RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14699
(195 letters)
>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 = 237 bits (607), Expect = 3e-79
Identities = 91/141 (64%), Positives = 111/141 (78%), Gaps = 2/141 (1%)
Query: 1 MKQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQ 60
MK+LH KVNI+PVIAKAD LT E+QR KK++ EI++ I IY PD +SDEDE+ KEQ
Sbjct: 135 MKKLHEKVNIIPVIAKADTLTPDELQRFKKRIRAEIERQNIKIYHFPDEESDEDEE-KEQ 193
Query: 61 VRQLKEAVPFAVCGANTVLEVGGNKVRGRQYPWGVVEVENPEHCDFTKLRTMLV-THMQD 119
QLK ++PFA+ G+NT +E G KVRGR+YPWGVVEVENP HCDF KLR ML+ TH+QD
Sbjct: 194 TEQLKSSIPFAIVGSNTEIENDGKKVRGRKYPWGVVEVENPSHCDFLKLRNMLIRTHLQD 253
Query: 120 LQEVTQEIHYENYRSERLVKG 140
L+EVT E+HYENYRSE+L
Sbjct: 254 LKEVTHELHYENYRSEKLSAL 274
>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 = 230 bits (590), Expect = 1e-76
Identities = 80/141 (56%), Positives = 107/141 (75%), Gaps = 3/141 (2%)
Query: 1 MKQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQ 60
MK+L KVNI+PVIAKAD LT +E+ KK++M++I++N I IY P+ + DE+E E+
Sbjct: 136 MKKLSKKVNIIPVIAKADTLTPEELTEFKKRIMEDIEENNIKIYKFPEDEEDEEE--IEE 193
Query: 61 VRQLKEAVPFAVCGANTVLEVGGNKVRGRQYPWGVVEVENPEHCDFTKLRTMLV-THMQD 119
++LK +PFA+ G+N +EV G KVRGR+YPWGVVEVEN EHCDF KLR +L+ TH+QD
Sbjct: 194 NKKLKSLIPFAIVGSNEEVEVNGKKVRGRKYPWGVVEVENEEHCDFVKLRNLLIRTHLQD 253
Query: 120 LQEVTQEIHYENYRSERLVKG 140
L+E T +HYENYRSE+L
Sbjct: 254 LKETTHNVHYENYRSEKLEAL 274
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 179 bits (456), Expect = 2e-55
Identities = 73/201 (36%), Positives = 119/201 (59%), Gaps = 16/201 (7%)
Query: 1 MKQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQ 60
MK+L +VN++PVIAKAD LT E+ K+++ ++++Q I ++ D + DEDE E+
Sbjct: 156 MKRLSKRVNLIPVIAKADTLTDDELAEFKERIREDLEQYNIPVFDPYDPEDDEDESL-EE 214
Query: 61 VRQLKEAVPFAVCGANTVLEVGGNKVRGRQYPWGVVEVENPEHCDFTKLRTMLV-THMQD 119
+ L+ +PFA+ G+NT +E GG +VRGR+YPWGVVE+++ EH DF KLR +L+ TH+Q+
Sbjct: 215 NQDLRSLIPFAIIGSNTEIENGGEQVRGRKYPWGVVEIDDEEHSDFKKLRNLLIRTHLQE 274
Query: 120 LQEVTQEIHYENYRSERLVKGVP------------VPKRTVSLTEDSKPTANNLEKDRIL 167
L+E T+ + YENYR+E+L + ++ R L
Sbjct: 275 LKETTENLLYENYRTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEKIREKEKR-L 333
Query: 168 QEKEAEL-QRMQEMIAKMQAQ 187
+E E L + +E+ +K++
Sbjct: 334 EELEQNLIEERKELNSKLEEI 354
>gnl|CDD|237428 PRK13564, PRK13564, anthranilate synthase component I; Provisional.
