RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13975
(415 letters)
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 472 bits (1217), Expect = e-165
Identities = 198/414 (47%), Positives = 257/414 (62%), Gaps = 41/414 (9%)
Query: 21 NILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAH 80
N+L++ ++ SGKTTLIAKLQG++ P+KG LEY Y+NV DE R+D TR VWILDG+ H
Sbjct: 47 NVLVLGEDGSGKTTLIAKLQGVEHPKKGRGLEYLYLNVHDEDRDDQTRCNVWILDGDLYH 106
Query: 81 SNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNIGAHDYQAGRC 140
LL+FALN E+L T+V+ VV M+ PW I++ L WASVL++HID L I + +
Sbjct: 107 KGLLKFALNAESLADTLVIFVVDMSRPWTIMESLQKWASVLREHIDKLKIPPEEMR---- 162
Query: 141 CKLLTFARLRAHLIELLSFYL---------------FYSSVS----VIP-GEGILERNLG 180
L L++ Y+ S ++P GE +L NLG
Sbjct: 163 -------ELEQRLVKDFQEYVEPGDDLPGSPQRRTPRLSGSDDDSVLLPLGENVLTHNLG 215
Query: 181 VDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLY 240
+ +VVV TK D MS LEK+ Y++EHFDF+Q +IR+FCL++GA L YTS KE+KN DLLY
Sbjct: 216 IPVVVVCTKCDAMSVLEKEHDYRDEHFDFIQSHIRRFCLQYGAALIYTSVKEEKNLDLLY 275
Query: 241 KYLAHRLYGFPFRTSALIVEKDAVLIPSGWDNMKKIGILYENMQSIKPDDYYTDVITKPI 300
KYL H++YGFPF T AL+VEKDAV IP+GWDN KKIGIL+EN Q++KP+D Y D I KP
Sbjct: 276 KYLVHKIYGFPFNTPALVVEKDAVFIPAGWDNEKKIGILHENFQTVKPEDPYEDFIVKPP 335
Query: 301 VRKPISREQDTLVEDEQSFLARQLALLQQNPAANPTTRQDNSLPQIRTPVGVQKTGDRRL 360
VRK + +++ EDEQ FL +Q +LL + PA TR S R+P G +T +R
Sbjct: 336 VRKLVH-DKEVQAEDEQVFLMKQQSLLAKQPAT--PTRGVESPA--RSPGGSPRTTNRSG 390
Query: 361 SNSPAMQGGGANSPKKMIDPTKVGATTPGGEGVLASFFNSLLLKKTAQSPLSKS 414
+ A S KK IDP EGVLA+FFNSLL KKT SP S
Sbjct: 391 PRNVASVSPMT-SVKK-IDPNMKPGAA--SEGVLANFFNSLLSKKTG-SPGSPG 439
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 34.6 bits (81), Expect = 0.074
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 15/93 (16%)
Query: 161 LFYSSVSVIPGEG---ILE--RNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIR 215
LF G G ILE + + +++V+ K D L KD KEE +++
Sbjct: 89 LFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKID----LVKD---KEELLPLLEELSE 141
Query: 216 KFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLY 248
F A + SA + N D L +A L
Sbjct: 142 LM--DF-AEIVPISALKGDNVDELLDVIAKYLP 171
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 32.4 bits (75), Expect = 0.17
Identities = 19/64 (29%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 181 VDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLY 240
+ I++V K+D LE + ++ + QQ+ ++ L F F TSAK +N D +
Sbjct: 106 IPIILVGNKSD----LEDE---RQVSTEEAQQFAKENGLLF----FETSAKTGENVDEAF 154
Query: 241 KYLA 244
+ LA
Sbjct: 155 ESLA 158
>gnl|CDD|213233 cd03266, ABC_NatA_sodium_exporter, ATP-binding cassette domain of
the Na+ transporter. NatA is the ATPase component of a
bacterial ABC-type Na+ transport system called NatAB,
which catalyzes ATP-dependent electrogenic Na+
extrusion without mechanically coupled proton or K+
uptake. NatB possess six putative membrane spanning
regions at its C-terminus. In B. subtilis, NatAB is
inducible by agents such as ethanol and protonophores,
which lower the proton-motive force across the
membrane. The closest sequence similarity to NatA is
exhibited by DrrA of the two-component daunorubicin-
and doxorubicin-efflux system. Hence, the functional
NatAB is presumably assembled with two copies of a
single ATP-binding protein and a single integral
membrane protein.
