: 6,723,972
Effective search space: 1089283464
Effective search space used: 1089283464
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.0 bits)