Length = 520
Score = 31.7 bits (73), Expect = 0.19
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 10/54 (18%)
Query: 24 EIQRLKKKVMDEIKQN---GITIYPLPDCDSDE------DEDYKEQVRQLKEAV 68
E QRL + + ++KQ P+ E DE++ VR+LKE +
Sbjct: 204 EKQRLAAR-LAQLKQQLTQPAPPLPVTSVPDMEVSVNISDEEFCAVVRKLKEHI 256
>gnl|CDD|187755 cd09294, SmpB, Small protein B (SmpB) is a component of the
trans-translation system in prokaryotes for releasing
stalled ribosome from damaged messenger RNAs. Small
protein B (SmpB) is a component of the
trans-translation system in prokaryotes for releasing
stalled ribosome from damaged messenger RNAs and
targeting incompletely synthesized protein fragments
for degradation. Trans-translation system is composed
of a ribonucleoprotein complex of tmRNA, a specialized
RNA with properties of both tRNA and mRNA, and SmpB.
SmpB is highly conserved and present in all bacterial
kingdoms and is also found in some chloroplasts and
mitochondria. This is suggesting Trans-translation
arose early in bacterial evolution and its mechanism is
a quality control for protein synthesis in spite of
challenges such as transcription errors, mRNA damage,
and translation frame shifting. SmpB deletion results
in phage development defects phenotype and absence of
tagged proteins translated from defective mRNAs.
Length = 116
Score = 28.9 bits (66), Expect = 0.68
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 20 LTRKEIQRLKKKVMDEIKQNGITIYPL 46
L +KEI +L KV +Q G+TI PL
Sbjct: 75 LHKKEIDKLIGKV----EQKGLTIVPL 97
>gnl|CDD|232819 TIGR00087, surE, 5'/3'-nucleotidase SurE. This protein family
originally was named SurE because of its role in
stationary phase survivalin Escherichia coli. In E.
coli, surE is next to pcm, an L-isoaspartyl protein
repair methyltransferase that is also required for
stationary phase survival. Recent work (PMID:15489502)
shows that viewing SurE as an acid phosphatase (3.1.3.2)
is not accurate. Rather, SurE in E. coli, Thermotoga
maritima, and Pyrobaculum aerophilum acts strictly on
nucleoside 5'- and 3'-monophosphates. E. coli SurE is
Recommended cutoffs are 15 for homology, 40 for probable
orthology, and 200 for orthology with full-length
homology [Cellular processes, Adaptations to atypical
conditions].
Length = 244
Score = 29.6 bits (67), Expect = 0.74
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 8/57 (14%)
Query: 8 VNI--VPVIA-KADCLTRKEIQRLKKKVMDEIKQNGITIY-----PLPDCDSDEDED 56
VN+ VP I +TR + V + G + Y P CD + D
Sbjct: 169 VNVPLVPSIQNTGIRITRLGRRMYATSVEERTDPRGRSYYWIGGDPGARCDREPGTD 225
>gnl|CDD|235455 PRK05422, smpB, SsrA-binding protein; Validated.
Length = 148
Score = 29.2 bits (67), Expect = 0.84
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 20 LTRKEIQRLKKKVMDEIKQNGITIYPL 46
L +KEI +L KV ++ G T+ PL
Sbjct: 83 LHKKEIDKLIGKV----ERKGYTLVPL 105
>gnl|CDD|225950 COG3416, COG3416, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 233
Score = 29.5 bits (66), Expect = 0.94
Identities = 9/41 (21%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 155 KPTANNLEKDRILQEKEAELQRMQEMIAKMQAQMQQAQSGQ 195
+P A R+L + E L++ I +++ ++ Q+G+
Sbjct: 39 QPDAAYYLAQRVLIQ-EQALKKASTQIKELEKRIAILQAGE 78
>gnl|CDD|237001 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase
subunit E2; Reviewed.
