RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8482
(122 letters)
>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 = 47.5 bits (114), Expect = 2e-07
Identities = 15/30 (50%), Positives = 24/30 (80%)
Query: 1 MLIRTNMEDMREKTHCRHYELYRKKRLEEV 30
+LIRT+++D++E TH HYE YR ++LE +
Sbjct: 245 LLIRTHLQDLKETTHNVHYENYRSEKLEAL 274
Score = 41.8 bits (99), Expect = 2e-05
Identities = 16/36 (44%), Positives = 25/36 (69%), Gaps = 4/36 (11%)
Query: 31 RDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEEL 66
R++L RT+++D++E TH HYE YR ++LE L
Sbjct: 243 RNLLI----RTHLQDLKETTHNVHYENYRSEKLEAL 274
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and chromosome
partitioning / Cytoskeleton].
Length = 373
Score = 41.9 bits (99), Expect = 2e-05
Identities = 32/101 (31%), Positives = 53/101 (52%), Gaps = 9/101 (8%)
Query: 1 MLIRTNMEDMREKTHCRHYELYRKKRLEEVRD----MLKHRHNRTNMEDMRE-KTHCRHY 55
+LIRT++++++E T YE YR ++L +++ LK H E+ RE K
Sbjct: 266 LLIRTHLQELKETTENLLYENYRTEKLSGLKNSGEPSLKEIHEARLNEEERELKKKFTEK 325
Query: 56 ELYRKKRLEE----LHAKFDKLKKDHADEKKRLEDARKKLE 92
++KRLEE L + +L + +K+LED K+LE
Sbjct: 326 IREKEKRLEELEQNLIEERKELNSKLEEIQKKLEDLEKRLE 366
>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 = 39.6 bits (93), Expect = 1e-04
Identities = 15/29 (51%), Positives = 22/29 (75%)
Query: 1 MLIRTNMEDMREKTHCRHYELYRKKRLEE 29
MLIRT+++D++E TH HYE YR ++L
Sbjct: 245 MLIRTHLQDLKEVTHELHYENYRSEKLSA 273
Score = 36.1 bits (84), Expect = 0.002
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 40 RTNMEDMREKTHCRHYELYRKKRLEELHAKFDK 72
RT+++D++E TH HYE YR ++L L K +
Sbjct: 248 RTHLQDLKEVTHELHYENYRSEKLSALGRKAEN 280
>gnl|CDD|222812 PHA00727, PHA00727, hypothetical protein.
Length = 278
Score = 32.1 bits (73), Expect = 0.041
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 20 ELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKFDKLKKDHAD 79
EL + + LEE LK ++ + KT R Y++Y K+ E +F++LK + +
Sbjct: 13 ELRKAQSLEE----LKQKYEEAQKQIADGKTLKRLYKVYEKREFELKKQQFEQLKAELSK 68
Query: 80 EKKRLEDAR 88
+KK+ + +
Sbjct: 69 KKKKFKKEK 77
>gnl|CDD|217933 pfam04156, IncA, IncA protein. Chlamydia trachomatis is an
obligate intracellular bacterium that develops within a
parasitophorous vacuole termed an inclusion. The
inclusion is non-fusogenic with lysosomes but intercepts
lipids from a host cell exocytic pathway. Initiation of
chlamydial development is concurrent with modification
of the inclusion membrane by a set of C.
trachomatis-encoded proteins collectively designated
Incs. One of these Incs, IncA, is functionally
associated with the homotypic fusion of inclusions. This
family probably includes members of the wider Inc family
rather than just IncA.
Length = 186
Score = 30.9 bits (70), Expect = 0.10
Identities = 10/46 (21%), Positives = 25/46 (54%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQM 105
K++L EL + + L++ A+ + LED ++ L+ ++++
Sbjct: 85 KQQLSELQEELEDLEERIAELESELEDLKEDLQLLRELLKSLEERL 130
>gnl|CDD|220533 pfam10034, Dpy19, Q-cell neuroblast polarisation. Dyp-19, formerly
known as DUF2211, is a transmembrane domain family that
is required to orient the neuroblast cells, QR and QL
accurately on the anterior-posterior axis: QL and QR are
born in the same anterior-posterior position, but
polarise and migrate left-right asymmetrically, QL
migrating towards the posterior and QR migrating towards
the anterior. It is also required, with unc-40, to
express mab-5 correctly in the Q cell descendants. The
Dpy-19 protein derives from the C. elegans DUMPY mutant.
