RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5168
(113 letters)
>gnl|CDD|239876 cd04413, NDPk_I, Nucleoside diphosphate kinase Group I
(NDPk_I)-like: NDP kinase domains are present in a
large family of structurally and functionally conserved
proteins from bacteria to humans that generally
catalyze the transfer of gamma-phosphates of a
nucleoside triphosphate (NTP) donor onto a nucleoside
diphosphate (NDP) acceptor through a phosphohistidine
intermediate. The mammalian nm23/NDP kinase gene family
can be divided into two distinct groups. The group I
genes encode proteins that generally have highly
homologous counterparts in other organisms and possess
the classic enzymatic activity of a kinase. This group
includes vertebrate NDP kinases A-D (Nm23- H1 to -H4),
and its counterparts in bacteria, archea and other
eukaryotes. NDP kinases exist in two different
quaternary structures; all known eukaryotic enzymes are
hexamers, while some bacterial enzymes are tetramers,
as in Myxococcus. They possess the NDP kinase active
site motif (NXXH[G/A]SD) and the nine residues that are
most essential for catalysis.
Length = 130
Score = 153 bits (390), Expect = 1e-49
Identities = 44/79 (55%), Positives = 58/79 (73%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT ++IKPDGVQRGL+G II RFE KG K+VA+K + +EEL ++HY++ KPFFP L
Sbjct: 1 ERTLVIIKPDGVQRGLIGEIISRFERKGLKIVALKMLQLTEELAEEHYAEHKGKPFFPEL 60
Query: 66 VKYMSSGPVVPMCWARPEV 84
V++M+SGPVV M
Sbjct: 61 VEFMTSGPVVAMVLEGENA 79
>gnl|CDD|201162 pfam00334, NDK, Nucleoside diphosphate kinase.
Length = 135
Score = 148 bits (375), Expect = 2e-47
Identities = 43/79 (54%), Positives = 57/79 (72%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT ++IKPD VQRGL+G II RFE KGFK+VA+K + + E ++HY++ KPFFPGL
Sbjct: 1 ERTLVIIKPDAVQRGLIGEIISRFEKKGFKIVALKMLQLTREQAEEHYAEHKGKPFFPGL 60
Query: 66 VKYMSSGPVVPMCWARPEV 84
V++M+SGPVV M
Sbjct: 61 VEFMTSGPVVAMVLEGENA 79
>gnl|CDD|173387 PTZ00093, PTZ00093, nucleoside diphosphate kinase, cytosolic;
Provisional.
Length = 149
Score = 142 bits (361), Expect = 3e-45
Identities = 52/81 (64%), Positives = 63/81 (77%)
Query: 4 PKERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFP 63
ERTF+M+KPDGVQRGLVG IIKRFE KG+KLVA+K + P+ E+ ++HY + KPFFP
Sbjct: 1 SSERTFIMVKPDGVQRGLVGEIIKRFEKKGYKLVALKMLQPTPEIAEEHYKEHKGKPFFP 60
Query: 64 GLVKYMSSGPVVPMCWARPEV 84
GLVKY+SSGPVV M W V
Sbjct: 61 GLVKYISSGPVVCMVWEGKNV 81
>gnl|CDD|179085 PRK00668, ndk, mulitfunctional nucleoside diphosphate
kinase/apyrimidinic endonuclease/3'-; Validated.
Length = 134
Score = 141 bits (357), Expect = 1e-44
Identities = 43/74 (58%), Positives = 54/74 (72%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERTF +IKPD VQRGL+G II RFE KG K+VA+K + S EL + HY++ KPFF L
Sbjct: 2 ERTFSIIKPDAVQRGLIGEIISRFEKKGLKIVALKMMQLSRELAEGHYAEHKEKPFFGEL 61
Query: 66 VKYMSSGPVVPMCW 79
V++M+SGPVV M
Sbjct: 62 VEFMTSGPVVVMVL 75
>gnl|CDD|197791 smart00562, NDK, Enzymes that catalyze nonsubstrate specific
conversions of nucleoside diphosphates to nucleoside
triphosphates. These enzymes play important roles in
bacterial growth, signal transduction and
pathogenicity.
