RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17351
(162 letters)
>gnl|CDD|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding
(OB)-fold. This family is found towards the C-terminus
of the DEAD-box helicases (pfam00270). In these
helicases it is apparently always found in association
with pfam04408. There do seem to be a couple of
instances where it occurs by itself - . The structure
PDB:3i4u adopts an OB-fold. helicases (pfam00270). In
these helicases it is apparently always found in
association with pfam04408. This C-terminal domain of
the yeast helicase contains an
oligonucleotide/oligosaccharide-binding (OB)-fold which
seems to be placed at the entrance of the putative
nucleic acid cavity. It also constitutes the binding
site for the G-patch-containing domain of Pfa1p. When
found on DEAH/RHA helicases, this domain is central to
the regulation of the helicase activity through its
binding of both RNA and G-patch domain proteins.
Length = 109
Score = 82.4 bits (204), Expect = 4e-21
Identities = 37/109 (33%), Positives = 52/109 (47%), Gaps = 36/109 (33%)
Query: 9 TQLKEILIQQKMK------LVSCGTDWDVIRKCICSALF----------GMGFT------ 46
QL EIL + + L S D+++IRK +C+ LF G T
Sbjct: 1 KQLLEILERLGLPEEPSSLLNSSSNDYELIRKALCAGLFPNVARLVDEKGEYKTLKEGQP 60
Query: 47 --------------PDYVVYHELIMTSKEYMQCVTAVDGQWLAELGPMF 81
P++VVYHEL+ T+KEYM+ VTA+D +WL EL P +
Sbjct: 61 VFIHPSSVLFGKKPPEWVVYHELVETTKEYMRDVTAIDPEWLLELAPHY 109
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 34.4 bits (79), Expect = 0.022
Identities = 22/106 (20%), Positives = 44/106 (41%), Gaps = 27/106 (25%)
Query: 1 MRKVREVRTQLKEILIQQKMKLVSCGTDWDVIRKCICSALFG-MGF-------------- 45
+R+ +++ QL +++ + +KL D+D I K + S L +G
Sbjct: 578 VREWQDIYRQLTQVVKELGLKLNEEPADYDAIHKALLSGLLSQIGMKDEKHEYDGARGRK 637
Query: 46 ------------TPDYVVYHELIMTSKEYMQCVTAVDGQWLAELGP 79
P +V+ EL+ TSK Y + V ++ +W+ +
Sbjct: 638 FHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAG 683
>gnl|CDD|223092 COG0013, AlaS, Alanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 879
Score = 34.2 bits (79), Expect = 0.024
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 75 AELGPMFFSVKETGKSGSTKR------RKALEHLHEMEDQMKQAQDEIQARKEEEER 125
++G F + E G + +R ALE+L E ED +K+ ++ E +
Sbjct: 678 GDIGL-FKIISEEGIAAGVRRIEAVTGEAALEYLQEQEDLLKEIASLLKVPPELLPK 733
>gnl|CDD|234701 PRK00252, alaS, alanyl-tRNA synthetase; Reviewed.
Length = 865
Score = 33.1 bits (77), Expect = 0.049
Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 18/71 (25%)
Query: 75 AELGPMFFSVKETGKSGSTKRR-------KALEHLHEMEDQMKQAQDEIQARKEE----- 122
++G +F V E+G + RR ALE+L+E E +K+ ++A+ E
Sbjct: 664 GDIG-LFKIVSESGV-AAGVRRIEAVTGEAALEYLNEQEALLKELAALLKAKPSELPERV 721
Query: 123 ----EERRQAQ 129
EE ++ +
Sbjct: 722 EALLEELKELE 732
>gnl|CDD|218912 pfam06148, COG2, COG (conserved oligomeric Golgi) complex
component, COG2. The COG complex comprises eight
proteins COG1-8. The COG complex plays critical roles in
Golgi structure and function. The proposed function of
the complex is to mediate the initial physical contact
between transport vesicles and their membrane targets. A
comparable role in tethering vesicles has been suggested
for at least six additional large multisubunit
complexes, including the exocyst, a complex that
mediates trafficking to the plasma membrane. COG2
structure reveals a six-helix bundle with few conserved
surface features but a general resemblance to recently
determined crystal structures of four different exocyst
subunits. These bundles inCOG2 may act as platforms for
interaction with other trafficing proteins including
SNAREs (soluble N-ethylmaleimide factor attachment
protein receptors) and Rabs.