Length = 637
Score = 30.8 bits (70), Expect = 0.15
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 26 RLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKFDKLKKDH 77
+L R ++ H H +RE+T + Y +Y +K EE++ D LK ++
Sbjct: 528 KLTTGRPIVNHPH--YEDVGLRERTK-KVYSIYSRKPAEEVYRTLDSLKVNY 576
>gnl|CDD|222242 pfam13584, BatD, Oxygen tolerance. This family of proteins carries
up to three membrane spanning regions and is involved in
tolerance to oxygen in in Bacteroides spp.
Length = 488
Score = 29.9 bits (68), Expect = 0.28
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 57 LYRKKRLEELHAKFDKLKKDHADEKKRLEDARKKLEED 94
LYRK+R ++ KK + KKRL++A+K L +
Sbjct: 448 LYRKRRARNADVAGNRTKKANKLAKKRLKEAKKALAGN 485
>gnl|CDD|163700 cd08069, MPN_RPN11_CSN5, Mov34/MPN/PAD-1 family: proteasomal
regulatory protein Rpn11 and signalosome complex subunit
CSN5. This family contains proteasomal regulatory
protein Rpn11 (26S proteasome regulatory subunit rpn11;
PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the
19S-proteasome; regulatory particle number 11) and
signalosomal CSN5 (COP9 signalosome complex subunit 5;
COP9 complex homolog subunit 5; c-Jun activation
domain-binding protein-1; CSN5/JAB1; JAB1). COP9
signalosome (CSN) and the proteasome lid are paralogous
complexes and their respective subunits CSN5 and Rpn11
are most closely related between the two complexes, both
containing the conserved JAMM (JAB1/MPN/Mov34
metalloenzyme) motif involved in zinc ion coordination
and providing the active site for isopeptidase activity.
Rpn11 is responsible for substrate deubiquitination
during proteasomal degradation. It is essential for
maintaining a correct cell cycle and normal
mitochondrial morphology and physiology; mutations in
Rpn11 cause cell cycle and mitochondrial defects,
temperature sensitivity and sensitivity to DNA damaging
reagents such as UV. It has been shown that the
C-terminal region of Rpn11 is involved in the regulation
of the mitochondrial fission and tubulation processes.
CSN5, one of the eight subunits of CSN, is critical for
nuclear export and the degradation of several tumor
suppressor proteins, including p53, p27, and Smad4. Its
MPN+ domain is critical for the physical interaction of
RUNX3 and Jab1. It has been suggested that the direct
interaction of CSN5/JAB1 with p27 provides p27 with a
leucine-rich nuclear export signal (NES), which is
required for binding to chromosomal region maintenance 1
(CRM1), and facilitates nuclear export. The
over-expression of CSN5/JAB1 also has been implicated in
cancer initiation and progression, including cancer of
the lung, pancreas, mouth, thyroid, and breast,
suggesting that the oncogenic activity of CSN5 is
associated with the down-regulation of RUNX3.