Length = 135
Score = 130 bits (329), Expect = 2e-40
Identities = 42/79 (53%), Positives = 55/79 (69%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT +IKPD VQRGL+G II RFE KGFK+VAMK + +EE ++ Y++ KPFF L
Sbjct: 1 ERTLAIIKPDAVQRGLIGEIISRFERKGFKIVAMKMLQLTEEQAEEFYAEHEGKPFFNDL 60
Query: 66 VKYMSSGPVVPMCWARPEV 84
V++M+SGPVV M +
Sbjct: 61 VEFMTSGPVVAMVLEGEDA 79
>gnl|CDD|223183 COG0105, Ndk, Nucleoside diphosphate kinase [Nucleotide transport
and metabolism].
Length = 135
Score = 129 bits (326), Expect = 5e-40
Identities = 41/74 (55%), Positives = 53/74 (71%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT +IKPD V+RGL+G II RFE KG K+VA+K V S EL + HY++ KPFF L
Sbjct: 3 ERTLSIIKPDAVKRGLIGEIISRFEKKGLKIVALKMVQLSRELAENHYAEHKGKPFFGEL 62
Query: 66 VKYMSSGPVVPMCW 79
V++++SGPVV M
Sbjct: 63 VEFITSGPVVAMVL 76
>gnl|CDD|178228 PLN02619, PLN02619, nucleoside-diphosphate kinase.
Length = 238
Score = 116 bits (292), Expect = 8e-34
Identities = 48/74 (64%), Positives = 57/74 (77%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERTF+ IKPDGVQRGL+ II RFE KGFKLVA+K V PS+E ++HY DL +PFF GL
Sbjct: 89 ERTFIAIKPDGVQRGLISEIISRFERKGFKLVAIKVVVPSKEFAQKHYHDLKERPFFNGL 148
Query: 66 VKYMSSGPVVPMCW 79
++SSGPVV M W
Sbjct: 149 CDFLSSGPVVAMVW 162
>gnl|CDD|238335 cd00595, NDPk, Nucleoside diphosphate kinases (NDP kinases,
NDPks): NDP kinases, responsible for the synthesis of
nucleoside triphosphates (NTPs), are involved in
numerous regulatory processes associated with
proliferation, development, and differentiation. They
are vital for DNA/RNA synthesis, cell division,
macromolecular metabolism and growth. The enzymes
generate NTPs or their deoxy derivatives by terminal
(gamma) phosphotransfer from an NTP such as ATP or GTP
to any nucleoside diphosphate (NDP) or its deoxy
derivative. The sequence of NDPk has been highly
conserved through evolution. There is a single
histidine residue conserved in all known NDK isozymes,
which is involved in the catalytic mechanism. The first
confirmed metastasis suppressor gene was the NDP kinase
protein encoded by the nm23 gene. Unicellular organisms
generally possess only one gene encoding NDP kinase,
while most multicellular organisms possess not only an
ortholog that provides most of the NDP kinase enzymatic
activity but also multiple divergent paralogous genes.
The human genome codes for at least nine NDP kinases
and can be classified into two groups, Groups I and II,
according to their genomic architecture and distinct
enzymatic activity. Group I isoforms (A-D) are
well-conserved, catalytically active, and share 58-88%
identity between each other, while Group II are more
divergent, with only NDPk6 shown to be active. NDP
kinases exist in two different quaternary structures;
all known eukaryotic enzymes are hexamers, while some
bacterial enzymes are tetramers, as in Myxococcus. The
hexamer can be viewed as trimer of dimers, while
tetramers are dimers of dimers, with the dimerization
interface conserved.
Length = 133
Score = 108 bits (272), Expect = 8e-32
Identities = 39/76 (51%), Positives = 52/76 (68%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT +IKPD V GL+G II R ED GF++VAMK + +EE ++ Y + +PFFP L
Sbjct: 1 ERTLALIKPDAVAEGLLGEIIMRIEDAGFEIVAMKELHLTEEQAEEFYVEHKGRPFFPDL 60
Query: 66 VKYMSSGPVVPMCWAR 81
V++MSSGPVV M +
Sbjct: 61 VQFMSSGPVVAMILEK 76
>gnl|CDD|184733 PRK14540, PRK14540, nucleoside diphosphate kinase; Provisional.
