RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12731
(107 letters)
>gnl|CDD|178174 PLN02560, PLN02560, enoyl-CoA reductase.
Length = 308
Score = 92.9 bits (231), Expect = 4e-24
Identities = 41/97 (42%), Positives = 59/97 (60%), Gaps = 5/97 (5%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAVRL-----EIKGKILKDSDDVKSLGLKNGDM 55
+EV S TV D+KK +HK K + YP RQ + L + + +L DS +K GL +G
Sbjct: 18 LEVPDSATVADLKKAIHKRKKKYYPSRQRLTLPLPPGKTRPTVLDDSKSLKDYGLGDGGT 77
Query: 56 VFIKDLGPQIGWSTVFMAEYAGPLFVYLIFYYRPWIF 92
V KDLGPQ+ + T+F EY GPL +Y +FY+ P ++
Sbjct: 78 VVFKDLGPQVSYRTLFFFEYLGPLLIYPLFYFFPQVY 114
>gnl|CDD|176396 cd01801, Tsc13_N, Ubiquitin-like domain of Tsc13. Tsc13_N
N-terminal domain of Tsc13. Tsc13 is an enoyl
reductase involved in elongation of long chain fatty
acids that localizes to the endoplasmic reticulum and
is highly enriched in a novel structure marking
nuclear-vacuolar junctions.
Length = 77
Score = 66.7 bits (163), Expect = 3e-16
Identities = 26/58 (44%), Positives = 39/58 (67%)
Query: 4 SGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFIKDL 61
SG T+ D+KK + K+ QL +RQ++RLE KGK LKD D + LG+ G ++++DL
Sbjct: 20 SGDATIADLKKLIAKSSPQLTVNRQSLRLEPKGKSLKDDDTLVDLGVGAGATLYVRDL 77
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which
also coordinate the ubls with their downstream
pathways.
Length = 69
Score = 41.9 bits (99), Expect = 1e-06
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFIKDL 61
EVS TV ++K ++ K + P++Q RL GKILKD + G+++G + +
Sbjct: 13 EVSPDDTVAELKAKIAA-KEGVPPEQQ--RLIYAGKILKDDKTLSDYGIQDGSTLHLVLR 69
>gnl|CDD|176400 cd01805, RAD23_N, Ubiquitin-like domain of RAD23. RAD23 belongs
to a family of adaptor molecules having affinity for
both the proteasome and ubiquitinylated proteins and
thought to shuttle these ubiquitinylated proteins to
the proteasome for destruction. RAD23 interacts with
ubiquitin through its C-terminal ubiquitin-associated
domains (UBA) and with the proteasome through its
N-terminal ubiquitin-like domain (UBL).
Length = 77
Score = 36.5 bits (85), Expect = 2e-04
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYP-DRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFI 58
EV TV ++K+++ + K YP ++Q +L GKILKD ++ + D V +
Sbjct: 16 EVDPDDTVAELKEKIEEEKGCDYPPEQQ--KLIYSGKILKDDTTLEEYKIDEKDFVVV 71
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 34.8 bits (80), Expect = 9e-04
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFI 58
V TV D+K+++ K K L P++Q RL + GKIL DS ++ GL++GD + +
Sbjct: 13 LVPSGTTVADLKEKLAK-KLGLPPEQQ--RLLVNGKILPDSLTLEDYGLQDGDELVL 66
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 33.8 bits (78), Expect = 0.002
Identities = 17/53 (32%), Positives = 32/53 (60%), Gaps = 3/53 (5%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGD 54
EV S TV ++K+++ + + P++Q RL KGK+L+D + G+++G
Sbjct: 16 EVKPSDTVSELKEKIAELT-GIPPEQQ--RLIYKGKVLEDDRTLADYGIQDGS 65
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 33.7 bits (78), Expect = 0.002
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVF 57
+EV S TV ++K+++ K + D+Q RL GK+L+D + G+++G +
Sbjct: 10 LEVDPSDTVSELKEKIED-KEGIPVDQQ--RLIFSGKVLEDDTTLSEYGIQDGSTLH 63
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The
small ubiquitin-related modifier SUMO-1 is a Ub/Ubl
family member, and although SUMO-1 shares structural
similarity to Ub, SUMO's cellular functions remain
