RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10457
(508 letters)
>gnl|CDD|221353 pfam11977, RNase_Zc3h12a, Zc3h12a-like Ribonuclease NYN domain.
This domain is found in the Zc3h12a protein which has
shown to be a ribonuclease that controls the stability
of a set of inflammatory genes. It has been suggested
that this domain belongs to the PIN domain superfamily.
This domain has also been identified as part of the NYN
domain family.
Length = 155
Score = 242 bits (619), Expect = 2e-78
Identities = 93/157 (59%), Positives = 123/157 (78%), Gaps = 2/157 (1%)
Query: 113 KLRPVVIDGSNVAMSHGNKELFSCIGIKICVDWFRARGHKEITVFVPKWRKESCRPDNLI 172
KLRP+VIDGSNVAMSHGNKE FSC G+ + VD+FR RGH+ ITVFVP WR + D +
Sbjct: 1 KLRPIVIDGSNVAMSHGNKEFFSCRGLLLAVDYFRKRGHEVITVFVPNWRYK--ARDGKV 58
Query: 173 KNQEVLSELEKDRILVYTPSRLIGGKRLVCYDDRFILRLAADTDGIVVSNDNYRDLCLES 232
+Q L L + ++V+TPSR + G+R+V YDDRFIL LA +TDG++VSNDN+RDL ES
Sbjct: 59 TDQHELERLIRLGLIVFTPSRTLDGRRIVSYDDRFILELAEETDGVIVSNDNFRDLADES 118
Query: 233 PDFRKVVEDRILMYSFVNDRFMPPEDPLGRSGPSLDK 269
P+++ ++E+R+LMY+FV D+FM P+DPLGR GPSL+
Sbjct: 119 PEWKDIIEERLLMYTFVGDKFMLPDDPLGRLGPSLND 155
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 35.9 bits (83), Expect = 0.037
Identities = 19/124 (15%), Positives = 36/124 (29%), Gaps = 7/124 (5%)
Query: 372 AHGSYSNLSQNSDQGAPLHQRLQRQLSLNPYEEVPQGAPPHQHIASQNSSHNGGSSNGLN 431
A + Q A L Q L + + +P G + + + + N ++ L
Sbjct: 45 AEFPWDPSPQAPPPVAQLPQPLPQPPPTQALQALPAGDQQQHNTPTGSPAANPPATFALP 104
Query: 432 GYLNGHGFH--NGHNAPNGSHNGMTRNP-----YEEQKERMRLHYHLASLFPEDQVVAAM 484
G G P +T+NP + ++R P + +
Sbjct: 105 AGPAGPTIQTEPGQLYPVQVPVMVTQNPANSPLDQPAQQRALQQLQQRYGAPASGQLPSQ 164
Query: 485 QAHP 488
Q
Sbjct: 165 QQSA 168
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 31.4 bits (72), Expect = 0.057
Identities = 8/24 (33%), Positives = 11/24 (45%), Gaps = 3/24 (12%)
Query: 282 APCPY---GRKCTYGSKCKFNHPE 302
C + C YG +CKF H +
Sbjct: 4 ELCRFFSRTGTCKYGDRCKFAHGQ 27
>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger.
Length = 27
Score = 29.5 bits (67), Expect = 0.24
Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 2/23 (8%)
Query: 282 APCPYGRK--CTYGSKCKFNHPE 302
C + ++ C G +CKF HP
Sbjct: 5 ELCKFFKRGYCPRGDRCKFAHPL 27
>gnl|CDD|143274 cd05866, Ig1_NCAM-2, First immunoglobulin (Ig)-like domain of
neural cell adhesion molecule NCAM-2. Ig1_NCAM-2:
first immunoglobulin (Ig)-like domain of neural cell
adhesion molecule NCAM-2 (OCAM/mamFas II, RNCAM). NCAM-2
is organized similarly to NCAM , including five
N-terminal Ig-like domains and two fibronectin type III
domains. NCAM-2 is differentially expressed in the
developing and mature olfactory epithelium (OE), and may
function like NCAM, as an adhesion molecule.