Length = 134
Score = 84.1 bits (208), Expect = 3e-22
Identities = 33/73 (45%), Positives = 53/73 (72%)
Query: 5 KERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPG 64
KERTF+ +KPD V+R L+G II+RFE+KGF++V MK + + E+ +++Y + K F+
Sbjct: 2 KERTFVALKPDAVERKLIGKIIQRFENKGFEIVEMKMLKLTREMAEEYYEEHKGKEFYER 61
Query: 65 LVKYMSSGPVVPM 77
L+ +M+SG +V M
Sbjct: 62 LINFMTSGRIVAM 74
>gnl|CDD|173008 PRK14542, PRK14542, nucleoside diphosphate kinase; Provisional.
Length = 137
Score = 80.9 bits (199), Expect = 7e-21
Identities = 36/76 (47%), Positives = 50/76 (65%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
RTF+MIKPDGV+ VGNI++R E +GFK++ +K++ S E KQ Y + +PF+ L
Sbjct: 2 SRTFIMIKPDGVKNKHVGNILQRIEKEGFKILGLKYLKLSLEDAKQFYKVHSARPFYNDL 61
Query: 66 VKYMSSGPVVPMCWAR 81
YMSSGP+V R
Sbjct: 62 CNYMSSGPIVAAALER 77
>gnl|CDD|184734 PRK14545, PRK14545, nucleoside diphosphate kinase; Provisional.
Length = 139
Score = 77.3 bits (190), Expect = 2e-19
Identities = 29/69 (42%), Positives = 42/69 (60%)
Query: 7 RTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGLV 66
RTF MIKPD V+ G +G I+ GF++VAMK + + Y+ A +PF+ LV
Sbjct: 5 RTFTMIKPDAVENGHIGGILDMITAAGFRIVAMKLTQLTVADAETFYAVHAERPFYGELV 64
Query: 67 KYMSSGPVV 75
++MS GP+V
Sbjct: 65 EFMSRGPIV 73
>gnl|CDD|173007 PRK14541, PRK14541, nucleoside diphosphate kinase; Provisional.
Length = 140
Score = 70.0 bits (171), Expect = 1e-16
Identities = 31/72 (43%), Positives = 48/72 (66%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT ++KPD V++ L+G +I + E GF++VAMK ++E + Y+ +PF+ L
Sbjct: 2 ERTLTILKPDCVRKQLIGAVIDKIERAGFRVVAMKKTRLTKETAGEFYAVHRERPFYGEL 61
Query: 66 VKYMSSGPVVPM 77
V++MSSGP VPM
Sbjct: 62 VEFMSSGPCVPM 73
>gnl|CDD|237749 PRK14543, PRK14543, nucleoside diphosphate kinase; Provisional.
Length = 169
Score = 70.3 bits (172), Expect = 2e-16
Identities = 30/74 (40%), Positives = 48/74 (64%), Gaps = 5/74 (6%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQH--YSDLATK---P 60
++T +IKPDGV+RGL+GN++ RFE G K+VA K + + ++H Y D+A +
Sbjct: 6 QKTLCIIKPDGVRRGLIGNVVSRFERVGLKIVAAKMLLVDRSMAEKHYLYDDIAVRHGEA 65
Query: 61 FFPGLVKYMSSGPV 74
+ L+K++SS PV
Sbjct: 66 VWKSLIKFISSSPV 79
>gnl|CDD|173010 PRK14544, PRK14544, nucleoside diphosphate kinase; Provisional.
Length = 183
Score = 69.5 bits (170), Expect = 4e-16
Identities = 41/107 (38%), Positives = 53/107 (49%), Gaps = 33/107 (30%)
Query: 4 PKERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHY---------- 53
P ERT +++KPD V+RGLVG II RFE G K+VAMK V + E +++ Y
Sbjct: 2 PIERTLVILKPDAVKRGLVGEIISRFEKAGLKIVAMKMVKATPEQIERFYPSSEEWYRSV 61
Query: 54 ----------------SDLATK-PFFPG------LVKYMSSGPVVPM 77
+ L T P G LVKYM+SGP+V M
Sbjct: 62 GNKLLKAYQELGIDPRARLGTDDPVEVGKKVKESLVKYMTSGPIVAM 108
>gnl|CDD|215503 PLN02931, PLN02931, nucleoside diphosphate kinase family protein.