Length = 411
Score = 29.8 bits (68), Expect = 0.99
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 21/62 (33%)
Query: 3 QLHNKVNI-----------VPVIAKADCLT----RKEIQRLKKKV------MDEIKQNGI 41
L VNI VPVI AD + +EI+ L +K +E++
Sbjct: 269 VLKKYVNIGIAVATDGGLIVPVIRDADKKSLFELAREIKDLAEKAREGKLKPEELQGGTF 328
Query: 42 TI 43
TI
Sbjct: 329 TI 330
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 28.6 bits (65), Expect = 1.5
Identities = 9/37 (24%), Positives = 20/37 (54%)
Query: 4 LHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNG 40
+ ++ V+ KAD L + E+ + KK+ +K++
Sbjct: 126 RERGIPVLIVLTKADKLKKSELNKQLKKIKKALKKDA 162
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 29.1 bits (65), Expect = 1.5
Identities = 14/77 (18%), Positives = 30/77 (38%), Gaps = 7/77 (9%)
Query: 2 KQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQV 61
++ +V ++ A R E +K+ GI + + D D ++ ++ +
Sbjct: 121 EKGWKRVALIYGDDGAYGRERLEG------FKAALKKAGIEVVAIEYGDLDTEKGFQALL 174
Query: 62 RQLKEAVPF-AVCGANT 77
+ LK A A+ N
Sbjct: 175 QLLKAAPKPDAIFACND 191
>gnl|CDD|178322 PLN02720, PLN02720, complex II.
Length = 140
Score = 28.2 bits (63), Expect = 1.7
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 7/38 (18%)
Query: 45 PLP---DCDSDE----DEDYKEQVRQLKEAVPFAVCGA 75
PLP D D DE D Y Q++ ++EA FAV GA
Sbjct: 36 PLPPWSDSDVDEFIASDPVYGPQLKTMREAATFAVTGA 73
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 29.0 bits (65), Expect = 1.8
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 47 PDCDSDEDEDYKEQVRQLKEAVPFAVCGANTVLEVGGNKVRGRQYPWGVVEVENPEHCDF 106
ED+ KE+V ++ + T+LE RG +P V V EH F
Sbjct: 334 IASVHSEDQHRKEKVEAFRDGK-ITLLITTTILE------RGVTFPNVDVFVLGAEHRVF 386
Query: 107 TK 108
T+
Sbjct: 387 TE 388
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 28.2 bits (64), Expect = 2.0
Identities = 10/42 (23%), Positives = 19/42 (45%)
Query: 4 LHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYP 45
+ ++ V+ KAD L + E ++ KKV +K +
Sbjct: 132 KEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVIL 173
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 28.3 bits (64), Expect = 2.4
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 11 VPVIAKADCLTRKEIQRLKKKVMDE 35
+PV+ KAD L+ +E++R+ K + D
Sbjct: 166 IPVLNKADLLSEEELERILKWLEDP 190
>gnl|CDD|202190 pfam02288, Dehydratase_MU, Dehydratase medium subunit. This family
contains the medium subunit of the trimeric diol
dehydratases and glycerol dehydratases. These enzymes
are produced by some enterobacteria in response to
growth substances.
Length = 112
Score = 27.5 bits (62), Expect = 2.5
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 12/44 (27%)
Query: 113 LVTHMQDLQE------VTQEIHY-ENYRS-----ERLVKGVPVP 144
+V H +DL Q + E R+ RLVKG P P
Sbjct: 69 VVIHQKDLPPLSPLELFPQPLLDLETLRAIGANAARLVKGEPFP 112
>gnl|CDD|178142 PLN02527, PLN02527, aspartate carbamoyltransferase.
Length = 306
Score = 28.2 bits (63), Expect = 2.5
Identities = 21/75 (28%), Positives = 31/75 (41%), Gaps = 25/75 (33%)
Query: 13 VIAKADCLTRKEIQR------------------LKKKVMDEIKQNGITIYPLP------- 47
V +K D L + IQR + KKVMD + ++ + ++PLP
Sbjct: 215 VASKCDVLYQTRIQRERFGERIDLYEAARGKYIVDKKVMDVLPKHAVVMHPLPRLDEITT 274
Query: 48 DCDSDEDEDYKEQVR 62
D DSD Y Q +
Sbjct: 275 DVDSDPRAAYFRQAK 289
>gnl|CDD|221016 pfam11180, DUF2968, Protein of unknown function (DUF2968). This
family of proteins has no known function.