Length = 92
Score = 30.4 bits (68), Expect = 0.61
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 117 VVIDGSNVAMSHGNKELFSC--IGIKICVDWFRARGHKEITVFVPKWRKESCRPDNLIKN 174
V I S V +S G + F+C IG +DW+ +G K ++ +KE R I N
Sbjct: 3 VSISLSKVELSVGESKFFTCTAIGEPESIDWYNPQGEKIVSSQRVVVQKEGVRSRLTIYN 62
Query: 175 QEV 177
+
Sbjct: 63 ANI 65
>gnl|CDD|177952 PLN02318, PLN02318, phosphoribulokinase/uridine kinase.
Length = 656
Score = 32.1 bits (73), Expect = 0.69
Identities = 27/124 (21%), Positives = 49/124 (39%), Gaps = 5/124 (4%)
Query: 330 NKTLSCPAVPNQYQHQEQQVTVHPQKTLLSRTRSYAPDSHPEAHGSYSNLSQNSDQGAPL 389
NK L + + Y Q + ++ R +S A + ++Q S+Q + L
Sbjct: 451 NKNLKSG-LSHSYSTQRDKNLSKLTGLAVTNRRFDERNSESPAALNQGAITQLSEQISSL 509
Query: 390 HQRLQRQLS----LNPYEEVPQGAPPHQHIASQNSSHNGGSSNGLNGYLNGHGFHNGHNA 445
++R+ S LN + + +P Q++A Q + NG + G+G G
Sbjct: 510 NERMDEFTSRIEELNSKLSIKKNSPSQQNLALQAEACNGSAPTSYFVSGLGNGSLTGSIL 569
Query: 446 PNGS 449
P S
Sbjct: 570 PLSS 573
>gnl|CDD|178200 PLN02590, PLN02590, probable tyrosine decarboxylase.
Length = 539
Score = 32.0 bits (72), Expect = 0.85
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 425 GSSNGLNGYLNGHGFHNGHNAPNGSHN 451
G SNG NGY NG+G NG+ NG+ +
Sbjct: 11 GYSNG-NGYTNGNGHTNGNGNYNGNGH 36
Score = 30.8 bits (69), Expect = 2.1
Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 421 SHNGGSSNGLNGYLNGHGFHNGHNAPNGS 449
S+ G +NG NG+ NG+G +NG+ NG+
Sbjct: 13 SNGNGYTNG-NGHTNGNGNYNGNGHVNGN 40
>gnl|CDD|222122 pfam13429, TPR_15, Tetratricopeptide repeat.
Length = 279
Score = 31.1 bits (71), Expect = 1.1
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 36 ESLSRQSTAEYDPGY-SARVDFALKLGYTED---LVQTALNKLGPNPSHNELLAELI 88
SL+ + AE G+ SAR ++ + G + + AL P+ ++L A L+
Sbjct: 133 ASLTPEEAAEQSAGFLSARAEYYRQTGQPDAALRDYRRALAL---PPASSDLRAALL 186
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 29.7 bits (67), Expect = 1.3
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 419 NSSHNGGSSNGLNGYLNGHGFHNGHNAPNGS 449
N GG NG G+ NG G+ NG NG
Sbjct: 83 NGGSGGGWVNGGGGWGNG-GWVNGGGWRNGY 112
>gnl|CDD|224827 COG1915, COG1915, Uncharacterized conserved protein [Function
unknown].