Length = 177
Score = 64.8 bits (158), Expect = 3e-14
Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 2 AEPKERTFLMIKPDGVQRGLVGNIIKRFE----DKGFKLVAMKFVWPSEELLKQHYSDLA 57
A +ERT MIKPDG L GN +R + + GF +V E+ Y++ +
Sbjct: 26 ASEEERTLAMIKPDG----LSGNYTERIKEVILESGFSIVKEMTTQLDEDRASLFYAEHS 81
Query: 58 TKPFFPGLVKYMSSGPVVPMCWARP 82
++ FFP LVKYM+SGPV+ M +
Sbjct: 82 SRSFFPSLVKYMTSGPVLVMVLEKE 106
>gnl|CDD|239878 cd04415, NDPk7A, Nucleoside diphosphate kinase 7 domain A
(NDPk7A): The nm23-H7 class of nucleoside diphosphate
kinase (NDPk7) consists of an N-terminal DM10 domain
and two functional catalytic NDPk modules, NDPk7A and
NDPk7B. The function of the DM10 domain, which also
occurs in multiple copies in other proteins, is
unknown. NDPk7 is predominantly expressed in testes,
although appreciable amount are also found in liver,
heart, brain, ovary, small intestine and spleen. The
nm23-H7 gene is located in or near the hereditary
prostrate cancer susceptibility locus. Nm23-H7 may be
involved in the development of colon and gastric
carcinoma, the latter possibly in a type-specific
manner.
Length = 131
Score = 62.5 bits (152), Expect = 8e-14
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 2/72 (2%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
E+T +IKPD + +G II+ ED GF + K S + + Y++ +KPF+ L
Sbjct: 1 EKTLALIKPDAYSK--IGKIIQIIEDAGFTITKAKMTKLSRKEAQDFYAEHQSKPFYNEL 58
Query: 66 VKYMSSGPVVPM 77
V++M+SGP+V M
Sbjct: 59 VQFMTSGPIVAM 70
>gnl|CDD|239880 cd04418, NDPk5, Nucleoside diphosphate kinase homolog 5 (NDP
kinase homolog 5, NDPk5, NM23-H5; Inhibitor of
p53-induced apoptosis-beta, IPIA-beta): In human, mRNA
for NDPk5 is almost exclusively found in testis,
especially in the flagella of spermatids and
spermatozoa, in association with axoneme microtubules,
and may play a role in spermatogenesis by increasing
the ability of late-stage spermatids to eliminate
reactive oxygen species. It belongs to the nm23 Group
II genes and appears to differ from the other human
NDPks in that it lacks two important catalytic site
residues, and thus does not appear to possess NDP
kinase activity. NDPk5 confers protection from cell
death by Bax and alters the cellular levels of several
antioxidant enzymes, including glutathione peroxidase 5
(Gpx5).
Length = 132
Score = 58.2 bits (141), Expect = 3e-12
Identities = 31/76 (40%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
ERT +IKPD V + I + GF +V + + S E Y++ K FFP L
Sbjct: 1 ERTLAIIKPDAVHK--AEEIEDIILESGFTIVQKRKLQLSPEQCSDFYAEHYGKMFFPHL 58
Query: 66 VKYMSSGPVVPMCWAR 81
V YMSSGP+V M AR
Sbjct: 59 VAYMSSGPIVAMVLAR 74
>gnl|CDD|239875 cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B
(NDPk7B): The nm23-H7 class of nucleoside diphosphate
kinase (NDPk7) consists of an N-terminal DM10 domain
and two functional catalytic NDPk modules, NDPk7A and
NDPk7B. The function of the DM10 domain, which also
occurs in multiple copies in other proteins, is
unknown. NDPk7 is predominantly expressed in testes,
although appreciable amount are also found in liver,
heart, brain, ovary, small intestine and spleen. The
nm23-H7 gene is located in or near the hereditary
prostrate cancer susceptibility locus. Nm23-H7 may be
involved in the development of colon and gastric
carcinoma, the latter possibly in a type-specific
manner.