Length = 218
Score = 33.1 bits (76), Expect = 0.18
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 15 DGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGV 71
G V G L+ N +GKTT + L G+ P+ G A +V E E RLG
Sbjct: 30 PGEVTG---LLGPNGAGKTTTLRMLAGLLEPDAGFA-TVDGFDVVKEPAEARRRLGF 82
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 32.6 bits (75), Expect = 0.19
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 11/65 (16%)
Query: 183 IVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKY 242
+V+V K D E + ++ GA F TSAK K + L+
Sbjct: 108 LVIVGNKIDL-----------ERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLS 156
Query: 243 LAHRL 247
LA R+
Sbjct: 157 LAKRM 161
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 32.8 bits (76), Expect = 0.21
Identities = 22/92 (23%), Positives = 36/92 (39%), Gaps = 26/92 (28%)
Query: 173 GILER------NLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLF 226
+L+R G++ V+V+ K D L D +E ++ Y K G +
Sbjct: 20 RLLDRYLVAAEASGIEPVIVLNKAD----LVDDEELEE----LLEIY-----EKLGYPVL 66
Query: 227 YTSAKEDKNCDLLYKYLAHRLYGFPFRTSALI 258
SAK + D L + L +TS L+
Sbjct: 67 AVSAKTGEGLDELRELLKG-------KTSVLV 91
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 32.5 bits (74), Expect = 0.24
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 7/65 (10%)
Query: 180 GVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLL 239
I + TK+D +E+D ++ F VQ + + A F TS+K +N D L
Sbjct: 105 HCKIYLCGTKSDL---IEQDRSLRQVDFHDVQDFADEI----KAQHFETSSKTGQNVDEL 157
Query: 240 YKYLA 244
++ +A
Sbjct: 158 FQKVA 162
>gnl|CDD|213187 cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of
polysaccharide transport system. The KpsT/Wzt ABC
transporter subfamily is involved in extracellular
polysaccharide export. Among the variety of
membrane-linked or extracellular polysaccharides
excreted by bacteria, only capsular polysaccharides,
lipopolysaccharides, and teichoic acids have been shown
to be exported by ABC transporters. A typical system is
made of a conserved integral membrane and an ABC. In
addition to these proteins, capsular polysaccharide
exporter systems require two 'accessory' proteins to
perform their function: a periplasmic (E.coli) or a
lipid-anchored outer membrane protein called OMA
(Neisseria meningitidis and Haemophilus influenza) and
a cytoplasmic membrane protein MPA2.
Length = 224
Score = 32.5 bits (75), Expect = 0.32
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G IG LI N +GK+TL+ L GI P+ G
Sbjct: 43 FEVPRGERIG---LIGRNGAGKSTLLRLLAGIYPPDSG 77
>gnl|CDD|132138 TIGR03094, sulfo_cyanin, sulfocyanin. Members of this family are
blue-copper redox proteins designated sulfocyanin, from
the archaeal genera Sulfolobus, Ferroplasma, and
Picrophilus. The most closely related proteins
characterized as functionally different are the
rustacyanins [Energy metabolism, Electron transport].
Length = 195
Score = 31.8 bits (72), Expect = 0.43
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 78 PAHSNLLRFALNQETLPHTMVMLVVSMTTP 107
PA N+ N E+LPH + +L S TP
Sbjct: 90 PAGWNVYVTFTNYESLPHNLKLLPNSTQTP 119
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 31.4 bits (72), Expect = 0.59
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
G +G +I N +GK+TL+ + GI P G
Sbjct: 48 FEIYKGERVG---IIGHNGAGKSTLLKLIAGIYKPTSG 82
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 31.7 bits (72), Expect = 0.69
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYIN---VSDEYREDHTRL 69
+ LI N SGK+TL L G+ P+ G ++ VS E ED+ +L
Sbjct: 352 VFLIGGNGSGKSTLAMLLTGLYQPQSG----EILLDGKPVSAEQLEDYRKL 398
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 30.9 bits (71), Expect = 0.71
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L G ++G ++ N +GK+TL+ L G+ P G
Sbjct: 20 LSIEAGEIVG---ILGPNGAGKSTLLKTLAGLLKPSSG 54
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 31.6 bits (72), Expect = 0.76
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLG 70
L G ++ L+ + +GK+TL+ + G+++P+ G I ++ D + L
Sbjct: 23 LDIKSGELVA---LLGPSGAGKSTLLRIIAGLETPDAG------RIRLNGRVLFDVSNLA 73
Query: 71 V 71
V
Sbjct: 74 V 74
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 30.1 bits (69), Expect = 0.90
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L N G IG L+ N +GK+TL+ + G P++G
Sbjct: 21 LTINPGDRIG---LVGRNGAGKSTLLKLIAGELEPDEG 55
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 30.4 bits (70), Expect = 1.1
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L G + G L+ N +GKTTLI + G+ P+ G