Length = 192
Score = 28.2 bits (63), Expect = 2.5
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 158 ANNLEKDRILQEKEAELQRMQEMIAKMQAQMQQAQSGQ 195
A + +R + EA +R+Q + QAQ QQ + Q
Sbjct: 112 AQKAQLERQIAASEARAERLQADLQLAQAQEQQVAARQ 149
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 27.7 bits (62), Expect = 3.1
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 165 RILQEKEAELQRMQEMIAKMQAQMQQAQSGQ 195
IL ++ A L++ I +++AQ Q QS
Sbjct: 49 TILVQEAA-LKQANARIEELEAQAQHPQSQS 78
>gnl|CDD|225711 COG3170, FimV, Tfp pilus assembly protein FimV [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 755
Score = 28.0 bits (62), Expect = 3.6
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 6/87 (6%)
Query: 109 LRTMLVTHMQDL--QEVTQEIHYENYRSERLVKGVPVPKRTVSLTEDSKPTANNLEKDRI 166
+L Q+ + Q + S+ G PV K + + +K A E
Sbjct: 248 AAQILRESPQEALAEVKAQTAAFAGEPSKADRVGKPVAK---APAKVAKERALA-ELPAR 303
Query: 167 LQEKEAELQRMQEMIAKMQAQMQQAQS 193
+ E +A+L + Q +A+ A + AQ+
Sbjct: 304 VAELQAQLNKAQHELAQKAAPLAAAQA 330
>gnl|CDD|234465 TIGR04092, LTA_DltD, D-alanyl-lipoteichoic acid biosynthesis
protein DltD. Members of this protein family are DltD,
part of the DltABCD system widely distributed in the
Firmicutes for D-alanylation of lipoteichoic acids. The
most common form of LTA, as in Staphylococcus aureus,
has a backbone of polyglycerolphosphate.
Length = 383
Score = 28.0 bits (63), Expect = 3.7
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 1 MKQLHNKVNIV--PVIAK-ADC--LTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDE 55
K+L V V PV K D L+++ Q+ KK+ ++K G I L D E E
Sbjct: 301 FKELGIDVLFVIPPVNGKWYDYTGLSKEMRQQYYKKIKYQLKSQGFNIADLSD---KEYE 357
Query: 56 DY 57
Y
Sbjct: 358 PY 359
>gnl|CDD|184826 PRK14799, thrS, threonyl-tRNA synthetase; Provisional.
Length = 545
Score = 27.9 bits (62), Expect = 3.8
Identities = 18/87 (20%), Positives = 34/87 (39%), Gaps = 8/87 (9%)
Query: 23 KEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQVRQLKEAVPFAVCGANTVLEVG 82
E+ +KV++++++ I + D + K + VP+ + G
Sbjct: 448 DEVNEYAEKVLNDMRKRRIRA----EIDYAGETLSKRIKNAYDQGVPYILIVGKKEASEG 503
Query: 83 GNKVRGRQYPWGVVEVENPEHCDFTKL 109
VR R G +EV N + F +L
Sbjct: 504 TVTVRAR----GNIEVRNVKFEKFLEL 526
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 27.2 bits (60), Expect = 4.5
Identities = 11/82 (13%), Positives = 22/82 (26%), Gaps = 7/82 (8%)
Query: 11 VPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQVRQLKEAVP- 69
+P+ + + + G + + E +R+L+EAVP
Sbjct: 58 LPLGVQLAINDAAAAVDIAAAA---ARAAGADGVEIHGAVGYLAREDLELIRELREAVPD 114
Query: 70 ---FAVCGANTVLEVGGNKVRG 88
L + G
Sbjct: 115 VKVVVKLSPTGELAAAAAEEAG 136
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 27.8 bits (62), Expect = 4.5
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 20 LTRKEIQRLKKKVM-DEIKQNGITIYP--LPDCDSDEDEDYKEQVRQLKEAV 68
KEI+ K V +EI++N + P + +ED D E +++L E
Sbjct: 416 REFKEIEGFSKSVSLEEIRENDYNLNPGRYVAEEEEEDIDLDELLQELSEID 467
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 26.4 bits (59), Expect = 5.1
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 162 EKDRILQEKEAELQRMQEMIAKMQAQMQQAQ 192
E + I + K ELQ+ + + Q + ++AQ
Sbjct: 2 ELEEIRRRKLEELQKQAQEQQQAQEEQEEAQ 32
>gnl|CDD|179580 PRK03449, PRK03449, putative inner membrane protein translocase
component YidC; Provisional.
