RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy224
(547 letters)
>gnl|CDD|239313 cd03015, PRX_Typ2cys, Peroxiredoxin (PRX) family, Typical 2-Cys PRX
subfamily; PRXs are thiol-specific antioxidant (TSA)
proteins, which confer a protective role in cells
through its peroxidase activity by reducing hydrogen
peroxide, peroxynitrite, and organic hydroperoxides. The
functional unit of typical 2-cys PRX is a homodimer. A
unique intermolecular redox-active disulfide center is
utilized for its activity. Upon reaction with peroxides,
its peroxidatic cysteine is oxidized into a sulfenic
acid intermediate which is resolved by bonding with the
resolving cysteine from the other subunit of the
homodimer. This intermolecular disulfide bond is then
reduced by thioredoxin, tryparedoxin or AhpF. Typical
2-cys PRXs, like 1-cys PRXs, form decamers which are
stabilized by reduction of the active site cysteine.
Typical 2-cys PRX interacts through beta strands at one
edge of the monomer (B-type interface) to form the
functional homodimer, and uses an A-type interface
(similar to the dimeric interface in atypical 2-cys PRX
and PRX5) at the opposite end of the monomer to form the
stable decameric (pentamer of dimers) structure.
Length = 173
Score = 330 bits (849), Expect = e-112
Identities = 116/171 (67%), Positives = 136/171 (79%), Gaps = 1/171 (0%)
Query: 359 KPAPEFEGQAVVN-GQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKI 417
K AP+F+ AVV G+FK I LS YKG++VVLFFYPLDFTFVCPTEIIAFSDR EEFKK+
Sbjct: 3 KKAPDFKATAVVPNGEFKEISLSDYKGKWVVLFFYPLDFTFVCPTEIIAFSDRYEEFKKL 62
Query: 418 NTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRG 477
N +V+ STDSHFSHLAW N PR +GGLG + P+L+D I+R YGVL+EE G+ RG
Sbjct: 63 NAEVLGVSTDSHFSHLAWRNTPRKEGGLGKINFPLLADPKKKISRDYGVLDEEEGVALRG 122
Query: 478 LFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPG 528
FIID + +R IT+NDLPVGRSVDETLR++ A QFV EHGEVCPA WKPG
Sbjct: 123 TFIIDPEGIIRHITVNDLPVGRSVDETLRVLDALQFVEEHGEVCPANWKPG 173
>gnl|CDD|140280 PTZ00253, PTZ00253, tryparedoxin peroxidase; Provisional.
Length = 199
Score = 312 bits (802), Expect = e-105
Identities = 122/192 (63%), Positives = 148/192 (77%), Gaps = 1/192 (0%)
Query: 357 LEKPAPEFEGQAVV-NGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFK 415
+ PAP FE A++ NG FK I LS YKG++VVLFFYPLDFTFVCPTEII FSD + F
Sbjct: 8 INHPAPSFEEVALMPNGSFKKISLSSYKGKWVVLFFYPLDFTFVCPTEIIQFSDSVKRFN 67
Query: 416 KINTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPY 475
++N +V+ACS DS ++HL W R KGGLG MAIP+L+DK+ SIARSYGVL EE G+ Y
Sbjct: 68 ELNCEVLACSMDSEYAHLQWTLQERKKGGLGTMAIPMLADKTKSIARSYGVLEEEQGVAY 127
Query: 476 RGLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKAD 535
RGLFIID K LRQIT+ND+PVGR+V+E LRL++AFQFV +HGEVCPA WK G TMK D
Sbjct: 128 RGLFIIDPKGMLRQITVNDMPVGRNVEEVLRLLEAFQFVEKHGEVCPANWKKGDPTMKPD 187
Query: 536 PSGSQEYFKTVN 547
P+ S+E F +
Sbjct: 188 PNKSKEGFFSKA 199
>gnl|CDD|223527 COG0450, AhpC, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 194
Score = 280 bits (719), Expect = 2e-92