Length = 133
Score = 29.2 bits (66), Expect = 0.57
Identities = 8/37 (21%), Positives = 19/37 (51%)
Query: 100 EHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGE 136
E L + + + E+++ + E E R +V +++ E
Sbjct: 69 EKLERIRVPLLALRKEVESVRSELEARLEEVEAKLEE 105
>gnl|CDD|216819 pfam01973, MAF_flag10, Protein of unknown function DUF115. This
family of archaebacterial proteins has no known
function.
Length = 170
Score = 29.1 bits (66), Expect = 0.74
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 10/42 (23%)
Query: 10 QLKEILIQQKMKLVSCGTDWDVIRKCICSALFGMGFTPDYVV 51
LK+ + K +++ + AL G PD VV
Sbjct: 42 LLKKN--RDKAVIIAADS--------ALKALLKHGIKPDIVV 73
>gnl|CDD|221397 pfam12054, DUF3535, Domain of unknown function (DUF3535). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 439 to 459 amino acids in length. This domain is
found associated with pfam00271, pfam02985, pfam00176.
This domain has two completely conserved residues (P and
K) that may be functionally important.
Length = 442
Score = 29.2 bits (66), Expect = 0.90
Identities = 19/77 (24%), Positives = 31/77 (40%), Gaps = 15/77 (19%)
Query: 68 AVDGQWLAELGPMFFSV------------KETGKSGSTKRRKALEHLHEMEDQMKQAQDE 115
AV Q E GP FS+ K ++ AL+ L ED ++
Sbjct: 221 AVVVQGEPEAGPEAFSIETAEKVVTTDFDKLKKSLSPKQKLTALQAL---EDARRRLLAA 277
Query: 116 IQARKEEEERRQAQVSS 132
I+ KE +E+R ++ +
Sbjct: 278 IEEAKEAKEKRHIRILA 294
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 27.9 bits (63), Expect = 1.2
Identities = 15/50 (30%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 95 RRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGEILTPGLKE 144
RR+ LE E++ Q ++ Q + ++E + + +AQ + + +ILTP +E
Sbjct: 7 RRRKLE---ELQKQAQEQQQAQEEQEEAQAQAEAQKQAILRQILTPEARE 53
>gnl|CDD|178850 PRK00083, frr, ribosome recycling factor; Reviewed.
Length = 185
Score = 28.1 bits (64), Expect = 1.4
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 7/30 (23%)
Query: 95 RRKALEHLHEM-------EDQMKQAQDEIQ 117
RR A + L ++ ED++K+A+DEIQ
Sbjct: 132 RRDANDKLKKLEKDKEISEDELKRAEDEIQ 161
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 28.2 bits (63), Expect = 2.0
Identities = 13/45 (28%), Positives = 24/45 (53%)
Query: 85 KETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQ 129
++ + ++RK E E Q KQA ++ + ++ E+ER AQ
Sbjct: 70 QQKSAKRAEEQRKKKEQQQAEELQQKQAAEQERLKQLEKERLAAQ 114
>gnl|CDD|213368 cd12834, ZntB_u1, Uncharacterized bacterial subgroup of the
Salmonella typhimurium Zn2+ transporter ZntB-like
subfamily. The MIT superfamily of essential membrane
proteins is involved in transporting divalent cations
(uptake or efflux) across membranes. The ZntB-like
subfamily includes the Zn2+ transporter Salmonella
typhimurium ZntB which mediates the efflux of Zn2+ (and
Cd2+). 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 which occur
in proteins belonging to this subfamily, 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 = 290
Score = 27.9 bits (63), Expect = 2.1
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 95 RRKALEHLH-------EMEDQMKQAQDEIQARKEEEERRQAQVSSRVGEILTP 140
R+ E L ++++ + Q+EI AR E+ R + S V +L P
Sbjct: 190 LRRLTERLDALDRDLVALQERARLLQEEIAARLAEQTNRSLYILSVVTALLLP 242
>gnl|CDD|149849 pfam08912, Rho_Binding, Rho Binding. Rho Binding Domain is
responsible for the recognition and binding of Rho
binding domain-containing proteins (such as ROCK) to
Rho, resulting in activation of the GTPase which in turn
modulates the phosphorylation of various signalling
proteins. This domain is within an amphipathic
alpha-helical coiled-coil and interacts with Rho through
predominantly hydrophobic interactions.