Length = 304
Score = 27.3 bits (61), Expect = 5.5
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 155 KPTANNLEKDRILQEKEAELQRMQEMIA----KMQAQMQQAQS 193
KP + R +QE + +++ +Q+ KM +MQ+ Q
Sbjct: 49 KPFVRQIRTTRKMQELQPQIKALQKKYGNDRQKMALEMQKLQK 91
>gnl|CDD|218397 pfam05044, Prox1, Homeobox prospero-like protein (PROX1). The
homeobox gene Prox1 is expressed in a subpopulation of
endothelial cells that, after budding from veins, gives
rise to the mammalian lymphatic system. Prox1 has been
found to be an early specific marker for the developing
liver and pancreas in the mammalian foregut endoderm.
This family contains an atypical homeobox domain.
Length = 908
Score = 27.3 bits (60), Expect = 5.7
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 130 ENYRSERLVKGVPVPKRTVSLTEDSKPTANNLEKDRILQEKE------AELQRMQEMIAK 183
E+Y + KR L + + + + L R Q++E +L+ MQ+ + +
Sbjct: 258 ESYGAAAAGLNSRENKRKQMLPQQQQQSFDQLVSPRKEQKREERRQLKQQLRDMQKQLRQ 317
Query: 184 MQAQMQQAQ 192
+Q + Q
Sbjct: 318 LQQKYVQIY 326
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 27.4 bits (62), Expect = 5.8
Identities = 17/81 (20%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 7 KVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQVRQLKE 66
+ P+ A LT + + L V + +++ +PL + + +E+ YK + +E
Sbjct: 301 GPKVFPISA----LTGQGLDELLYAVAELLEE--TPEFPLEEEEVEEEVYYKFE----EE 350
Query: 67 AVPFAVCG-ANTVLEVGGNKV 86
F + + V V G K+
Sbjct: 351 EKDFTITRDEDGVFVVSGEKI 371
>gnl|CDD|129194 TIGR00086, smpB, SsrA-binding protein. This model describes the
SsrA-binding protein, also called tmRNA binding protein,
small protein B, and SmpB. The small, stable RNA SsrA
(also called tmRNA or 10Sa RNA) recognizes stalled
ribosomes such as occur during translation from message
that lacks a stop codon. It becomes charged with Ala
like a tRNA, then acts as mRNA to resume translation
started with the defective mRNA. The short C-terminal
peptide tag added by the SsrA system marks the
abortively translated protein for degradation. SmpB
binds SsrA after its aminoacylation but before the
coupling of the Ala to the nascent polypeptide chain and
is an essential part of the SsrA peptide tagging system.
SmpB has been associated with the survival of bacterial
pathogens in conditions of stress. It is universal in
the first 100 sequenced bacterial genomes [Protein
synthesis, Other].
Length = 144
Score = 26.4 bits (59), Expect = 6.2
Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 4/27 (14%)
Query: 20 LTRKEIQRLKKKVMDEIKQNGITIYPL 46
L +KEI +L+ K +K+ G+T+ PL
Sbjct: 79 LHKKEIDKLQGK----VKEKGLTLVPL 101
>gnl|CDD|223763 COG0691, SmpB, tmRNA-binding protein [Posttranslational
modification, protein turnover, chaperones].
Length = 153
Score = 26.4 bits (59), Expect = 7.2
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 20 LTRKEIQRLKKKVMDEIKQNGITIYPL 46
L ++EI +L KV +Q G T+ PL
Sbjct: 85 LHKREIDKLIGKV----EQEGYTLVPL 107
>gnl|CDD|184470 PRK14037, PRK14037, citrate synthase; Provisional.
Length = 377
Score = 27.0 bits (60), Expect = 7.3
Identities = 14/35 (40%), Positives = 23/35 (65%), Gaps = 4/35 (11%)
Query: 21 TRKEIQRLKKKVMD--EIKQNGI-TIYPLP-DCDS 51
T+KE+ LK+K+ + E+ Q I +IY +P D D+
Sbjct: 58 TKKELNDLKEKLNEEYEVPQEVIDSIYLMPRDSDA 92
>gnl|CDD|191367 pfam05761, 5_nucleotid, 5' nucleotidase family. This family of
eukaryotic proteins includes 5' nucleotidase enzymes,
such as purine 5'-nucleotidase EC:3.1.3.5.