Identities = 104/188 (55%), Positives = 129/188 (68%), Gaps = 2/188 (1%)
Query: 359 KPAPEFEGQAVVNGQ-FKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKI 417
K AP+F AV+ G+ F+ I LS Y G++VVLFFYP DFTFVCPTEIIAF+ R EEF+K
Sbjct: 7 KKAPDFTANAVLGGEIFEEITLSDYYGKWVVLFFYPADFTFVCPTEIIAFAKRYEEFQKR 66
Query: 418 NTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRG 477
+VI STDS FSH AW R GG+G + P+++D IAR+YGVL+ E G+ RG
Sbjct: 67 GVEVIGVSTDSVFSHKAWKATIREAGGIGKIKFPMIADPKGEIARAYGVLHPEEGLALRG 126
Query: 478 LFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKADPS 537
FIID +R I +N L +GR+VDE LR++ A QFVA+HGEVCPA WKPG KT+K P
Sbjct: 127 TFIIDPDGVIRHILVNPLTIGRNVDEILRVIDALQFVAKHGEVCPANWKPGDKTIKPSPD 186
Query: 538 GSQEYFKT 545
EY K
Sbjct: 187 L-GEYLKE 193
>gnl|CDD|212661 cd07777, FGGY_SHK_like, sedoheptulokinase-like proteins; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is predominantly composed of
uncharacterized bacterial and eukaryotic proteins with
similarity to human sedoheptulokinase (SHK, also known
as D-altro-heptulose or heptulokinase, EC 2.7.1.14)
encoded by the carbohydrate kinase-like (CARKL/SHPK)
gene. SHK catalyzes the ATP-dependent phosphorylation of
sedoheptulose to produce sedoheptulose 7-phosphate and
ADP. The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subfamily belong to
the FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 448
Score = 288 bits (739), Expect = 6e-92
Identities = 130/290 (44%), Positives = 183/290 (63%), Gaps = 33/290 (11%)
Query: 89 QDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTI 148
QDF+VAMLC L PVMS NAASWGYF+ + + WN +IL+ FP+HLLP++ P GTI
Sbjct: 163 QDFVVAMLCGLSRPVMSPHNAASWGYFDLETNAWNSEILQ--AAGFPVHLLPEVVPPGTI 220
Query: 149 VGTLTRDWLGINKDTPINVALGDLQCSVLATLQYHSDAIVNISTSAQIAFID-------- 200
GTL DW GI K TP+ VALGDLQCSVLA LQ +DA++NI TSAQ++F+
Sbjct: 221 AGTLGGDWYGIPKGTPVGVALGDLQCSVLACLQEETDAVLNIGTSAQLSFLPVFKPETVP 280
Query: 201 ----EM-----------GASMNGGNCLATFVCTLQNWFKEFGFNVPQNQIWAKLINASDP 245
E AS+NGGN LA FV LQ+W +E GF+VPQ++++ +LI +
Sbjct: 281 PASPEYRPYFKNHYLAVAASLNGGNVLAAFVKMLQSWVEELGFSVPQDEVYDRLIALALA 340
Query: 246 INHITRHHSTLRVTPTLLGDRHVIAESASVTHITIQNLGVTKLFVALCEGIINNIHDIMN 305
+ L++ PTL G+RH ASV++IT+ NL + + ALC+GI+ N+H++
Sbjct: 341 ES-----DPPLKIDPTLFGERHDPDLRASVSNITLSNLTLGHITRALCQGIVENLHEMFP 395
Query: 306 RSVLHRSGINRIIGIGSCLTRNHILQHYIERIYGLQLIVEQDQAMRDASY 355
R +L +GI RI+G GS L RN +L+ +E+++GL L++ + DA+
Sbjct: 396 RELLKSAGIERIVGSGSALRRNPVLRDEVEKVFGLPLVLSKG---EDAAL 442
Score = 104 bits (261), Expect = 7e-24
Identities = 45/77 (58%), Positives = 57/77 (74%), Gaps = 3/77 (3%)
Query: 4 QVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLH 63
VLGIDIGTTSVK CL+D+ T+E L+S+SK T AN+PS P EQ+V KI+STL
Sbjct: 1 MYVLGIDIGTTSVKACLLDSETKEVLASQSKPTSANVPSD---GPLGSEQDVDKILSTLD 57
Query: 64 NCILRLPKDHLKQVKHI 80
+C+ RLPK+ LK+VK I
Sbjct: 58 SCLKRLPKELLKKVKAI 74
>gnl|CDD|239269 cd02971, PRX_family, Peroxiredoxin (PRX) family; composed of the
different classes of PRXs including many proteins
originally known as bacterioferritin comigratory
proteins (BCP), based on their electrophoretic mobility