distinct insomuch as SUMO modification alters protein
function through changes in activity, cellular
localisation, or by protecting substrates from
ubiquitination. Rad60 family members contain
functionally enigmatic, integral SUMO-like domains
(SLDs). Despite their divergence from SUMO, each Rad60
SLD interacts with a subset of SUMO pathway enzymes:
SLD2 specifically binds the SUMO E2 conjugating enzyme
(Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also
called Uba2) activating and E3 (Pli1, also called Siz1
and Siz2) specificity enzymes. Structural analysis of
PDB:2uyz reveals a mechanistic basis for the
near-synonymous roles of Rad60 and SUMO in survival of
genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 32.9 bits (76), Expect = 0.004
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMV 56
++V + T+ + K + P Q VRL G+ L +D V +++GD +
Sbjct: 15 IKVKPTTTLSKLINAYRKKRGI--PADQQVRLIFDGERLDPNDTVADYDIEDGDTI 68
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N
N-terminal ubiquitin-like (Ubl) domain of the BAG1
protein. This domain occurs together with the BAG
domain and is closely related to the Ubl domain of a
family of deubiquitinases that includes Rpn11, UBP6
(USP14), USP7 (HAUSP).
Length = 71
Score = 33.1 bits (76), Expect = 0.004
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFI 58
+ +S T D+KK + + + P Q +L KGK D++ + G+K+G V +
Sbjct: 14 LSISSQATFGDLKKML-APVTGVEPRDQ--KLIFKGKERDDAETLDMSGVKDGSKVML 68
>gnl|CDD|176404 cd01809, Scythe_N, Ubiquitin-like domain of Scythe protein.
Scythe protein (also known as Bat3) is an apoptotic
regulator that is highly conserved in eukaryotes and
contains a ubiquitin-like domain near its N-terminus.
Scythe binds reaper, a potent apoptotic inducer, and
Scythe/Reaper are thought to signal apoptosis, in part
through regulating the folding and activity of
apoptotic signaling molecules.
Length = 72
Score = 32.2 bits (74), Expect = 0.009
Identities = 13/52 (25%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNG 53
V TV D+K+++ + + + ++Q RL G++LKD + + +++G
Sbjct: 16 TVEEEITVLDLKEKIAE-EVGIPVEQQ--RLIYSGRVLKDDETLSEYKVEDG 64
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC
protein. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 378
Score = 31.0 bits (70), Expect = 0.070
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQ-LYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMV 56
+++ TVK++K+++ + + YP Q +L GKIL D VK +K D V
Sbjct: 15 IDMEPDETVKELKEKIEAEQGKDAYPVAQ-QKLIYSGKILSDDKTVKEYKIKEKDFV 70
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 30.2 bits (69), Expect = 0.17
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 18 KAKSQLYPDRQA--VR-LEIKGKILKDSDDVKSLGLKNGDMVFIKDLGP-QIGWSTVFMA 73
+AK L+PDR R + + GK+ SDD+++ G MV + DL +I +V A
Sbjct: 431 EAKIPLHPDRPERGEREIPVGGKVYVSSDDLEAE----GKMVRLMDLFNVEITGVSVDKA 486
Query: 74 EYAG 77
Y
Sbjct: 487 RYHS 490
>gnl|CDD|176408 cd01813, UBP_N, UBP ubiquitin processing protease. The UBP
(ubiquitin processing protease) domain (also referred
to as USP which stands for "ubiquitin-specific
protease") is present at in a large family of cysteine
proteases that specifically cleave ubiquitin
conjugates. This family includes Rpn11, UBP6 (USP14),
USP7 (HAUSP). This domain is closely related to the
amino-terminal ubiquitin-like domain of BAG1
(Bcl2-associated anthanogene1) protein and is found
only in eukaryotes.