Sbjct: 21 LTVEKGEIYG---LLGPNGAGKTTLIKIILGLLKPDSG 55
>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 = 30.1 bits (69), Expect = 1.2
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 13/77 (16%)
Query: 174 ILERNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKF--GAGLFYTSAK 231
ILE +++VV K D +EKD +E ++ +R+ L F A + + SA
Sbjct: 109 ILEEGKA--LIIVVNKWD---LVEKDEKTMKE----FEKELRRK-LPFLDYAPIVFISAL 158
Query: 232 EDKNCDLLYKYLAHRLY 248
+ D L+ +Y
Sbjct: 159 TGQGVDKLFD-AIKEVY 174
>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 = 30.1 bits (69), Expect = 1.3
Identities = 27/92 (29%), Positives = 40/92 (43%), Gaps = 15/92 (16%)
Query: 161 LFYSSVSVIPGEG---ILER--NLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIR 215
LF S GEG ILE +++V+ K D L KD KE+ +++
Sbjct: 87 LFVVDASEWIGEGDEFILELLKKSKTPVILVLNKID----LVKD---KEDLLPLLEKL-- 137
Query: 216 KFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRL 247
L A +F SA + +N D L +Y+ L
Sbjct: 138 -KELHPFAEIFPISALKGENVDELLEYIVEYL 168
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 30.7 bits (70), Expect = 1.5
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKG 48
I ++ N +GK+TL+ L G P G
Sbjct: 351 IAIVGPNGAGKSTLLKLLAGELGPLSG 377
Score = 29.9 bits (68), Expect = 2.9
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L N G IG L+ N +GK+TL+ L G P+ G
Sbjct: 24 LTLNPGERIG---LVGRNGAGKSTLLKILAGELEPDSG 58
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 29.5 bits (67), Expect = 1.6
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 8/50 (16%)
Query: 4 PYYDVFVLR-----FNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
Y L G ++ L+ N SGK+TL+ + G+ P G
Sbjct: 8 RYGGRTALDNVSLTLKAGEIVA---LVGPNGSGKSTLLRAIAGLLKPTSG 54
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 30.4 bits (70), Expect = 1.7
Identities = 16/77 (20%), Positives = 26/77 (33%), Gaps = 15/77 (19%)
Query: 174 ILERNLGVDIVVVVTKTDYMSTLEKDFYYKE--EHFDFVQQYIRKFCLKFGAGLFYTSAK 231
LE +V+VV K D + + + KE F+ A + + SA
Sbjct: 280 ALEAGRA--LVIVVNKWDLVDEKTMEEFKKELRRRLPFL----------DYAPIVFISAL 327
Query: 232 EDKNCDLLYKYLAHRLY 248
+ D L + Y
Sbjct: 328 TGQGVDKLLE-AIDEAY 343
>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 = 29.9 bits (68), Expect = 1.8
Identities = 27/90 (30%), Positives = 40/90 (44%), Gaps = 35/90 (38%)
Query: 31 GKTTLIAKLQGIDS---PE---KGLALE--YAYINVSDEYREDHTRLGVWILDGEPAHSN 82
GKTTLI L GI++ PE +G+ ++ +AY+++ D RLG +D P H
Sbjct: 11 GKTTLIKALTGIETDRLPEEKKRGITIDLGFAYLDL-----PDGKRLG--FID-VPGH-- 60
Query: 83 LLRFALNQETLPHTM---------VMLVVS 103
E M V+LVV+
Sbjct: 61 --------EKFVKNMLAGAGGIDAVLLVVA 82
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 30.7 bits (70), Expect = 1.8
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEK-----GLALEYAYINVSDEYRED 65
I LI N GKTTL+ + G + G LE AY D++R +
Sbjct: 348 IALIGPNGCGKTTLLKLMLGQLQADSGRIHCGTKLEVAYF---DQHRAE 393
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 29.9 bits (68), Expect = 1.9
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L G +I L N +GKTTL L G+ G
Sbjct: 21 LDLYAGEIIA---LTGKNGAGKTTLAKILAGLIKESSG 55
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.9 bits (68), Expect = 1.9
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKGL 49
+LLI N SGK+TL+ L G+ P G
Sbjct: 33 VLLIGPNGSGKSTLLKLLNGLLKPTSGE 60
>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 = 30.2 bits (68), Expect = 2.2
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 17/66 (25%)
Query: 31 GKTTLIAKLQGIDS---PE---KGLALE--YAYINVSDEYREDHTRLGVWILDGEPAHSN 82
GKTTL+ L GI + PE +G+ ++ +AY + D RLG +D P H
Sbjct: 12 GKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPD------YRLG--FIDV-PGHEK 62
Query: 83 LLRFAL 88
+ A+
Sbjct: 63 FISNAI 68
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of
RNase L inhibitor. The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis,
formation of translation preinitiation complexes, and
assembly of HIV capsids. RLI's are not transport
proteins, and thus cluster with a group of soluble
proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains, which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 177
Score = 29.5 bits (66), Expect = 2.4
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 7/52 (13%)
Query: 1 MTNPYYDVFVL----RFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
Y F+L +G VIG ++ N +GKTT + L G P
Sbjct: 6 CVKRYGVFFLLVELGVVKEGEVIG---IVGPNGTGKTTAVKILAGQLIPNGD 54
>gnl|CDD|107050 PHA01633, PHA01633, putative glycosyl transferase group 1.