before their function was identified. PRXs are
thiol-specific antioxidant (TSA) proteins also known as
TRX peroxidases and alkyl hydroperoxide reductase C22
(AhpC) proteins. They confer a protective antioxidant
role in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either TRX, glutathione,
trypanothione and AhpF. They are distinct from other
peroxidases in that they have no cofactors such as
metals or prosthetic groups. The first step of
catalysis, common to all PRXs, is the nucleophilic
attack by the catalytic cysteine (also known as the
peroxidatic cysteine) on the peroxide leading to
cleavage of the oxygen-oxygen bond and the formation of
a cysteine sulfenic acid intermediate. The second step
of the reaction, the resolution of the intermediate,
distinguishes the different types of PRXs. The presence
or absence of a second cysteine (the resolving cysteine)
classifies PRXs as either belonging to the 2-cys or
1-cys type. The resolving cysteine of 2-cys PRXs is
either on the same chain (atypical) or on the second
chain (typical) of a functional homodimer. Structural
and motif analysis of this growing family supports the
need for a new classification system. The peroxidase
activity of PRXs is regulated in vivo by irreversible
cysteine over-oxidation into a sulfinic acid,
phosphorylation and limited proteolysis.
Length = 140
Score = 182 bits (465), Expect = 2e-55
Identities = 62/149 (41%), Positives = 82/149 (55%), Gaps = 12/149 (8%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINT 419
AP+F + + LS +KG++VVLFFYP DFT VC TE+ AF D AEEF K
Sbjct: 1 KAPDFT---LPATDGGEVSLSDFKGKWVVLFFYPKDFTPVCTTELCAFRDLAEEFAKGGA 57
Query: 420 QVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEE---TGIPYR 476
+V+ S DS FSH AW G + P+LSD A++YGVL E+ G+ R
Sbjct: 58 EVLGVSVDSPFSHKAWAEK------EGGLNFPLLSDPDGEFAKAYGVLIEKSAGGGLAAR 111
Query: 477 GLFIIDDKQNLRQITINDLPVGRSVDETL 505
FIID +R + + LP GR+ +E L
Sbjct: 112 ATFIIDPDGKIRYVEVEPLPTGRNAEELL 140
>gnl|CDD|184962 PRK15000, PRK15000, peroxidase; Provisional.
Length = 200
Score = 182 bits (463), Expect = 1e-54
Identities = 82/188 (43%), Positives = 119/188 (63%), Gaps = 3/188 (1%)
Query: 359 KPAPEFEGQAVV-NGQF-KNIKLSQY-KGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFK 415
+ AP+F AV+ +G+ Q+ G+ VLFF+P+DFTFVCP+E+IAF R EEF+
Sbjct: 6 RQAPDFTAAAVLGSGEIVDKFNFKQHTNGKTTVLFFWPMDFTFVCPSELIAFDKRYEEFQ 65
Query: 416 KINTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPY 475
K +V+ S DS F H AW N P +KGG+G + +++D I ++YG+ + + G+
Sbjct: 66 KRGVEVVGVSFDSEFVHNAWRNTPVDKGGIGPVKYAMVADVKREIQKAYGIEHPDEGVAL 125
Query: 476 RGLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKAD 535
RG F+ID +R +NDLP+GR++DE LR+V A QF EHG+VCPA W+ G + M A
Sbjct: 126 RGSFLIDANGIVRHQVVNDLPLGRNIDEMLRMVDALQFHEEHGDVCPAQWEKGKEGMNAS 185
Query: 536 PSGSQEYF 543
P G +Y
Sbjct: 186 PDGVAKYL 193
>gnl|CDD|211789 TIGR03137, AhpC, peroxiredoxin. This peroxiredoxin (AhpC,
alkylhydroperoxide reductase subunit C) is one subunit
of a two-subunit complex with subunit F(TIGR03140).