Length = 68
Score = 26.3 bits (58), Expect = 2.2
Identities = 10/20 (50%), Positives = 17/20 (85%)
Query: 104 EMEDQMKQAQDEIQARKEEE 123
E+ +++K+AQ+E+Q KEEE
Sbjct: 13 ELNNKLKKAQEELQKLKEEE 32
>gnl|CDD|224643 COG1729, COG1729, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 262
Score = 27.8 bits (62), Expect = 2.2
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 99 LEHLHEMEDQMKQ---AQDEIQARKEEEERRQAQVSSRVGEILTPGLKETAPGTP 150
L + E++ Q Q Q+E +AR + E + ++ +G+ T PG+
Sbjct: 75 LRGIQELQYQNNQNVERQEENEARLDSLESGRQALAQGIGDQSGAAPDATTPGSA 129
>gnl|CDD|220506 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
(DUF2229). Members of this family include various
bacterial hypothetical proteins, as well as CoA enzyme
activases. The exact function of this domain has not, as
yet, been defined.
Length = 218
Score = 27.9 bits (63), Expect = 2.3
Identities = 19/78 (24%), Positives = 33/78 (42%), Gaps = 12/78 (15%)
Query: 50 VVYHELIMTSKEYMQCVTAVDGQWLAELGPMF-FSVKETGKSGSTKRRKALEHLHEMEDQ 108
++ L + KE + + L ELG S +E K+ KALE +
Sbjct: 115 LLSPFLNLKDKEALA-------KRLYELGKKLGISKEEIKKAV----EKALEEQEAFKKD 163
Query: 109 MKQAQDEIQARKEEEERR 126
+++ +E A EEE ++
Sbjct: 164 LRKKGEEALAYLEEEGKK 181
>gnl|CDD|235360 PRK05183, hscA, chaperone protein HscA; Provisional.
Length = 616
Score = 28.2 bits (64), Expect = 2.4
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 106 EDQMKQAQDEIQARKEEEERRQAQVSSRVGEILTPGLKE 144
+D M A++++QAR E++ +A+ RV E L L
Sbjct: 514 KDSMSHAEEDMQARALAEQKVEAE---RVLEALQAALAA 549
>gnl|CDD|216828 pfam01984, dsDNA_bind, Double-stranded DNA-binding domain. This
domain is believed to bind double-stranded DNA of 20
bases length.
Length = 105
Score = 26.7 bits (60), Expect = 2.5
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 95 RRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGEILTPGLKE 144
RR L L + + +++ Q + + +++EE ++QA + ILTP +E
Sbjct: 2 RRARLAELQQQQGGLEEQQQQEEQQQQEEAQKQAILRQ----ILTPEARE 47
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 28.1 bits (63), Expect = 2.5
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 11/44 (25%)
Query: 47 PDYVVYHELIMTSKEY-----------MQCVTAVDGQWLAELGP 79
+++ Y E + T K Y +Q + + WL E
Sbjct: 664 LEWIKYAEFLRTRKGYLREGRGERWPDVQTLIELLKLWLKEQVK 707
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the CF(0)
(base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the ab
CF(1) proteins (in the head of the ATP synthase) which
are found in pfam00006.
