RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7331
(139 letters)
>gnl|CDD|214625 smart00332, PP2Cc, Serine/threonine phosphatases, family 2C,
catalytic domain. The protein architecture and deduced
catalytic mechanism of PP2C phosphatases are similar to
the PP1, PP2A, PP2B family of protein Ser/Thr
phosphatases, with which PP2C shares no sequence
similarity.
Length = 252
Score = 89.4 bits (222), Expect = 1e-22
Identities = 38/115 (33%), Positives = 60/115 (52%), Gaps = 8/115 (6%)
Query: 14 STNHEGSNLTCGASSMQGWRIYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVYTSQHLP 73
S + + L G SSMQG R EDAH + D ++ F V+DGHGGSE A + S++LP
Sbjct: 1 SVSGKNLGLRYGLSSMQGVRKPMEDAHVITPDLSDSGGFFGVFDGHGGSEAAKFLSKNLP 60
Query: 74 EFIKKTEQFKKGNY---KQALIDAFMEFDESLIKDEVMAILKTLKKENEVMAILK 125
E + + +K ++AL AF+ DE ++++ T V+A++
Sbjct: 61 EILAEELIKEKDELEDVEEALRKAFLSTDEEILEELEALSGSTA-----VVALIS 110
>gnl|CDD|238083 cd00143, PP2Cc, Serine/threonine phosphatases, family 2C, catalytic
domain; The protein architecture and deduced catalytic
mechanism of PP2C phosphatases are similar to the PP1,
PP2A, PP2B family of protein Ser/Thr phosphatases, with
which PP2C shares no sequence similarity.
Length = 254
Score = 79.3 bits (196), Expect = 7e-19
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 5/84 (5%)
Query: 24 CGASSMQGWRIYQEDAHNVIIDFDENK-SLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQF 82
G S G R EDA + + + LF V+DGHGG + S+ L E + + +
Sbjct: 3 AGVSDKGGDRKTNEDAVVIKPNLNNEDGGLFGVFDGHGGHAAGEFASKLLVEELLEELEE 62
Query: 83 KK----GNYKQALIDAFMEFDESL 102
+ ++AL AF+ DE +
Sbjct: 63 TLTLSEEDIEEALRKAFLRADEEI 86
>gnl|CDD|215938 pfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is
a Mn++ or Mg++ dependent protein serine/threonine
phosphatase.
Length = 252
Score = 78.2 bits (193), Expect = 2e-18
Identities = 32/90 (35%), Positives = 44/90 (48%), Gaps = 5/90 (5%)
Query: 22 LTCGASSMQGWRIYQEDAHNVIIDF-----DENKSLFAVYDGHGGSEVAVYTSQHLPEFI 76
L G MQG+R + EDAH + ++ FAV+DGHGGS+ A Y +HL +
Sbjct: 1 LDVGGPRMQGFRKFMEDAHIAGKNLNASSGKDSFGFFAVFDGHGGSQAAKYAGKHLETIL 60
Query: 77 KKTEQFKKGNYKQALIDAFMEFDESLIKDE 106
F + AL +F+E DE L D
Sbjct: 61 ALRRSFLTLDKLDALRKSFLEADEELRSDA 90
>gnl|CDD|223704 COG0631, PTC1, Serine/threonine protein phosphatase [Signal
transduction mechanisms].
Length = 262
Score = 58.9 bits (143), Expect = 2e-11
Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 20 SNLTCGASSMQGWRIYQEDAHNVIIDFDENKS-LFAVYDGHGGSEVAVYTSQHLPE---- 74
S G S + R + EDA + + + N LFAV DG GG S+ E
Sbjct: 7 SLKVAGLSDVGTVRKHNEDAFLIKPNENGNLLLLFAVADGMGGHAAGEVASKLAVEALAR 66
Query: 75 -FIKKTEQFKKGNYKQALIDAFMEFDESLIKDEVM 108
F + + ++ L +A ++ +E++ ++ +
Sbjct: 67 LFDETNFNSLNESLEELLKEAILKANEAIAEEGQL 101
>gnl|CDD|240318 PTZ00224, PTZ00224, protein phosphatase 2C; Provisional.