Usually these are found as an apparent operon. The gene
has been characterized in Bacteroides fragilis where it
is important in oxidative stress defense. This gene
contains two invariant cysteine residues, one near the
N-terminus and one near the C-terminus, each followed
immediately by a proline residue [Cellular processes,
Detoxification, Cellular processes, Adaptations to
atypical conditions].
Length = 187
Score = 180 bits (458), Expect = 8e-54
Identities = 75/177 (42%), Positives = 108/177 (61%), Gaps = 6/177 (3%)
Query: 362 PEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINTQV 421
F+ A NG+F + KG++ V FFYP DFTFVCPTE+ +D E KK+ +V
Sbjct: 9 KPFKATAYHNGEFVEVTDEDVKGKWSVFFFYPADFTFVCPTELEDLADNYAELKKLGVEV 68
Query: 422 IACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRGLFII 481
+ STD+HF H AW + +G + P+L D + + R++GVL EE G+ RG F+I
Sbjct: 69 YSVSTDTHFVHKAWHD---TSEAIGKITYPMLGDPTGVLTRNFGVLIEEAGLADRGTFVI 125
Query: 482 DDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEH-GEVCPAGWKPGSKTMKADPS 537
D + ++ + I+D +GR E LR ++A Q+VA H GEVCPA WK G++T+K PS
Sbjct: 126 DPEGVIQAVEIHDNGIGRDASELLRKIKAAQYVAAHPGEVCPAKWKEGAETLK--PS 180
>gnl|CDD|173427 PTZ00137, PTZ00137, 2-Cys peroxiredoxin; Provisional.
Length = 261
Score = 177 bits (450), Expect = 7e-52
Identities = 77/191 (40%), Positives = 113/191 (59%), Gaps = 3/191 (1%)
Query: 359 KPAPEFEGQAVVNGQFKNIKLSQY-KGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKI 417
K P F+G A++N S Y K Y +L FYPLDFTFVCP+E++ FS+R +EF++
Sbjct: 72 KLMPSFKGTALLNDDLVQFNSSDYFKDSYGLLVFYPLDFTFVCPSELLGFSERLKEFEER 131
Query: 418 NTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRG 477
+V+ S DS FSH AW + +GG+ + P+ SD S +++S+G+L +E G +R
Sbjct: 132 GVKVLGVSVDSPFSHKAWKELDVRQGGVSPLKFPLFSDISREVSKSFGLLRDE-GFSHRA 190
Query: 478 LFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKADPS 537
++D ++ + + DL +GRSVDETLRL A QF + G VCP WK G + MK D
Sbjct: 191 SVLVDKAGVVKHVAVYDLGLGRSVDETLRLFDAVQFAEKTGNVCPVNWKQGDQAMKPDSQ 250
Query: 538 GSQEY-FKTVN 547
++Y N
Sbjct: 251 SVKQYLSNRFN 261
>gnl|CDD|216002 pfam00578, AhpC-TSA, AhpC/TSA family. This family contains
proteins related to alkyl hydroperoxide reductase (AhpC)
and thiol specific antioxidant (TSA).