Length = 134
Score = 57.3 bits (139), Expect = 8e-12
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 7 RTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPS----EELLKQHYSDLATKPFF 62
T +IKP V GL+G I+++ D+GF++ A++ + EE L+ Y + P
Sbjct: 2 CTVCIIKPHAVSHGLLGEILQQILDEGFEITALQMFNLTRANAEEFLE-VYKGVV--PEL 58
Query: 63 PGLVKYMSSGPVVPM 77
P +V ++SGP + +
Sbjct: 59 PAMVDELTSGPCIAL 73
>gnl|CDD|239879 cd04416, NDPk_TX, NDP kinase domain of thioredoxin
domain-containing proteins (TXNDC3 and TXNDC6): Txl-2
(TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of
Group II N-terminal thioredoxin domains followed by one
or three NDP kinase domains, respectively. Sptrx-2,
which has a tissue specific distribution in human
testis, has been considered as a member of the nm23
family (nm23-H8) and exhibits a high homology with sea
urchin IC1 (intermediate chain-1) protein, a component
of the sperm axonemal outer dynein arm complex. Txl-2
is mainly represented in close association with
microtubules within tissues with cilia and flagella
such as seminiferous epithelium (spermatids) and lung
airway epithelium, suggesting possible role in control
of microtubule stability and maintenance.
Length = 132
Score = 53.4 bits (129), Expect = 2e-10
Identities = 22/73 (30%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPGL 65
E T +IKPD V I+++ ++ GF+++A K + +EE ++ Y + + +F L
Sbjct: 1 EYTLALIKPDAVAEK-KDEILEKIKEAGFEILAQKEMVLTEEQAREFYKEHEEEDYFEDL 59
Query: 66 VKYMSSGPVVPMC 78
V++M+SGP + +
Sbjct: 60 VEFMTSGPSLILV 72
>gnl|CDD|239877 cd04414, NDPk6, Nucleoside diphosphate kinase 6 (NDP kinase 6,
NDPk6, NM23-H6; NME6; Inhibitor of p53-induced
apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding
NDPk6 is expressed mainly in mitochondria, but also
found at a lower level in most tissues. NDPk6 has all
nine residues considered crucial for enzyme structure
and activity, and has been found to have NDP kinase
activity. It may play a role in cell growth and cell
cycle progression. The nm23-H6 gene locus has been
implicated in a variety of malignant tumors.
Length = 135
Score = 49.7 bits (119), Expect = 7e-09
Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 1/80 (1%)
Query: 6 ERTFLMIKPDGVQRGLVGNIIKRF-EDKGFKLVAMKFVWPSEELLKQHYSDLATKPFFPG 64
+ T +IKPD V L +++ GF +V K + + E ++ Y++ K F+
Sbjct: 1 QLTLALIKPDAVAHPLALEAVRQLILSNGFTIVRKKELRWTTEDAERFYAEHKGKFFYDR 60
Query: 65 LVKYMSSGPVVPMCWARPEV 84
LV +M+SGP + A
Sbjct: 61 LVSFMTSGPSWALILAHENA 80
>gnl|CDD|132883 cd07062, Peptidase_S66_mccF_like, Microcin C7 self-immunity
protein determines resistance to exogenous microcin C7.
Microcin C7 self-immunity protein (mccF): MccF, a
homolog of the LD-carboxypeptidase family, mediates
resistance against exogenously added microcin C7
(MccC7), a ribosomally-encoded peptide antibiotic that
contains a phosphoramidate linkage to adenosine
monophosphate at its C-terminus. The plasmid-encoded
mccF gene is transcribed in the opposite direction to
the other five genes (mccA-E) and is required for the
full expression of immunity but not for production. The
catalytic triad residues (Ser, His, Glu) of
LD-carboxypeptidase are also conserved in MccF,
strongly suggesting that MccF shares the hydrolytic
activity with LD-carboxypeptidases. Substrates of MccF
have not been deduced, but could likely be microcin C7
precursors. The possible role of MccF is to defend
producer cells against exogenous microcin from
re-entering after having been exported. It is
suggested that MccF is involved in microcin degradation
or sequestration in the periplasm.
Length = 308
Score = 31.4 bits (72), Expect = 0.065
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 26 IKRFEDKGFKLVAMKFVWPSEELLKQH 52
KR E+ GF++V ++ L
Sbjct: 24 KKRLENLGFEVVEGPNALKGDKYLSAS 50
>gnl|CDD|238712 cd01424, MGS_CPS_II, Methylglyoxal synthase-like domain from type
II glutamine-dependent carbamoyl phosphate synthetase
(CSP). CSP, a CarA and CarB heterodimer, catalyzes the
production of carbamoyl phosphate which is subsequently
employed in the metabolic pathways responsible for the
synthesis of pyrimidine nucleotides or arginine. The
MGS-like domain is the C-terminal domain of CarB and
appears to play a regulatory role in CPS function by
binding allosteric effector molecules, including UMP
and ornithine.