Length = 335
Score = 29.9 bits (67), Expect = 2.5
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 163 YSSVSVIPGEGILE--RNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLK 220
YSS+S + E I E R G +IV + Y+ EK + H + Y+ +
Sbjct: 10 YSSISNV-SEDIAEVLRENG-EIVTITKNPFYIPKAEKLIVFIPFHPPSLNPYLYAYYQF 67
Query: 221 FGAGLFYTSAKEDKNCDLLYKYL 243
G FYT+ N +++ KYL
Sbjct: 68 KGKKYFYTTCDGIPNIEIVNKYL 90
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 29.0 bits (66), Expect = 2.5
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 7/71 (9%)
Query: 177 RNLGVDIVVVVTKTDYMSTLEKDFYYKEEHFDFVQQYIRKFCLKFGAGLFYTSAKEDKNC 236
LG+ ++V+TK D + E + +++ + F + S+K+
Sbjct: 107 EELGIPFLIVLTKADKLKKSELA-----KVLKKIKEELNLF--NILPPVILFSSKKGTGI 159
Query: 237 DLLYKYLAHRL 247
D L +A L
Sbjct: 160 DELRALIAEWL 170
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 29.7 bits (67), Expect = 2.7
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 13 FNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
++ VIG ++ N GKTT I L G+ P++G
Sbjct: 22 ISESEVIG---ILGPNGIGKTTFIKMLAGVLKPDEG 54
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.9 bits (64), Expect = 2.8
Identities = 25/106 (23%), Positives = 40/106 (37%), Gaps = 12/106 (11%)
Query: 20 GNILLISDNSSGKTTLIAKLQG-IDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEP 78
IL++ SGKTTL L + P G YI+ D E +L + I+ G+
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGG----VIYIDGEDILEEVLDQLLLIIVGGKK 58
Query: 79 AHSNLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDH 124
A + L + V+ I+DE+ + Q+
Sbjct: 59 ASGSGELRLRLALALARKLKPDVL-------ILDEITSLLDAEQEA 97
>gnl|CDD|227297 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
[Intracellular trafficking and secretion].
Length = 355
Score = 29.6 bits (67), Expect = 3.0
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 11/75 (14%)
Query: 21 NILLISDNSSGKTTLIAKLQG-IDSPEKGLALE------YAYINVSDEYREDHTRLGVWI 73
NIL+ SGKTTL+ L G IDS E+ + +E A+ +V TR
Sbjct: 175 NILISGGTGSGKTTLLNALSGFIDSDERVITIEDTAELQLAHPHVV----RLETRPPNVE 230
Query: 74 LDGEPAHSNLLRFAL 88
GE +L++ AL
Sbjct: 231 GTGEVTMRDLVKNAL 245
>gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter
ATP-binding subunit. This model describes daunorubicin
resistance ABC transporter, ATP binding subunit in
bacteria and archaea. This model is restricted in its
scope to preferentially recognize the ATP binding
subunit associated with effux of the drug,
daunorubicin. This transport system belong to the
larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP
hydrolysis to substrate translocation. The minimal
configuration of bacterial ABC transport system: an
ATPase or ATP binding subunit; An integral membrane
protein; a hydrophilic polypetpide, which likely
functions as substrate binding protein. In eukaryotes
proteins of similar function include p-gyco proteins,
multidrug resistance protein etc [Transport and binding
proteins, Other].