Length = 124
Score = 159 bits (405), Expect = 6e-47
Identities = 56/132 (42%), Positives = 75/132 (56%), Gaps = 10/132 (7%)
Query: 359 KPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
AP+FE + K + LS YKG++VVLFFYP DFT VC TE+ A +D EEFKK+
Sbjct: 3 DKAPDFELP---DLDGKEVSLSDYKGKWVVLFFYPKDFTPVCTTELPALADLYEEFKKLG 59
Query: 419 TQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRGL 478
+V+ S DS SH + + P+LSD +A++YGVLNEE G+ R
Sbjct: 60 VEVLGVSVDSPESHKKFAEKL-------GLPFPLLSDPDGEVAKAYGVLNEEEGLALRTT 112
Query: 479 FIIDDKQNLRQI 490
F+ID +R I
Sbjct: 113 FVIDPDGKIRYI 124
>gnl|CDD|239314 cd03016, PRX_1cys, Peroxiredoxin (PRX) family, 1-cys PRX subfamily;
composed of PRXs containing only one conserved cysteine,
which serves as the peroxidatic cysteine. They are
homodimeric thiol-specific antioxidant (TSA) proteins
that confer a protective role in cells by reducing and
detoxifying hydrogen peroxide, peroxynitrite, and
organic hydroperoxides. As with all other PRXs, a
cysteine sulfenic acid intermediate is formed upon
reaction of 1-cys PRX with its substrates. Having no
resolving cysteine, the oxidized enzyme is resolved by
an external small-molecule or protein reductant such as
thioredoxin or glutaredoxin. Similar to typical 2-cys
PRX, 1-cys PRX forms a functional dimeric unit with a
B-type interface, as well as a decameric structure which
is stabilized in the reduced form of the enzyme. Other
oligomeric forms, tetramers and hexamers, have also been
reported. Mammalian 1-cys PRX is localized cellularly in
the cytosol and is expressed at high levels in brain,
eye, testes and lung. The seed-specific plant 1-cys PRXs
protect tissues from reactive oxygen species during
desiccation and are also called rehydrins.
Length = 203
Score = 161 bits (409), Expect = 2e-46
Identities = 68/186 (36%), Positives = 95/186 (51%), Gaps = 11/186 (5%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKG-QYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
AP FE + IK Y G + +LF +P DFT VC TE+ AF+ A EFKK N
Sbjct: 4 TAPNFE----ADTTHGPIKFHDYLGDSWGILFSHPADFTPVCTTELGAFAKLAPEFKKRN 59
Query: 419 TQVIACSTDSHFSHLAWC-NIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPY-- 475
++I S DS SH+ W +I G ++ PI++D +A+ G+++ + G
Sbjct: 60 VKLIGLSVDSVESHIKWIEDIEEYTG--VEIPFPIIADPDREVAKLLGMIDPDAGSTLTV 117
Query: 476 RGLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKAD 535
R +FIID + +R I GR+ DE LR+V A Q +H PA WKPG +
Sbjct: 118 RAVFIIDPDKKIRLILYYPATTGRNFDEILRVVDALQLTDKHKVATPANWKPGDDVIVP- 176
Query: 536 PSGSQE 541
PS S E
Sbjct: 177 PSVSDE 182
>gnl|CDD|237297 PRK13189, PRK13189, peroxiredoxin; Provisional.
Length = 222
Score = 151 bits (383), Expect = 1e-42
Identities = 70/171 (40%), Positives = 96/171 (56%), Gaps = 7/171 (4%)
Query: 360 PAPEFEGQAVVNGQFKNIKLS-QYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
PEFE V IKL YKG++ VLF +P DFT VC TE +AF R +EF+++N
Sbjct: 14 KFPEFE----VKTTHGPIKLPDDYKGKWFVLFSHPADFTPVCTTEFVAFQKRYDEFRELN 69
Query: 419 TQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETG-IPYRG 477
T++I S D FSH+ W + K G+ ++ PI++D IA+ G+++ G R
Sbjct: 70 TELIGLSIDQVFSHIKWVEWIKEKLGV-EIEFPIIADDRGEIAKKLGMISPGKGTNTVRA 128
Query: 478 LFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPG 528
+FIID K +R I VGR++DE LRLV+A Q E G PA W P
Sbjct: 129 VFIIDPKGIIRAILYYPQEVGRNMDEILRLVKALQTSDEKGVATPANWPPN 179
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 141 bits (356), Expect = 6e-39
Identities = 70/191 (36%), Positives = 108/191 (56%), Gaps = 5/191 (2%)
Query: 357 LEKPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKK 416
L + AP+F VN I LS+YKG++V+LF +P DFT VC TE IAFS R E+FKK
Sbjct: 4 LGQKAPDFT----VNTTKGPIDLSKYKGKWVLLFSHPADFTPVCTTEFIAFSRRYEDFKK 59
Query: 417 INTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYR 476
+ +++ S DS +SH+AW + G+ + P+++D +AR Y +++E +G R
Sbjct: 60 LGVELVGLSVDSIYSHIAWLRDIEERFGI-KIPFPVIADIDKELAREYNLIDENSGATVR 118
Query: 477 GLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGWKPGSKTMKADP 536
G+FIID Q +R + GR++DE +R+ +A Q + PA W+PG + + P
Sbjct: 119 GVFIIDPNQIVRWMIYYPAETGRNIDEIIRITKALQVNWKRKVATPANWQPGQEGIVPAP 178
Query: 537 SGSQEYFKTVN 547
S E +
Sbjct: 179 STLDEAEMRIK 189
>gnl|CDD|182423 PRK10382, PRK10382, alkyl hydroperoxide reductase subunit C;
Provisional.