Length = 268
Score = 29.9 bits (68), Expect = 0.28
Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 9/90 (10%)
Query: 15 HCRH-YEL---YRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKF 70
H + Y L Y K L+ R +L + N+ + + + Y K++ +L
Sbjct: 175 HNKQYYSLPIEYFKSSLD--RKLLLNLWNKYWVNTLSLSPLLENSNEYTIKQILDLA--- 229
Query: 71 DKLKKDHADEKKRLEDARKKLEEDLLEFNR 100
+KL+K E++ + L+ R
Sbjct: 230 EKLEKAEQQEERLTGEELDIANVGKLDKAR 259
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 29.5 bits (67), Expect = 0.28
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQMA 106
+ L+ A++ K K + E K LE K+ E + + + A
Sbjct: 69 RAELQAKIARYKKEKARYRSEAKELEAKAKEAEAESDHALHQHHRFA 115
Score = 27.2 bits (61), Expect = 1.8
Identities = 8/45 (17%), Positives = 12/45 (26%), Gaps = 1/45 (2%)
Query: 63 LEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFN-RRKQQMA 106
A+ + EK R K+LE E +
Sbjct: 65 AAAPRAELQAKIARYKKEKARYRSEAKELEAKAKEAEAESDHALH 109
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 29.3 bits (65), Expect = 0.53
Identities = 27/98 (27%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 4 RTNMEDMREKTHCRHYELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRL 63
R +E ++ KKR+E + + R R ME + E ++RL
Sbjct: 437 RARIEKENAHRKALEMKILEKKRIERLEREERERLERERMERIER-------ERLERERL 489
Query: 64 EELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRR 101
E + D+L++D D +R R LE D LE RR
Sbjct: 490 ERERLERDRLERDRLDRLERERVDR--LERDRLEKARR 525
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 28.9 bits (65), Expect = 0.62
Identities = 15/59 (25%), Positives = 27/59 (45%), Gaps = 11/59 (18%)
Query: 64 EELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQM-----------ATMSGS 111
+ L + L+K +K+ LE K+ + L + NR++ + AT+SGS
Sbjct: 70 DALANQLTALQKAQESQKQELEGILKQQAKALDQANRQQAALAKQLDELQQKVATISGS 128
>gnl|CDD|163506 TIGR03794, NHLM_micro_HlyD, NHLM bacteriocin system secretion
protein. Members of this protein family are homologs of
the HlyD membrane fusion protein of type I secretion
systems. Their occurrence in prokaryotic genomes is
associated with the occurrence of a novel class of
microcin (small bacteriocins) with a leader peptide
region related to nitrile hydratase. We designate the
class of bacteriocin as Nitrile Hydratase Leader
Microcin, or NHLM. This family, therefore, is designated
as NHLM bacteriocin system secretion protein. Some but
not all NHLM-class putative microcins belong to the TOMM
(thiazole/oxazole modified microcin) class as assessed
by the presence of the scaffolding protein and/or
cyclodehydratase in the same gene clusters [Transport
and binding proteins, Amino acids, peptides and amines,
Cellular processes, Biosynthesis of natural products].
Length = 421
Score = 27.9 bits (62), Expect = 1.5
Identities = 22/120 (18%), Positives = 44/120 (36%), Gaps = 20/120 (16%)
Query: 10 MREKTHCRHYELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRH--------YELYRKK 61
+RE+ E+ +++ L R + + +R + RE+ Y L K
Sbjct: 144 LREELAALSREVGKQRGLLS-RGLATFKRDRILQQQWREEQEKYDAADKARAIYALQTKA 202
Query: 62 RLEELHAKFDKLK-----------KDHADEKKRLEDARKKLEEDLLEFNRRKQQMATMSG 110
L L K+ + R+++AR ++EE + N + ++ SG
Sbjct: 203 DERNLETVLQSLSQADFQLAGVAEKELETVEARIKEARYEIEELENKLNLNTRIVSQHSG 262
>gnl|CDD|223945 COG1013, PorB, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, beta subunit
[Energy production and conversion].
