RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5052
(172 letters)
>gnl|CDD|215513 PLN02951, PLN02951, Molybderin biosynthesis protein CNX2.
Length = 373
Score = 286 bits (734), Expect = 8e-98
Identities = 106/171 (61%), Positives = 136/171 (79%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDD 61
K+AGL S+NISLDTL P K+EF+TRRKG RVL ID A++LGY+ +KVN VVM+ FNDD
Sbjct: 156 KEAGLTSLNISLDTLVPAKFEFLTRRKGHDRVLESIDTAIELGYNPVKVNCVVMRGFNDD 215
Query: 62 EILDFVLLTRDRPIDVRFIEYMPFSGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPND 121
EI DFV LTRD+PI+VRFIE+MPF GN WN K++P++EM+ +I++ P L L++ P D
Sbjct: 216 EICDFVELTRDKPINVRFIEFMPFDGNVWNVKKLVPYAEMMDRIEQRFPSLKRLQDHPTD 275
Query: 122 TSKAYKVPEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
T+K +++ G V FITSMTEHFC CNRLRL+ADG+LKVCLFG +E+SL
Sbjct: 276 TAKNFRIDGHCGSVSFITSMTEHFCAGCNRLRLLADGNLKVCLFGPSEVSL 326
>gnl|CDD|233967 TIGR02666, moaA, molybdenum cofactor biosynthesis protein A,
bacterial. The model for this family describes
molybdenum cofactor biosynthesis protein A, or MoaA, as
found in bacteria. It does not include the family of
probable functional equivalent proteins from the
archaea. MoaA works together with MoaC to synthesize
precursor Z from guanine [Biosynthesis of cofactors,
prosthetic groups, and carriers, Molybdopterin].
Length = 334
Score = 209 bits (534), Expect = 7e-68
Identities = 76/176 (43%), Positives = 114/176 (64%), Gaps = 5/176 (2%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
K+AGL +N+SLD+L P+++ ITRR G +VLAGID A+ G + +K+N VVM+ ND
Sbjct: 109 KEAGLKRVNVSLDSLDPERFAKITRRGGRLEQVLAGIDAALAAGLEPVKLNTVVMRGVND 168
Query: 61 DEILDFVLLTRDRPIDVRFIEYMPFS-GNQWNNTKIMPFSEMLTKIKEAHPDLLTLENA- 118
DEI+D ++R + +RFIE MP GN W K + E+L ++++A L + +
Sbjct: 169 DEIVDLAEFAKERGVTLRFIELMPLGEGNGWREKKFVSADEILERLEQAFGPLEPVPSPR 228
Query: 119 PNDTSKAYKV--PEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
N + AY+ P KG++GFI+ +++ FCGTCNRLRL ADG L++CLF + + L
Sbjct: 229 GNGPAPAYRWRLPGGKGRIGFISPVSDPFCGTCNRLRLTADGKLRLCLFADDGVDL 284
>gnl|CDD|234672 PRK00164, moaA, molybdenum cofactor biosynthesis protein A;
Reviewed.
Length = 331
Score = 206 bits (528), Expect = 5e-67
Identities = 69/172 (40%), Positives = 101/172 (58%), Gaps = 2/172 (1%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDD 61
K AGLD +N+SLD+L P++++ IT R +VLAGID A+ G +KVN V+MK NDD
Sbjct: 115 KDAGLDRVNVSLDSLDPERFKAITGRDRLDQVLAGIDAALAAGLTPVKVNAVLMKGVNDD 174
Query: 62 EILDFVLLTRDRPIDVRFIEYMPFS-GNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPN 120
EI D + +DR I +RFIE MP GN+W + +E+ ++ L
Sbjct: 175 EIPDLLEWAKDRGIQLRFIELMPTGEGNEWFRKHHLSGAEIRARL-AERGWTLQPRARSG 233
Query: 121 DTSKAYKVPEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
++ ++ P++ G++G I +T FC +CNRLRL ADG L +CLF + L
Sbjct: 234 GPAQYFRHPDYGGEIGLIAPVTHDFCASCNRLRLTADGKLHLCLFAEDGVDL 285
>gnl|CDD|225449 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme
metabolism].
