RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4598
(369 letters)
>gnl|CDD|130724 TIGR01663, PNK-3'Pase, polynucleotide 5'-kinase 3'-phosphatase.
This model represents the metazoan
5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is
believed to be involved in repair of oxidative DNA
damage. Removal of 3' phosphates is essential for the
further processing of the break by DNA polymerases. The
central phosphatase domain is a member of the IIIA
subfamily (TIGR01662) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. As is
common in this superfamily, the enzyme is magnesium
dependent. A difference between this enzyme and other
HAD-superfamily phosphatases is in the third conserved
catalytic motif which usually contains two conserved
aspartate residues believed to be involved in binding
the magnesium ion. Here, the second aspartate is
replaced by a conserved arginine residue which may
indicate an interaction with the phosphate backbone of
the substrate. Very close relatives of this domain are
also found separate from the N- and C-terminal domains
seen here, as in the 3'-phosphatase found in plants. The
larger family of these domains is described by
TIGR01664. Outside of the phosphatase domain is a P-loop
ATP-binding motif associated with the kinase activity.
The entry for the mouse homolog, GP|7108591, appears to
be missing a large piece of sequence corresponding to
the first conserved catalytic motif of the phosphatase
domain as well as the conserved threonine of the second
motif. Either this is a sequencing artifact or this may
represent a pseudo- or non-functional gene. Note that
the EC number for the kinase function is: 2.7.1.78.
Length = 526
Score = 316 bits (810), Expect = e-104
Identities = 149/374 (39%), Positives = 191/374 (51%), Gaps = 58/374 (15%)
Query: 2 KGSWDIVDNGKLLVFTSNDVCNSAKIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIES 61
KG+ + KLL+FT+ V KIA FDLDGT+I TKSGKVFP DW+++F I
Sbjct: 145 KGNPGWENLEKLLIFTAAGVKGQEKIAGFDLDGTIIKTKSGKVFPKGPDDWQIIFPEIPE 204
Query: 62 VLKQYLDDGYKLVIFTNQGAIGRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYRKP 121
LK+ DG+K+ IFTNQG I R K++ DF+AK E I+ L VP Q+F+A YRKP
Sbjct: 205 KLKELEADGFKICIFTNQGGIARGKINADDFKAKIEAIVAKLGVPFQVFIAIGAGFYRKP 264
Query: 122 VPGMWEYLSQEKNGDLAIDISQSFYAGDAAGRAAN-WAP-KKKKDFACTDHLFAFNLNLA 179
+ GMW++L +E N I F+ GDAAGR AN A KKKKDF+C D LFA NL +
Sbjct: 265 LTGMWDHLKEEANDGTEIQEDDCFFVGDAAGRPANGKAAGKKKKDFSCADRLFAANLGIP 324
Query: 180 FFTPEQIFLNEKAPDFPNLPTFKPREVYQKAQSQTIPNIPHDKKQVLIMIGSQGSGKSSF 239
F TPE+ FL + A F P F PR V Q Q P D
Sbjct: 325 FATPEEFFLGKPAAGF-EKPAFDPRSV----QDQGPLCDPDDL----------------- 362
Query: 240 VSTYLKPLNYTTVNRDTLGSWQKCVSVMKAALDS----VLIMIGSQGSGKSSFVSTYLKP 295
ALD ++I +G G+GKS F + +P
Sbjct: 363 ------------------------------ALDDAPCEMVIAVGFPGAGKSHFCKKFFQP 392
Query: 296 LNYTTVNRDTLGSWQKCVSVMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAV 355
Y VN DTLGS Q C++ + ALD G +DNTNPD SR ++++ A+ G+ C
Sbjct: 393 AGYKHVNADTLGSTQNCLTACERALDQGKRCAIDNTNPDAASRAKFLQCARAAGIPCRCF 452
Query: 356 HMNISKEHAKHNIK 369
N AKHNI
Sbjct: 453 LFNAPLAQAKHNIA 466
>gnl|CDD|219952 pfam08645, PNK3P, Polynucleotide kinase 3 phosphatase.
Polynucleotide kinase 3 phosphatases play a role in the
repair of single breaks in DNA induced by DNA-damaging
agents such as gamma radiation and camptothecin.
Length = 158
Score = 215 bits (551), Expect = 5e-70
Identities = 87/163 (53%), Positives = 114/163 (69%), Gaps = 6/163 (3%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRK 85
KIA+FDLDGTLI TKSGKVFP D DWK L+ ++ LK+ +DGYK+VIFTNQG I K
Sbjct: 1 KIAAFDLDGTLIKTKSGKVFPKDADDWKWLYPSVPEKLKKLHEDGYKIVIFTNQGGISTK 60
Query: 86 -KMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEKNGDLAIDISQS 144
K S F+ K E I+K L+VP+Q++ AT+ D+YRKP GMW+ L ++ N + ID+ +S
Sbjct: 61 GKKSAESFKNKIESILKKLDVPLQVYAATKKDKYRKPNTGMWDELLEDYNDGITIDLEKS 120
Query: 145 FYAGDAAGRAANWAPKKKKDFACTDHLFAFNLNLAFFTPEQIF 187
FY GDAAGR P +KKDF+ +D FA N+ + F TPE+ F
Sbjct: 121 FYVGDAAGR-----PARKKDFSDSDRKFALNVGIKFKTPEEFF 158
>gnl|CDD|211680 TIGR01664, DNA-3'-Pase, DNA 3'-phosphatase. This model represents
a family of proteins and protein domains which catalyze
the dephosphorylation of DNA 3'-phosphates. It is
believed that this activity is important for the repair
of single-strand breaks in DNA caused by radiation or
oxidative damage. This domain is often (TIGR01663), but
not always linked to a DNA 5'-kinase domain. The central
phosphatase domain is a member of the IIIA subfamily
(TIGR01662) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. As is
common in this superfamily, the enzyme is magnesium
dependent. A difference between this enzyme and other
HAD-superfamily phosphatases is in the third conserved
catalytic motif which usually contains two conserved
aspartate residues believed to be involved in binding
the magnesium ion. Here, the second aspartate is usually
replaced by an arginine residue which may indicate an
interaction with the phosphate backbone of the
substrate. Alternatively, there is an additional
conserved aspartate downstream of the ususal site which
may indicate slightly different fold in this region.
Length = 166
Score = 194 bits (494), Expect = 3e-61
Identities = 86/176 (48%), Positives = 112/176 (63%), Gaps = 10/176 (5%)
Query: 13 LLVFTSNDVCNSAKIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYK 72
L VFT++ +K+A+FDLDGTLITT+SGKVFP DW+ L+ I + L++ D+GYK
Sbjct: 1 LFVFTADGPKPQSKVAAFDLDGTLITTRSGKVFPTSASDWRFLYPEIPAKLQELDDEGYK 60
Query: 73 LVIFTNQGAIGRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQE 132
+VIFTNQ IGR K+S F+ K E ++ L VP+Q+ AT YRKP+ GMWEYL +
Sbjct: 61 IVIFTNQSGIGRGKLSAESFKNKIEAFLEKLKVPIQVLAATHAGLYRKPMTGMWEYLQSQ 120
Query: 133 KNGDLAIDISQSFYAGDAAGRAANWAPKKKKDFACTDHLFAFNLNLAFFTPEQIFL 188
N I +++SFY GDAAGR K DF+ D FA NL L F PE+ FL
Sbjct: 121 YNSP--IKMTRSFYVGDAAGR--------KLDFSDADIKFAKNLGLEFKYPEEFFL 166
>gnl|CDD|233517 TIGR01662, HAD-SF-IIIA, HAD-superfamily hydrolase, subfamily IIIA.
This subfamily falls within the Haloacid Dehalogenase
(HAD) superfamily of aspartate-nucleophile hydrolases.
The Class III subfamilies are characterized by the lack
of any domains located between either between the first
and second conserved catalytic motifs (as in the Class I
subfamilies, TIGR01493, TIGR01509, TIGR01488 and
TIGR01494) or between the second and third conserved
catalytic motifs (as in the Class II subfamilies,
TIGR01460 and TIGR01484) of the superfamily domain. The
IIIA subfamily contains five major clades:
histidinol-phosphatase (TIGR01261) and
histidinol-phosphatase-related protein (TIGR00213) which
together form a subfamily (TIGR01656), DNA
3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668)
and YrbI (TIGR01670). In the case of histidinol
phosphatase and PNK-3'-phosphatase, this model
represents a domain of a bifunctional system. In the
histidinol phosphatase HisB, a C-terminal domain is an
imidazoleglycerol-phosphate dehydratase which catalyzes
a related step in histidine biosynthesis. In
PNK-3'-phosphatase, N- and C-terminal domains constitute
the polynucleotide kinase and DNA-binding components of
the enzyme [Unknown function, Enzymes of unknown
specificity].