Length = 110
Score = 27.4 bits (62), Expect = 0.78
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 25 IIKRFEDKGFKLVA 38
I KR + GFKLVA
Sbjct: 18 IAKRLAELGFKLVA 31
>gnl|CDD|234087 TIGR03013, EpsB_2, sugar transferase, PEP-CTERM system associated.
Members of this protein family belong to the family of
bacterial sugar transferases (pfam02397). Nearly all are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria (notable exceptions appear to
include Magnetococcus sp. MC-1 and Myxococcus xanthus DK
1622 ). These genes are generally found near one or more
of the PrsK, PrsR or PrsT genes that have been related
to the PEP-CTERM system by phylogenetic profiling
methods. The nature of the sugar transferase reaction
catalyzed by members of this clade is unknown and may
conceivably be variable with respect to substrate by
species. These proteins are homologs of the EpsB protein
found in Methylobacillus sp. strain 12S , which is also
associated with a PEP-CTERM system, but of a distinct
type. A name which appears attached to a number of genes
(by transitive annotation) in this family is
"undecaprenyl-phosphate galactose phosphotransferase",
which comes from relatively distant characterized
enterobacterial homologs, and is considerably more
specific than warranted from the currently available
evidence.
Length = 442
Score = 26.2 bits (58), Expect = 4.0
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 11 MIKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWP 44
+I +G + + I KR D L+ + P
Sbjct: 240 LIFSNGFRNSSLRRITKRSFDVVASLILLILTLP 273
>gnl|CDD|178370 PLN02771, PLN02771, carbamoyl-phosphate synthase
(glutamine-hydrolyzing).
Length = 415
Score = 26.1 bits (57), Expect = 5.6
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 20 GLVGNIIKRFEDKGFKLVAMKFVWPSEELLK 50
G+ NI++R G K+ + WP+ E LK
Sbjct: 249 GIKHNILRRLASYGCKITVVPSTWPASEALK 279
>gnl|CDD|201571 pfam01047, MarR, MarR family. The Mar proteins are involved in
the multiple antibiotic resistance, a non-specific
resistance system. The expression of the mar operon is
controlled by a repressor, MarR. A large number of
compounds induce transcription of the mar operon. This
is thought to be due to the compound binding to MarR,
and the resulting complex stops MarR binding to the
DNA. With the MarR repression lost, transcription of
the operon proceeds. The structure of MarR is known and
shows MarR as a dimer with each subunit containing a
winged-helix DNA binding motif.
Length = 59
Score = 24.4 bits (54), Expect = 6.1
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 16 GVQRGLVGNIIKRFEDKGF 34
GV R V ++ R E KG
Sbjct: 28 GVDRSTVTRVLDRLEKKGL 46
>gnl|CDD|216847 pfam02016, Peptidase_S66, LD-carboxypeptidase.
Muramoyl-tetrapeptide carboxypeptidase hydrolyses a
peptide bond between a di-basic amino acid and the
C-terminal D-alanine in the tetrapeptide moiety in
peptidoglycan. This cleaves the bond between an L- and
a D-amino acid. The function of this activity is in
murein recycling. This family also includes the
microcin c7 self-immunity protein. This family
corresponds to Merops family S66.
Length = 281
Score = 25.6 bits (57), Expect = 7.0
Identities = 7/32 (21%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 12 IKPDGVQRGLVGNIIKRFEDKGFKLVAMKFVW 43
+ P+ ++R I R E G ++V
Sbjct: 10 LDPERLERA-----IARLESLGLEVVVGPHAL 36
>gnl|CDD|216660 pfam01717, Meth_synt_2, Cobalamin-independent synthase, Catalytic
domain. This is a family of vitamin-B12 independent
methionine synthases or
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferases, EC:2.1.1.14 from bacteria and
plants. Plants are the only higher eukaryotes that have
the required enzymes for methionine synthesis. This
enzyme catalyzes the last step in the production of
methionine by transferring a methyl group from
5-methyltetrahydrofolate to homocysteine. The aligned
region makes up the carboxy region of the approximately
750 amino acid protein except in some hypothetical
archaeal proteins present in the family, where this
region corresponds to the entire length. This domain
contains the catalytic residues of the enzyme.