Length = 415
Score = 31.3 bits (71), Expect = 1.5
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 13/48 (27%)
Query: 75 GPNPSH-NELLAELIKLGAQVPTSFIQDNEQDCMPYPQAKLRPVVIDG 121
P+ H E+L+ELI LGA +P I++ +L P DG
Sbjct: 55 APDHEHLEEILSELIDLGAVIPE--IEE----------VELEPAPQDG 90
>gnl|CDD|238222 cd00379, Ribosomal_L10_P0, Ribosomal protein L10 family; composed
of the large subunit ribosomal protein called L10 in
bacteria, P0 in eukaryotes, and L10e in archaea, as well
as uncharacterized P0-like eukaryotic proteins. In all
three kingdoms, L10 forms a tight complex with multiple
copies of the small acidic protein L12(e). This complex
forms a stalk structure on the large subunit of the
ribosome. The N-terminal domain (NTD) of L10 interacts
with L11 protein and forms the base of the L7/L12 stalk,
while the extended C-terminal helix binds to two or
three dimers of the NTD of L7/L12 (L7 and L12 are
identical except for an acetylated N-terminus). The
L7/L12 stalk is known to contain the binding site for
elongation factors G and Tu (EF-G and EF-Tu,
respectively); however, there is disagreement as to
whether or not L10 is involved in forming the binding
site. The stalk is believed to be associated with GTPase
activities in protein synthesis. In a neuroblastoma cell
line, L10 has been shown to interact with the SH3 domain
of Src and to activate the binding of the Nck1 adaptor
protein with skeletal proteins such as the
Wiskott-Aldrich Syndrome Protein (WASP) and the
WASP-interacting protein (WIP). Some eukaryotic P0
sequences have an additional C-terminal domain
homologous with acidic proteins P1 and P2.
Length = 155
Score = 29.8 bits (68), Expect = 2.0
Identities = 24/69 (34%), Positives = 26/69 (37%), Gaps = 17/69 (24%)
Query: 47 DPGYSARV--DFA-------LKLGYTEDLV-----QTALNKLGPNPSHNELLAELIKLGA 92
DP A+V DFA K G V TAL KL PS ELLA LI L
Sbjct: 83 DPVEVAKVLKDFAKENKKLFAKGGVVAGKVLDPAGVTALAKL---PSREELLAMLIGLLK 139
Query: 93 QVPTSFIQD 101
+
Sbjct: 140 APIAKLARL 148
>gnl|CDD|236510 PRK09428, pssA, phosphatidylserine synthase; Provisional.
Length = 451
Score = 30.2 bits (69), Expect = 2.9
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 139 IKICVDWFRAR 149
IK+ VDW RA+
Sbjct: 83 IKVLVDWHRAQ 93
>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3. The
C.elegans Notch pathway, involved in the control of
growth, differentiation and patterning in animal
development, relies on either of the receptors GLP-1 or
LIN-12. Both these receptors promote signalling by the
recruitment of LAG-3 to target promoters, where it then
acts as a transcriptional activator. LAG-3 works as a
ternary complex together with the DNA binding protein,
LAG-1.
Length = 476
Score = 29.9 bits (66), Expect = 3.1
Identities = 35/143 (24%), Positives = 59/143 (41%), Gaps = 15/143 (10%)
Query: 314 RLMEHAQKQMSEKRQVNKTLSCPAVPNQYQHQEQQVTVHPQKTLL--SRTRSYAPDSHPE 371
RL++ + +M Q + +QHQ+QQ H Q+ +L + + + H +
Sbjct: 333 RLLQQQEMEMQRIEQQRQQ------QIMHQHQQQQQQEHQQQQMLLQQQQQMHQLQQHHQ 386
Query: 372 AHGSYSNLSQNSDQGAPLHQRLQRQLSLNPYEEVPQGAPPHQHIASQNSSHNGGSSNGLN 431
+G +Q A L Q++Q + Q A HQ Q H + +G
Sbjct: 387 MNGGGQFATQAHQHAAYL-QQMQHMRLQEQIQHQQQQAQHHQQAQQQ---HQQPAQHGQM 442
Query: 432 GY--LNGHGFH-NGHNAPNGSHN 451
GY NG+ H +GH G+H+
Sbjct: 443 GYGIPNGYPAHMHGHAPAYGAHH 465
>gnl|CDD|239052 cd02137, Nitroreductase_1, Nitroreductase-like family 1. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 148
Score = 29.1 bits (66), Expect = 3.2
Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 21/68 (30%)
Query: 81 NELLAELIKLGAQVPTSF---------IQDNEQ------DCMPYPQAKLRPVVI------ 119
E L E+++L P+SF ++D E+ M PQ VI
Sbjct: 21 REELKEILELATLAPSSFNLQPWRFVVVRDPEKKAKLAEAAMNQPQVTTASAVILVLGDL 80
Query: 120 DGSNVAMS 127
+ AM+
Sbjct: 81 NAGLAAMN 88
>gnl|CDD|240420 PTZ00441, PTZ00441, sporozoite surface protein 2 (SSP2);
Provisional.