Length = 132
Score = 107 bits (269), Expect = 2e-28
Identities = 43/145 (29%), Positives = 60/145 (41%), Gaps = 14/145 (9%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRK 85
K DLDGTL V VD D ++L+ + L + + GYK+VI TNQ IGR
Sbjct: 1 KGVVLDLDGTLTD----DVPYVDDEDERILYPEVPDALAELKEAGYKVVIVTNQSGIGRG 56
Query: 86 KMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEKNGDLAIDISQSF 145
K + + ++ L VP+ + A RKP PGM+ + N ID +S
Sbjct: 57 KF----SSGRVARRLEELGVPIDILYACP--HCRKPKPGMFLEALKRFNE---IDPEESV 107
Query: 146 YAGDAAGRAANWAPK-KKKDFACTD 169
Y GD A +
Sbjct: 108 YVGDQDLTDLQAAKRAGLAFILVAP 132
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 93.9 bits (234), Expect = 3e-23
Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 20/116 (17%)
Query: 274 VLIMIGSQGSGKSSFVSTYLKPLNYTTVNRDTLGS--------------------WQKCV 313
+++M+G GSGKS+F L+ L ++ DTL +Q+ +
Sbjct: 1 LILMVGLPGSGKSTFARRLLRELGAVVLSSDTLRKRLRGDGPPDISYYARASGRVYQRLL 60
Query: 314 SVMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHMNISKEHAKHNIK 369
+ + AL +G V+VD TN +E R R I+ A+++G V++ +E +
Sbjct: 61 ELAREALRAGRPVIVDATNLSREERARLIDLARRYGAPVRIVYLEAPEEVLRERNA 116
>gnl|CDD|223319 COG0241, HisB, Histidinol phosphatase and related phosphatases
[Amino acid transport and metabolism].
Length = 181
Score = 78.5 bits (194), Expect = 3e-17
Identities = 43/140 (30%), Positives = 58/140 (41%), Gaps = 20/140 (14%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
D DGT+ K V +D D++ + I L + GYKLV+ TNQ IGR +
Sbjct: 10 LDRDGTINIDKGDYVDSLD--DFQFIPGVIP-ALLKLQRAGYKLVVVTNQSGIGRGYFTE 66
Query: 90 RDFQAKAEKIIKSL---NVPVQMF-----VATQYDRYRKPVPGMWEYLSQEKNGDLAIDI 141
DF K++K L V + RKP PGM +E N ID+
Sbjct: 67 ADFDKLHNKMLKILASQGVKIDGILYCPHHPEDNCDCRKPKPGMLLSALKEYN----IDL 122
Query: 142 SQSFYAGDA-----AGRAAN 156
S+S+ GD A A
Sbjct: 123 SRSYVVGDRLTDLQAAENAG 142
>gnl|CDD|233512 TIGR01656, Histidinol-ppas, histidinol-phosphate phosphatase family
domain. This domain is found in authentic
histidinol-phosphate phosphatases which are sometimes
found as stand-alone entities and sometimes as fusions
with imidazoleglycerol-phosphate dehydratase
(TIGR01261). Additionally, a family of proteins
including YaeD from E. coli (TIGR00213) and various
other proteins are closely related but may not have the
same substrate specificity. This domain is a member of
the haloacid-dehalogenase (HAD) superfamily of
aspartate-nucleophile hydrolases. This superfamily is
distinguished by the presence of three motifs: an
N-terminal motif containing the nucleophilic aspartate,
a central motif containing an conserved serine or
threonine, and a C-terminal motif containing a conserved
lysine (or arginine) and conserved aspartates. More
specifically, the domian modelled here is a member of
subfamily III of the HAD-superfamily by virtue of
lacking a "capping" domain in either of the two common
positions, between motifs 1 and 2, or between motifs 2
and 3.
Length = 147
Score = 52.0 bits (125), Expect = 2e-08
Identities = 38/147 (25%), Positives = 56/147 (38%), Gaps = 23/147 (15%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
D DG + +P DW+L + ++L GY +V+ TNQ IGR S
Sbjct: 5 LDRDGVINEDTVSD-YPRSLDDWQLRPGAVPALLT-LRAAGYTVVVVTNQSGIGRGYFSA 62
Query: 90 RDF---QAKAEKIIKSLNVPVQMFVATQYDRY-----RKPVPGMWEYLSQEKNGDLAIDI 141
F + ++++ L V V + + RKP PG+ E L +D
Sbjct: 63 EAFRAPNGRVLELLRQLGVAVDGVLFCPHHPADNCSCRKPKPGLIL----EALKRLGVDA 118
Query: 142 SQSFYAGD---------AAGRAANWAP 159
S+S GD AG AA
Sbjct: 119 SRSLVVGDRLRDLQAARNAGLAAVLLV 145
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 51.2 bits (123), Expect = 3e-07
Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 22/100 (22%)
Query: 273 SVLIMIGSQGSGKSSFVSTYLKPL-NYTTVNRDTL-------GSW---------QKCVSV 315
+++ +G GSGKS++ + VNRD L G W + V+
Sbjct: 3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVNRDDLRQSLFGHGEWGEYKFTKEKEDLVTK 62
Query: 316 M-----KAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGV 350
AAL SG SV++ +TN + E R ++ E AK+ G
Sbjct: 63 AQEAAALAALKSGKSVIISDTNLNPERRRKWKELAKELGA 102
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase. Members
of this protein family are the bacterial polynucleotide
kinase-phosphatase (Pnkp) whose genes occur paired with
genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis is
that the combination of Pnkp (RNA repair) and Hen1 (RNA
modification) serves to first repair RNA damage from
ribotoxins and then perform a modification that prevents
the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 50.0 bits (120), Expect = 1e-06
Identities = 26/105 (24%), Positives = 46/105 (43%), Gaps = 23/105 (21%)
Query: 273 SVLIMIGSQGSGKSSFVSTYLKPLNYTTVNRDTLGSW-------QKCVSVMKAALD---- 321
S+++++G+ GSGKS+F + KP ++ D Q S A D
Sbjct: 9 SLVVLVGASGSGKSTFARKHFKP--TEVLSSDFCRGLVSDDENDQ---SASSDAFDVLYY 63
Query: 322 -------SGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHMNI 359
GL V+D TN E R + A+++ V +A+ +++
Sbjct: 64 IAGKRLARGLLTVIDATNVQPEDRKGLVALAREYHVLPVAIVLDL 108
>gnl|CDD|130328 TIGR01261, hisB_Nterm, histidinol-phosphatase. This model
describes histidinol phosphatase. All known examples in
the scope of this model are bifunctional proteins with a
histidinol phosphatase domain followed by an
imidazoleglycerol-phosphate dehydratase domain. These
enzymatic domains catalyze the ninth and seventh steps,
respectively, of histidine biosynthesis [Amino acid
biosynthesis, Histidine family].
Length = 161
Score = 45.9 bits (109), Expect = 5e-06
Identities = 42/163 (25%), Positives = 58/163 (35%), Gaps = 33/163 (20%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSN-IESVLKQYLDDGYKLVIFTNQGAIGR 84
KI D DGTLI F VD + KL F + L + GYK V+ TNQ +G
Sbjct: 2 KILFIDRDGTLIEEPPSD-FQVDALE-KLRFEKGVIPALLKLKKAGYKFVMVTNQDGLGT 59
Query: 85 KKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRY--------RKPVPGMWE-YLSQEKNG 135
DF +++ +F + RKP + E YL +
Sbjct: 60 PSFPQADFDGPHNLMLQIFRSQGIIFDDVLICPHFPDDNCDCRKPKIKLLEPYLKKNL-- 117
Query: 136 DLAIDISQSFYAGDAAGRAANWAPKKKKDFACTDHLFAFNLNL 178
ID ++S+ GD TD A NL +
Sbjct: 118 ---IDKARSYVIGDRE----------------TDMQLAENLGI 141
>gnl|CDD|119389 cd01427, HAD_like, Haloacid dehalogenase-like hydrolases. The
haloacid dehalogenase-like (HAD) superfamily includes
L-2-haloacid dehalogenase, epoxide hydrolase,
phosphoserine phosphatase, phosphomannomutase,
phosphoglycolate phosphatase, P-type ATPase, and many
others, all of which use a nucleophilic aspartate in
their phosphoryl transfer reaction. All members possess
a highly conserved alpha/beta core domain, and many also
possess a small cap domain, the fold and function of
which is variable. Members of this superfamily are
sometimes referred to as belonging to the DDDD
superfamily of phosphohydrolases.