Length = 381
Score = 58.2 bits (141), Expect = 7e-11
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 2/78 (2%)
Query: 1 MGAYLSQPITKKESTNHEGSNLTCGASSMQGWRIYQEDAHNVIIDFDENKSLFAVYDGHG 60
MG L +P+ K S C ++ + G+R EDAH + + D F V+DGH
Sbjct: 1 MGIMLPKPVLSKLVDRAGNSIFRCASACVNGYRESMEDAHLLYLTDDWG--FFGVFDGHV 58
Query: 61 GSEVAVYTSQHLPEFIKK 78
E + Y ++ P+ ++K
Sbjct: 59 NDECSQYLARAWPQALEK 76
>gnl|CDD|215603 PLN03145, PLN03145, Protein phosphatase 2c; Provisional.
Length = 365
Score = 47.2 bits (112), Expect = 4e-07
Identities = 27/90 (30%), Positives = 43/90 (47%), Gaps = 11/90 (12%)
Query: 25 GASSMQGWRIYQEDAH----NVIIDF------DENKSLFAVYDGHGGSEVAVYTSQHLPE 74
GA + G R ED + N + DF D + + V+DGHGG A + HLP
Sbjct: 68 GAWADIGSRSSMEDVYICVDNFMSDFGLKNSEDGPSAFYGVFDGHGGKHAADFACYHLPR 127
Query: 75 FIKKTEQFKKGNYKQALIDAFMEFDESLIK 104
FI + E F + ++ + AF++ D + +
Sbjct: 128 FIVEDEDFPR-EIEKVVSSAFLQTDTAFAE 156
>gnl|CDD|234829 PRK00750, lysK, lysyl-tRNA synthetase; Reviewed.
Length = 510
Score = 33.6 bits (78), Expect = 0.023
Identities = 20/65 (30%), Positives = 27/65 (41%), Gaps = 20/65 (30%)
Query: 73 PEFIKKTEQFKKGNYKQALIDAFMEFDESLIKDEVMAILKTLKKENEVMAIL-KTLKKEI 131
EFI TE +K G +DE AIL L+ +E+M IL L +E
Sbjct: 127 YEFISATECYKSG-----------RYDE--------AILTALENRDEIMEILLPYLGEER 167
Query: 132 TVSYF 136
+Y
Sbjct: 168 QATYS 172
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 31.3 bits (71), Expect = 0.13
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 9/72 (12%)
Query: 34 IYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQFKKGNYKQALID 93
I ED +ID E K+ F ++G G++ + +P + EQ K+ ++ L++
Sbjct: 166 IGAEDNFIGVIDLVEMKAYF--FNGDKGTK---AIEKEIPSDLL--EQAKE--LRENLVE 216
Query: 94 AFMEFDESLIKD 105
A EFDE L++
Sbjct: 217 AVAEFDEELMEK 228
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 29.8 bits (68), Expect = 0.40
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 34 IYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQFKKGNYKQALID 93
I ED ++D E K+L +DG G ++ +PE + E+ ++ ++ LI+
Sbjct: 155 IGAEDDFEGVVDLIEMKAL--YWDGELGEKIEE---TDIPEDLL--EEAEE--AREELIE 205
Query: 94 AFMEFDESL 102
E D+ L
Sbjct: 206 TLAEVDDEL 214
>gnl|CDD|216786 pfam01921, tRNA-synt_1f, tRNA synthetases class I (K). This family
includes only lysyl tRNA synthetases from prokaryotes.
Length = 357
Score = 29.9 bits (68), Expect = 0.44
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 20/65 (30%)
Query: 73 PEFIKKTEQFKKGNYKQALIDAFMEFDESLIKDEVMAILKTLKKENEVMAIL-KTLKKEI 131
EFI TE +K G +DE AIL L+ +E+M IL +E
Sbjct: 123 YEFISATELYKSG-----------LYDE--------AILLALENRDEIMEILLPYRGEER 163
Query: 132 TVSYF 136
+Y
Sbjct: 164 QETYS 168
>gnl|CDD|235326 PRK04976, torD, chaperone protein TorD; Validated.
Length = 202
Score = 29.2 bits (66), Expect = 0.54
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 72 LPEFIKKTEQFKKGNYKQALID---AFMEFD 99
LPEF K Q+ + AL AF++ D
Sbjct: 166 LPEFAAKCTQYDSFGFYAALSQLLLAFVQLD 196
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 28.9 bits (66), Expect = 0.86
Identities = 19/90 (21%), Positives = 36/90 (40%), Gaps = 21/90 (23%)
Query: 34 IYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQFKKGNYKQALID 93
I + D ++D K+ YD G SE +P + + ++ L++
Sbjct: 151 IGEGDDFTGVVDLLSMKAY--RYDEGGPSEEI-----EIPAELLDRAE----EAREELLE 199
Query: 94 AFMEFDESLI----------KDEVMAILKT 113
A EFD+ L+ ++E+ A L+
Sbjct: 200 ALAEFDDELMEKYLEGEELSEEEIKAGLRK 229
>gnl|CDD|234905 PRK01122, PRK01122, potassium-transporting ATPase subunit B;
Provisional.