Length = 294
Score = 27.7 bits (62), Expect = 1.6
Identities = 16/89 (17%), Positives = 31/89 (34%), Gaps = 18/89 (20%)
Query: 36 HRHNRTNM----EDMREKTHCRHYELYR--KKRLEELHAKFDKLKKDHADE--------- 80
N N E+ + ++ LYR + EE K + + E
Sbjct: 206 PTGNGRNTMKTIEEAKLAVETGYWPLYRYEPGKAEEEKGKDIPIGIFYPVEEYLEYEERF 265
Query: 81 ---KKRLEDARKKLEEDLLEFNRRKQQMA 106
K + +KL++D+ E +++A
Sbjct: 266 KHLTKSNPELIQKLQKDVDERWEELKRLA 294
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 27.7 bits (62), Expect = 1.6
Identities = 17/59 (28%), Positives = 35/59 (59%)
Query: 57 LYRKKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQMATMSGSHTLT 115
L R++ +EEL K ++L++ A+ +K L + RK+LEE E + ++++ +S +
Sbjct: 673 LERRREIEELEEKIEELEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISAL 731
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 27.8 bits (62), Expect = 1.7
Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 17 RHYELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKFDKLKKD 76
+ E + L E +++L N+ E RE+ + E ++ E+L A+ +KL
Sbjct: 44 KEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQLDARAEKLD-- 101
Query: 77 HADEKKRLEDARKKLEEDLLEFNRRKQQ 104
+ + +LE+ K L LE ++Q
Sbjct: 102 --NLENQLEEREKALSARELELEELEKQ 127
>gnl|CDD|224486 COG1570, XseA, Exonuclease VII, large subunit [DNA replication,
recombination, and repair].
Length = 440
Score = 27.6 bits (62), Expect = 1.8
Identities = 18/92 (19%), Positives = 34/92 (36%), Gaps = 7/92 (7%)
Query: 11 REKTHCRHYELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKF 70
R R +K+RLE + L+ R + + +++ RL
Sbjct: 276 RLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLD------ELAIRLRRALENQ 329
Query: 71 DKLKKDHAD-EKKRLEDARKKLEEDLLEFNRR 101
LKK + +RL ++ ++ L + RR
Sbjct: 330 LALKKQRLERLTQRLNPQIQRQQQRLQQLERR 361
Score = 26.8 bits (60), Expect = 2.7
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)
Query: 47 REKTHCRHYELYRKKRLEELHAKFDKLKKD--HADEKKRLEDARKKLEEDLLEFNRRKQQ 104
R R +K+RLE L + + +++++RL++ +L L K+Q
Sbjct: 276 RLHRALRRLLDQKKQRLEHLARRLQFRSPERLLSEQQQRLDELAIRLRRALENQLALKKQ 335
>gnl|CDD|236892 PRK11281, PRK11281, hypothetical protein; Provisional.
Length = 1113
Score = 27.6 bits (62), Expect = 2.0
Identities = 11/43 (25%), Positives = 17/43 (39%)
Query: 65 ELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQMAT 107
L K D+ K++ K++L A KL + E K
Sbjct: 70 ALLDKIDRQKEETEQLKQQLAQAPAKLRQAQAELEALKDDNDE 112
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 27.4 bits (62), Expect = 2.1
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKL 91
K + EL + + L ++ + +K LE + KL
Sbjct: 711 KAKPSELPERVEALLEELKELEKELEQLKAKL 742
>gnl|CDD|233228 TIGR00998, 8a0101, efflux pump membrane protein (multidrug
resistance protein A). [Transport and binding proteins,
Other].
Length = 334
Score = 27.5 bits (61), Expect = 2.1
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 61 KRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQ 103
++ ++L +L+ K +LE AR+KL + L+ RR
Sbjct: 94 RQTKQLEITVQQLQAKVESLKIKLEQAREKLLQAELDLRRRVP 136
>gnl|CDD|239285 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd
subfamily; Phd is a cytosolic regulator of G protein
functions. It specifically binds G protein betagamma
(Gbg)-subunits with high affinity, resulting in the
solubilization of Gbg from the plasma membrane. This
impedes the formation of a functional G protein trimer
(G protein alphabetagamma), thereby inhibiting G
protein-mediated signal transduction. Phd also inhibits
the GTPase activity of G protein alpha. Phd can be
phosphorylated by protein kinase A and G
protein-coupled receptor kinase 2, leading to its
inactivation. Phd was originally isolated from the
retina, where it is highly expressed and has been
implicated to play an important role in light
adaptation. It is also found in the pineal gland,
liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain.