Length = 302
Score = 29.7 bits (67), Expect = 3.0
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 10/73 (13%)
Query: 5 YYDVFV------LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINV 58
Y F + +G V G + N +GKTT I L + P G A Y +V
Sbjct: 2 VYGDFKAVDGVNFKVREGEVFG---FLGPNGAGKTTTIRMLTTLLRPTSGTARVAGY-DV 57
Query: 59 SDEYREDHTRLGV 71
E R+ +G+
Sbjct: 58 VREPRKVRRSIGI 70
>gnl|CDD|226982 COG4635, HemG, Flavodoxin [Energy production and conversion /
Coenzyme metabolism].
Length = 175
Score = 29.0 bits (65), Expect = 3.2
Identities = 29/120 (24%), Positives = 42/120 (35%), Gaps = 26/120 (21%)
Query: 285 SIKPDDYYTDVITKPIVRKPISREQDTLVEDEQSFLARQLALLQQNPAA----NPTTRQD 340
+DY VI I E QSF+ + L P+A N T R++
Sbjct: 42 EPALEDYDAVVIGASI-------RYGHFHEAVQSFVKKHAEALSTKPSAFFSVNLTARKE 94
Query: 341 NSLPQIRTPVGVQKTGDRRLSNSP------AMQGGGANSPK-KMIDPT--KVGATTPGGE 391
P+ + V + L SP A+ GG P+ + D K+ GGE
Sbjct: 95 KRTPETNSYV------RKFLMKSPWQPVAIAVFGGALRYPRYRWFDRFMIKLIMKMSGGE 148
>gnl|CDD|203280 pfam05579, Peptidase_S32, Equine arteritis virus serine
endopeptidase S32. Serine peptidases involved in
processing nidovirus polyprotein.
Length = 425
Score = 29.7 bits (67), Expect = 3.4
Identities = 23/97 (23%), Positives = 35/97 (36%), Gaps = 9/97 (9%)
Query: 86 FALNQETLPHTMVMLVVSMT-------TPWNI-IDELHNWASVLQDHIDSLNIGAHDYQA 137
F LN E LP +V LV S TP + + + + L ++ SL A
Sbjct: 213 FLLN-EILPKVLVRLVFSFALFLLCWFTPLSAQVLLIRLLTAALNRNVISLAFYALGAGT 271
Query: 138 GRCCKLLTFARLRAHLIELLSFYLFYSSVSVIPGEGI 174
++ + + LS YLF V V+
Sbjct: 272 SFLAEMWFLGGIPLQALGFLSTYLFLPRVLVVTSPVP 308
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 29.5 bits (66), Expect = 3.4
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG-LALEYAYINVSDEYREDHTRL 69
LR G ++ ++ +N GK+TL G+ P++G + L+ A VS + R+D+ L
Sbjct: 363 LRIAQGDIV---FIVGENGCGKSTLAKLFCGLYIPQEGEILLDGA--AVSADSRDDYRDL 417
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 26.8 bits (60), Expect = 3.7
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 5 YYDVFVLRFNDGSVIGNILLISDNSSGKTTLIAKLQ 40
+D + + LL + SGK+TLI +Q
Sbjct: 11 TFDGHTIPID----PKGTLLTGPSGSGKSTLIDAIQ 42
>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 = 28.8 bits (65), Expect = 3.9
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 3/66 (4%)
Query: 183 IVVVVTKTDYMSTLEKDFYYKEEH-FDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYK 241
I+V V K D E+DF + ++ F + SA + + L
Sbjct: 117 IIVAVNKID--RVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGIEELLD 174
Query: 242 YLAHRL 247
+ L
Sbjct: 175 AIVEHL 180
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 29.3 bits (66), Expect = 4.1
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEK 47
L F +G +LI +N+SGK++L+ L+ + PE
Sbjct: 19 LEFEEG----LNVLIGENNSGKSSLLDALRLLLDPES 51
>gnl|CDD|219971 pfam08690, GET2, GET complex subunit GET2. This family corresponds
to the GET complex subunit GET2. The GET complex is
involved in the retrieval of ER resident proteins from
the Golgi.