Length = 322
Score = 189 bits (482), Expect = 3e-60
Identities = 77/172 (44%), Positives = 104/172 (60%), Gaps = 3/172 (1%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDD 61
K+AGLD +N+SLD+L P+K+ IT R RVL GID AV+ G +K+N V+MK NDD
Sbjct: 108 KEAGLDRVNVSLDSLDPEKFRKITGRDRLDRVLEGIDAAVEAGLTPVKLNTVLMKGVNDD 167
Query: 62 EILDFVLLTRDRPIDVRFIEYMPF-SGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPN 120
EI D + ++R +RFIE MP GN W K + E+L K++E LL + +
Sbjct: 168 EIEDLLEFAKERGAQLRFIELMPLGEGNSWRLDKYLSLDEILRKLEE-RATLLPVRKRLH 226
Query: 121 DTSKAYKVPEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
+K + P+ G++GFI ++ FC TCNRLRL ADG LK CLF I L
Sbjct: 227 GRAKYFIHPDG-GEIGFIAPVSNPFCATCNRLRLTADGKLKPCLFREDGIDL 277
>gnl|CDD|237364 PRK13361, PRK13361, molybdenum cofactor biosynthesis protein A;
Provisional.
Length = 329
Score = 152 bits (386), Expect = 7e-46
Identities = 61/171 (35%), Positives = 96/171 (56%), Gaps = 4/171 (2%)
Query: 4 AGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDDEI 63
AGL +NISLDTL+P+ + +TR RV+AGID A G++ +K+N V+++ NDDE+
Sbjct: 113 AGLKRLNISLDTLRPELFAALTRNGRLERVIAGIDAAKAAGFERIKLNAVILRGQNDDEV 172
Query: 64 LDFVLLTRDRPIDVRFIEYMPFSG-NQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPND- 121
LD V R+R +D+ FIE MP ++ + E+ I+ +P LT N
Sbjct: 173 LDLVEFCRERGLDIAFIEEMPLGEIDERRRARHCSSDEVRAIIETRYP--LTPSNKRTGG 230
Query: 122 TSKAYKVPEFKGQVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
++ Y + + +GFI+ + +FC CNR+R+ A+G L +CL L
Sbjct: 231 PARYYTMADSPIHIGFISPHSHNFCHECNRVRVTAEGQLLLCLGNEHASDL 281
>gnl|CDD|115139 pfam06463, Mob_synth_C, Molybdenum Cofactor Synthesis C. This
region contains two iron-sulphur (3Fe-4S) binding sites.
Mutations in this region of human MOCS1 cause MOCOD
(Molybdenum Co-Factor Deficiency) type A.
Length = 127
Score = 129 bits (327), Expect = 3e-39
Identities = 43/99 (43%), Positives = 60/99 (60%), Gaps = 2/99 (2%)
Query: 75 IDVRFIEYMPF-SGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPNDTSKAYKVPEFKG 133
I++RFIE MP GN W K + ++E+L +++E P LL ++ Y++P G
Sbjct: 1 IELRFIELMPVGEGNGWRRKKFVSYAEILDRLEERFP-LLAARKRTGGPARRYRIPGGGG 59
Query: 134 QVGFITSMTEHFCGTCNRLRLMADGSLKVCLFGNTEISL 172
++GFI M+ FC +CNRLRL ADG LK CLF N I L
Sbjct: 60 RIGFIAPMSNPFCASCNRLRLTADGKLKTCLFRNDGIDL 98
>gnl|CDD|233968 TIGR02668, moaA_archaeal, probable molybdenum cofactor biosynthesis
protein A, archaeal. This model describes an archaeal
family related, and predicted to be functionally
equivalent, to molybdenum cofactor biosynthesis protein
A (MoaA) of bacteria (see TIGR02666) [Biosynthesis of
cofactors, prosthetic groups, and carriers,
Molybdopterin].