Length = 139
Score = 43.9 bits (104), Expect = 2e-05
Identities = 27/138 (19%), Positives = 48/138 (34%), Gaps = 19/138 (13%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIG-RKKMS 88
FDLDGTL+ ++ G + L+ ++ LK+ + G KL + TN+ + +
Sbjct: 4 FDLDGTLLDSEPGIAEIEELE----LYPGVKEALKELKEKGIKLALATNKSRREVLELLE 59
Query: 89 TRDFQAKAEKII-----KSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEKNGDLAIDISQ 143
+ +I +F+ KP P + L +D +
Sbjct: 60 ELGLDDYFDPVITSNGAAIYYPKEGLFLGGGPFDIGKPNPDKLLAALKL----LGVDPEE 115
Query: 144 SFYAGD-----AAGRAAN 156
GD +AA
Sbjct: 116 VLMVGDSLNDIEMAKAAG 133
>gnl|CDD|226986 COG4639, COG4639, Predicted kinase [General function prediction
only].
Length = 168
Score = 44.0 bits (104), Expect = 3e-05
Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 16/99 (16%)
Query: 273 SVLIMIGSQGSGKSSFVSTYLKP-----LNYTTVNRDTLGS-----------WQKCVSVM 316
++++ G+ GSGKS+F L+ + S W +
Sbjct: 3 ILVVLRGASGSGKSTFAKENFLQNYVLSLDDLRLLLGVSASKENSQKNDELVWDILYKQL 62
Query: 317 KAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAV 355
+ L G ++D TN +E R + I+ AK +G + A+
Sbjct: 63 EQRLRRGKFTIIDATNLRREDRRKLIDLAKAYGYKIYAI 101
>gnl|CDD|236354 PRK08942, PRK08942, D,D-heptose 1,7-bisphosphate phosphatase;
Validated.
Length = 181
Score = 44.0 bits (105), Expect = 3e-05
Identities = 44/152 (28%), Positives = 62/152 (40%), Gaps = 40/152 (26%)
Query: 31 DLDGTLITTKSGKVFPVDTHDWKLLFSNIESV--LKQYLDDGYKLVIFTNQGAIGRKKMS 88
D DG + G V D +W + +IE++ LKQ GY++V+ TNQ I R +
Sbjct: 9 DRDGVINVDSDGYVKSPD--EWIPIPGSIEAIARLKQA---GYRVVVATNQSGIARGLFT 63
Query: 89 TRDFQAKAEKIIKSLNVPVQMFVATQYDR-----Y-----------RKPVPGMWEYLSQE 132
A EK+ SL A + R Y RKP PGM +++
Sbjct: 64 EAQLNALHEKMDWSL--------ADRGGRLDGIYYCPHHPEDGCDCRKPKPGMLLSIAER 115
Query: 133 KNGDLAIDISQSFYAGDA-----AGRAANWAP 159
L ID++ S GD+ A AA P
Sbjct: 116 ----LNIDLAGSPMVGDSLRDLQAAAAAGVTP 143
>gnl|CDD|129317 TIGR00213, GmhB_yaeD, D,D-heptose 1,7-bisphosphate phosphatase.
This family of proteins formerly designated yaeD
resembles the histidinol phosphatase domain of the
bifunctional protein HisB. The member from E. coli has
been characterized as D,D-heptose 1,7-bisphosphate
phosphatase, GmhB, involved in inner core LPS assembly
(PMID:11751812) [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 176
Score = 41.8 bits (98), Expect = 1e-04
Identities = 44/146 (30%), Positives = 63/146 (43%), Gaps = 27/146 (18%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
D DGT I G V +D +++ + I++ L++ GY LV+ TNQ I R +
Sbjct: 6 LDRDGT-INIDHGYVHEID--NFEFIDGVIDA-LRELKKMGYALVLVTNQSGIARGYFTE 61
Query: 90 RDFQAKAEKIIKSL--------------NVPVQMFVATQYDRYRKPVPGMWEYLSQEKNG 135
F+ E + SL + P + Q RKP PGM L K
Sbjct: 62 AQFEQLTEWMDWSLAERDVDLDGIYYCPHHPEGVEEFRQVCDCRKPKPGM--LLQARK-- 117
Query: 136 DLAIDISQSFYAGDA-----AGRAAN 156
+L ID++QS+ GD AG AA
Sbjct: 118 ELHIDMAQSYMVGDKLEDMQAGVAAK 143
>gnl|CDD|235471 PRK05446, PRK05446, imidazole glycerol-phosphate
dehydratase/histidinol phosphatase; Provisional.
Length = 354
Score = 40.5 bits (96), Expect = 0.001
Identities = 40/136 (29%), Positives = 55/136 (40%), Gaps = 17/136 (12%)
Query: 24 SAKIASFDLDGTLITTKSGKVFPVDTHDWKLLF-SNIESVLKQYLDDGYKLVIFTNQGAI 82
KI D DGTLI F VD+ D KL F + L + GYKLV+ TNQ +
Sbjct: 1 MQKILFIDRDGTLIEEPPTD-FQVDSLD-KLAFEPGVIPALLKLQKAGYKLVMVTNQDGL 58
Query: 83 GRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRY--------RKPVPGMWE-YLSQEK 133
G DF +++ F + RKP G+ E YL++
Sbjct: 59 GTDSFPQEDFDPPHNLMMQIFESQGIKFDEVLICPHFPEDNCSCRKPKTGLVEEYLAEGA 118
Query: 134 NGDLAIDISQSFYAGD 149
ID++ S+ GD
Sbjct: 119 -----IDLANSYVIGD 129
>gnl|CDD|233526 TIGR01681, HAD-SF-IIIC, HAD-superfamily phosphatase, subfamily
IIIC. This model represents the IIIC subfamily of the
Haloacid Dehalogenase (HAD) superfamily of aspartate
nucleophile hydrolases. Subfamily III (also including
IIIA - TIGR01662 and IIIB - pfam03767) contains
sequences which do not contain either of the insert
domains (between the 1st and 2nd conserved catalytic
motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549,
TIGR01488, TIGR01494, TIGR01658, TIGR01544 and
TIGR01545, or between the 2nd and 3rd, subfamily II -
TIGR01460 and TIGR01484). Subfamily IIIC contains five
relatively distantly related clades: a family of viral
proteins (TIGR01684), a family of eukaryotic proteins
called MDP-1 and a family of archaeal proteins most
closely related to MDP-1 (TIGR01685), a family of
bacteria including the Streptomyces FkbH protein
(TIGR01686), and a small clade including the Pasteurella
BcbF and EcbF proteins. The overall lack of species
overlap among these clades may indicate a conserved
function, but the degree of divergence between the
clades and the differences in archetecture outside of
the domain in some clades warns against such a
conclusion. No member of this subfamily is characterized
with respect to function, however the MDP-1 protein is a
characterized phosphatase. All of the characterized
enzymes within subfamily III are phosphatases, and all
of the active site residues characteristic of
HAD-superfamily phosphatases are present in subfamily
IIIC.
Length = 128
Score = 38.2 bits (89), Expect = 0.001
Identities = 20/121 (16%), Positives = 37/121 (30%), Gaps = 18/121 (14%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVI------FTNQ 79
K+ FDLD TL T ++ V D ++ I L+ +G+ L +
Sbjct: 1 KVIVFDLDNTLWTGENIVVGEDPIIDLEVTIKEIRDKLQTLKKNGFLLALASYNDDPHVA 60
Query: 80 GAIGRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEKNGDLAI 139
+ + + + + F Y P ++ + NG L
Sbjct: 61 YELLKIF-----------EDFGIIFPLAEYFDPLT-IGYWLPKSPRLVEIALKLNGVLKP 108
Query: 140 D 140
Sbjct: 109 K 109
>gnl|CDD|201133 pfam00289, CPSase_L_chain, Carbamoyl-phosphate synthase L chain,
N-terminal domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. This important enzyme initiates both the
urea cycle and the biosynthesis of arginine and/or
pyrimidines. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain. The small chain promotes the hydrolysis of
glutamine to ammonia, which is used by the large chain
to synthesise carbamoyl phosphate. See pfam00988. The
small chain has a GATase domain in the carboxyl
terminus. See pfam00117.
Length = 108
Score = 35.5 bits (83), Expect = 0.006
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 25/68 (36%)
Query: 312 CVSVMKAALDSGLSVVVDNTNPDKESRHR-----------------Y------IEAAKQH 348
V +++A + G+ V N+NPD S H Y ++ A++
Sbjct: 13 AVRIIRALRELGIETVAVNSNPDTVSTHVRLADEAYFLGPGPASESYLNIERILDIAEKE 72
Query: 349 GVRCIAVH 356
G A+H
Sbjct: 73 G--ADAIH 78
>gnl|CDD|221729 pfam12710, HAD, haloacid dehalogenase-like hydrolase.