Length = 74
Score = 28.7 bits (64), Expect = 0.17
Identities = 16/45 (35%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 8 TVKDIKKEVHKAKSQLYPDRQAV-RLEIKGKILKDSDDVKSLGLK 51
TV D+K+ + K + + P+RQ + L++KGK +D + +L LK
Sbjct: 21 TVLDLKQFI-KTLTGVLPERQKLLGLKVKGKPAEDDVKISALKLK 64
>gnl|CDD|221132 pfam11543, UN_NPL4, Nuclear pore localisation protein NPL4. Npl4
is part of the heterodimer UN along with Ufd1 which is
involved in the recruitment of p97, an AAA ATPase, for
tasks involving the ubiquitin pathway. Npl4 has a
ubiquitin-like domain which has within its structure a
beta-grasp fold with a helical insert.
Length = 80
Score = 28.5 bits (64), Expect = 0.27
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 2 EVSGSFTVKDIKKEVHKAKSQLYPDRQ-AVRLEIKGKIL---KDSDDVKSLGLKNGDMVF 57
E+S + T+ + +V + +P+ ++ LE S V LGLK+GDM++
Sbjct: 19 EISSTSTLSTLLSKVAEELG--FPNNGFSLYLERNKTTELVSSGSKSVSELGLKHGDMLY 76
Query: 58 IK 59
+
Sbjct: 77 LF 78
>gnl|CDD|176403 cd01808, hPLIC_N, Ubiquitin-like domain of hPLIC-1 and hPLIC2.
hPLIC-1 and hPLIC-2 (human homologs of the yeast
ubiquitin-like Dsk2 protein) are type2 UBL's
(ubiquitin-like) proteins that are thought to serve as
adaptors that link the ubiquitination machinery to the
proteasome. The hPLIC's have an N-terminal UBL domain
that binds the S5a subunit of the proteasome and a
C-terminal UBA (ubiquitin-associated) domain that binds
a ubiquitylated protein.
Length = 71
Score = 27.0 bits (60), Expect = 0.68
Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFI 58
+E++ +VKD K+ V K + +++ + L GKILKD+D + +K+G V +
Sbjct: 14 IEIAEDASVKDFKEAVSK---KFKANQEQLVLIFAGKILKDTDTLTQHNIKDGLTVHL 68
>gnl|CDD|235115 PRK03317, PRK03317, histidinol-phosphate aminotransferase;
Provisional.
Length = 368
Score = 27.9 bits (63), Expect = 0.90
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 9 VKDIKKEVHKAKSQL--YPDRQAVRL 32
V DI + V +A + L YPDR AV L
Sbjct: 45 VADIAEAVAEAAAGLNRYPDRDAVAL 70
>gnl|CDD|216576 pfam01568, Molydop_binding, Molydopterin dinucleotide binding
domain. This domain is found in various molybdopterin
- containing oxidoreductases and tungsten
formylmethanofuran dehydrogenase subunit d (FwdD) and
molybdenum formylmethanofuran dehydrogenase subunit
(FmdD); where the domain constitutes almost the entire
subunit. The formylmethanofuran dehydrogenase catalyzes
the first step in methane formation from CO2 in
methanogenic archaea and has a molybdopterin
dinucleotide cofactor. This domain corresponds to the
C-terminal domain IV in dimethyl sulfoxide
(DMSO)reductase which interacts with the 2-amino
pyrimidone ring of both molybdopterin guanine
dinucleotide molecules.