Length = 132
Score = 27.2 bits (61), Expect = 2.6
Identities = 12/55 (21%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 83 SVKETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQ-----ARKEEEERRQAQVSS 132
+ K + ++A L E E Q+ QA+ E A+KE ++ ++ ++
Sbjct: 34 KIANNIKEAEERLKQAAALLAEAEQQLAQARAEASEIINNAKKEAQKLKEEILAE 88
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 27.7 bits (62), Expect = 3.2
Identities = 12/54 (22%), Positives = 25/54 (46%), Gaps = 3/54 (5%)
Query: 94 KRRKALEHLHEMEDQMK-QAQDEIQAR--KEEEERRQAQVSSRVGEILTPGLKE 144
KRRK LE + E Q+K + + + +E +++ + + + G K+
Sbjct: 287 KRRKELEREAKEEKQLKKKLAQLARLKEIAKEVAQKEKARARKKEQRKERGEKK 340
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 27.8 bits (62), Expect = 3.4
Identities = 10/47 (21%), Positives = 26/47 (55%)
Query: 83 SVKETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQ 129
++E + + + E L E+E + ++ +DE++ +EE+E + +
Sbjct: 846 ELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEE 892
>gnl|CDD|216689 pfam01765, RRF, Ribosome recycling factor. The ribosome recycling
factor (RRF / ribosome release factor) dissociates the
ribosome from the mRNA after termination of translation,
and is essential bacterial growth. Thus ribosomes are
"recycled" and ready for another round of protein
synthesis.
Length = 165
Score = 27.1 bits (61), Expect = 3.7
Identities = 13/52 (25%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 95 RRKALEHLHEM-------EDQMKQAQDEIQA-RKEEEERRQAQVSSRVGEIL 138
RR A + L ++ ED++K+A+ EIQ + ++ + + EI+
Sbjct: 114 RRDANDKLKKLEKDKEISEDEVKRAEKEIQKLTDKYIKKIDELLKKKEKEIM 165
>gnl|CDD|225232 COG2357, COG2357, PpGpp synthetase catalytic domain [General
function prediction only].
Length = 231
Score = 27.3 bits (61), Expect = 3.9
Identities = 8/39 (20%), Positives = 21/39 (53%)
Query: 98 ALEHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGE 136
A E ++++M + + EIQ +E ++R+ + ++
Sbjct: 191 AAEAAAGLDEEMSEIRKEIQEAQEYFDQREQALEEKIKN 229
>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of
pre-ribosomes [Translation, ribosomal structure and
biogenesis / Intracellular trafficking and secretion].
Length = 657
Score = 27.3 bits (60), Expect = 4.0
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 92 STKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQV 130
S K RK + ++ +M+ A+D +A EEE+ Q+++
Sbjct: 368 SKKLRKIEKERLRIQSEMRDAEDIEEA--IEEEKNQSEI 404
>gnl|CDD|221028 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
However, the cis-regulatory yjdF motif, just upstream
from the gene encoding the proteins for this family, is
a small non-coding RNA, Rfam:RF01764. The yjdF motif is
found in many Firmicutes, including Bacillus subtilis.
In most cases, it resides in potential 5' UTRs of
homologues of the yjdF gene whose function is unknown.
However, in Streptococcus thermophilus, a yjdF RNA motif
is associated with an operon whose protein products
synthesise nicotinamide adenine dinucleotide (NAD+).
Also, the S. thermophilus yjdF RNA lacks typical yjdF
motif consensus features downstream of and including the
P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the
S. thermophilus RNAs might sense a distinct compound
that structurally resembles the ligand bound by other
yjdF RNAs. On the ohter hand, perhaps these RNAs have an
alternative solution forming a similar binding site, as
is observed with some SAM riboswitches.