Length = 122
Score = 34.9 bits (80), Expect = 0.018
Identities = 18/125 (14%), Positives = 35/125 (28%), Gaps = 19/125 (15%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
FDLDGTL + + + + + L D +L+ + +
Sbjct: 3 FDLDGTLTDSDTALLL------LLEALAEDRRLGLLGLSDAEELLELV--------VIVS 48
Query: 90 RDFQAKAEKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEK-----NGDLAIDISQS 144
+ + K+L + V T+ + + + K I
Sbjct: 49 GSPEPLVRPVAKALGIDDVNVVGTELENVLVDGRLTGKLDGEGKAAALKRLAQKIGRYPV 108
Query: 145 FYAGD 149
GD
Sbjct: 109 VAVGD 113
>gnl|CDD|226648 COG4185, COG4185, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 187
Score = 34.4 bits (79), Expect = 0.045
Identities = 24/121 (19%), Positives = 42/121 (34%), Gaps = 28/121 (23%)
Query: 273 SVLIMIGSQGSGKSSFVSTYLKPL--NYTTVNRDTL----GSW----------QKCVSVM 316
+ I+ G GSGKS+ ++ L PL VN D + + + +
Sbjct: 3 RLDIVAGPNGSGKSTVYASTLAPLLPGIVFVNADEIAAQISPDNPTSAAIQAARVAIDRI 62
Query: 317 KAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHMN--------ISKEHAKHNI 368
+D G + + T S I+ AK G + +N ++ E K +
Sbjct: 63 ARLIDLGRPFIAETTLSGP-SILELIKTAKAAG---FYIVLNYIVIDSVELAVERVKLRV 118
Query: 369 K 369
Sbjct: 119 A 119
Score = 27.8 bits (62), Expect = 6.1
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 223 KQVLIMIGSQGSGKSSFVSTYLKPLN 248
K++ I+ G GSGKS+ ++ L PL
Sbjct: 2 KRLDIVAGPNGSGKSTVYASTLAPLL 27
>gnl|CDD|236315 PRK08633, PRK08633, 2-acyl-glycerophospho-ethanolamine
acyltransferase; Validated.
Length = 1146
Score = 35.7 bits (83), Expect = 0.046
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 43 KVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMSTRDFQAKAEKIIKS 102
V P+ + K ++E +++ LDDG + IF +GAI R +F+ E I+K
Sbjct: 488 GVIPISSGGSK---ESLEF-IRKALDDGEVVCIFP-EGAITRNGQ-LNEFKRGFELIVKG 541
Query: 103 LNVPV 107
+VP+
Sbjct: 542 TDVPI 546
>gnl|CDD|223635 COG0561, Cof, Predicted hydrolases of the HAD superfamily
[General function prediction only].
Length = 264
Score = 34.7 bits (80), Expect = 0.059
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 17/67 (25%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRK 85
K+ +FDLDGTL+ + + E L + + G K+V+ T GR
Sbjct: 4 KLLAFDLDGTLL-----------DSNKTISPETKE-ALARLREKGVKVVLAT-----GRP 46
Query: 86 KMSTRDF 92
Sbjct: 47 LPDVLSI 53
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 33.5 bits (77), Expect = 0.098
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 272 DSVLIMIGSQGSGKSSFVST 291
D VLI+ G+QGSGKS+F+
Sbjct: 52 DHVLILQGAQGSGKSTFLKK 71
Score = 32.4 bits (74), Expect = 0.25
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 219 PHDK-KQVLIMIGSQGSGKSSFVST 242
P K VLI+ G+QGSGKS+F+
Sbjct: 47 PGCKFDHVLILQGAQGSGKSTFLKK 71
>gnl|CDD|107287 cd06292, PBP1_LacI_like_10, 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 = 273
Score = 33.8 bits (78), Expect = 0.10
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 312 CVSVMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHMNISKEHA 364
++ A G +V++ NT S Y+E GVR + IS HA
Sbjct: 18 AEAIEAALAQYGYTVLLCNTYRGGVSEADYVEDLLARGVRGVVF---ISSLHA 67
>gnl|CDD|238948 cd01990, Alpha_ANH_like_I, This is a subfamily of Adenine
nucleotide alpha hydrolases superfamily. Adenine
nucleotide alpha hydrolases superfamily includes N type
ATP PPases and ATP sulphurylases. It forms a
apha/beta/apha fold which binds to Adenosine group.
This subfamily of proteins probably binds ATP. This
domain is about 200 amino acids long with a strongly
conserved motif SGGKD at the N terminus.
Length = 202
Score = 33.4 bits (77), Expect = 0.12
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 317 KAALDSGLSVVVDNTNPDKESRHRY-IEAAKQHGVRCIAVHMNISKEH 363
+ A + GL VV+D TN D +R ++A ++ GVR + K
Sbjct: 89 EIAEELGLDVVLDGTNADDLGDYRPGLKALRELGVRSPLAEAGLGKAE 136
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 33.2 bits (76), Expect = 0.13
Identities = 12/40 (30%), Positives = 18/40 (45%)
Query: 317 KAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVH 356
+ L SG SVV+D T + R A+ GV + +
Sbjct: 70 ELLLSSGHSVVLDATFDRPQERALARALARDVGVAFVLIR 109
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 33.3 bits (77), Expect = 0.22
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 16/59 (27%)
Query: 188 LNEKAPDFPNLPTFKPRE-----VYQK-----AQSQTIPNIPHDKKQVLIMIGSQGSGK 236
L E+ P PRE VY++ + +P K Q ++++G QGSGK
Sbjct: 56 LEEEPP-----KGLTPREHVIKIVYEELVKLLGEETEPLVLPL-KPQTIMLVGLQGSGK 108
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 32.5 bits (75), Expect = 0.24
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 273 SVLIMIGSQGSGKSSFV---STYLKPLNYTT--VNRDT 305
++ +G+ GSGK++ S +L+ Y VN D
Sbjct: 3 YIVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVNLDP 40
Score = 32.5 bits (75), Expect = 0.26
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 225 VLIMIGSQGSGKSSFV---STYLKPLNYTT--VNRDT 256
++ +G+ GSGK++ S +L+ Y VN D
Sbjct: 4 IVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVNLDP 40
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 31.7 bits (72), Expect = 0.45
Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 18/102 (17%)
Query: 274 VLIMIGSQGSGKSSFVSTYLKPLNY---------TTVNRDTLGSWQKCVS---------V 315
++I+ G G GKS+F K L+ T + R++ W++ +
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIRESFPVWKEKYEEFIRDSTLYL 60
Query: 316 MKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHM 357
+K AL + SV+VD+TN R I AK++ I +++
Sbjct: 61 IKTALKNKYSVIVDDTNYYNSMRRDLINIAKEYNKNYIIIYL 102
>gnl|CDD|107250 cd01537, PBP1_Repressors_Sugar_Binding_like, Ligand-binding domain
of the LacI-GalR family of transcription regulators and
the sugar-binding domain of ABC-type transport systems.
Ligand-binding domain of the LacI-GalR family of
transcription regulators and the sugar-binding domain of
ABC-type transport systems, all of which contain the
type I periplasmic binding protein-like fold. Their
specific ligands include lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars.
The LacI family of proteins consists of transcriptional
regulators related to the lac repressor; in general the
sugar binding domain in this family binds a sugar, which
in turn changes the DNA binding activity of the
repressor domain. The core structure of the periplasmic
binding proteins is classified into two types and they
differ in number and order of beta strands in each
domain: type I, which has six beta strands, and type II,
which has five beta strands. These two distinct
structural arrangements may have originated from a
common ancestor.
Length = 264
Score = 31.6 bits (72), Expect = 0.61
Identities = 10/43 (23%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 309 WQKCVSVMK-AALDSGLSVVVDNTNPDKESRHRYIEAAKQHGV 350
+ + + ++ AA +G V++ N+ D E + +E GV
Sbjct: 14 FAQVLKGIEEAAKAAGYQVLLANSQNDAEKQLSALENLIARGV 56
>gnl|CDD|233434 TIGR01484, HAD-SF-IIB, HAD-superfamily hydrolase, subfamily IIB.
This subfamily falls within the Haloacid Dehalogenase
(HAD) superfamily of aspartate-nucleophile hydrolases.