Length = 302
Score = 115 bits (290), Expect = 8e-32
Identities = 59/178 (33%), Positives = 84/178 (47%), Gaps = 26/178 (14%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDD 61
K+AGLD +N+SLDTL P+KY+ IT R RV+ GI+ AV G +K+N+VV+K ND+
Sbjct: 105 KEAGLDRVNVSLDTLDPEKYKKITGRGALDRVIEGIESAVDAGLTPVKLNMVVLKGINDN 164
Query: 62 EILDFVLLTRDRPIDVRFIEYMPFSGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPND 121
EI D V + ++ IE MP E + K+ H D+ +E
Sbjct: 165 EIPDMVEFAAEGGAILQLIEL-------------MPPGEGEKEFKKYHEDIDPIEEELEK 211
Query: 122 TSKAYKVPEF----------KGQVGFITSM--TEHFCGTCNRLRLMADGSLKVCLFGN 167
+ + +V + M FC C RLRL +DG LK CL +
Sbjct: 212 MADRVRTRRMHNRPKYFIPGGVEVEVVKPMDNPV-FCAHCTRLRLTSDGKLKTCLLRD 268
>gnl|CDD|217866 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyze diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 59.9 bits (145), Expect = 7e-12
Identities = 19/69 (27%), Positives = 37/69 (53%)
Query: 1 YKKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
K+AGLD ++ISL + + + I R + VL ++L + G + N+V + ND
Sbjct: 96 LKEAGLDRVSISLQSGDDEVLKIINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGEND 155
Query: 61 DEILDFVLL 69
+++ + + L
Sbjct: 156 EDLEETLEL 164
>gnl|CDD|223609 COG0535, COG0535, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 347
Score = 48.1 bits (114), Expect = 5e-07
Identities = 27/108 (25%), Positives = 46/108 (42%), Gaps = 4/108 (3%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
K+AGLD ++ISLD L P+ ++ I KG + R + I + G L V + N
Sbjct: 115 KEAGLDYVSISLDGLDPETHDPIRGVKGVFKRAVEAIKNLKEAGI--LVVINTTVTKINY 172
Query: 61 DEILDFVLLTRDRPID-VRFIEYMPFSGNQWNNTKIMPFSEMLTKIKE 107
DE+ + L + +D + +P + N + E +
Sbjct: 173 DELPEIADLAAELGVDELNVFPLIPVGRGEENLELDLTPEEEELLLVL 220
>gnl|CDD|214792 smart00729, Elp3, Elongator protein 3, MiaB family, Radical SAM.
This superfamily contains MoaA, NifB, PqqE,
coproporphyrinogen III oxidase, biotin synthase and MiaB
families, and includes a representative in the
eukaryotic elongator subunit, Elp-3. Some members of the
family are methyltransferases.
Length = 216
Score = 45.1 bits (107), Expect = 3e-06
Identities = 18/113 (15%), Positives = 48/113 (42%), Gaps = 10/113 (8%)
Query: 1 YKKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVV-MKNFN 59
K+AG++ +++ + + + + I R VL ++L + G + +++V +
Sbjct: 106 LKEAGVNRVSLGVQSGDDEVLKAINRGHTVEDVLEAVELLREAGPIKVSTDLIVGLPGET 165
Query: 60 DDEILDFVLLTRDRPID-VRFIEYMPFSGNQWNNTKIMPFSEMLTKIKEAHPD 111
+++ + + L ++ D V P G P ++M ++K +
Sbjct: 166 EEDFEETLKLLKELGPDRVSIFPLSPRPG--------TPLAKMYKRLKPPTKE 210
>gnl|CDD|225011 COG2100, COG2100, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 414
Score = 41.7 bits (98), Expect = 6e-05
Identities = 31/113 (27%), Positives = 53/113 (46%), Gaps = 9/113 (7%)
Query: 3 KAGLDSINISLDTLKPDKYEFITRRKGWS--RVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
+AGLD IN+S+D L P + + RK + +VL + G D L + V + ND
Sbjct: 212 EAGLDRINLSVDALDPKLAKMLAGRKDYDVKKVLEVAEYIANAGIDVL-IAPVWLPGVND 270
Query: 61 DEILDFVLLTRD-----RPIDVRFIEYMPFS-GNQWNNTKIMPFSEMLTKIKE 107
DE+ + R+ + + +Y+P+ G + K+ PF E ++E
Sbjct: 271 DEMPKIIEWAREIGAGKKWPPLGIQKYIPYKFGRKPVIAKVWPFKEFYRWLRE 323
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin.