Length = 448
Score = 26.8 bits (60), Expect = 7.4
Identities = 5/28 (17%), Positives = 12/28 (42%)
Query: 168 QEKEAELQRMQEMIAKMQAQMQQAQSGQ 195
Q + ELQR+ ++ ++ +
Sbjct: 337 QYRFEELQRLDILLERLYDHLDVHAELS 364
>gnl|CDD|225075 COG2164, COG2164, Uncharacterized conserved protein [Function
unknown].
Length = 126
Score = 26.1 bits (57), Expect = 7.4
Identities = 7/22 (31%), Positives = 14/22 (63%)
Query: 49 CDSDEDEDYKEQVRQLKEAVPF 70
C + DE+ E VR++ +++P
Sbjct: 15 CTGELDEENPESVRRIYDSLPI 36
>gnl|CDD|205181 pfam12997, DUF3881, Domain of unknown function, E. rectale Gene
description (DUF3881). Based on Eubacterium rectale
gene EUBREC_3695. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 283
Score = 26.7 bits (60), Expect = 7.7
Identities = 38/190 (20%), Positives = 72/190 (37%), Gaps = 56/190 (29%)
Query: 21 TRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQVRQLKEAVPFAVCGANTVLE 80
++KE+ + K+V + + + DE D+ E ++ + + VCG E
Sbjct: 11 SKKELDEILKEVEESPTRKKVVSD-------DEGTDFCELSKEFGDGMGITVCG-----E 58
Query: 81 VGGNKVRGRQY--PW----GV-----VEVENPEH---------CDFTKLRTMLVTHMQDL 120
+ + R+Y P+ G+ V +E H CD K+ L+ ++Q++
Sbjct: 59 MDEDGTFSREYYFPYFRGSGITTYEEVSIE--RHADKESYAGICDDYKIGISLIFYLQNV 116
Query: 121 QEVTQEIHYENYRSERLVKGVPVPKRTVSLTEDSK------PTANNLEKDR--ILQEKEA 172
E Y E+ + + ++V+L+ S P KD E+E
Sbjct: 117 IE---------YLKEKQLGKDSIKAKSVTLSGLSVSGKILLPV----NKDEEQERNEREE 163
Query: 173 ELQRMQEMIA 182
R +IA
Sbjct: 164 SKNRNN-LIA 172
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 27.1 bits (61), Expect = 7.9
Identities = 14/75 (18%), Positives = 33/75 (44%), Gaps = 17/75 (22%)
Query: 22 RKEIQRLKKKVMDEIKQ---------NGITIYPLPDCDSDEDEDYKEQVRQLKEAVPFAV 72
+KEI++L+K++ + + G+ + D+DEDE ++ +L +
Sbjct: 774 KKEIEKLRKELAELLASELLSKAEEVGGVKVVVEEV-DADEDE-LRKIANELAKE----- 826
Query: 73 CGANTVLEVGGNKVR 87
G ++ +G +
Sbjct: 827 -GKVALVVLGNGGGQ 840
>gnl|CDD|239273 cd02975, PfPDO_like_N, Pyrococcus furiosus protein disulfide
oxidoreductase (PfPDO)-like family, N-terminal TRX-fold
subdomain; composed of proteins with similarity to
PfPDO, a redox active thermostable protein believed to
be the archaeal counterpart of bacterial DsbA and
eukaryotic protein disulfide isomerase (PDI), which are
both involved in oxidative protein folding. PfPDO
contains two redox active CXXC motifs in two contiguous
TRX-fold subdomains. The active site in the N-terminal
TRX-fold subdomain is required for isomerase but not
for reductase activity of PfPDO. The exclusive presence
of PfPDO-like proteins in extremophiles may suggest
that they have a special role in adaptation to extreme
conditions.