Length = 298
Score = 29.0 bits (65), Expect = 4.4
Identities = 17/70 (24%), Positives = 27/70 (38%)
Query: 296 ITKPIVRKPISREQDTLVEDEQSFLARQLALLQQNPAANPTTRQDNSLPQIRTPVGVQKT 355
I + I E D + + +QLA +QQ + D+S + + +
Sbjct: 71 ILEAIDPPKDESESPAENIDPEVEMFQQLAKMQQQGNGSDNPPADDSTADLFSMLLQMGG 130
Query: 356 GDRRLSNSPA 365
GD S SPA
Sbjct: 131 GDGPDSESPA 140
>gnl|CDD|238193 cd00316, Oxidoreductase_nitrogenase, The nitrogenase enzyme system
catalyzes the ATP-dependent reduction of dinitrogen to
ammonia. This group contains both alpha and beta
subunits of component 1 of the three known genetically
distinct types of nitrogenase systems: a
molybdenum-dependent nitrogenase (Mo-nitrogenase), a
vanadium-dependent nitrogenase (V-nitrogenase), and an
iron-only nitrogenase (Fe-nitrogenase) and, both
subunits of Protochlorophyllide (Pchlide) reductase and
chlorophyllide (chlide) reductase. The nitrogenase
systems consist of component 1 (MoFe protein, VFe
protein or, FeFe protein respectively) and, component 2
(Fe protein). The most widespread and best characterized
nitrogenase is the Mo-nitrogenase. MoFe is an
alpha2beta2 tetramer, the alternative nitrogenases are
alpha2beta2delta2 hexamers whose alpha and beta subunits
are similar to the alpha and beta subunits of MoFe. For
MoFe, each alphabeta pair contains one P-cluster (at the
alphabeta interface) and, one molecule of iron
molybdenum cofactor (FeMoco) contained within the alpha
subunit. The Fe protein contains a single [4Fe-4S]
cluster from which, electrons are transferred to the
P-cluster of the MoFe and in turn, to FeMoCo at the site
of substrate reduction. The V-nitrogenase requires an
iron-vanadium cofactor (FeVco), the iron
only-nitrogenase an iron only cofactor (FeFeco). These
cofactors are analogous to the FeMoco. The V-nitrogenase
has P clusters identical to those of MoFe. Pchlide
reductase and chlide reductase participate in the
Mg-branch of the tetrapyrrole biosynthetic pathway.
Pchlide reductase catalyzes the reduction of the D-ring
of Pchlide during the synthesis of chlorophylls (Chl)
and bacteriochlorophylls (BChl). Chlide-a reductase
catalyzes the reduction of the B-ring of Chlide-a during
the synthesis of BChl-a. The Pchlide reductase NB
complex is a an N2B2 heterotetramer resembling
nitrogenase FeMo, N and B proteins are homologous to the
FeMo alpha and beta subunits respectively. The NB
complex may serve as a catalytic site for Pchlide
reduction and, the ZY complex as a site of chlide
reduction, similar to MoFe for nitrogen reduction.
Length = 399
Score = 29.2 bits (66), Expect = 4.6
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 22/120 (18%)
Query: 147 ARLRAHLIELLSFYLFYSS--VSVIPGEG-------ILERNLGVDIVVVVTKTDYMSTLE 197
AR RA L++ L+ Y Y I G+G LG+++V T + + E
Sbjct: 260 ARERARLLDALADYHEYLGGKKVAIFGDGDLLLALARFLLELGMEVVAAGTTFGHKADYE 319
Query: 198 KDFYYKEE----HFDFVQQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFPFR 253
+ E D + + + + L +K +Y+A +L G P
Sbjct: 320 RREELLGEGTEVVDDGDLEELEELIRELKPDLIIGGSKG--------RYIAKKL-GIPLV 370
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 28.9 bits (65), Expect = 5.1
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKG 48
L+ N +GK+TL+ L GI P++G
Sbjct: 34 TALLGPNGAGKSTLLLHLNGIYLPQRG 60
>gnl|CDD|226493 COG4004, COG4004, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 96
Score = 27.1 bits (60), Expect = 5.4
Identities = 13/60 (21%), Positives = 22/60 (36%)
Query: 350 VGVQKTGDRRLSNSPAMQGGGANSPKKMIDPTKVGATTPGGEGVLASFFNSLLLKKTAQS 409
V + GDR +++SP + K + T + A +N L K T +
Sbjct: 26 WTVSEEGDRIVASSPGISRIEIKPENKKLLVNTTDYTDDETKLQTAKTYNDFLEKLTGYT 85
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 28.5 bits (65), Expect = 5.9
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 22 ILLISDNSSGKTTLIAKL 39
IL++ N GKTT I KL
Sbjct: 117 ILVVGVNGVGKTTTIGKL 134
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 28.2 bits (64), Expect = 6.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 30 SGKTTLIAKLQGIDSPEKG 48
SGK+TL+ L G+D P G
Sbjct: 42 SGKSTLLNLLGGLDKPTSG 60
>gnl|CDD|215407 PLN02762, PLN02762, pyruvate kinase complex alpha subunit.