Length = 204
Score = 39.2 bits (91), Expect = 3e-04
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
K+ GLD + +SLD+ + + I + L + + G L ++V D
Sbjct: 95 KELGLDGVGVSLDSGDEEVADKIRGSGESFKERLEALKELREAGL-GLSTTLLVGLGDED 153
Query: 61 -DEILDFVLLTRD--RPIDVRFIEYMPFSGNQ 89
++ L+ + L + P V +P G
Sbjct: 154 EEDDLEELELLAEFRSPDRVSLFRLLPEEGTP 185
>gnl|CDD|234449 TIGR04053, sam_11, radical SAM protein, BA_1875 family. Members of
this subfamily of the radical SAM domain superfamily
show closer sequence relationships to peptide-modifying
proteins of bacteriocin and PQQ biosynthesis than to
other characterized radical SAM proteins. Within this
subfamily, targets are likely to be diverse [Unknown
function, Enzymes of unknown specificity].
Length = 365
Score = 34.2 bits (79), Expect = 0.025
Identities = 15/70 (21%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMK-NFN 59
K+AG+ ++++SLD + ++ G + R + I A++LG +++N V N +
Sbjct: 106 KEAGVSAVSLSLDGATAETHDAFRGVPGSFDRTVNAIRAALELGI-PVQINTTVTAENVH 164
Query: 60 D-DEILDFVL 68
+ ++ +
Sbjct: 165 ELPDVAKLLK 174
>gnl|CDD|188570 TIGR04055, rSAM_NirJ2, putative heme d1 biosynthesis radical SAM
protein NirJ2. Members of this radical SAM protein
subfamily, designated NirJ2, occur in genomic contexts
with a paralog NirJ1 and with other nitrite reductase
operon genes associated with heme d1 biosynthesis, as in
Heliobacillus mobilis and Heliophilum fasciatum. NirJ2
is presumed by bioinformatics analysis (Xiong, et al.)
to be a heme d1 biosynthesis protein by context.
Length = 325
Score = 33.5 bits (77), Expect = 0.039
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 2 KKAGLDSINISLDTLKPDKYEFITRRKG-WSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
KKAG + ISLD+L K++ G W + G++ + G +++ VM +N
Sbjct: 94 KKAGAMRVGISLDSLDAKKHDAFRGYPGAWEGAVRGMENCRKAGLP-FQIHTTVMD-WNR 151
Query: 61 DEILD 65
DE+
Sbjct: 152 DEVEA 156
>gnl|CDD|234542 TIGR04321, spiroSPASM, spiro-SPASM protein. This three-domain
protein is restricted to the spirochetes and widely
distributed (excepting Borrelia). It has a conserved
C-terminal SPASM domain, a 4Fe-4S binding domain shared
by a number of peptide-modifying and heme-modifying
radical SAM proteins. It has a central radical SAM
domain, although half the members have lost the
signature 4Fe-4S-binding Cys residues, fail to register
with the radical SAM domain definition of pfam04055, and
must be considered pseudo-SAM proteins. PSI-BLAST shows
a relationship between the N-terminal domain and various
predicted glycosyltransferases (e.g. Bacillus subtilis
SpsF) and cytidyltransferases. In some Treponema
species, this protein appears to split into two tandem
genes.