The Class II subfamilies are characterized by a domain
that is located between the second and third conserved
catalytic motifs of the superfamily domain. The IIB
subfamily is distinguished from the IIA subfamily
(TIGR01460) by homology and the predicted secondary
structure of this domain by PSI-PRED. The IIB
subfamily's Class II domain has the following predicted
structure: Helix-Sheet-Sheet-(Helix or
Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB
subfamily consists of Trehalose-6-phosphatase
(TIGR00685), plant and cyanobacterial
Sucrose-phosphatase and a closely related group of
bacterial and archaeal sequences, eukaryotic
phosphomannomutase (pfam03332), a large subfamily
("Cof-like hydrolases", TIGR00099) containing many
closely related bacterial sequences, a hypothetical
equivalog containing the E. coli YedP protein, as well
as two small clusters containing OMNI|TC0379 and
OMNI|SA2196 whose relationship to the other groups is
unclear [Unknown function, Enzymes of unknown
specificity].
Length = 204
Score = 31.2 bits (71), Expect = 0.64
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 23/81 (28%)
Query: 27 IASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKK 86
+ FDLDGTL+ + ++ P L++ + G K+V+ T GR
Sbjct: 1 LLFFDLDGTLLDPNAHELSP-----------ETIEALERLREAGVKVVLVT-----GRS- 43
Query: 87 MSTRDFQAKAEKIIKSLNVPV 107
A+ ++++K L +P+
Sbjct: 44 ------LAEIKELLKQLPLPL 58
>gnl|CDD|234729 PRK00331, PRK00331, glucosamine--fructose-6-phosphate
aminotransferase; Reviewed.
Length = 604
Score = 31.6 bits (73), Expect = 0.71
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 13/48 (27%)
Query: 97 EKIIKSLNVPVQMFVATQYDRYRKPVPGMWEYLSQEKNGDLAIDISQS 144
E + +PV++ +A+++ RYR PV L I ISQS
Sbjct: 312 ESLAG---IPVEVEIASEF-RYRDPVLS---------PKTLVIAISQS 346
>gnl|CDD|233443 TIGR01509, HAD-SF-IA-v3, haloacid dehalogenase superfamily,
subfamily IA, variant 3 with third motif having DD or
ED. This model represents part of one structural
subfamily of the Haloacid Dehalogenase (HAD) superfamily
of aspartate-nucleophile hydrolases. The superfamily is
defined by the presence of three short catalytic motifs.
The subfamilies are defined based on the location and
the observed or predicted fold of a so-called "capping
domain", or the absence of such a domain. Subfamily I
consists of sequences in which the capping domain is
found in between the first and second catalytic motifs.
Subfamily II consists of sequences in which the capping
domain is found between the second and third motifs.
Subfamily III sequences have no capping domain in either
of these positions.The Subfamily IA and IB capping
domains are predicted by PSI-PRED to consist of an alpha
helical bundle. Subfamily I encompasses such a wide
region of sequence space (the sequences are highly
divergent) that representing it with a single model is
impossible, resulting in an overly broad description
which allows in many unrelated sequences. Subfamily IA
and IB are separated based on an aparrent phylogenetic
bifurcation. Subfamily IA is still too broad to model,
but cannot be further subdivided into large chunks based
on phylogenetic trees. Of the three motifs defining the
HAD superfamily, the third has three variant forms : (1)
hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s
where _s_ refers to a small amino acid and _h_ to a
hydrophobic one. All three of these variants are found
in subfamily IA. Individual models were made based on
seeds exhibiting only one of the variants each. Variant
3 (this model) is found in the enzymes
beta-phosphoglucomutase (TIGR01990) and
deoxyglucose-6-phosphatase, while many other enzymes of
subfamily IA exhibit this variant as well as variant 1
(TIGR01549). These three variant models were created
withthe knowledge that there will be overlap among them
- this is by design and serves the purpose of
eliminating the overlap with models of more distantly
relatedHAD subfamilies caused by an overly broad single
model [Unknown function, Enzymes of unknown
specificity].
Length = 177
Score = 30.8 bits (70), Expect = 0.75
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 18/104 (17%)
Query: 58 NIESVLKQYLDDGYKLVIFTNQGAIGRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQYDR 117
+ ++L+ G KL + TN K + +A + +I S +V +
Sbjct: 83 GVRALLEALRARGKKLALLTNSPRADAKLVLELGLRALFDVVIDSSDVGL---------- 132
Query: 118 YRKPVPGMWEYLSQEKNGD----LAIDISQSFYAGDAAGRAANW 157
KP P ++ ++ L +D S AG A +AA
Sbjct: 133 -GKPDPDIYLQALKKLGLKPSECLFVDDSP---AGIDAAKAAGM 172
>gnl|CDD|205524 pfam13344, Hydrolase_6, Haloacid dehalogenase-like hydrolase. This
family is part of the HAD superfamily.
Length = 101
Score = 29.3 bits (67), Expect = 0.91
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 17/77 (22%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
FD+DG L + G+ P E L G +V TN + R++ +
Sbjct: 3 FDVDGVLW--RGGEPIP----------GAAE-ALNALRAAGKPVVFVTNNSSRSREQYAK 49
Query: 90 R----DFQAKAEKIIKS 102
+ F +++I S
Sbjct: 50 KLRKLGFDVDEDEVITS 66
>gnl|CDD|223943 COG1011, COG1011, Predicted hydrolase (HAD superfamily) [General
function prediction only].
Length = 229
Score = 30.6 bits (69), Expect = 0.98
Identities = 19/112 (16%), Positives = 28/112 (25%), Gaps = 6/112 (5%)
Query: 26 KIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRK 85
K FDLDGTL+ S + V ++ L F G
Sbjct: 5 KAILFDLDGTLLDFDSAEFRAVLAEFAEIGVPETLEELALLKLIEKLEARFLRGEYTGEY 64
Query: 86 KMSTRDFQAKAEKIIKSLNVPVQMFVATQYDRYR---KPVPGMWEYLSQEKN 134
++ E++ L V P E L +
Sbjct: 65 GLTLERLLELLERL---LGDEDAELVEELLAALAKLLPDYPEALEALKELGK 113
>gnl|CDD|219777 pfam08282, Hydrolase_3, haloacid dehalogenase-like hydrolase. This
family contains haloacid dehalogenase-like hydrolase
enzymes.
Length = 254
Score = 30.3 bits (69), Expect = 1.5
Identities = 20/76 (26%), Positives = 30/76 (39%), Gaps = 24/76 (31%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMST 89
DLDGTL+ D K+ E +K+ + G K+VI T GR
Sbjct: 3 SDLDGTLL-----------NSDKKISERTKE-AIKKLQEKGIKVVIAT-----GR---PY 42
Query: 90 RDFQAKAEKIIKSLNV 105
R A +++ L +
Sbjct: 43 RG----ALPVLEELGL 54
>gnl|CDD|223620 COG0546, Gph, Predicted phosphatases [General function prediction
only].
Length = 220
Score = 29.7 bits (67), Expect = 1.9
Identities = 24/109 (22%), Positives = 41/109 (37%), Gaps = 23/109 (21%)
Query: 55 LFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMSTRDFQAKAEKIIKSLNV--PVQMFVA 112
LF ++ +L GYKL I TN+ + ++K+L + + V
Sbjct: 90 LFPGVKELLAALKSAGYKLGIVTNKP---------ERE---LDILLKALGLADYFDVIVG 137
Query: 113 TQYDRYRKPVPGMWEYLSQEKNGDLAIDISQSFYAGDA-----AGRAAN 156
KP P L ++ L +D ++ GD+ A +AA
Sbjct: 138 GDDVPPPKPDPEPLLLLLEK----LGLDPEEALMVGDSLNDILAAKAAG 182
>gnl|CDD|237336 PRK13288, PRK13288, pyrophosphatase PpaX; Provisional.
Length = 214
Score = 29.6 bits (67), Expect = 2.1
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 12/43 (27%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYK 72
FDLDGTLI +T++ L+ S+ LK Y + YK
Sbjct: 8 FDLDGTLI----------NTNE--LIISSFLHTLKTYYPNQYK 38
>gnl|CDD|107278 cd06283, PBP1_RegR_EndR_KdgR_like, Ligand-binding domain of DNA
transcription repressor RegR and other putative
regulators such as KdgR and EndR. Ligand-binding domain
of DNA transcription repressor RegR and other putative
regulators such as KdgR and EndR, all of which are
members of the LacI-GalR family of bacterial
transcription regulators. RegR regulates bacterial
competence and the expression of virulence factors,
including hyaluronidase. 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 = 267
Score = 29.9 bits (68), Expect = 2.1
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 313 VSVMKAALDS----GLSVVVDNTNPDKESRHRYIEAAKQHGV 350
V+K D G V+V N++ D E Y+E+ + V
Sbjct: 15 SLVLKGIEDVCRAHGYQVLVCNSDNDPEKEKEYLESLLAYQV 56
>gnl|CDD|222115 pfam13419, HAD_2, Haloacid dehalogenase-like hydrolase.