Length = 679
Score = 28.6 bits (65), Expect = 1.0
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 77 KKTEQFKKGNYKQALIDAFMEFD-ESLIKDEVMAILKTLKKENEVMAILKTL 127
K+ + F + AL DAF + D I++ VM ++ EV +IL T+
Sbjct: 4 KQAKLFDPALVRPALKDAFKKLDPRVQIRNPVMFVV-------EVGSILTTI 48
>gnl|CDD|217017 pfam02399, Herpes_ori_bp, Origin of replication binding protein.
This Pfam family represents the herpesvirus origin of
replication binding protein, probably involved in DNA
replication.
Length = 829
Score = 28.5 bits (64), Expect = 1.1
Identities = 12/31 (38%), Positives = 18/31 (58%), Gaps = 5/31 (16%)
Query: 102 LIKDEVMAILK-----TLKKENEVMAILKTL 127
LI DEVM+ + T+++ EV A+L L
Sbjct: 146 LILDEVMSTIGQLYSPTMRRLKEVDALLLRL 176
>gnl|CDD|173900 cd00674, LysRS_core_class_I, catalytic core domain of class I
lysyl tRNA synthetase. Class I lysyl tRNA synthetase
(LysRS) catalytic core domain. This class I enzyme is a
monomer which aminoacylates the 2'-OH of the nucleotide
at the 3' of the appropriate tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding. The class I LysRS is found only in archaea and
some bacteria and has evolved separately from class II
LysRS, as the two do not share structural or sequence
similarity.
Length = 353
Score = 28.4 bits (64), Expect = 1.1
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 6/39 (15%)
Query: 73 PEFIKKTEQFKKGNYKQALIDAFMEFDESLIKDEVMAIL 111
EFI +++ +K G Y + ++ A + +DE+MAIL
Sbjct: 121 VEFISQSQMYKSGLYDENILIALEK------RDEIMAIL 153
>gnl|CDD|225126 COG2216, KdpB, High-affinity K+ transport system, ATPase chain B
[Inorganic ion transport and metabolism].
Length = 681
Score = 28.4 bits (64), Expect = 1.4
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 77 KKTEQFKKGNYKQALIDAFMEFD-ESLIKDEVMAILKTLKKENEVMAILKTL 127
KK F +QAL DAF + + L+K+ VM ++ EV +IL T
Sbjct: 3 KKASLFDPALVRQALKDAFKKLNPRVLVKNPVMFVV-------EVGSILTTF 47
>gnl|CDD|130561 TIGR01497, kdpB, K+-transporting ATPase, B subunit. This model
describes the P-type ATPase subunit of the complex
responsible for translocating potassium ions across
biological membranes in microbes. In E. coli and other
species, this complex consists of the proteins KdpA,
KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while
KdpA is the potassium-ion translocating subunit. The
function of KdpC is unclear, although cit has been
suggested to couple the ATPase subunit to the
ion-translocating subunit , while KdpF serves to
stabilize the complex. The potassium P-type ATPases have
been characterized as Type IA based on a phylogenetic
analysis which places this clade closest to the
heavy-metal translocating ATPases (Type IB). Others
place this clade closer to the Na+/K+ antiporter type
(Type IIC) based on physical characteristics. This model
is very clear-cut, with a strong break between trusted
hits and noise. All members of the seed alignment, from
Clostridium, Anabaena and E. coli are in the
characterized table. One sequence above trusted,
OMNI|NTL01TA01282, is apparently mis-annotated in the
primary literature, but properly annotated by TIGR