Length = 507
Score = 33.4 bits (77), Expect = 0.040
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 1/77 (1%)
Query: 11 ISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFNDDEILDFVLLT 70
+SLD ++ + Y I L+ ID ++ N+ V MK N+DE+ F
Sbjct: 344 VSLDAVEQELYAKIRGDGELEEALSNIDALSKIFPGNVYVQFTRMKE-NEDELESFYRFW 402
Query: 71 RDRPIDVRFIEYMPFSG 87
+ + +V +Y F G
Sbjct: 403 KKKGGEVIIQKYNRFCG 419
>gnl|CDD|222144 pfam13458, Peripla_BP_6, Periplasmic binding protein. This family
includes a diverse range of periplasmic binding
proteins.
Length = 343
Score = 30.3 bits (69), Expect = 0.51
Identities = 16/69 (23%), Positives = 22/69 (31%), Gaps = 13/69 (18%)
Query: 81 EYMPFSGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPNDTSKAYK-VPEF----KGQV 135
Y P FS ++ +IK + PD++ L D K E KG
Sbjct: 170 VYYPLGTTD--------FSSVVLQIKASGPDVVLLTLVGADAVAFIKAAREAGLDPKGIP 221
Query: 136 GFITSMTEH 144
S E
Sbjct: 222 LVSLSGYEA 230
>gnl|CDD|129630 TIGR00539, hemN_rel, putative oxygen-independent coproporphyrinogen
III oxidase. Experimentally determined examples of
oxygen-independent coproporphyrinogen III oxidase, an
enzyme that replaces HemF function under anaerobic
conditions, belong to a family of proteins described by
the model hemN. This model, hemN_rel, models a closely
related protein, shorter at the amino end and lacking
the region containing the motif PYRT[SC]YP found in
members of the hemN family. Several species, including
E. coli, Helicobacter pylori, Aquifex aeolicus, and
Chlamydia trachomatis, have members of both this family
and the E. coli hemN family. The member of this family
from Bacillus subtilis was shown to complement an
hemF/hemN double mutant of Salmonella typimurium and to
prevent accumulation of coproporphyrinogen III under
anaerobic conditions, but the exact role of this protein
is still uncertain. It is found in a number of species
that do not synthesize heme de novo [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 360
Score = 30.3 bits (68), Expect = 0.52
Identities = 11/53 (20%), Positives = 31/53 (58%)
Query: 1 YKKAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGIDLAVQLGYDNLKVNVV 53
K AG++ +++ + + + DK F+ R+ + I+ A++ G +N+ ++++
Sbjct: 106 LKGAGINRLSLGVQSFRDDKLLFLGRQHSAKNIAPAIETALKSGIENISLDLM 158
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 29.5 bits (67), Expect = 0.58
Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 11/37 (29%)
Query: 43 LGYDNLKVNVVVMKNFNDDEILDF------VLLTRDR 73
LGYD + +F DDE+L +LLTRDR
Sbjct: 19 LGYD-----TLYDNDFEDDELLAIAAKEGRILLTRDR 50
>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 29.6 bits (67), Expect = 0.75
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 107 EAHPDLLTLENAPNDTSKAYK----VPEFKGQVGFITS 140
AH LLTLE + N+ K + V E + + F
Sbjct: 98 GAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGL 135
>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 = 29.2 bits (66), Expect = 1.1
Identities = 20/106 (18%), Positives = 42/106 (39%), Gaps = 9/106 (8%)
Query: 3 KAGLDSINISLDTLKPDKYEFITRRKGWSRVLAGI----DLAVQLG--YDNLKVNVVVMK 56
G+D I +S+D L Y I ++VL + ++ ++ G ++ + V K
Sbjct: 100 GLGVDKIYVSIDALPDKPYR-IIGHGDLAKVLENLKKLYEIKIKKGSDKPHVGIEFVATK 158
Query: 57 NFNDDEILDFVLLTRDRPID-VRFIEYMPFSGNQWNNTKIMPFSEM 101
N E+ + V L R + + +P++ + E+
Sbjct: 159 -ENYKELPELVELARKLGVSSIIVSNLLPYTEEYIDEILYDGPGEL 203
>gnl|CDD|188566 TIGR04051, rSAM_NirJ, heme d1 biosynthesis radical SAM protein
NirJ. Heme d1 occurs in the cytochrome cd1 subunit of
nitrite reductase in species such as Pseudomonas
stutzeri. NirJ is a radical SAM protein involved in its
bioynthesis. In a number of species, distinct genes
NirJ1 and NirJ2 are found in similar genomic regions;
this model describe authentic NirJ from genomes with
NirJ only [Biosynthesis of cofactors, prosthetic groups,
and carriers, Heme, porphyrin, and cobalamin].