Length = 509
Score = 28.9 bits (65), Expect = 6.0
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 178 NLGVDIVVVVTKTDYMSTL 196
NLGVD + V TK +M++L
Sbjct: 407 NLGVDAIFVYTKHGHMASL 425
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and
TFIID) that are involved in accurate initiation of
transcription by RNA polymerase II in eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs to
show the relationship between TAF orthologs and
paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 28.4 bits (64), Expect = 6.2
Identities = 31/138 (22%), Positives = 50/138 (36%), Gaps = 23/138 (16%)
Query: 211 QQYIRKFCLKFGAGLFYTSAKEDKNCDLLYKYLAHRLYGFP----FRTSALIVEKDAVLI 266
+ + G Y EDK DL + L P + L +E LI
Sbjct: 75 SEPLPFRVSTGGGQELYY--VEDKEIDL-KDLINTPLPKVPLDVSVKAHWLAIEGVQPLI 131
Query: 267 P-----SGWDNMKKIGILYENMQSIKPDDYYTDVITKPIVRKPISREQ--------DTLV 313
P S + KK + ++ +K D+ V+ KP+VR +S+E + LV
Sbjct: 132 PENPPPSAIEVQKKESLANAAVKRLKKDE---QVLLKPLVRHVLSKELQLYFEEITEALV 188
Query: 314 EDEQSFLARQLALLQQNP 331
+ L L+ +P
Sbjct: 189 GSNEEKRREALQSLRTDP 206
>gnl|CDD|106587 PRK13644, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 28.4 bits (63), Expect = 6.4
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 16 GSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLAL 51
G IG +I N SGK+TL L G+ P+KG L
Sbjct: 28 GEYIG---IIGKNGSGKSTLALHLNGLLRPQKGKVL 60
>gnl|CDD|236554 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 28.7 bits (64), Expect = 6.5
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L +GS++G L+ N +GKTTL+ + G +P G
Sbjct: 24 LSVREGSLVG---LVGPNGAGKTTLLRAINGTLTPTAG 58
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho 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 Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 28.1 bits (62), Expect = 6.9
Identities = 23/109 (21%), Positives = 40/109 (36%), Gaps = 4/109 (3%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYREDHTRLGVWILDGEPAHS 81
++L+ D GKT ++ L PE + + E E L +W G P +
Sbjct: 16 LVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYD 75
Query: 82 NLLRFALNQETLPHTMVMLVVSMTTPWNIIDELHNWASVLQDHIDSLNI 130
N+ + V+L ++ P L W + + D+ S I
Sbjct: 76 NVRPLCYSDS----DAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRI 120
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 28.8 bits (65), Expect = 7.0
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 4 PYYDVFVLRFNDGSVIGNILLISDNSSGKTTLIAKL 39
P+Y F D V+G+ L+ SGKTTL+ L
Sbjct: 421 PFY--FNFHVRDAKVLGHTLIFGPTGSGKTTLLNFL 454
>gnl|CDD|213198 cd03231, ABC_CcmA_heme_exporter, Cytochrome c biogenesis
ATP-binding export protein. CcmA, the ATP-binding
component of the bacterial CcmAB transporter. The CCM
family is involved in bacterial cytochrome c
biogenesis. Cytochrome c maturation in E. coli requires
the ccm operon, which encodes eight membrane proteins
(CcmABCDEFGH). CcmE is a periplasmic heme chaperon that
binds heme covalently and transfers it onto
apocytochrome c in the presence of CcmF, CcmG, and
CcmH. The CcmAB proteins represent an ABC transporter
and the CcmCD proteins participate in heme transfer to
CcmE.
Length = 201
Score = 27.8 bits (62), Expect = 7.5
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 20 GNILLIS-DNSSGKTTLIAKLQGIDSPEKG 48
G L ++ N SGKTTL+ L G+ P G
Sbjct: 26 GEALQVTGPNGSGKTTLLRILAGLSPPLAG 55
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 28.1 bits (63), Expect = 7.7
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L G + ++ + SGK+TL+A L G+D P G
Sbjct: 31 LVVKRGETVA---IVGPSGSGKSTLLAVLAGLDDPSSG 65
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain.