Length = 110
Score = 27.2 bits (61), Expect = 1.1
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 43 DDVKSLGLKNGDMVFIK 59
+D +LG+K+GD+V +
Sbjct: 37 EDAAALGIKDGDLVEVT 53
>gnl|CDD|216993 pfam02359, CDC48_N, Cell division protein 48 (CDC48), N-terminal
domain. This domain has a double psi-beta barrel fold
and includes VCP-like ATPase and N-ethylmaleimide
sensitive fusion protein N-terminal domains. Both the
VAT and NSF N-terminal functional domains consist of
two structural domains of which this is at the
N-terminus. The VAT-N domain found in AAA ATPases
pfam00004 is a substrate 185-residue recognition
domain.
Length = 84
Score = 26.8 bits (60), Expect = 1.1
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 8/44 (18%)
Query: 16 VHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFIK 59
V +A + R RL D+ LGL GD+V IK
Sbjct: 3 VAEAPNDRDVGRGIARL--------SPKDMDELGLFPGDIVEIK 38
>gnl|CDD|239180 cd02779, MopB_CT_Arsenite-Ox, This CD contains the
molybdopterin_binding C-terminal (MopB_CT) region of
Arsenite oxidase (Arsenite-Ox) and related proteins.
Arsenite oxidase oxidizes arsenite to the less toxic
arsenate; it transfers the electrons obtained from the
oxidation of arsenite towards the soluble periplasmic
electron carriers cytochrome c and/or amicyanin.
Length = 115
Score = 27.0 bits (60), Expect = 1.3
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 9/49 (18%)
Query: 43 DDVKSLGLKNGDMVFI-KDLGPQIGWSTVFMA---EYAGPLFVYLIFYY 87
+D K GLKNGD+V + D G ST MA P +++ +
Sbjct: 40 EDAKREGLKNGDLVEVYNDYG-----STTAMAYVTNTVKPGQTFMLMAH 83
>gnl|CDD|212152 cd11545, NTP-PPase_YP_001813558, Nucleoside Triphosphate
Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found
in Exiguobacterium sibiricum YP_001813558.1 protein and
its bacterial homologs. This family contains a putative
NTP_PPase (YP_001813558.1) from Exiguobacterium
sibiricum and its bacterial homologs. Unlike normal
dimeric dUTPase-like proteins with a central four-helix
bundle forming the active site, YP_001813558.1 displays
a very unusual interlaced segment-swapped dimer that
might be important for it to adapt to an extremely cold
environment. Moreover, structural analysis and
comparisons indicate that YP_001813558.1 potentially
prefers to hydrolyze dCTPs or its derivatives.
Length = 115
Score = 26.5 bits (59), Expect = 1.8
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 5 GSFTVKDIKKE-----VHKAK-SQLYPDRQAVRLEIKGKILK 40
GSF ++ + VHKA +L+PD + GKILK
Sbjct: 60 GSFVEMGVEPDPLFEIVHKANMGKLFPDGKPRYDPEDGKILK 101
>gnl|CDD|239176 cd02775, MopB_CT, Molybdopterin-Binding, C-terminal (MopB_CT)
domain of the MopB superfamily of proteins, a large,
diverse, heterogeneous superfamily of enzymes that, in
general, bind molybdopterin as a cofactor. The MopB
domain is found in a wide variety of molybdenum- and
tungsten-containing enzymes, including formate
dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms
of nitrate reductase (Nap, Nas, NarG),
dimethylsulfoxide reductase (DMSOR), thiosulfate
reductase, formylmethanofuran dehydrogenase, and
arsenite oxidase. Molybdenum is present in most of
these enzymes in the form of molybdopterin, a modified
pterin ring with a dithiolene side chain, which is
responsible for ligating the Mo. In many bacterial and
archaeal species, molybdopterin is in the form of a
dinucleotide, with two molybdopterin dinucleotide units
per molybdenum. These proteins can function as
monomers, heterodimers, or heterotrimers, depending on
the protein and organism. Also included in the MopB
superfamily is the eukaryotic/eubacterial protein
domain family of the 75-kDa subunit/Nad11/NuoG (second
domain) of respiratory complex 1/NADH-quinone
oxidoreductase which is postulated to have lost an
ancestral formate dehydrogenase activity and only
vestigial sequence evidence remains of a molybdopterin
binding site. This hierarchy is of the conserved
MopB_CT domain present in many, but not all, MopB
homologs.