Length = 354
Score = 28.9 bits (65), Expect = 1.2
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 4 AGLDSINISLDTLKPDKYEFITRRK--GWSRVLAGIDLAVQLGYDNLKVNV-VVMKNFND 60
AG D + IS+D L+ F RR + LAGI L G +KV + + N
Sbjct: 99 AGFDYVGISIDGLEATHDRF--RRLKGAFDAALAGIRLCKAAG---IKVGLRFTLTEDNA 153
Query: 61 DEILDFVLLTRDRPIDVRFIEYMPFSG 87
++ + L + +D ++ ++ ++G
Sbjct: 154 AQLPALLDLMEEEGVDKFYLSHLNYAG 180
>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2,) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 27.7 bits (62), Expect = 2.8
Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 46 DNLKVNVVVMKNFNDDE--ILDFVLLTRDRPIDVRFIEYMPF 85
N+ + + V+ FND E I R V I+ +P+
Sbjct: 215 KNVVIRIPVIPGFNDSEENIEAIAAFLRKLEPGVDEIDLLPY 256
>gnl|CDD|99819 cd05776, DNA_polB_alpha_exo, inactive DEDDy 3'-5' exonuclease
domain of eukaryotic DNA polymerase alpha, a family-B
DNA polymerase. The 3'-5' exonuclease domain of
eukaryotic DNA polymerase alpha. DNA polymerase alpha
is a family-B DNA polymerase with a catalytic subunit
that contains a DnaQ-like 3'-5' exonuclease domain. It
is one of the three DNA-dependent type B DNA polymerases
(delta and epsilon are the other two) that have been
identified as essential for nuclear DNA replication in
eukaryotes. DNA polymerase alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. It
associates with DNA primase and is the only enzyme able
to start DNA synthesis de novo. The catalytic subunit
contains both polymerase and 3'-5' exonuclease domains,
but only exhibits polymerase activity. The 3'-5'
exonuclease domain contains three sequence motifs termed
ExoI, ExoII and ExoIII, without the four conserved
acidic residues that are crucial for metal binding and
catalysis. This explains why in most organisms, that no
specific repair role, other than check point control,
has been assigned to this enzyme. The exonuclease domain
may have a structural role.
Length = 234
Score = 27.6 bits (62), Expect = 2.8
Identities = 14/76 (18%), Positives = 29/76 (38%), Gaps = 12/76 (15%)
Query: 50 VNVVVMKNFNDD-----EILDFVLLTRDRPIDVRFIEYMPFSGNQWNNTKIMPF------ 98
++++V +N + D T RP+ + + TK+ F
Sbjct: 26 ISMLVHRNVSLDKPTPPPPFQSHTCTLTRPLGRSPPPDLFEKNAKKKKTKVRIFENERAL 85
Query: 99 -SEMLTKIKEAHPDLL 113
+ L K+++ PD+L
Sbjct: 86 LNFFLAKLQKIDPDVL 101
>gnl|CDD|235397 PRK05301, PRK05301, pyrroloquinoline quinone biosynthesis protein
PqqE; Provisional.
Length = 378
Score = 27.5 bits (62), Expect = 4.1
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 6/71 (8%)
Query: 2 KKAGLDSINISLDTLKPDKYEFIT-RRKGWSRVLAGIDLAVQLGYDNLKVNVVVMKNFND 60
K AGLD I +S P+ + + + +++ LA L GY L +N V+ + N
Sbjct: 111 KDAGLDHIQLSFQDSDPELNDRLAGTKGAFAKKLAVARLVKAHGYP-LTLNAVIHR-HNI 168
Query: 61 D---EILDFVL 68
D I++ +
Sbjct: 169 DQIPRIIELAV 179
>gnl|CDD|200384 TIGR04133, rSAM_w_lipo, radical SAM enzyme, rSAM/lipoprotein
system. Members of this protein family are radical SAM
enzymes with an additional 4Fe4S cluster-binding
C-terminal domain (TIGR04085) shared with PqqE and many
other peptide and protein-modifying radical SAM enzymes.