Length = 175
Score = 26.9 bits (60), Expect = 2.3
Identities = 8/34 (23%), Positives = 19/34 (55%)
Query: 42 NMEDMREKTHCRHYELYRKKRLEELHAKFDKLKK 75
+D ++ + YR++R++E+HAK ++
Sbjct: 27 QEDDDDDEDKEEFLQQYREQRMQEMHAKLPFGRR 60
Score = 26.5 bits (59), Expect = 3.0
Identities = 6/44 (13%), Positives = 18/44 (40%)
Query: 6 NMEDMREKTHCRHYELYRKKRLEEVRDMLKHRHNRTNMEDMREK 49
+D ++ + YR++R++E+ L + ++
Sbjct: 27 QEDDDDDEDKEEFLQQYREQRMQEMHAKLPFGRRFGKVYELDSG 70
>gnl|CDD|234715 PRK00290, dnaK, molecular chaperone DnaK; Provisional.
Length = 627
Score = 27.4 bits (62), Expect = 2.3
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 6/34 (17%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEE 93
+K L+EL K ADEK+++E A K+L+E
Sbjct: 540 EKTLKELGDKVP------ADEKEKIEAAIKELKE 567
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 27.0 bits (60), Expect = 2.7
Identities = 11/35 (31%), Positives = 23/35 (65%)
Query: 61 KRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDL 95
L+++ +FDKLKK+ +K++++ A+ L+ D
Sbjct: 212 LELQKIKEEFDKLKKEGKADKQKIKSAKNDLQNDK 246
>gnl|CDD|130161 TIGR01089, fucI, L-fucose isomerase. This enzyme catalyzes the
first step in fucose metabolism, and has been
characterized in Escherichia coli and Bacteroides
thetaiotaomicron [Energy metabolism, Sugars].
Length = 587
Score = 27.2 bits (60), Expect = 2.8
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 91 LEEDLLEFNRRKQQMATMSGSHTLTLG 117
+EE LL F R +A+M G L+LG
Sbjct: 152 VEEKLLRFARAGLAVASMRGKSYLSLG 178
>gnl|CDD|218679 pfam05661, DUF808, Protein of unknown function (DUF808). This
family consists of several bacterial proteins of unknown
function.
Length = 293
Score = 26.7 bits (60), Expect = 3.2
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 64 EELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRK 102
E+L KF L + A+E + +A DL+ F + K
Sbjct: 104 EKLAHKF--LHHEDAEEHEERLEALADPAVDLVAFEKDK 140
>gnl|CDD|223647 COG0574, PpsA, Phosphoenolpyruvate synthase/pyruvate phosphate
dikinase [Carbohydrate transport and metabolism].
Length = 740
Score = 26.9 bits (60), Expect = 3.2
Identities = 14/93 (15%), Positives = 29/93 (31%), Gaps = 11/93 (11%)
Query: 19 YELYRKKRLEEVRDMLKHRHNRTNMED-MREKTH--CRHYELYRKKRLEELHAKFDKLKK 75
+ + +E ML R E RE CR +L + L + ++
Sbjct: 546 LKGGEEYEPKEENPMLGFRGASRYPEIYYREAFALECRAIKLVEEMGLTNVEIMIPFVRT 605
Query: 76 DHADEKKRLEDARKKLEEDLLEFNRRKQQMATM 108
+ E+ K + + + ++ M
Sbjct: 606 E--------EEREKVIILEEGLKRGKNYKVGQM 630
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 26.7 bits (60), Expect = 3.5
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 61 KRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDL 95
+ E L + +KLK++ ++K++L++ KL E+
Sbjct: 537 EEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEA 571
>gnl|CDD|213355 cd12821, EcCorA_ZntB-like, Escherichia coli CorA-Salmonella
typhimurium ZntB_like family. A family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. Members of this family are found in all three
kingdoms of life. It is a functionally diverse family,
including the Mg2+ transporters Escherichia coli and
Salmonella typhimurium CorAs (which can also transport
Co2+, and Ni2+ ), and the Zn2+ transporter Salmonella
typhimurium ZntB which mediates the efflux of Zn2+ (and
Cd2+). It also includes two Saccharomyces cerevisiae
members: the inner membrane Mg2+ transporters
Mfm1p/Lpe10p, and Mrs2p, and a family of Arabidopsis
thaliana members (AtMGTs) some of which are localized to
distinct tissues, and not all of which can transport
Mg2+. Structures of the intracellular domain of Vibrio
parahaemolyticus and Salmonella typhimurium ZntB form