Length = 101
Score = 26.5 bits (59), Expect = 1.9
Identities = 7/14 (50%), Positives = 12/14 (85%)
Query: 43 DDVKSLGLKNGDMV 56
+D +LG+K+GD+V
Sbjct: 30 EDAAALGIKDGDLV 43
>gnl|CDD|220681 pfam10302, DUF2407, DUF2407 ubiquitin-like domain. This is a
family of proteins found in fungi. The function is not
known. This domain is related to the ubiquitin domain.
Length = 90
Score = 26.1 bits (58), Expect = 1.9
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 6 SFTVKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFIKDLGPQI 65
S TV +KK + +++ + +RL G++L DS + S+ G +I
Sbjct: 23 STTVAWLKKLI-RSRLPQELSNRRLRLIYAGRLLNDSSKLASILKLPGKGKGKAPERVRI 81
>gnl|CDD|215198 PLN02348, PLN02348, phosphoribulokinase.
Length = 395
Score = 27.1 bits (60), Expect = 2.0
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 15/81 (18%)
Query: 21 SQLYPDRQAVRLEIKGKILKDSDDVKSLGLKNGDMVFIKDLGPQIGW---STVFMAEYAG 77
+QL PD +GK+L+ +K G+KN D V++ D G I W Y G
Sbjct: 246 TQLIPDDN------EGKVLRVRLIMKE-GVKNFDPVYLFDEGSTISWIPCGRKLTCSYPG 298
Query: 78 PLFVYLIFYYRPWIFYGSEAA 98
+ F+Y P ++G E +
Sbjct: 299 -----IKFFYGPDTYFGHEVS 314
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 27.0 bits (61), Expect = 2.2
Identities = 6/26 (23%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 43 DDVKSLGLKNGDMVFIK---DLGPQI 65
D+++ ++ GD V ++ D+ P++
Sbjct: 361 DEIERKDIRIGDTVVVRRAGDVIPEV 386
>gnl|CDD|131740 TIGR02693, arsenite_ox_L, arsenite oxidase, large subunit. This
model represents the large subunit of an arsenite
oxidase complex. The small subunit is a Rieske protein.
Homologs to both large and small subunits that score in
the gray zone between the set trusted and noise bit
score cutoffs for the respective models are found in
Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7.
This enzyme acts in energy metabolim by arsenite
oxidation, rather than detoxification by reduction of
arsenate to arsenite prior to export [Energy metabolism,
Electron transport].
Length = 806
Score = 26.8 bits (59), Expect = 2.3
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 9/49 (18%)
Query: 43 DDVKSLGLKNGDMVFI-KDLGPQIGWSTVFMA---EYAGPLFVYLIFYY 87
+D K LGLK+GD+V + D G +T MA + P +++F +
Sbjct: 732 EDAKRLGLKSGDLVEVYNDEG-----NTTAMAYPTDAVKPGTTFMLFGH 775
>gnl|CDD|219187 pfam06813, Nodulin-like, Nodulin-like. This family represents a
conserved region within plant nodulin-like proteins.
Length = 248
Score = 26.5 bits (59), Expect = 2.9
Identities = 12/28 (42%), Positives = 14/28 (50%)
Query: 57 FIKDLGPQIGWSTVFMAEYAGPLFVYLI 84
KDLG GW + AEY P V L+
Sbjct: 44 VAKDLGKNFGWLSGLAAEYLPPWVVLLV 71
>gnl|CDD|101162 PRK03002, prsA, peptidylprolyl isomerase; Reviewed.