Length = 132
Score = 26.4 bits (59), Expect = 5.4
Identities = 17/44 (38%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 85 KETGKSG-STKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQ 127
KE K G STK ++AL+ HE Q K+ + + + +E+E +RQ
Sbjct: 76 KEVKKPGISTKAQQALKLEHERNKQEKKKRSKEKKEEEKERKRQ 119
>gnl|CDD|205940 pfam13767, DUF4168, Domain of unknown function (DUF4168).
Length = 78
Score = 25.6 bits (57), Expect = 5.6
Identities = 7/28 (25%), Positives = 14/28 (50%)
Query: 102 LHEMEDQMKQAQDEIQARKEEEERRQAQ 129
+ +E ++ EIQA ++ E + Q
Sbjct: 13 VLAIEPIRQEYYQEIQAAEDPAEAQALQ 40
>gnl|CDD|150747 pfam10107, Endonuc_Holl, Endonuclease related to archaeal Holliday
junction resolvase. This domain is found in various
predicted bacterial endonucleases which are distantly
related to archaeal Holliday junction resolvases.
Length = 153
Score = 26.2 bits (58), Expect = 6.2
Identities = 11/43 (25%), Positives = 20/43 (46%)
Query: 95 RRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGEI 137
+ K + E+ +Q + A+ E QA +E E + + EI
Sbjct: 17 QGKVEKRARELFEQWRNAEREAQAMREAEAKFEEWQKKEEKEI 59
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 26.9 bits (61), Expect = 6.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 82 FSVKETGKSGSTKRR 96
+SV ETG+ GS RR
Sbjct: 385 YSVGETGRVGSPGRR 399
>gnl|CDD|233957 TIGR02635, RhaI_grampos, L-rhamnose isomerase, Streptomyces
subtype. This clade of sequences is closely related to
the L-rhamnose isomerases found in Pseudomonas stutzeri
and in a number of the Rhizobiales (TIGR02629). The
genes of the family represented here are found in
similar genomic contexts which contain genes apparently
involved in rhamnose catabolism such as
rhamnulose-1-phosphate aldolase (TIGR02632), sugar
kinases, and sugar transporters [Energy metabolism,
Sugars].
Length = 378
Score = 26.7 bits (59), Expect = 6.7
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 17/58 (29%)
Query: 95 RRKALEHLHEMEDQMKQ-----------------AQDEIQARKEEEERRQAQVSSRVG 135
RRKA++HL E D K+ QD+ ++RK+ E A+V +G
Sbjct: 111 RRKAIDHLLECVDIAKKTGSKDISLWLADGTNYPGQDDFRSRKDRLEESLAEVYEHLG 168
>gnl|CDD|237292 PRK13182, racA, polar chromosome segregation protein; Reviewed.
Length = 175
Score = 26.2 bits (58), Expect = 6.8
Identities = 18/74 (24%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 94 KRRKALEHLHEMEDQMKQAQDEI------QARKEEEERRQ--AQVSSRVGEILTPGLKET 145
+ L E+E Q++Q D++ Q R+E EE + ++ +R+ + L P
Sbjct: 93 QLNTITRRLDELERQLQQKADDVVSYQLLQHRREMEEMLERLQKLEARLKK-LEPIYITP 151
Query: 146 APGTPYTPRRTPKR 159
Y + PKR
Sbjct: 152 DTEPTYEREKKPKR 165
>gnl|CDD|215195 PLN02341, PLN02341, pfkB-type carbohydrate kinase family protein.