funnel-shaped homopentamers, the tip of the funnel is
formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, such as
occur in some ZntB family proteins, may be associated
with the transport of different divalent cations, such
as zinc and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 285
Score = 26.5 bits (59), Expect = 4.4
Identities = 13/73 (17%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 25 KRLEEVRDMLKHRHNRTNMEDM----REKTHCRHYELYRKKRLEELHAKFDKLKKDHADE 80
++LEE+ L +N ++ + RE + +++ L L F +L +++
Sbjct: 125 EKLEELEWDLLEGNNAIKLDRILELRRELLRLTNLIEPQQEVLMALQEAFAELLF--SED 182
Query: 81 KKRLEDARKKLEE 93
++ L ++E
Sbjct: 183 EEELRRTLDRIER 195
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 26.6 bits (59), Expect = 4.7
Identities = 12/52 (23%), Positives = 30/52 (57%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQMATMSGS 111
K+++ EL A+ L++ A++++ LEDA ++L + E ++ ++ +
Sbjct: 293 KEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELERE 344
Score = 26.2 bits (58), Expect = 5.5
Identities = 12/88 (13%), Positives = 31/88 (35%), Gaps = 4/88 (4%)
Query: 25 KRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKFDKLKKDHADEKKRL 84
K E + LK N E R + + + L +L+A ++ + ++
Sbjct: 388 KDYREKLEKLKREINELKRELDRLQEELQR----LSEELADLNAAIAGIEAKINELEEEK 443
Query: 85 EDARKKLEEDLLEFNRRKQQMATMSGSH 112
ED ++++ + + ++
Sbjct: 444 EDKALEIKKQEWKLEQLAADLSKYEQEL 471
Score = 25.8 bits (57), Expect = 7.2
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 62 RLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNR 100
LEE+ +F + + + D +++LE ++++ E E +R
Sbjct: 372 ELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDR 410
>gnl|CDD|236272 PRK08475, PRK08475, F0F1 ATP synthase subunit B; Validated.
Length = 167
Score = 25.7 bits (57), Expect = 5.7
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 61 KRLEELHAKFDKLKKDHADEKKRLEDARKKLEE 93
KRLEE+ K + K+ D K+LE+A++K E
Sbjct: 60 KRLEEIQEKLKESKEKKEDALKKLEEAKEKAEL 92
>gnl|CDD|219050 pfam06478, Corona_RPol_N, Coronavirus RPol N-terminus. This family
covers the N-terminal region of the coronavirus
RNA-directed RNA Polymerase.
Length = 356
Score = 25.8 bits (57), Expect = 5.8
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 50 THCRHYELYRKKRLEELHAKFDKLKKDHADEKKRL 84
T+C E + K + + +D LK D + K L
Sbjct: 237 TNCLASECFVKSDIGKDFKTYDLLKYDFTEHKLEL 271
>gnl|CDD|153279 cd07595, BAR_RhoGAP_Rich-like, The Bin/Amphiphysin/Rvs (BAR) domain
of Rich-like Rho GTPase Activating Proteins. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. This subfamily is composed of Rho and
Rac GTPase activating proteins (GAPs) with similarity to
GAP interacting with CIP4 homologs proteins (Rich).
Members contain an N-terminal BAR domain, followed by a
Rho GAP domain, and a C-terminal prolin-rich region.
Vertebrates harbor at least three Rho GAPs in this
subfamily including Rich1, Rich2, and SH3-domain binding
protein 1 (SH3BP1). Rich1 and Rich2 play complementary
roles in the establishment and maintenance of cell
polarity. Rich1 is a Cdc42- and Rac-specific GAP that
binds to polarity proteins through the scaffold protein
angiomotin and plays a role in maintaining the integrity
of tight junctions. Rich2 is a Rac GAP that interacts
with CD317 and plays a role in actin cytoskeleton
organization and the maintenance of microvilli in
polarized epithelial cells. SH3BP1 is a Rac GAP that
inhibits Rac-mediated platelet-derived growth factor
(PDGF)-induced membrane ruffling. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions. The BAR domain of Rich1
has been shown to form oligomers, bind membranes and
induce membrane tubulation.