Length = 113
Score = 25.8 bits (57), Expect = 8.2
Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 2 KQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYK 58
K++ N V++V +K C + ++L +++ + + + IY D D ++ E Y
Sbjct: 17 KEMKNPVDLVVFSSKEGCQYCEVTKQLLEELSELSDKLKLEIYD-FDEDKEKAEKYG 72
>gnl|CDD|235652 PRK05950, sdhB, succinate dehydrogenase iron-sulfur subunit;
Reviewed.
Length = 232
Score = 26.7 bits (60), Expect = 8.3
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 30 KKVMDEIKQNGITIYPLP 47
+ ++K+ I I PLP
Sbjct: 73 ITPISDLKKGKIVIRPLP 90
>gnl|CDD|133394 cd04766, HTH_HspR, Helix-Turn-Helix DNA binding domain of the HspR
transcription regulator. Helix-turn-helix (HTH)
transcription regulator HspR, N-terminal domain. Heat
shock protein regulators (HspR) have been shown to
regulate expression of specific regulons in response to
high temperature or high osmolarity in Streptomyces and
Helicobacter, respectively. These proteins share the
N-terminal DNA binding domain with other transcription
regulators of the MerR superfamily that promote
transcription by reconfiguring the spacer between the
-35 and -10 promoter elements. A typical MerR regulator
is comprised of distinct domains that harbor the
regulatory (effector-binding) site and the active
(DNA-binding) site. Their conserved N-terminal domains
contain predicted winged HTH motifs that mediate DNA
binding, while the dissimilar C-terminal domains bind
specific coactivator molecules.
Length = 91
Score = 25.3 bits (56), Expect = 8.8
Identities = 7/32 (21%), Positives = 19/32 (59%)
Query: 160 NLEKDRILQEKEAELQRMQEMIAKMQAQMQQA 191
NL + + E E EL ++ + +++A++++
Sbjct: 60 NLAGVKRILELEEELAELRAELDELRARLRRE 91
>gnl|CDD|224431 COG1514, LigT, 2'-5' RNA ligase [Translation, ribosomal structure
and biogenesis].
Length = 180
Score = 26.1 bits (58), Expect = 9.0
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 41 ITIYPLPDCDSDEDEDYKEQVRQLKEAVPF 70
IT+ L + D D+ ++ E + ++ PF
Sbjct: 40 ITLKFLGEVDEDKADELIEALARIAAPEPF 69
>gnl|CDD|148137 pfam06339, Ectoine_synth, Ectoine synthase. This family consists
of several bacterial ectoine synthase proteins. The
ectABC genes encode the diaminobutyric acid
acetyltransferase (EctA), the diaminobutyric acid
aminotransferase (EctB), and the ectoine synthase
(EctC). Together these proteins constitute the ectoine
biosynthetic pathway.
Length = 127
Score = 26.0 bits (58), Expect = 9.1
Identities = 8/27 (29%), Positives = 18/27 (66%)
Query: 112 MLVTHMQDLQEVTQEIHYENYRSERLV 138
M+V ++D++ +++ EN+ S RL+
Sbjct: 1 MIVRTLEDIEGTDRDVKAENWESRRLL 27
>gnl|CDD|217555 pfam03433, EspA, EspA-like secreted protein. EspA is the
prototypical member of this family. EspA, together with
EspB, EspD and Tir are exported by a type III secretion
system. These proteins are essential for attaching and
effacing lesion formation. EspA is a structural protein
and a major component of a large, transiently expressed,
filamentous surface organelle which forms a direct link
between the bacterium and the host cell.
Length = 188
Score = 26.3 bits (58), Expect = 9.5
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 8/59 (13%)
Query: 2 KQLHNKVNIVPVIAKADCLTRKEIQRLKKKVMDEIKQNGITIYPLPDCDSDEDEDYKEQ 60
+++ N+V+ VIAK K+ +L + V+ +K NGI + D DY ++
Sbjct: 75 QEMANRVD--AVIAKVAKSDDKKKVKLPQDVIKYMKDNGILV------DGKSILDYLDK 125
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.130 0.368
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,773,509
Number of extensions: 909538
Number of successful extensions: 1671
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1633
Number of HSP's successfully gapped: 138
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
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: 42 (22.0 bits)
S2: 56 (25.2 bits)