Length = 176
Score = 29.2 bits (66), Expect = 2.4
Identities = 22/108 (20%), Positives = 43/108 (39%), Gaps = 19/108 (17%)
Query: 55 LFSNIESVLKQYLDDGYKLVIFTNQGAIGRKKMSTRDFQAKAEKIIKSLNVPVQMFVATQ 114
F ++ +L++ G KLVI +N +R+ + + + L++ +F +
Sbjct: 78 PFPDVVELLRRLKAKGVKLVILSN---------GSREAVERLLEKLGLLDLFDAVFTS-D 127
Query: 115 YDRYRKPVPGMWEYLSQEKNGDLAIDISQSFYAGD-----AAGRAANW 157
RKP P +E + + L + + + D A RAA
Sbjct: 128 DVGARKPDPEAYERVLER----LGLPPEEILFIDDSPEDLEAARAAGI 171
>gnl|CDD|227415 COG5083, SMP2, Uncharacterized protein involved in plasmid
maintenance [General function prediction only].
Length = 580
Score = 29.8 bits (67), Expect = 2.5
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 14/76 (18%)
Query: 10 NGKLLVFTSNDVCNSAKIASFDLDGTLITTKS-GKVFPVDTHDWKLLFSNIESVLKQYLD 68
+ V+ +N KI D+DGT+ + + G V + DW V K Y D
Sbjct: 365 TMYIFVWRNNK-----KIVVSDIDGTITKSDALGHVKQMIGKDW-----THNGVAKLYTD 414
Query: 69 ---DGYKLVIFTNQGA 81
+GYK+ T++
Sbjct: 415 IDRNGYKIKYLTSRSY 430
>gnl|CDD|217564 pfam03447, NAD_binding_3, Homoserine dehydrogenase, NAD binding
domain. This domain adopts a Rossmann NAD binding fold.
The C-terminal domain of homoserine dehydrogenase
contributes a single helix to this structural domain,
which is not included in the Pfam model.
Length = 116
Score = 28.1 bits (63), Expect = 2.9
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 319 ALDSGLSVVVDNT--NPDKESRHRYIEAAKQHGVR 351
AL +G VV + D R R EAA+ GVR
Sbjct: 78 ALKAGKHVVTASKGALADLALRERLREAAEASGVR 112
>gnl|CDD|227832 COG5545, COG5545, Predicted P-loop ATPase and inactivated
derivatives [General function prediction only].
Length = 517
Score = 29.5 bits (66), Expect = 3.2
Identities = 17/74 (22%), Positives = 27/74 (36%), Gaps = 21/74 (28%)
Query: 219 PHDK-KQVLIMIGSQGSGKSSFVST-------------------YLKPLNYTTVNRDTLG 258
P K +L++ G QGS KS+F+S Y V +
Sbjct: 197 PGAKVDFMLVLEGPQGSHKSTFLSELFGTYWFTDTAESPTGKDFYQVIQGCWIVEIGEMD 256
Query: 259 SWQKC-VSVMKAAL 271
S+ K V+ +K +
Sbjct: 257 SFGKADVTALKVFI 270
Score = 28.0 bits (62), Expect = 8.4
Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 20/72 (27%)
Query: 269 AALDSVLIMIGSQGSGKSSFVST-------------------YLKPLNYTTVNRDTLGSW 309
A +D +L++ G QGS KS+F+S Y V + S+
Sbjct: 199 AKVDFMLVLEGPQGSHKSTFLSELFGTYWFTDTAESPTGKDFYQVIQGCWIVEIGEMDSF 258
Query: 310 QKC-VSVMKAAL 320
K V+ +K +
Sbjct: 259 GKADVTALKVFI 270
>gnl|CDD|107262 cd06267, PBP1_LacI_sugar_binding_like, Ligand binding domain of the
LacI tanscriptional regulator family belonging to the
type I periplasmic-binding fold protein superfamily.
Ligand binding domain of the LacI tanscriptional
regulator family belonging to the type I
periplasmic-binding fold protein superfamily. In most
cases, ligands are monosaccharide including lactose,
ribose, fructose, xylose, arabinose, galactose/glucose,
and other sugars. The LacI family of proteins consists
of transcriptional regulators related to the lac
repressor. In this case, the domain sugar binding
changes the DNA binding activity of the repressor
domain.
Length = 264
Score = 29.1 bits (66), Expect = 3.5
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 314 SVMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGV 350
+ +AA ++G SV++ N++ D E +E V
Sbjct: 20 GIEEAAREAGYSVLLCNSDEDPEKEREALELLLSRRV 56
>gnl|CDD|224525 COG1609, PurR, Transcriptional regulators [Transcription].
Length = 333
Score = 29.2 bits (66), Expect = 3.7
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 315 VMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGV 350
+ +AA ++G S+++ NT+ D E Y+E Q V
Sbjct: 80 IEEAAREAGYSLLLANTDDDPEKEREYLETLLQKRV 115
>gnl|CDD|216130 pfam00809, Pterin_bind, Pterin binding enzyme. This family
includes a variety of pterin binding enzymes that all
adopt a TIM barrel fold. The family includes
dihydropteroate synthase EC:2.5.1.15 as well as a group
methyltransferase enzymes including
methyltetrahydrofolate, corrinoid iron-sulfur protein
methyltransferase (MeTr) that catalyzes a key step in
the Wood-Ljungdahl pathway of carbon dioxide fixation.
It transfers the N5-methyl group from
methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide
centre in another protein, the corrinoid iron-sulfur
protein. MeTr is a member of a family of proteins that
includes methionine synthase and methanogenic enzymes
that activate the methyl group of
methyltetra-hydromethano(or -sarcino)pterin.
Length = 210
Score = 28.8 bits (65), Expect = 3.8
Identities = 10/55 (18%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 315 VMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHMNISKEHAKHNIK 369
V +AAL +G ++ D++ + A ++G + +HM+ + + + +
Sbjct: 84 VAEAALKAGADIINDSSGGKDDPEM--APLAAEYGAPVVLMHMDGNPQGMQETPE 136
>gnl|CDD|224522 COG1606, COG1606, ATP-utilizing enzymes of the PP-loop superfamily
[General function prediction only].
Length = 269
Score = 28.9 bits (65), Expect = 3.9
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 314 SVMKAALDSGLSVVVDNTNPDKESRHR-YIEAAKQHGVRCIAVHMNISKE 362
++++ A G VV D TN +R + A K+ G+R I+K+
Sbjct: 104 TLVEEAEKRGYDVVADGTNASDLFDYRPGLRALKELGIRSPLAEFGITKK 153
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 27.8 bits (62), Expect = 3.9
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 229 IGSQGSGKSSFVSTYLK 245
IG +GSGKSS +S +
Sbjct: 5 IGDKGSGKSSLLSQLVG 21
Score = 27.8 bits (62), Expect = 3.9
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 278 IGSQGSGKSSFVSTYLK 294
IG +GSGKSS +S +
Sbjct: 5 IGDKGSGKSSLLSQLVG 21
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 28.9 bits (65), Expect = 4.2
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 220 HDKKQVLIMIGSQGSGKSSFVSTYL 244
K V++++G SGKS+ +TYL
Sbjct: 70 AGKVGVVMVVGPVDSGKSTL-TTYL 93
>gnl|CDD|129369 TIGR00268, TIGR00268, TIGR00268 family protein. The N-terminal
region of the model shows similarity to
Argininosuccinate synthase proteins using PSI-blast and
using the recognize protein identification server
[Hypothetical proteins, Conserved].
Length = 252
Score = 28.6 bits (64), Expect = 4.4
Identities = 16/50 (32%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 314 SVMKAALDSGLSVVVDNTNPDKESRHRY-IEAAKQHGVRCIAVHMNISKE 362
++K A G VVVD TN D HR A K+ I+K+
Sbjct: 98 ILVKEAEKRGYDVVVDGTNADDLFDHRPGYRAVKEFNGVSPWAEFGITKK 147
>gnl|CDD|188099 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic phosphate.
In the model species Escherichia coli, a constitutive
transporter for inorganic phosphate, with low affinity,
is also present. The high affinity transporter that
includes this polypeptide is induced when extracellular
phosphate concentrations are low. The proteins most
similar to the members of this family but not included
appear to be amino acid transporters [Transport and
binding proteins, Anions].