Length = 244
Score = 25.8 bits (57), Expect = 5.8
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 53 RHYELYRKKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEF 98
R+ ++ + AK D LK ++ + + +LE R L D+ EF
Sbjct: 143 RYNAAHKSSGGQGAAAKVDALKDEYEEAELKLEQCRDALATDMYEF 188
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 26.1 bits (58), Expect = 5.9
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFN--RR 101
+K L+EL + L+K A E++ L+ +K+L E +F RR
Sbjct: 440 EKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDERR 483
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 26.2 bits (58), Expect = 6.2
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 62 RLEELHAKFDKLKKDHADEKKRLEDARKKLEEDLLEFNR 100
L +L ++K++ D K +L ++LEE+L E ++
Sbjct: 374 ELTQLEVLIQQVKRELQDAKSQLLKELRELEEELAEVDK 412
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 26.3 bits (57), Expect = 6.4
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 3/87 (3%)
Query: 8 EDMREKTHCRHYELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELH 67
E+ R + + YE +K + EE + K + E++++ + KK+ E
Sbjct: 1590 EEARIEEVMKLYEEEKKMKAEEAK---KAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEK 1646
Query: 68 AKFDKLKKDHADEKKRLEDARKKLEED 94
K ++LKK + K + + KK EED
Sbjct: 1647 KKAEELKKAEEENKIKAAEEAKKAEED 1673
>gnl|CDD|161783 TIGR00237, xseA, exodeoxyribonuclease VII, large subunit. This
family consist of exodeoxyribonuclease VII, large
subunit XseA which catalyses exonucleolytic cleavage in
either the 5'->3' or 3'->5' direction to yield
5'-phosphomononucleotides. Exonuclease VII consists of
one large subunit and four small subunits [DNA
metabolism, Degradation of DNA].
Length = 432
Score = 26.0 bits (57), Expect = 6.8
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 5/68 (7%)
Query: 59 RKKRLEELHAKFDKL--KKDHADEKKRLEDARKKL---EEDLLEFNRRKQQMATMSGSHT 113
+K RLE+L A + + A ++ + E K+ LE R+K+ T + T
Sbjct: 282 KKARLEQLVASLQRQHPQNKLALQQLQFEKLEKRKQAALNKQLERTRQKKTRLTKRLTQT 341
Query: 114 LTLGKSKK 121
+ +
Sbjct: 342 NPSPQILR 349
>gnl|CDD|215656 pfam00012, HSP70, Hsp70 protein. Hsp70 chaperones help to fold
many proteins. Hsp70 assisted folding involves repeated
cycles of substrate binding and release. Hsp70 activity
is ATP dependent. Hsp70 proteins are made up of two
regions: the amino terminus is the ATPase domain and the
carboxyl terminus is the substrate binding region.
Length = 598
Score = 25.7 bits (57), Expect = 7.1
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 64 EELHAKFDKLKKDHADEKKRLE----DARKKLEED 94
E +A DK +K+ + K E K L+E+
Sbjct: 513 AEEYAAEDKKRKERIEAKNEAEEYVYSLEKSLKEE 547
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 25.8 bits (57), Expect = 7.6
Identities = 24/86 (27%), Positives = 41/86 (47%), Gaps = 10/86 (11%)
Query: 27 LEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKK---RLEELHAKFDKLKKDHADEKKR 83
+ V++ LK R +++ EK + RKK +EEL AK ++L K K +
Sbjct: 11 PDLVKESLKARGL--SVDIDLEKL--IALDDERKKLLSEIEELQAKRNELSKQIGKAKGQ 66
Query: 84 LEDARKKLEEDLLEFNRRKQQMATMS 109
+D K+EE E K+++ +S
Sbjct: 67 KKD---KIEEIKKELKELKEELTELS 89
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 25.7 bits (57), Expect = 7.9
Identities = 9/40 (22%), Positives = 22/40 (55%)
Query: 69 KFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQMATM 108
K + ++ A ++ +E+A++ L + L EF + K ++
Sbjct: 546 KLEMIRTGKATREEVIEEAKETLNKLLEEFKKNKDEIGEE 585
>gnl|CDD|181856 PRK09436, thrA, bifunctional aspartokinase I/homoserine
dehydrogenase I; Provisional.
