RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 046160
(114 letters)
>gnl|CDD|233145 TIGR00836, amt, ammonium transporter. The Ammonium Transporter
(Amt) Family (TC 2.A.49) All functionally characterized
members of the Amt family are ammonia or ammonium uptake
transporters. Some, but not others, also transport
methylammonium. The mechanism of energy coupling, if
any, to methyl-NH2 or NH3 uptake by the AmtB protein of
E. coli is not entirely clear. NH4+ uniport driven by
the pmf, energy independent NH3 facilitation, and
NH4+/K+ antiport have been proposed as possible
transport mechanisms. In Corynebacterium glutamicum and
Arabidopsis thaliana, uptake via the Amt1 homologues of
AmtB has been reported to be driven by the pmf
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 403
Score = 61.5 bits (150), Expect = 2e-12
Identities = 27/112 (24%), Positives = 42/112 (37%), Gaps = 29/112 (25%)
Query: 9 WVLIGLNILAIKLNFDDPLEATRLHGGWGFIGS--------------------------- 41
+ ++ L KL DDPL+A +HG G G
Sbjct: 292 LCYLAVSKLKKKLKIDDPLDAFAVHGVGGIWGLIATGLFAAPKVGGVGTGGLLGGNGKQL 351
Query: 42 --QVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEITGLDISSDSGYAY 91
Q+ ++ I+ W + L K LR+ E+EE GLD++ +AY
Sbjct: 352 GVQLIGIAAIIAWAFVVTFIILKILDKTIGLRVSEEEEKIGLDLAEHGEFAY 403
>gnl|CDD|216185 pfam00909, Ammonium_transp, Ammonium Transporter Family.
Length = 399
Score = 49.6 bits (119), Expect = 3e-08
Identities = 27/113 (23%), Positives = 40/113 (35%), Gaps = 30/113 (26%)
Query: 9 WVLIGLNILAIKLNFDDPLEATRLHGGWGFIG---------------------------- 40
++G L KL DDPL+ +HG G G
Sbjct: 287 VSVLGYKKLKEKLGIDDPLDVFPVHGVGGIWGGIAVGIFAAPYVPTSGIYGGLLGGGFKQ 346
Query: 41 --SQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEITGLDISSDSGYAY 91
Q+ ++VI+ + L L LR+ E+EE GLD++ AY
Sbjct: 347 LGVQLIGIAVILAYAFGVTFILGLLLGLTLGLRVSEEEEEVGLDVAEHGETAY 399
>gnl|CDD|234292 TIGR03644, marine_trans_1, probable ammonium transporter, marine
subtype. Members of this protein family are well
conserved subclass of putative ammonimum transporters,
belonging to the much broader set of
ammonium/methylammonium transporter described by
TIGR00836. Species with this transporter tend to be
marine bacteria. Partial phylogenetic profiling (PPP)
picks a member of this protein family as the single
best-scoring protein vs. a reference profile for the
marine environment Genome Property for a large number of
different query genomes. This finding by PPP suggests
that this transporter family represents an important
adaptation to the marine environment.
Length = 404
Score = 39.3 bits (92), Expect = 1e-04
Identities = 26/90 (28%), Positives = 42/90 (46%), Gaps = 15/90 (16%)
Query: 10 VLIGLNILAI-KLNFDDPLEATRLHGGWGFIG--------------SQVTELSVIVGWVR 54
V++ +I+ + KL DDP+ A +HG G G +Q+ + I WV
Sbjct: 305 VIVVFSIVLLDKLKIDDPVGAISVHGVAGIWGTLVVPITNGDASFGAQLIGAATIFAWVF 364
Query: 55 ETMGPLFHALHKLKMLRILEDEEITGLDIS 84
T ++ L +R+ E+EE GLDI+
Sbjct: 365 VTSLIVWFILKATMGIRVSEEEEYEGLDIA 394
>gnl|CDD|223083 COG0004, AmtB, Ammonia permease [Inorganic ion transport and
metabolism].
Length = 409
Score = 34.1 bits (79), Expect = 0.008
Identities = 30/126 (23%), Positives = 46/126 (36%), Gaps = 39/126 (30%)
Query: 5 YFEPW--VLIGL----------NILAIKLNFDDPLEATRLHG------------------ 34
+ PW ++IGL +L KL DD L+ +HG
Sbjct: 277 FVSPWGALIIGLIAGVICYFAVKLLKKKLGVDDALDVFGVHGVGGIVGAILTGIFAAPAV 336
Query: 35 ---------GWGFIGSQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEITGLDISS 85
G +G Q+ + V + + + L + LR+ E+EE+ GLDIS
Sbjct: 337 GGGGGLFYGGGVQLGVQLLGVLVTIVYAFVVTFIILKVLKLIIGLRVSEEEELEGLDISE 396
Query: 86 DSGYAY 91
AY
Sbjct: 397 HGESAY 402
>gnl|CDD|236156 PRK08125, PRK08125, bifunctional UDP-glucuronic acid
decarboxylase/UDP-4-amino-4-deoxy-L-arabinose
formyltransferase; Validated.