Length = 285
Score = 26.4 bits (58), Expect = 3.3
Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 11 DIKKEVHKAKSQLYPDRQAVRLEIKGKILKDSDDVKS 47
D+ KEV KAKSQ Y D+ L+ G LKD D K+
Sbjct: 75 DVDKEVQKAKSQ-YGDQFKNVLKNNG--LKDEADFKN 108
>gnl|CDD|223311 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
structure and biogenesis].
Length = 187
Score = 26.0 bits (58), Expect = 3.3
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 11/47 (23%)
Query: 9 VKDIKKEVHKAKSQLYPDRQAVRLEIKGKILKD-------SDDVKSL 48
VK KK +AK + + +R + KI K D+VK
Sbjct: 116 VKVAKKYAEEAKVAV----RNIRRDANDKIKKLEKDKEISEDEVKKA 158
>gnl|CDD|238282 cd00508, MopB_CT_Fdh-Nap-like, This CD includes formate
dehydrogenases (Fdh) H and N; nitrate reductases, Nap
and Nas; and other related proteins. Formate
dehydrogenase H is a component of the anaerobic formate
hydrogen lyase complex and catalyzes the reversible
oxidation of formate to CO2 with the release of a
proton and two electrons. Formate dehydrogenase N
(alpha subunit) is the major electron donor to the
bacterial nitrate respiratory chain and nitrate
reductases, Nap and Nas, catalyze the reduction of
nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is
of the conserved molybdopterin_binding C-terminal
(MopB_CT) region present in many, but not all, MopB
homologs.
Length = 120
Score = 25.9 bits (58), Expect = 3.5
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 43 DDVKSLGLKNGDMV 56
+D LG+K+GD+V
Sbjct: 42 EDAARLGIKDGDLV 55
>gnl|CDD|223321 COG0243, BisC, Anaerobic dehydrogenases, typically
selenocysteine-containing [Energy production and
conversion].
Length = 765
Score = 26.3 bits (58), Expect = 3.6
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 43 DDVKSLGLKNGDMV 56
+D LG+K+GD+V
Sbjct: 678 EDAAKLGIKDGDLV 691
>gnl|CDD|215012 smart01073, CDC48_N, Cell division protein 48 (CDC48) N-terminal
domain. This domain has a double psi-beta barrel fold
and includes VCP-like ATPase and N-ethylmaleimide
sensitive fusion protein N-terminal domains. Both the
VAT and NSF N-terminal functional domains consist of
two structural domains of which this is at the
N-terminus. The VAT-N domain found in AAA ATPases is a
substrate 185-residue recognition domain.
Length = 82
Score = 24.9 bits (55), Expect = 5.9
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 35 KGKILKDSDDVKSLGLKNGDMVFIK 59
+G +D+ LGL GD V I
Sbjct: 14 RGIARLSPEDMDELGLFPGDYVLIT 38
>gnl|CDD|237290 PRK13146, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 209
Score = 25.5 bits (57), Expect = 6.3
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 43 DDVKSLGLKNGDMVFIKDLG-----PQIGWSTVFMAEYAGPLF 80
D LGL G++V + G P +GW+TV PLF
Sbjct: 98 GDTPGLGLIPGEVVRFQPDGPALKVPHMGWNTVDQTR-DHPLF 139
>gnl|CDD|220030 pfam08817, YukD, WXG100 protein secretion system (Wss), protein
YukD. The YukD protein family members participate in
the formation of a translocon required for the
secretion of WXG100 proteins (pfam06013) in monoderm
bacteria, with the WXG100 protein secretion system
(Wss). Like the cytoplasmic protein EsaC in
Staphylococcus aureus, YukD was hypothesized to play a
role of a chaperone. YukD adopts a ubiquitin-like fold.