Length = 324
Score = 25.4 bits (56), Expect = 7.1
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 66 VKYMSSGPVVPMCWARPEVQRPRRAQ 91
VK M +GPV + W+ + R AQ
Sbjct: 123 VKGMLTGPVTILNWSFVRDDQDREAQ 148
>gnl|CDD|215264 PLN02475, PLN02475,
5-methyltetrahydropteroyltriglutamate--homocysteine
methyltransferase.
Length = 766
Score = 25.5 bits (56), Expect = 8.0
Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 54 SDLATKPFFPGLVKYMSSGPVVPMCWARPEVQRPRRAQ 91
+ +P +K M +GPV + W+ +PR
Sbjct: 548 QSMTKRP-----MKGMLTGPVTILNWSFVRNDQPRHET 580
>gnl|CDD|235065 PRK02733, PRK02733, photosystem I reaction center subunit IX;
Provisional.
Length = 42
Score = 23.9 bits (52), Expect = 8.0
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 64 GLVKYMSSGPVVPMCW 79
GL K++S+ PVV W
Sbjct: 3 GLTKFLSTAPVVAAIW 18
>gnl|CDD|233381 TIGR01371, met_syn_B12ind,
5-methyltetrahydropteroyltriglutamate--homocysteine
S-methyltransferase. This model describes the
cobalamin-independent methionine synthase. A family of
uncharacterized archaeal proteins is homologous to the
C-terminal region of this family. That family is
excluded from this model but, along with this family,
belongs to Pfam model pfam01717 [Amino acid
biosynthesis, Aspartate family].
Length = 750
Score = 25.4 bits (56), Expect = 8.2
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 56 LATKPFFPGLVKYMSSGPVVPMCWARPEVQRPRR 89
L +KP VK M +GPV + W+ PR+
Sbjct: 539 LTSKP-----VKGMLTGPVTILNWSFVRDDIPRK 567
>gnl|CDD|132882 cd07025, Peptidase_S66, LD-Carboxypeptidase, a serine protease,
includes microcin C7 self immunity protein.
LD-carboxypeptidase (Muramoyltetrapeptide
carboxypeptidase; EC 3.4.17.13; Merops family S66;
initially described as Carboxypeptidase II) family also
includes the microcin c7 self-immunity protein (MccF)
as well as uncharacterized proteins including
hypothetical proteins. LD-carboxypeptidase hydrolyzes
the amide bond that links the dibasic amino acids to
C-terminal D-amino acids. The physiological substrates
of LD-carboxypeptidase are tetrapeptide fragments (such
as UDP-MurNAc-tetrapeptides) that are produced when
bacterial cell walls are degraded; they contain an
L-configured residue (L-lysine or meso-diaminopimelic
acid residue) as the penultimate residue and D-alanine
as the ultimate residue. A possible role of
LD-carboxypeptidase is in peptidoglycan recycling
whereby the resulting tripeptide (precursor for murein
synthesis) can be reconverted into peptidoglycan by
attachment of preformed D-Ala-D-Ala dipeptides. Some
enzymes possessing LD-carboxypeptidase activity also
act as LD-transpeptidase by replacing the terminal
D-Ala with another D-amino acid. MccF contributes to
self-immunity towards microcin C7 (MccC7), a
ribosomally encoded peptide antibiotic that contains a
phosphoramidate linkage to adenosine monophosphate at
its C-terminus. Its possible biological role is to
defend producer cells against exogenous microcin from
re-entering after having been exported. It is
suggested that MccF is involved in microcin degradation
or sequestration in the periplasm.
Length = 282
Score = 25.2 bits (56), Expect = 9.2
Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 5/37 (13%)
Query: 13 KPDGVQRGLVGNIIKRFEDKGFKLVAMKFVWPSEELL 49
+ + ++R I R E G ++V V + L
Sbjct: 12 EEERLERA-----IARLESLGLEVVVGPHVLARDGYL 43
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
0.322 0.140 0.446
Gapped
Lambda K H
0.267 0.0656 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,989,842
Number of extensions: 514047
Number of successful extensions: 607
Number of sequences better than 10.0: 1
Number of HSP's gapped: 600
Number of HSP's successfully gapped: 50
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (21.9 bits)
S2: 53 (24.3 bits)