Length = 247
Score = 28.8 bits (65), Expect = 4.5
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 217 NIPHDKKQVLIMIGSQGSGKSSFVSTYLKPLN 248
N+ K QV +IG G GK ST L+ LN
Sbjct: 21 NLDIPKNQVTALIGPSGCGK----STLLRSLN 48
>gnl|CDD|233439 TIGR01496, DHPS, dihydropteroate synthase. This model represents
dihydropteroate synthase, the enzyme that catalyzes the
second to last step in folic acid biosynthesis. The gene
is usually designated folP (folic acid biosynthsis) or
sul (sulfanilamide resistance). This model represents
one branch of the family of pterin-binding enzymes
(pfam00809) and of a cluster of dihydropteroate synthase
and related enzymes (COG0294). Other members of
pfam00809 and COG0294 are represented by model TIGR00284
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Folic acid].
Length = 257
Score = 28.8 bits (65), Expect = 4.7
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 314 SVMKAALDSGLSVVVD---NTNPDKESRHRYIEAAKQHGVRCIAVHM 357
V +AAL++G ++ D +P +E A ++GV + +HM
Sbjct: 86 EVARAALEAGADIINDVSGGQDPAM------LEVAAEYGVPLVLMHM 126
>gnl|CDD|217230 pfam02784, Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase,
pyridoxal binding domain. These pyridoxal-dependent
decarboxylases acting on ornithine, lysine, arginine and
related substrates This domain has a TIM barrel fold.
Length = 245
Score = 28.8 bits (65), Expect = 4.7
Identities = 13/74 (17%), Positives = 26/74 (35%), Gaps = 16/74 (21%)
Query: 306 LGSWQKCVS------VMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVHM-- 357
LG C S V+ A + ++ N + + A +HGV C+ V
Sbjct: 41 LGLGFDCASKGELERVLAAGVPPE-RIIFANPCKSRS----ELRYALEHGVVCVTVDNVE 95
Query: 358 ---NISKEHAKHNI 368
+++ + +
Sbjct: 96 ELEKLARLAPEARL 109
>gnl|CDD|217328 pfam03031, NIF, NLI interacting factor-like phosphatase. This
family contains a number of NLI interacting factor
isoforms and also an N-terminal regions of RNA
polymerase II CTC phosphatase and FCP1 serine
phosphatase. This region has been identified as the
minimal phosphatase domain.
Length = 153
Score = 28.0 bits (63), Expect = 4.8
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 25/83 (30%)
Query: 30 FDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLK---------QYLDDGYKLVIFTNQG 80
DLD TL+ + P D +L N +K Q L Y++VIFT
Sbjct: 5 LDLDETLVHSSFEPDLPFDF----VLNFNHGVYVKKRPGLDEFLQELSKYYEIVIFT--- 57
Query: 81 AIGRKKMSTRDFQAKAEKIIKSL 103
S++++ A+ ++ L
Sbjct: 58 ------ASSKEY---ADPVLDKL 71
>gnl|CDD|234615 PRK00075, cbiD, cobalt-precorrin-6A synthase; Reviewed.
Length = 361
Score = 28.6 bits (65), Expect = 5.1
Identities = 13/66 (19%), Positives = 23/66 (34%), Gaps = 11/66 (16%)
Query: 38 TTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFTNQGAIGRK--KMSTRDFQAK 95
TT G V P+ + ++I+ L +G V+ G + +
Sbjct: 173 TT--GIVEPMSEEAYL---ASIKQELDVARANGLDHVVLV----TGNNGEDYARKLLGLP 223
Query: 96 AEKIIK 101
+ IIK
Sbjct: 224 EDAIIK 229
>gnl|CDD|184023 PRK13392, PRK13392, 5-aminolevulinate synthase; Provisional.
Length = 410
Score = 28.7 bits (64), Expect = 5.6
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 209 KAQSQTIPNIPHDKKQVLIMIGSQGSGKS------SFVSTYLKPLNYTTVNRDT 256
K + IP +P V +M+G K+ S Y++P+NY TV R T
Sbjct: 315 KLNANGIPVMPSPSHIVPVMVGDPTLCKAISDRLMSEHGIYIQPINYPTVPRGT 368
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 28.6 bits (64), Expect = 5.8
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 10/76 (13%)
Query: 169 DHLFAFNLNLAFFTPEQIFLNEKAPDFPNLPTFKPREV---YQKAQSQTIP-NIPHDKKQ 224
+ + L + F +A FP+ T + R V YQ P N+ + +
Sbjct: 297 NKIAKLELA----PYKADFPRPQA--FPDWKTLELRNVRFAYQDNAFHVGPINLTIKRGE 350
Query: 225 VLIMIGSQGSGKSSFV 240
++ +IG GSGKS+
Sbjct: 351 LVFLIGGNGSGKSTLA 366
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 28.4 bits (64), Expect = 5.9
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 222 KKQVLIMIGSQGSGKSSFVS 241
+KQ+L ++G G GKSS V
Sbjct: 77 RKQILYLLGPVGGGKSSLVE 96
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 28.7 bits (64), Expect = 5.9
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 214 TIPNIPHDKKQVLIMIGSQGSGKSSFVS 241
+ I + KK+V I++G G GK++ ++
Sbjct: 165 SGSIIDNLKKRVFILVGPTGVGKTTTIA 192
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 28.7 bits (64), Expect = 6.1
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 5/65 (7%)
Query: 180 FFTPEQIFLNEKAPDFPNLPTFKPREVYQKAQSQTIPNIPHDKKQVLIMIGSQGSGKSSF 239
E + L+E FP P+++ Q+ + H L++ G+ GSGKS
Sbjct: 492 PPLRELLDLDEFLERFPLGVIDLPKDIRQEPIVIDLAKAGH-----LLIAGATGSGKSVA 546
Query: 240 VSTYL 244
++T +
Sbjct: 547 LNTMI 551
>gnl|CDD|237646 PRK14237, PRK14237, phosphate transporter ATP-binding protein;
Provisional.
Length = 267
Score = 28.1 bits (63), Expect = 6.1
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 4/27 (14%)
Query: 222 KKQVLIMIGSQGSGKSSFVSTYLKPLN 248
K ++ +IG GSGK STYL+ LN
Sbjct: 45 KNKITALIGPSGSGK----STYLRSLN 67
>gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated.
Length = 226
Score = 28.1 bits (63), Expect = 6.2
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 225 VLIMIGSQGSGKSSFVSTYLKPLNYTTVNRDTLGSWQKCVSVMKAALDSVLI 276
V+++ G GSGK+ S + + + ++ + +GS + AA VLI
Sbjct: 46 VVVLAGPVGSGKTHLASIWREKSDALLIHPNEIGS----DAANAAAEGPVLI 93
>gnl|CDD|222146 pfam13460, NAD_binding_10, NADH(P)-binding.
Length = 182
Score = 28.0 bits (63), Expect = 6.5
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 318 AALDSGLSVVVDNTN---PDKESRHRYIEAAKQHGVRCIAV 355
A +G+ VVD D + ++AA + GVR I V
Sbjct: 54 AEALAGVDAVVDAFGARPDDSDGVKHLLDAAARAGVRRIVV 94
>gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 358
Score = 28.2 bits (63), Expect = 6.8
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 221 DKKQVLIMIGSQGSGKSSFV 240
++KQ+L ++G G GKSS
Sbjct: 83 ERKQILYLLGPVGGGKSSLA 102
>gnl|CDD|223536 COG0460, ThrA, Homoserine dehydrogenase [Amino acid transport and
metabolism].
Length = 333
Score = 28.3 bits (64), Expect = 7.2
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 311 KCVSVMKAALDSGLSVVVDNTNPDKESRHRYIEAAKQHGVR 351
+ + AL++G VV N H EAA+++GV+
Sbjct: 94 EPADLYLKALENGKHVVTANKALLALHYHELREAAEKNGVK 134
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 28.6 bits (64), Expect = 7.2
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 11/46 (23%)
Query: 193 PDFPNLPTFKPREVYQKAQSQTIPNIPHDKKQVLIMIGSQGSGKSS 238
PD NLP RE +A ++ QV+I+ G GSGK++
Sbjct: 63 PD--NLPVSAKREDIAEAIAE---------NQVVIIAGETGSGKTT 97
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 28.2 bits (63), Expect = 7.2
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 258 GSWQKCVSVMKAALDSV------LIMIGSQGSGKSSFVST 291
G+ QK VS++K A+ + + + G G+GKSSF++
Sbjct: 15 GNLQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFINA 54
>gnl|CDD|182523 PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase;
Provisional.