Length = 660
Score = 30.7 bits (70), Expect = 0.12
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 31/68 (45%)
Query: 37 GFIGSQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDE--EITGLDISSDSGYAYVCS 94
GFIG+ +TE R+L D+ E+ GLDI SD+ +
Sbjct: 325 GFIGNHLTE-------------------------RLLRDDNYEVYGLDIGSDA----ISR 355
Query: 95 SKNHPRFY 102
HPRF+
Sbjct: 356 FLGHPRFH 363
>gnl|CDD|233828 TIGR02348, GroEL, chaperonin GroL. This family consists of GroEL,
the larger subunit of the GroEL/GroES cytosolic
chaperonin. It is found in bacteria, organelles derived
from bacteria, and occasionally in the Archaea. The
bacterial GroEL/GroES group I chaperonin is replaced a
group II chaperonin, usually called the thermosome in
the Archaeota and CCT (chaperone-containing TCP) in the
Eukaryota. GroEL, thermosome subunits, and CCT subunits
all fall under the scope of pfam00118 [Protein fate,
Protein folding and stabilization].
Length = 524
Score = 27.3 bits (61), Expect = 2.1
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 14/64 (21%)
Query: 20 KLNFDDPLEATRLHGGWGFIGSQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEIT 79
KL +D L ATR + V E V G V L A L+ L+ ++E
Sbjct: 391 KLRIEDALNATR---------AAVEEGIVPGGGV-----ALLRAAAALEGLKGDGEDEAI 436
Query: 80 GLDI 83
G+DI
Sbjct: 437 GIDI 440
>gnl|CDD|200495 cd09295, Sema, The Sema domain, a protein interacting module, of
semaphorins and plexins. Both semaphorins and plexins
have a Sema domain on their N-termini. Plexins function
as receptors for the semaphorins. Evolutionarily,
plexins may be the ancestor of semaphorins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems,
and cancer. Semaphorins can be divided into 7 classes.
Vertebrates have members in classes 3-7, whereas classes
1 and 2 are known only in invertebrates. Class 2 and 3
semaphorins are secreted; classes 1 and 4 through 6 are
transmembrane proteins; and class 7 is membrane
associated via glycosylphosphatidylinositol (GPI)
linkage. Plexins are a large family of transmembrane
proteins, which are divided into four types (A-D)
according to sequence similarity. In vertebrates, type A
plexins serve as co-receptors for neuropilins to mediate
the signalling of class 3 semaphorins. Plexins serve as
direct receptors for several other members of the
semaphorin family: class 6 semaphorins signal through
type A plexins and class 4 semaphorins through type B
plexins. This family also includes the MET and RON
receptor tyrosine kinases. The Sema domain is located at
the N-terminus and contains four disulfide bonds formed
by eight conserved cysteine residues. It serves to
recognize and bind receptors.
Length = 392
Score = 26.4 bits (58), Expect = 3.3
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 40 GSQVTELSVIVGWVRETMGPLF-HALHKLKMLRILED-EEITGLDISSDSGYAYVCSS 95
G QV L + +G + + + F + H ++ ++ +D IT LD+S Y YV S
Sbjct: 326 GYQVVFLGLKLGSLGKALAFFFLYKGHIIEEWKVFKDSSRITNLDLSRPPLYLYVGSE 383
>gnl|CDD|236013 PRK07409, PRK07409, threonine synthase; Validated.
Length = 353
Score = 26.3 bits (59), Expect = 3.4
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 10 VLIGLNILAIKLNFDDPLEATR 31
V+ G I+ I NFDD LE R
Sbjct: 122 VMYGAEIIQIDGNFDDALEIVR 143
>gnl|CDD|234573 PRK00013, groEL, chaperonin GroEL; Reviewed.
Length = 542
Score = 26.6 bits (60), Expect = 3.4
Identities = 20/64 (31%), Positives = 27/64 (42%), Gaps = 14/64 (21%)
Query: 20 KLNFDDPLEATRLHGGWGFIGSQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEIT 79
K +D L ATR + V E V G V L A L+ L+ L +E T
Sbjct: 392 KDRVEDALHATR---------AAVEEGIVPGGGV-----ALLRAAPALEALKGLNGDEAT 437
Query: 80 GLDI 83
G++I
Sbjct: 438 GINI 441
>gnl|CDD|200540 cd11279, Sema_RON, The Sema domain, a protein interacting module,
of RON Receptor Tyrosine Kinase. RON receptor tyrosine
kinase is a Macrophage-stimulating protein (MSP)
receptor. Upon binding of MSP, RON is activated via
autophosphorylation within its kinase catalytic domain,
resulting in a wide range of effects, including
proliferation, tubular morphogenesis, angiogenesis,
cellular motility and invasiveness. By interacting with
downstream signaling molecules, it regulates macrophage
migration, phagocytosis, and nitric oxide production.