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 675
Score = 28.3 bits (63), Expect = 1.5
Identities = 11/36 (30%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 77 KKTEQFKKGNYKQALIDAFMEFD-ESLIKDEVMAIL 111
KK + F K QA+ +AF + + ++ ++ VM I+
Sbjct: 3 KKLKLFTKTIVVQAIKEAFKKLNPKAQWRNPVMFIV 38
>gnl|CDD|239311 cd03013, PRX5_like, Peroxiredoxin (PRX) family, PRX5-like
subfamily; members are similar to the human protein,
PRX5, a homodimeric TRX peroxidase, widely expressed in
tissues and found cellularly in mitochondria,
peroxisomes and the cytosol. The cellular location of
PRX5 suggests that it may have an important antioxidant
role in organelles that are major sources of reactive
oxygen species (ROS), as well as a role in the control
of signal transduction. PRX5 has been shown to reduce
hydrogen peroxide, alkyl hydroperoxides and
peroxynitrite. As with all other PRXs, the N-terminal
peroxidatic cysteine of PRX5 is oxidized into a
sulfenic acid intermediate upon reaction with
peroxides. Human PRX5 is able to resolve this
intermediate by forming an intramolecular disulfide
bond with its C-terminal cysteine (the resolving
cysteine), which can then be reduced by TRX, just like
an atypical 2-cys PRX. This resolving cysteine,
however, is not conserved in other members of the
subfamily. In such cases, it is assumed that the
oxidized cysteine is directly resolved by an external
small-molecule or protein reductant, typical of a 1-cys
PRX. In the case of the H. influenza PRX5 hybrid, the
resolving glutaredoxin domain is on the same protein
chain as PRX. PRX5 homodimers show an A-type interface,
similar to atypical 2-cys PRXs.
Length = 155
Score = 27.5 bits (62), Expect = 1.5
Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 4/32 (12%)
Query: 68 TSQHLPEFIKKTEQFKKGNYKQALI----DAF 95
++QHLP +++ ++ K + + D F
Sbjct: 46 SAQHLPGYVENADELKAKGVDEVICVSVNDPF 77
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 28.1 bits (64), Expect = 1.5
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 73 PEFIKKTEQFKKGNYKQAL-IDAFMEFDESL--IKDEVMAILKTLK----KENEVMAILK 125
E ++ + K+A I E + +L IK+EV+ L + E E+ K
Sbjct: 239 EELKAAVKELAEAKLKEAYQITDKQEREAALDAIKEEVLEALAAEEEEEEDEKEIKEAFK 298
Query: 126 TLKKEI 131
L+K+I
Sbjct: 299 KLEKKI 304
>gnl|CDD|235723 PRK06170, PRK06170, amidase; Provisional.
Length = 490
Score = 28.1 bits (63), Expect = 1.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 8 PITKKESTNHEGSNLTCGASSMQGWRIYQEDA 39
P+T KES N G T G ++ + EDA
Sbjct: 80 PVTVKESFNVAGLPTTWGFPDLRD-YVPAEDA 110
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 27.9 bits (63), Expect = 1.6
Identities = 19/89 (21%), Positives = 34/89 (38%), Gaps = 21/89 (23%)
Query: 34 IYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQFKKGNYKQALID 93
I + D ++D K+ YD S +PE + K ++ L++
Sbjct: 155 IGEGDEFTGVVDLLSEKAY--RYDPGEPSVEIE-----IPE----ELKEKVAEAREELLE 203
Query: 94 AFMEFDESLI----------KDEVMAILK 112
A E DE L+ ++E+ A L+
Sbjct: 204 AVAETDEELMEKYLEEGELTEEELRAGLR 232
>gnl|CDD|224302 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
ribosomal structure and biogenesis].