Length = 272
Score = 28.1 bits (63), Expect = 7.3
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 24 SAKIASFDLDGTLITTKSGKVFPVDTHDWKLLFSNIESVLKQYLDDGYKLVIFT 77
+ ++ + DLDGTL+T K +L ++E L + + GYK++I T
Sbjct: 2 TYRVIALDLDGTLLTPKK-----------TILPESLE-ALARAREAGYKVIIVT 43
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 28.1 bits (63), Expect = 7.4
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 217 NIPHDKKQVLIMIGSQGSGKSSF---VSTYLKP 246
I + + +IGS G+GKS+ ++ LKP
Sbjct: 28 EIA--EGDFVTVIGSNGAGKSTLLNAIAGDLKP 58
>gnl|CDD|236707 PRK10522, PRK10522, multidrug transporter membrane
component/ATP-binding component; Provisional.
Length = 547
Score = 28.4 bits (64), Expect = 7.4
Identities = 25/75 (33%), Positives = 35/75 (46%), Gaps = 12/75 (16%)
Query: 173 AFN----LNLAFFTPEQIFLNEKAPDFPNLPTFKPREV---YQKAQSQTIP-NIPHDKKQ 224
AFN L LA + E F + FP+ T + R V YQ P N+ + +
Sbjct: 295 AFNKLNKLALAPYKAE--F--PRPQAFPDWQTLELRNVTFAYQDNGFSVGPINLTIKRGE 350
Query: 225 VLIMIGSQGSGKSSF 239
+L +IG GSGKS+
Sbjct: 351 LLFLIGGNGSGKSTL 365
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.0 bits (62), Expect = 7.5
Identities = 4/20 (20%), Positives = 13/20 (65%)
Query: 226 LIMIGSQGSGKSSFVSTYLK 245
++++G G GK++ ++ +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVG 27
Score = 28.0 bits (62), Expect = 7.5
Identities = 4/20 (20%), Positives = 13/20 (65%)
Query: 275 LIMIGSQGSGKSSFVSTYLK 294
++++G G GK++ ++ +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVG 27
>gnl|CDD|226961 COG4598, HisP, ABC-type histidine transport system, ATPase
component [Amino acid transport and metabolism].
Length = 256
Score = 27.8 bits (62), Expect = 7.7
Identities = 14/27 (51%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 262 KCVSVMKAALDSVLIMIGSQGSGKSSF 288
K VS ++A V+ +IGS GSGKS+F
Sbjct: 23 KGVS-LQANAGDVISIIGSSGSGKSTF 48
Score = 27.8 bits (62), Expect = 8.9
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 222 KKQVLIMIGSQGSGKSSF 239
V+ +IGS GSGKS+F
Sbjct: 31 AGDVISIIGSSGSGKSTF 48
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 27.9 bits (62), Expect = 7.8
Identities = 10/52 (19%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 308 SWQKCVSVMKAALD---SGLSVVVDNTNPDKESRHRYIEAAKQHGVRCIAVH 356
+ ++ ++ A + GL V++ ++ D E + Q GV I
Sbjct: 14 FGAQLLAGIELAAEEIGRGLEVILADSQSDPERALEALRDLIQQGVDGIIGP 65
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 27.9 bits (62), Expect = 8.0
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 221 DKKQVLIMIGSQGSGKSSFV 240
+ Q L +IG GSGKS+
Sbjct: 37 REGQTLAIIGENGSGKSTLA 56
>gnl|CDD|99961 cd03785, GT1_MurG, MurG is an N-acetylglucosaminyltransferase, the
last enzyme involved in the intracellular phase of
peptidoglycan biosynthesis. It transfers
N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the
C4 hydroxyl of a lipid-linked N-acetylmuramoyl
pentapeptide (NAM). The resulting disaccharide is then
transported across the cell membrane, where it is
polymerized into NAG-NAM cell-wall repeat structure.
MurG belongs to the GT-B structural superfamily of
glycoslytransferases, which have characteristic N- and
C-terminal domains, each containing a typical Rossmann
fold. The two domains have high structural homology
despite minimal sequence homology. The large cleft that
separates the two domains includes the catalytic center
and permits a high degree of flexibility.
Length = 350
Score = 27.8 bits (63), Expect = 8.5
Identities = 7/31 (22%), Positives = 14/31 (45%)
Query: 204 REVYQKAQSQTIPNIPHDKKQVLIMIGSQGS 234
E+ + + + K +L+ GSQG+
Sbjct: 163 EEILALDRERARLGLRPGKPTLLVFGGSQGA 193
>gnl|CDD|233271 TIGR01098, 3A0109s03R, phosphate/phosphite/phosphonate ABC
transporters, periplasmic binding protein. Phosphonates
are a varied class of phosphorus-containing organic
compound in which a direct C-P bond is found, rather
than a C-O-P linkage of the phosphorus through an oxygen
atom. They may be toxic but also may be used as sources
of phosphorus and energy by various bacteria.
Phosphonate utilization systems typically are encoded in
14 or more genes, including a three gene ABC
transporter. This family includes the periplasmic
binding protein component of ABC transporters for
phosphonates as well as other, related binding
components for closely related substances such as
phosphate and phosphite. A number of members of this
family are found in genomic contexts with components of
selenium metabolic processes suggestive of a role in
selenate or other selenium-compound transport. A subset
of this model in which nearly all members exhibit
genomic context with elements of phosphonate metabolism,
particularly the C-P lyase system (GenProp0232) has been
built (TIGR03431) as an equivalog. Nevertheless, there
are members of this subfamily (TIGR01098) which show up
sporadically on a phylogenetic tree that also show
phosphonate context and are most likely competent to
transport phosphonates [Transport and binding proteins,
Anions].
Length = 254
Score = 27.7 bits (62), Expect = 8.8
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 89 TRDFQAKAEKIIKSLNVPVQMFVATQYD 116
TR ++ A+ + K L + VQ+FVAT Y
Sbjct: 48 TRRWEPLADYLEKKLGIKVQLFVATDYS 75
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 27.9 bits (62), Expect = 9.2
Identities = 9/56 (16%), Positives = 24/56 (42%)
Query: 246 PLNYTTVNRDTLGSWQKCVSVMKAALDSVLIMIGSQGSGKSSFVSTYLKPLNYTTV 301
++ T + + W+ ++ + ++G + +GKS+ V+ N T+
Sbjct: 136 SVSATQIRENPFQHWKHIPREVRPFFVKTVAILGGESTGKSTLVNKLAAVFNTTSA 191
>gnl|CDD|184907 PRK14943, PRK14943, DNA polymerase III subunit beta; Provisional.
Length = 374
Score = 28.0 bits (62), Expect = 9.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 192 APDFPNLPTFKPREVYQKAQSQ 213
A +FP LP+F+ V+Q QS+
Sbjct: 112 AEEFPPLPSFEQATVFQLEQSE 133
>gnl|CDD|224042 COG1117, PstB, ABC-type phosphate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 253
Score = 27.5 bits (62), Expect = 9.6
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 217 NIPHDKKQVLIMIGSQGSGKSSFVSTYLKPLN 248
+IP K +V +IG G GK ST L+ LN
Sbjct: 29 DIP--KNKVTALIGPSGCGK----STLLRCLN 54
>gnl|CDD|213256 cd03289, ABCC_CFTR2, ATP-binding cassette domain 2 of
CFTR,subfamily C. The cystic fibrosis transmembrane
regulator (CFTR), the product of the gene mutated in
patients with cystic fibrosis, has adapted the ABC
transporter structural motif to form a tightly regulated
anion channel at the apical surface of many epithelia.
Use of the term assembly of a functional ion channel
implies the coming together of subunits or at least
smaller not-yet functional components of the active
whole. In fact, on the basis of current knowledge only
the CFTR polypeptide itself is required to form an ATP-
and protein kinase A-dependent low-conductance chloride
channel of the type present in the apical membrane of
many epithelial cells. CFTR displays the typical
organization (IM-ABC)2 and carries a characteristic
hydrophilic R-domain that separates IM1-ABC1 from
IM2-ABC2.
Length = 275
Score = 27.5 bits (61), Expect = 9.8
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 8/52 (15%)
Query: 224 QVLIMIGSQGSGKSSFVSTYLKPLNY--------TTVNRDTLGSWQKCVSVM 267
Q + ++G GSGKS+ +S +L+ LN + N L W+K V+
Sbjct: 31 QRVGLLGRTGSGKSTLLSAFLRLLNTEGDIQIDGVSWNSVPLQKWRKAFGVI 82
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
0.318 0.132 0.392
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,285,175
Number of extensions: 1708493
Number of successful extensions: 2817
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2794
Number of HSP's successfully gapped: 114
Length of query: 369
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 271
Effective length of database: 6,590,910
Effective search space: 1786136610
Effective search space used: 1786136610
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 (21.7 bits)
S2: 60 (26.9 bits)