Length = 173
Score = 27.9 bits (63), Expect = 7.7
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 22 ILLISDNSSGKTTLIAKL 39
ILL+ GKTT AKL
Sbjct: 3 ILLVGLQGVGKTTTAAKL 20
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 28.4 bits (64), Expect = 7.8
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 22 ILLISDNSSGKTTLIAKL 39
IL + N GKTT IAKL
Sbjct: 142 ILFVGVNGVGKTTTIAKL 159
>gnl|CDD|227254 COG4917, EutP, Ethanolamine utilization protein [Amino acid
transport and metabolism].
Length = 148
Score = 27.5 bits (61), Expect = 8.7
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDS-PEKGLALEYAYINVSDEYRED 65
I + GKTTL L G D+ +K A+E+ +D+ D
Sbjct: 4 IAFVGQVGCGKTTLFQSLYGNDTLYKKTQAVEF-----NDKGDID 43
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 28.3 bits (63), Expect = 8.9
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 11/56 (19%)
Query: 16 GSVIGN-----ILLISDNSSGKTTLIAKL---QGIDSPEKGLALEYAYINVSDEYR 63
GS+I N +L+ GKTT IAKL GI+S +K L ++ I D YR
Sbjct: 166 GSIIDNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITI---DNYR 218
>gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter,
ATP-binding protein. This small clade of ABC-type
transporter ATP-binding protein components is found as
a three gene cassette along with a periplasmic
substrate-binding protein (TIGR03868) and a permease
(TIGR03869). The organisms containing this cassette are
all Actinobacteria and all contain numerous genes
requiring the coenzyme F420. This model was defined
based on five such organisms, four of which are lacking
all F420 biosynthetic capability save the final
side-chain polyglutamate attachment step (via the gene
cofE: TIGR01916). In Jonesia denitrificans DSM 20603
and marine actinobacterium PHSC20C1 this cassette is in
an apparent operon with the cofE gene and, in PHSC20C1,
also with a F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this ATP-binding protein is a component
of an F420-0 (that is, F420 lacking only the
polyglutamate tail) transporter.
Length = 256
Score = 27.9 bits (62), Expect = 8.9
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 16 GSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
GS+ G L+ N SGK+TL+ L G P+ G
Sbjct: 27 GSLTG---LLGPNGSGKSTLLRLLAGALRPDAG 56
>gnl|CDD|182569 PRK10584, PRK10584, putative ABC transporter ATP-binding protein
YbbA; Provisional.
Length = 228
Score = 27.8 bits (62), Expect = 9.0
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 22 ILLISDNSSGKTTLIAKLQGIDSPEKG 48
I LI ++ SGK+TL+A L G+D G
Sbjct: 39 IALIGESGSGKSTLLAILAGLDDGSSG 65
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 27.5 bits (62), Expect = 9.4
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 22 ILLISDNSSGKTTLIAKL 39
ILL+ SGKTT IAKL
Sbjct: 4 ILLVGLQGSGKTTTIAKL 21
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain
of the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 27.6 bits (62), Expect = 9.5
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
L G + G + N +GKTT + + G+ P+ G
Sbjct: 21 LHVKKGEIYG---FLGPNGAGKTTTMKIILGLIKPDSG 55
>gnl|CDD|184198 PRK13638, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 271
Score = 28.0 bits (62), Expect = 9.5
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLAL 51
L F+ V G L+ N GK+TL L G+ P+KG L
Sbjct: 22 LDFSLSPVTG---LVGANGCGKSTLFMNLSGLLRPQKGAVL 59
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 27.8 bits (62), Expect = 9.7
Identities = 25/85 (29%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 15 DGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKGLALEYAYINVSDEYRE-DHTRLGVWI 73
+G + G L+ +N +GKTTL+ + + P+ G I+ D R+ R + +
Sbjct: 27 EGEITG---LLGENGAGKTTLLRMIATLLIPDSGK----VTIDGVDTVRDPSFVRRKIGV 79
Query: 74 LDGE-------PAHSNLLRFA-LNQ 90
L GE A NL FA LN
Sbjct: 80 LFGERGLYARLTARENLKYFARLNG 104
>gnl|CDD|237455 PRK13637, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 27.7 bits (62), Expect = 10.0
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 11 LRFNDGSVIGNILLISDNSSGKTTLIAKLQGIDSPEKG 48
+ DG +G LI SGK+TLI L G+ P G
Sbjct: 28 IEIEDGEFVG---LIGHTGSGKSTLIQHLNGLLKPTSG 62
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.401
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,540,568
Number of extensions: 2135266
Number of successful extensions: 2138
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2131
Number of HSP's successfully gapped: 105
Length of query: 415
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 316
Effective length of database: 6,546,556
Effective search space: 2068711696
Effective search space used: 2068711696
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.6 bits)