Length = 521
Score = 27.7 bits (62), Expect = 2.0
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 73 PEFIKKTEQFKKGNYKQALIDAFMEFDESLIKDEVMAIL-KTLKKE 117
EF+ TE +K G Y +A+ A +DE+M IL + +E
Sbjct: 123 VEFVSATELYKSGLYDEAIRIALER------RDEIMEILNEYRGRE 162
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 26.5 bits (59), Expect = 4.3
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 9/69 (13%)
Query: 32 WRIYQEDAHN---VIIDFDENKSLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQ--FKKGN 86
W++ + + +++ ++ + V G G V T I++T F+ GN
Sbjct: 90 WKLGDKAQDDGVLLLVAMNDRRVRIEVGYGLEG----VLTDAQAGRIIRETIAPAFRDGN 145
Query: 87 YKQALIDAF 95
Y L
Sbjct: 146 YAGGLEAGI 154
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 26.7 bits (60), Expect = 4.6
Identities = 21/83 (25%), Positives = 35/83 (42%), Gaps = 12/83 (14%)
Query: 61 GSEVAVYTSQHLPEFIKK--TEQFKKGNYKQAL-IDAFMEFDESL--IKDEVMAILKTLK 115
G E + + + E +K E + K+A I E +L IK+EV+ L +
Sbjct: 218 GKEKWEFVAPEVDEELKAKVKELAYEAGLKEAYQITEKQERYAALDAIKEEVLEALAEEE 277
Query: 116 K-------ENEVMAILKTLKKEI 131
+ E E+ K L+K+I
Sbjct: 278 EEEEEADREKEIKEAFKDLEKKI 300
>gnl|CDD|238844 cd01709, RT_like_1, RT_like_1: A subfamily of reverse
transcriptases (RTs). An RT gene is usually indicative
of a mobile element such as a retrotransposon or
retrovirus. RTs occur in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 346
Score = 26.5 bits (59), Expect = 4.6
Identities = 22/86 (25%), Positives = 35/86 (40%), Gaps = 17/86 (19%)
Query: 51 SLFAVYDGHGGSEVAVYTSQHLPEFIKKTEQFKKGNYKQALIDAFMEFDESL----IKDE 106
LF G GGS E++++ + + G + D F F E L +K+
Sbjct: 261 RLFPDAGGGGGSVT---------EYLRQMIESRFG--VSDIPDGFFYFPEELGGLGLKNP 309
Query: 107 VMAILKTL--KKENEVMAILKTLKKE 130
+++L KE+ I K LK E
Sbjct: 310 FISLLLVRDSIKEDPEELIDKFLKAE 335
>gnl|CDD|234539 TIGR04317, W_rSAM_matur, tungsten cofactor oxidoreducase radical
SAM maturase. Members of this family are radical SAM
enzymes involved in the maturation of tungsten
(W)-containing cofactors in the enzymes aldehyde
ferredoxin oxidoreductase, formaldehyde ferredoxin
oxidoreductase, and others, and tend to be encoded by an
adjacent gene.
Length = 349
Score = 26.6 bits (59), Expect = 4.6
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 45 DFDENKSLFAVYDGHGGSEVA--VYTSQHLPEFI----KKTEQFKKGNYKQ-ALID 93
+F EN++ +DG V+ + E++ KK GN + +LID
Sbjct: 237 NFVENRAAVIRWDG----GVSPCYRFLHNYKEYVFGRKKKVYAHSFGNVNEESLID 288
>gnl|CDD|215816 pfam00246, Peptidase_M14, Zinc carboxypeptidase.
Length = 277
Score = 26.6 bits (59), Expect = 4.7
Identities = 23/96 (23%), Positives = 35/96 (36%), Gaps = 20/96 (20%)
Query: 15 TNHEGSNL---------TCGASSMQGWRIYQEDAHNV------IIDFDENKSLFAVYDGH 59
+N G +L GASS Y+ A + DF + D H
Sbjct: 114 SNANGVDLNRNFPDLWNEVGASSNPCSETYRGPAPFSEPETRAVADFIRSYKFKLYIDLH 173
Query: 60 GGSEVAVY----TSQHLPEFIKKTEQFKKGNYKQAL 91
G S++ +Y T LP ++ + K Y +AL
Sbjct: 174 GYSQLILYPYGYTYSSLPPDDEELKSLAKR-YAKAL 208
>gnl|CDD|218760 pfam05812, Herpes_BLRF2, Herpesvirus BLRF2 protein. This family
consists of several Herpesvirus BLRF2 proteins.
Length = 118
Score = 25.8 bits (57), Expect = 5.3
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 88 KQALI----DAFMEFDESLIKDEVMAILKTLKKENEVMAILKTLKKEITVSY 135
K+ALI I+ +V + L + E+ L L I VS
Sbjct: 46 KEALITSAVSKLTSQAMKKIEAKVRKLTAPLVTKEEIEEALANLTIRIDVSM 97
>gnl|CDD|224676 COG1762, PtsN, Phosphotransferase system mannitol/fructose-specific
IIA domain (Ntr-type) [Carbohydrate transport and
metabolism / Signal transduction mechanisms].