Length = 576
Score = 29.9 bits (67), Expect = 3.7
Identities = 9/47 (19%), Positives = 20/47 (42%)
Query: 418 QNSSHNGGSSNGLNGYLNGHGFHNGHNAPNGSHNGMTRNPYEEQKER 464
+ G N + Y HG +N + N ++ + ++P + E+
Sbjct: 453 NKQVNPGNRHNSEDRYTRPHGRNNENRNYNNKNSDIPKHPERSEHEQ 499
>gnl|CDD|129401 TIGR00300, TIGR00300, TIGR00300 family protein. All members of the
family come from genome projects. A partial length
search brings in two plant lysine-ketoglutarate
reductase/saccharopine dehydrogenase bifunctional
enzymes hitting the N-terminal region of the family
[Hypothetical proteins, Conserved].
Length = 407
Score = 29.8 bits (67), Expect = 3.9
Identities = 26/108 (24%), Positives = 40/108 (37%), Gaps = 18/108 (16%)
Query: 75 GPNPSH-NELLAELIKLGAQVPTSFIQDNEQDCMPYPQAKLRPVVIDGSNVAMSHGNKEL 133
+ H E+L ELI LGA +P I++ E + PQ + P D V +H
Sbjct: 55 ARDHQHLEEILTELIDLGAVIPE--IEEVELE--TAPQDGVLP---DDFYVTTNHPTFVR 107
Query: 134 FSCIGIKICVDWFRARGHK--EITVFVPKWRKESCRP-DNLIKNQEVL 178
+W G + V P + C+P + K V+
Sbjct: 108 VGG-------EWVEVEGQRMDAAIVVTPNPPRARCKPIREIKKGDRVV 148
>gnl|CDD|178374 PLN02775, PLN02775, Probable dihydrodipicolinate reductase.
Length = 286
Score = 29.2 bits (66), Expect = 4.7
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 433 YLNGHGFHNGH-NAPNGS------HNGMTRNPYEE 460
+LNGH FH +P+G+ HN R+ Y E
Sbjct: 218 HLNGHAFHTYRLTSPDGTVSFEFQHNVCGRSIYAE 252
>gnl|CDD|219042 pfam06468, Spond_N, Spondin_N. This conserved region is found at
the in the N-terminal half of several Spondin proteins.
Spondins are involved in patterning axonal growth
trajectory through either inhibiting or promoting
adhesion of embryonic nerve cells.
Length = 197
Score = 28.9 bits (65), Expect = 5.3
Identities = 12/45 (26%), Positives = 17/45 (37%)
Query: 315 LMEHAQKQMSEKRQVNKTLSCPAVPNQYQHQEQQVTVHPQKTLLS 359
L + Q + R V K PA PN + V + L+S
Sbjct: 67 LESEIEAQGEKIRTVIKAFGAPAYPNGTGATSAEFEVDSRHHLVS 111
>gnl|CDD|223055 PHA03361, PHA03361, UL7 tegument protein; Provisional.