RON has been implicated in cancers of the breast, colon,
pancreas and ovaries because both splice variants and
receptor overexpression have been identified in these
tumors. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as ligand recognition and
binding model. RON is composed of an alpha-beta
heterodimer. The extracellular alpha chain is disulfide
linked to the beta chain, which contains an
extracellular ligand-binding region with a Sema domain,
a PSI domain and four IPT repeats, a transmembrane
segment, and an intracellular catalytic tyrosine kinase
domain. The Sema domain of RON may be necessary for
receptor dimerization and activation.
Length = 493
Score = 26.7 bits (59), Expect = 3.6
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 78 ITGLDISSDSGYAYVCSSKNHPR 100
I+ L+ + D G CSS N R
Sbjct: 342 ISLLNEAIDEGMEKCCSSSNSDR 364
>gnl|CDD|233933 TIGR02568, LcrE, type III secretion regulator YopN/LcrE/InvE/MxiC.
This protein is found in type III secretion operons and,
in Yersinia is localized to the cell surface and is
involved in the Low-Calicium Response (LCR), possibly by
sensing the calcium concentration. In Salmonella, the
gene is known as InvE and is believed to perform an
essential role in the secretion process and interacts
with the proteins SipBCD and SicA.//Altered name to
reflect regulatory role. Added GO and role IDs. Negative
regulation of type III secretion in Y pestis is mediated
in part by a multiprotein complex that has been proposed
to act as a physical impediment to type III secretion by
blocking the entrance to the secretion apparatus prior
to contact with mammalian cells. This complex is
composed of YopN, its heterodimeric secretion chaperone
SycN-YscB, and TyeA. PMID: 15701523[SS 6/3/05] [Protein
fate, Protein and peptide secretion and trafficking,
Cellular processes, Pathogenesis].
Length = 240
Score = 26.2 bits (58), Expect = 3.7
Identities = 11/51 (21%), Positives = 17/51 (33%), Gaps = 2/51 (3%)
Query: 28 EATRLHGGWGF-IGSQVTELSVIVGWV-RETMGPLFHALHKLKMLRILEDE 76
A R F I + +LS + L L +L+ L D+
Sbjct: 182 GAQRFDIVLDFLIRALAADLSAQGPSTDSAQLQVLMSDLTQLRHLLTALDQ 232
>gnl|CDD|151420 pfam10973, DUF2799, Protein of unknown function (DUF2799). Some
members in this family of proteins are annotated as yfiL
which has no known function.
Length = 89
Score = 25.0 bits (55), Expect = 6.9
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 87 SGYAY--VCSSKNHPRFYADYKR 107
SG +Y VC ++ PRF Y++
Sbjct: 62 SGKSYYGVCPDEDEPRFREAYQK 84
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 25.4 bits (56), Expect = 8.1
Identities = 17/49 (34%), Positives = 19/49 (38%), Gaps = 10/49 (20%)
Query: 40 GSQVTELSVIVGWVRETMGPLF----HALHKLKMLRILEDEEITGLDIS 84
G V EL + W PL+ HAL LK D GLDI
Sbjct: 121 GMSVEELYTKIIW------PLYKKYGHALDALKEALTNPDNVFEGLDIP 163
>gnl|CDD|182630 PRK10666, PRK10666, ammonium transporter; Provisional.
Length = 428
Score = 25.5 bits (56), Expect = 8.8
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 70 LRILEDEEITGLDISSDSGYAY 91
LR+ E++E GLD++S AY
Sbjct: 405 LRVPEEQEREGLDVNSHGENAY 426
>gnl|CDD|187567 cd05257, Arna_like_SDR_e, Arna decarboxylase_like, extended (e)
SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme
involved in the modification of outer membrane protein
lipid A of gram-negative bacteria. It is a bifunctional
enzyme that catalyzes the NAD-dependent decarboxylation
of UDP-glucuronic acid and
N-10-formyltetrahydrofolate-dependent formylation of
UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent
decaboxylating activity is in the C-terminal 360
residues. This subgroup belongs to the extended SDR
family, however the NAD binding motif is not a perfect
match and the upstream Asn of the canonical active site
tetrad is not conserved. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately 100
amino acids. Extended SDRs are a diverse collection of
proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 316
Score = 25.3 bits (56), Expect = 9.2
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 24/68 (35%)
Query: 34 GGWGFIGSQVTELSVIVGWVRETMGPLFHALHKLKMLRILEDEEITGLDISSDSGYAYVC 93
G GFIGS +TE + G E+ LDI + +
Sbjct: 6 GADGFIGSHLTERLLREGH------------------------EVRALDIYNSFNSWGLL 41
Query: 94 SSKNHPRF 101
+ H RF
Sbjct: 42 DNAVHDRF 49
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
0.322 0.141 0.444
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,948,365
Number of extensions: 508684
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 507
Number of HSP's successfully gapped: 26
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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 (21.9 bits)
S2: 53 (24.3 bits)