Usually, ubiquitin covalently binds to protein and
flags them for protein degradation, however conjugation
assays have indicated that the classical YukD lacks the
capacity for covalent bond formation with other
proteins. In contrast to the situation in firmicutes,
YukD-like proteins in actinobacteria are often fused to
a transporter involved in the ESAT-6/ESX/Wss secretion
pathway. Members of the YukD family are also associated
in gene neighborhoods with other enzymatic members of
the ubiquitin signaling and degradation pathway such as
the E1, E2 and E3 trienzyme complex that catalyze
ubiquitin transfer to substrates, and the JAB family
metallopeptidases that are involved in its release.
This suggests that a subset of the YukD family in
bacteria are conjugated and released from proteins as
in the eukaryotic ubiquitin-mediated signaling and
degradation pathway.
Length = 77
Score = 24.5 bits (54), Expect = 6.3
Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 3/58 (5%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQAV---RLEIKGKILKDSDDVKSLGLKNGDM 55
+ + VK++ + +A D RL KG L D D + G+ +GD+
Sbjct: 16 LVLPADVPVKELIPLLVEALKLPGTDPSGQGVYRLARKGIPLSDDDTLADAGVTDGDI 73
>gnl|CDD|227704 COG5417, COG5417, Uncharacterized small protein [Function
unknown].
Length = 81
Score = 24.7 bits (54), Expect = 6.4
Identities = 10/60 (16%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 1 MEVSGSFTVKDIKKEVHKAKSQLYPDRQA--VRLEIKGKILKDSDDVKSLGLKNGDMVFI 58
+ + +K + V ++ DR+ +++ K ++L D + + +GD++ I
Sbjct: 21 LRLPDYLPIKKLIDIVWESLKISIFDREGTQIKVMNKAQLLSGDDKLIDYQIADGDILEI 80
>gnl|CDD|237289 PRK13143, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 200
Score = 25.2 bits (56), Expect = 7.4
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 44 DVKSLGLKNGDMVFIKDLG--PQIGWSTVFMAEYAGPLF 80
V+ LGL G +V P +GW+TV + + PLF
Sbjct: 93 GVRGLGLFPGRVVRFPAGVKVPHMGWNTVKVVKD-CPLF 130
>gnl|CDD|215512 PLN02950, PLN02950, 4-alpha-glucanotransferase.
Length = 909
Score = 25.5 bits (56), Expect = 7.7
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 6/34 (17%)
Query: 11 DIKKEVHKAKSQL------YPDRQAVRLEIKGKI 38
D+K E+ KA+ QL Y A +L I K+
Sbjct: 345 DLKAEIQKARKQLDKKDVDYEATLATKLSIAKKV 378
>gnl|CDD|223918 COG0849, ftsA, Cell division ATPase FtsA [Cell division and
chromosome partitioning].
Length = 418
Score = 25.3 bits (56), Expect = 8.2
Identities = 11/46 (23%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 8 TVKDIKKEVHKAKSQ-LYPDRQAVRLEIKGKILKDSDDVKS-LGLK 51
T +DI++ + AK+ + P+R+ + + + I+ + +K LG+
Sbjct: 104 TQEDIERVLEAAKAVAIPPEREILHVIPQEYIVDGQEGIKDPLGMS 149
>gnl|CDD|223196 COG0118, HisH, Glutamine amidotransferase [Amino acid transport and
metabolism].
Length = 204
Score = 24.9 bits (55), Expect = 8.6
Identities = 14/42 (33%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 42 SDDVKSLGLKNGDMVFIKDLG---PQIGWSTVFMAEYAGPLF 80
VK LGL G +V P +GW+ V PLF
Sbjct: 94 GGGVKGLGLIPGKVVRFPAEDLKVPHMGWNQVEFVR-GHPLF 134
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
0.320 0.138 0.412
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,465,702
Number of extensions: 472952
Number of successful extensions: 567
Number of sequences better than 10.0: 1
Number of HSP's gapped: 563
Number of HSP's successfully gapped: 66
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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 (21.8 bits)
S2: 53 (24.1 bits)