All members occur in the context of a predicted
lipoprotein that usually is encoded by an adjacent gene.
Length = 350
Score = 26.6 bits (59), Expect = 6.7
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 4 AGLDSINISLDTLKPDKYEFITRR-KGWSRVLAGIDLAV---QLGYD 46
+GL SI ISLD + D + ++ + R L I L +L +D
Sbjct: 124 SGLRSITISLDGFE-DSHNWLRGNPHSFERALNAIRLIAKTPELTFD 169
>gnl|CDD|119177 pfam10657, RC-P840_PscD, Photosystem P840 reaction centre protein
PscD. The photosynthetic reaction centres (RCs) of
aerotolerant organisms contain a heterodimeric core,
built up of two strongly homologous polypeptides each of
which contributes five transmembrane peptide helices to
hold a pseudo-symmetric double set of redox components.
Two molecules of PscD are housed within a subunit. PscD
may be involved in stabilising the PscB component since
it is found to co-precipitate with FMO
(Fenna-Mathews-Olson BChl a-protein) and PscB. It may
also be involved in the interaction with ferredoxin.
Length = 144
Score = 26.4 bits (58), Expect = 7.0
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 4/41 (9%)
Query: 80 IEYMPFSGNQWNNTKIMPFSEMLTKIKEAHPDLLTLENAPN 120
I P SG K+ P EM+ K+ +L L P+
Sbjct: 49 ITISPASGR----RKLSPTKEMIDKLISGEIELFVLTTQPD 85
>gnl|CDD|107322 cd06327, PBP1_SBP_like_1, Periplasmic solute-binding domain of
active transport proteins that belong to the type I
periplasmic binding fold protein family. Periplasmic
solute-binding domain of active transport proteins that
belong to the type I periplasmic binding fold protein
family. Solute binding proteins are the primary specific
receptors that initiate uptake of a broad range of
solutes, including amino acids, peptides and inorganic
ions. The members are predicted to have a similar
function to an active transport system for short chain
amides and urea by sequence comparison and phylogenetic
analysis. Moreover, this binding domain has high
sequence identity to the family of hydrophobic amino
acid transporters (HAAT), and thus may also be involved
in transport of amino acids.
Length = 334
Score = 26.7 bits (60), Expect = 7.1
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 98 FSEMLTKIKEAHPDLLTLENAPNDTSKAYK 127
FS L + + + D+L L NA DT A K
Sbjct: 179 FSSYLLQAQASGADVLVLANAGADTVNAIK 208
>gnl|CDD|197984 smart00916, L51_S25_CI-B8, Mitochondrial ribosomal protein L51 /
S25 / CI-B8 domain. Proteins containing this domain
are located in the mitochondrion and include ribosomal
protein L51, and S25. This domain is also found in
mitochondrial NADH-ubiquinone oxidoreductase B8 subunit
(CI-B8) . It is not known whether all members of this
family form part of the NADH-ubiquinone oxidoreductase
and whether they are also all ribosomal proteins.
Length = 70
Score = 24.8 bits (55), Expect = 9.0
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 45 YDNLKVNVVVMKNFNDDEILDFVLLTRDR 73
Y+N + + ++N + +EIL + L +
Sbjct: 42 YENGREKEISLRNLSAEEILKKLQLLVNS 70
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
0.321 0.139 0.414
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,784,872
Number of extensions: 805321
Number of successful extensions: 772
Number of sequences better than 10.0: 1
Number of HSP's gapped: 760
Number of HSP's successfully gapped: 45
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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: 55 (24.8 bits)