Length = 819
Score = 25.5 bits (57), Expect = 8.5
Identities = 9/24 (37%), Positives = 10/24 (41%)
Query: 61 KRLEELHAKFDKLKKDHADEKKRL 84
RL EL A+F E K L
Sbjct: 720 ARLPELDAEFAARVAKARAEGKVL 743
>gnl|CDD|218845 pfam05991, NYN_YacP, YacP-like NYN domain. This family consists of
bacterial proteins related to YacP. This family is
uncharacterized functionally, but it has been suggested
that these proteins are nucleases due to them containing
a NYN domain. NYN (for N4BP1, YacP-like Nuclease)
domains were discovered by Anantharaman and Aravind.
Based on gene neighborhoods it was suggested that the
bacterial YacP proteins interact with the Ribonuclease
III and TrmH methylase in a processome complex that
catalyzes the maturation of rRNA and tRNA.
Length = 165
Score = 25.2 bits (56), Expect = 8.7
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 69 KFDKLKKDHADEKKRLEDARKKLEEDLLEFNRRKQQ 104
+ +LKK ++ LE AR KL E L + K
Sbjct: 11 AWPELKKL--KDRGSLEAARDKLLEILANYQAFKGY 44
>gnl|CDD|221371 pfam12004, DUF3498, Domain of unknown function (DUF3498). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 433 to 538 amino acids in length. This domain is
found associated with pfam00616, pfam00168. This domain
has two conserved sequence motifs: DLQ and PLSFQNP.
Length = 489
Score = 25.4 bits (55), Expect = 8.7
Identities = 21/91 (23%), Positives = 40/91 (43%), Gaps = 6/91 (6%)
Query: 19 YELYRKKRLEEVRDMLKHRHNRTNMEDMREKTHCRHYELYRKKRLEELHAKFDKLKKDHA 78
YE + ++++ +L+ R + R + + K + L A ++LKKDHA
Sbjct: 389 YERRLLGQEQQMQKLLQEYQARLEDSEERLRRQQEEKDSQMKSIISRLMAVEEELKKDHA 448
Query: 79 ------DEKKRLEDARKKLEEDLLEFNRRKQ 103
D K+++ DA+++ L N R
Sbjct: 449 DMQAVVDSKQKIIDAQERRIASLDAANTRLM 479
>gnl|CDD|235580 PRK05724, PRK05724, acetyl-CoA carboxylase carboxyltransferase
subunit alpha; Validated.
Length = 319
Score = 25.5 bits (57), Expect = 8.9
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 60 KKRLEELHAKFDKLKKDHADEKKRLEDARKKLEEDL 95
+ ++EEL A + D ++E +RLE ++L + +
Sbjct: 16 EAKIEELRAVAEDSDVDLSEEIERLEKKLEELTKKI 51
>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 435 to 791 amino acids in
length. This family is related to pfam00589 suggesting
it may be an integrase enzyme.
Length = 418
Score = 25.4 bits (56), Expect = 8.9
Identities = 11/46 (23%), Positives = 22/46 (47%)
Query: 45 DMREKTHCRHYELYRKKRLEELHAKFDKLKKDHADEKKRLEDARKK 90
D +K Y K + L+ + +K +++ +E++RL KK
Sbjct: 298 DHLKKEIIALYGQVAKAKGTPLYERLEKRRREVRNERQRLRRELKK 343
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
0.318 0.130 0.369
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,280,366
Number of extensions: 580097
Number of successful extensions: 2179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1969
Number of HSP's successfully gapped: 514
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.3 bits)