Length = 152
Score = 26.1 bits (58), Expect = 5.5
Identities = 10/42 (23%), Positives = 18/42 (42%)
Query: 89 QALIDAFMEFDESLIKDEVMAILKTLKKENEVMAILKTLKKE 130
+ A + L+ +E L K E E++AIL+ +
Sbjct: 111 NHHLKALSQLARLLLDEEFREQLLNAKSEEEIIAILENVLSS 152
>gnl|CDD|188641 cd00954, NAL, N-Acetylneuraminic acid aldolase, also called
N-acetylneuraminate lyase (NAL). N-Acetylneuraminic
acid aldolase, also called N-acetylneuraminate lyase
(NAL), which catalyses the reversible aldol reaction of
N-acetyl-D-mannosamine and pyruvate to give
N-acetyl-D-neuraminic acid (D-sialic acid). It has a
widespread application as biocatalyst for the synthesis
of sialic acid and its derivatives. This enzyme has been
shown to be quite specific for pyruvate as the donor,
but flexible to a variety of D- and, to some extent,
L-hexoses and pentoses as acceptor substrates. NAL is
member of dihydrodipicolinate synthase family that
comprises several pyruvate-dependent class I aldolases.
Length = 288
Score = 26.1 bits (58), Expect = 6.4
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 2/50 (4%)
Query: 73 PEFIKKTEQFKKGNYKQA--LIDAFMEFDESLIKDEVMAILKTLKKENEV 120
+ K E F G+ A L + LIK+ + LK + + +
Sbjct: 213 KRYRKIFEAFNAGDIDTARELQHVINDVITVLIKNGLYPTLKAILRLMGL 262
>gnl|CDD|107285 cd06290, PBP1_LacI_like_9, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 265
Score = 26.1 bits (58), Expect = 6.6
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 9/51 (17%)
Query: 87 YKQALIDAFMEFDESLIKDEVMAILKTLKKENEVMAILKTLKKEITVSYFT 137
Y++AL +A +E LI ++E+ + A+ + L++ FT
Sbjct: 137 YRKALEEAGLEVQPDLIVQ------GDFEEESGLEAVEELLQRGP---DFT 178
>gnl|CDD|143498 cd06825, PLPDE_III_VanT, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, VanT and similar proteins.
This subfamily is composed of Enterococcus gallinarum
VanT and similar proteins. VanT is a membrane-bound
serine racemase (EC 5.1.1.18) that is essential for
vancomycin resistance in Enterococcus gallinarum. It
converts L-serine into its D-enantiomer (D-serine) for
peptidoglycan synthesis. The C-terminal region of this
protein contains a PLP-binding TIM-barrel domain
followed by beta-sandwich domain, which is homologous to
the fold type III PLP-dependent enzyme, bacterial
alanine racemase (AR). AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. On the basis of this
similarity, it has been suggested that dimer formation
of VanT is required for its catalytic activity, and that
it catalyzes the racemization of serine in a
mechanistically similar manner to that of alanine by
bacterial AR. Some biochemical evidence indicates that
VanT also exhibits alanine racemase activity and plays a
role in the racemization of L-alanine. VanT contains a
unique N-terminal transmembrane domain, which may
function as an L-serine transporter. VanT serine
racemases are not related to eukaryotic serine
racemases, which are fold type II PLP-dependent enzymes.
Length = 368
Score = 26.2 bits (58), Expect = 7.6
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 94 AFMEFDESLIKDEVMAILKTLKKENEVMAILK 125
A++E D S ++ V I + L ++MA++K
Sbjct: 2 AWLEIDLSALEHNVKEIKRLLPSTCKLMAVVK 33
>gnl|CDD|216094 pfam00747, Viral_DNA_bp, ssDNA binding protein. This protein is
found in herpesviruses and is needed for replication.
Length = 1111
Score = 26.2 bits (58), Expect = 8.1
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 98 FDESLIKDEVMAILK--TLKKENEVMAILKTLK 128
F+ LI+ V IL+ + + A+++ L
Sbjct: 1020 FEVELIRQRVGIILEGGANVVDPVLAALVEALG 1052
>gnl|CDD|215888 pfam00384, Molybdopterin, Molybdopterin oxidoreductase.
Length = 358
Score = 25.8 bits (57), Expect = 9.0
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 34 IYQEDAHNVIIDFDENKSLFAVYDGHGGSEVAVY 67
+ D + V+ E LF VYDGH G + A Y
Sbjct: 276 VTHADENRVV-KALEKLDLFVVYDGHHGDKTAKY 308
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 0.362
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,874,779
Number of extensions: 610680
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 608
Number of HSP's successfully gapped: 65
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
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: 54 (24.6 bits)