Length = 302
Score = 29.2 bits (66), Expect = 5.7
Identities = 22/73 (30%), Positives = 29/73 (39%), Gaps = 20/73 (27%)
Query: 204 DDRFILRLAADTDGIVVSNDNYRDLCLESPDFR-------KVVEDR---------ILMYS 247
R +L L +G VS+++Y CL P FR EDR +L +
Sbjct: 75 GGRLMLTLDGR-EGAEVSSEDYFAQCLAQPAFRGFAFAVLTAAEDRVHSLAVPPLVLPHR 133
Query: 248 FVNDRFMPPEDPL 260
V F PED L
Sbjct: 134 LV--LFR-PEDLL 143
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 29.3 bits (65), Expect = 6.2
Identities = 16/54 (29%), Positives = 23/54 (42%)
Query: 317 EHAQKQMSEKRQVNKTLSCPAVPNQYQHQEQQVTVHPQKTLLSRTRSYAPDSHP 370
+ Q+ ++ + Q + A QYQ +Q V PQ TLL DS P
Sbjct: 805 QQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQDTLLHPLLMRNGDSRP 858
Score = 28.9 bits (64), Expect = 9.0
Identities = 29/113 (25%), Positives = 38/113 (33%), Gaps = 13/113 (11%)
Query: 307 PHKTV-TERLMEHAQKQMSEKRQVNKTLSCPAVPNQYQHQEQQVTVHPQKTLLSRTRSYA 365
PH+ + T + Q Q Q V Q Q+Q+ Q V PQ + A
Sbjct: 740 PHEPLFTPIVEPVQQPQQPVAPQQQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVA 799
Query: 366 PDSHPEAHGSYSNLSQNSDQGAPLHQRLQRQLSLNPYEEVPQGAPPHQHIASQ 418
P + Q AP Q Q Q + P PQ P Q +A Q
Sbjct: 800 PQPQYQ---------QPQQPVAPQPQYQQPQQPVAPQ---PQYQQPQQPVAPQ 840
>gnl|CDD|188151 TIGR01517, ATPase-IIB_Ca, plasma-membrane calcium-translocating
P-type ATPase. This model describes the P-type ATPase
responsible for translocating calcium ions across the
plasma membrane of eukaryotes , out of the cell. In some
organisms, this type of pump may also be found in
vacuolar membranes. In humans and mice, at least, there
are multiple isoforms of the PMCA pump with overlapping
but not redundant functions. Accordingly, there are no
human diseases linked to PMCA defects, although
alterations of PMCA function do elicit physiological
effects. The calcium P-type ATPases have been
characterized as Type IIB based on a phylogenetic
analysis which distinguishes this group from the Type
IIA SERCA calcium pump. A separate analysis divides Type
IIA into sub-types (SERCA and PMR1) which are modelled
by TIGR01116 and TIGR01522. This model is well separated
from those.
Length = 944
Score = 29.4 bits (66), Expect = 6.5
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 228 LCLESPDFRKVVEDRILMYSFVNDRFMPPEDPLGRSGPSLDKFL 271
L +E +FR +V + + D +P L RS P LDK L
Sbjct: 627 LAMEGKEFRSLVYEEM-------DPILPKLRVLARSSP-LDKQL 662
>gnl|CDD|233311 TIGR01208, rmlA_long, glucose-1-phosphate thymidylylransferase,
long form. The family of known and putative
glucose-1-phosphate thymidyltransferase (also called
dTDP-glucose synthase) shows a deep split into a short
form (see TIGR01207) and a long form described by this
model. The homotetrameric short form is found in
numerous bacterial species that incorporate
dTDP-L-rhamnose, which it helps synthesize, into the
cell wall. It is subject to feedback inhibition. This
form, in contrast, is found in many species for which it
serves as a sugar-activating enzyme for antibiotic
biosynthesis and or other, unknown pathways, and in
which dTDP-L-rhamnose is not necessarily produced.
Alternate name: dTDP-D-glucose synthase.
Length = 353
Score = 28.9 bits (65), Expect = 6.7
Identities = 15/55 (27%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 143 VDWFRARGHKEITVFVPKWRKESCRPDNLIK-NQEVLSELEKDRILVYTPSRLIG 196
+ W +G+K V W K++ +P++L+ N+ +L E+E++ V S++ G
Sbjct: 199 IQWLIEKGYKVGGSKVTGWWKDTGKPEDLLDANRLILDEVEREVQGVDDESKIRG 253
>gnl|CDD|227877 COG5590, COG5590, Uncharacterized conserved protein [Function
unknown].