Length = 470
Score = 26.7 bits (59), Expect = 7.1
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 16/91 (17%)
Query: 31 VIRKCICSALFGMGFTPDYVVYHELIMTSKEYMQCVTAVDGQWLAELGPMFFSVKETGKS 90
IR+ ALF G+ D + I ++ +Y V +FF GKS
Sbjct: 221 AIRQS--KALFCNGYVFDEL-SPSAIASAVDYAIDVGTA----------VFFDPGPRGKS 267
Query: 91 ---GSTKRRKALEHLHEMEDQMKQAQDEIQA 118
G+ R+ALEHL M D + +E +A
Sbjct: 268 LLVGTPDERRALEHLLRMSDVLLLTSEEAEA 298
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 26.6 bits (59), Expect = 7.3
Identities = 21/76 (27%), Positives = 36/76 (47%), Gaps = 18/76 (23%)
Query: 75 AELGPMFFSVKETGKSGSTKR------RKALEHLHEMEDQMKQAQDE-----------IQ 117
E+G +F VKE+G + +R A+E+L+E ED++K+ D I+
Sbjct: 671 GEIG-LFKIVKESGIAAGVRRIEAVTGNAAIEYLNEQEDKLKELADILKVTPNELPKKIE 729
Query: 118 ARKEEEERRQAQVSSR 133
EE + Q ++ S
Sbjct: 730 RFFEEWKALQKELESL 745
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 26.4 bits (58), Expect = 7.5
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 69 VDGQWLAELGPMFFSVKETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQARKEEEERR 126
+ AE KS R+++ + + + Q E + +K+EE+RR
Sbjct: 134 LGDVKNAEKFEKECRALSRKKSDDEHRKRSGKQKEKRRVEDSQKHKEDRRKKQEEKRR 191
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 26.7 bits (60), Expect = 7.6
Identities = 10/32 (31%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 97 KALEHLHEMEDQMKQAQDEIQA-RKEEEERRQ 127
+ L+ L E+E + ++ + +Q RK+E E R+
Sbjct: 387 EILKQLEEIEKEQEKLSEMLQGLRKDELEARE 418
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 26.6 bits (58), Expect = 8.1
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 86 ETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQVSSRVGE 136
E K ++KA E ED+ K A E ++ EE ++ ++ + E
Sbjct: 1665 EEAKKAEEDKKKAEEAKKAEEDEKKAA--EALKKEAEEAKKAEELKKKEAE 1713
Score = 26.3 bits (57), Expect = 9.3
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 86 ETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQARKEEEERRQAQ 129
E K R + + L+E E +MK + A+K EE + +A+
Sbjct: 1584 EEAKKAEEARIEEVMKLYEEEKKMKAEE----AKKAEEAKIKAE 1623
>gnl|CDD|221198 pfam11740, KfrA_N, Plasmid replication region DNA-binding N-term.
The broad host-range plasmid RK2 is able to replicate in
and be inherited in a stable manner in diverse
Gram-negative bacterial species. It encodes a number of
co-ordinately regulated operons including a central
control korF1 operon that represses the kfrA operon. The
KfrA polypeptide is a site-specific DNA-binding protein
whose operator overlaps the kfrA promoter. The
N-terminus, containing an helix-turn-helix motif, is
essential for function. Downstream from this family is
an extended coiled-coil domain containing a heptad
repeat segment which is probably responsible for
formation of multimers, and may provide an example of a
bridge to host structures required for plasmid
partitioning.
Length = 120
Score = 25.3 bits (56), Expect = 9.5
Identities = 8/40 (20%), Positives = 17/40 (42%), Gaps = 1/40 (2%)
Query: 96 RKALEHLHEM-EDQMKQAQDEIQARKEEEERRQAQVSSRV 134
E E E+++ A+ +A + E E A+ ++
Sbjct: 72 AALWEAAQEEAEERLAAARAAAEAERAELEAELAEAAAEA 111
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 25.6 bits (57), Expect = 9.8
Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 85 KETGKSGSTKRRKALEHLHEMEDQMKQAQDEIQAR-KEEEERRQAQVSSR 133
KE K R+ A + E++ ++A+ E R +E +RQA+ +
Sbjct: 22 KEKRKQRKQARKGADDGDDELKQAAEEAKAEKAERDRELNRQRQAEAEQK 71
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.133 0.391
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: 8,356,887
Number of extensions: 747990
Number of successful extensions: 1797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1734
Number of HSP's successfully gapped: 165
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (24.9 bits)