Length = 229
Score = 28.3 bits (63), Expect = 7.5
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 9/57 (15%)
Query: 43 TAEYDPGYSARVDFALKL----GYTEDLVQTALNKLGPNPSHNELLA-----ELIKL 90
+ + L+L G+ L+ AL LG + ++ +L ELIK
Sbjct: 22 YEKESIKKIVFLQSLLELVPFNGWNNRLIVEALEALGYSKGYSLILFPEGPMELIKF 78
>gnl|CDD|130919 TIGR01860, VNFD, nitrogenase vanadium-iron protein, alpha chain.
This model represents the alpha chain of the
vanadium-containing component of the vanadium-iron
nitrogenase compound I. The complex also includes a
second alpha chain, two beta chains and two delta
chains. Compount I interacts with compound II also known
as the iron-protein which transfers electrons to
compound I where the catalysis occurs [Central
intermediary metabolism, Nitrogen fixation].
Length = 461
Score = 28.8 bits (64), Expect = 7.8
Identities = 18/47 (38%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 433 YLNGHGFHNG-HNAPNGSHNGMTRNPYEEQKERMRLHYHLASLFPED 478
Y+NGHG+HNG + G+ N M R+ Y +R HLA++ D
Sbjct: 418 YVNGHGYHNGPYMGFEGAVN-MARDMYNAIYSPLR---HLAAVDIRD 460
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 28.5 bits (64), Expect = 8.0
Identities = 9/46 (19%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 208 ILRLAADTDGIVVSNDNYRDLCLES--PDFRKVVEDR---ILMYSF 248
+ LA +++S++ Y +L + P +++ I++ SF
Sbjct: 157 LAELAKKHGILIISDEAYAELVYDGEPPPALALLDAYERVIVLRSF 202
>gnl|CDD|197232 cd09134, PLDc_PSS_G_neg_1, Catalytic domain, repeat 1, of
phosphatidylserine synthases from gram-negative
bacteria. Catalytic domain, repeat 1, of
phosphatidylserine synthases (PSSs) from gram-negative
bacteria. There are two subclasses of PSS enzymes in
bacteria: subclass I of gram-negative bacteria and
subclass II of gram-positive bacteria. It is common that
PSSs in gram-positive bacteria and yeast are tight
membrane-associated enzymes. By contrast, the
gram-negative bacterial PSSs, such as Escherichia coli
PSS, are commonly bound to the ribosomes. They are
peripheral membrane proteins that can interact with the
surface of the inner membrane by binding to the lipid
substrate (CDP-diacylglycerol) and the lipid product
(phosphatidylserine). The prototypical member of this
subfamily is Escherichia coli PSS (also called
CDP-diacylglycerol-L-serine O-phosphatidyltransferase,
EC 2.7.8.8), which catalyzes the exchange reactions
between CMP and CDP-diacylglycerol, and between serine
and phosphatidylserine. The phosphatidylserine is then
decarboxylated by phosphatidylserine decarboxylase to
yield phosphatidylethanolamine, the major phospholipid
in Escherichia coli. It also catalyzes the hydrolysis of
CDP-diacylglycerol to form phosphatidic acid with the
release of CMP. PSS may utilize a ping-pong mechanism
involving a phosphatidyl-enzyme intermediate, which is
distinct from those of gram-positive bacterial
phosphatidylserine synthases. Moreover, all members in
this subfamily have two HKD motifs (H-x-K-x(4)-D, where
x represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
constitute an active site for the formation of a
covalent substrate-enzyme intermediate.
Length = 173
Score = 28.0 bits (63), Expect = 8.2
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 139 IKICVDWFRAR 149
IK+ VDW RA+
Sbjct: 67 IKVLVDWHRAQ 77
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
0.316 0.133 0.407
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,601,447
Number of extensions: 2453555
Number of successful extensions: 2165
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2152
Number of HSP's successfully gapped: 35
Length of query: 508
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 407
Effective length of database: 6,457,848
Effective search space: 2628344136
Effective search space used: 2628344136
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 (21.6 bits)
S2: 61 (27.2 bits)