Length = 187
Score = 139 bits (352), Expect = 1e-38
Identities = 61/170 (35%), Positives = 100/170 (58%), Gaps = 4/170 (2%)
Query: 364 FEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINTQVIA 423
F+ QA NG+F + +G++ V FFYP DFTFVCPTE+ +D EE +K+ V +
Sbjct: 11 FKNQAFKNGEFIEVTEKDTEGRWSVFFFYPADFTFVCPTELGDVADHYEELQKLGVDVYS 70
Query: 424 CSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRGLFIIDD 483
STD+HF+H AW + + + + ++ D + ++ R++ + E+ G+ R F++D
Sbjct: 71 VSTDTHFTHKAWHS---SSETIAKIKYAMIGDPTGALTRNFDNMREDEGLADRATFVVDP 127
Query: 484 KQNLRQITINDLPVGRSVDETLRLVQAFQFVAEH-GEVCPAGWKPGSKTM 532
+ ++ I + +GR + LR ++A Q+VA H GEVCPA WK G T+
Sbjct: 128 QGIIQAIEVTAEGIGRDASDLLRKIKAAQYVASHPGEVCPAKWKEGEATL 177
>gnl|CDD|183885 PRK13191, PRK13191, putative peroxiredoxin; Provisional.
Length = 215
Score = 128 bits (323), Expect = 4e-34
Identities = 64/166 (38%), Positives = 97/166 (58%), Gaps = 7/166 (4%)
Query: 362 PEFEGQAVVNGQFKNIKL-SQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINTQ 420
PE E V IKL YKG++ VLF +P DFT VC TE +F+ + EEFKK+NT+
Sbjct: 14 PEME----VITTHGKIKLPDDYKGRWFVLFSHPGDFTPVCTTEFYSFAKKYEEFKKLNTE 69
Query: 421 VIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIP-YRGLF 479
+I S DS+ SH+ W + ++ PI++D ++A+ G+++ E+ R +F
Sbjct: 70 LIGLSVDSNISHIEWVMWIEKNLKV-EVPFPIIADPMGNVAKRLGMIHAESSTATVRAVF 128
Query: 480 IIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCPAGW 525
I+DDK +R I + +GR++DE LR ++A Q V + G V PA W
Sbjct: 129 IVDDKGTVRLILYYPMEIGRNIDEILRAIRALQLVDKAGVVTPANW 174
>gnl|CDD|224146 COG1225, Bcp, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 157
Score = 118 bits (298), Expect = 2e-31
Identities = 53/159 (33%), Positives = 75/159 (47%), Gaps = 17/159 (10%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINT 419
AP+FE +G + + LS +G+ VVL+FYP DFT C TE F D EEF+K+
Sbjct: 9 KAPDFELPDQ-DG--ETVSLSDLRGKPVVLYFYPKDFTPGCTTEACDFRDLLEEFEKLGA 65
Query: 420 QVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGI------ 473
V+ S DS SH + K GL P+LSD+ +A +YGV E+
Sbjct: 66 VVLGISPDSPKSHKKFA----EKHGL---TFPLLSDEDGEVAEAYGVWGEKKMYGKEYMG 118
Query: 474 PYRGLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQ 512
R F+ID +R + + V DE L ++
Sbjct: 119 IERSTFVIDPDGKIRYV-WRKVKVKGHADEVLAALKKLA 156
>gnl|CDD|239316 cd03018, PRX_AhpE_like, Peroxiredoxin (PRX) family, AhpE-like
subfamily; composed of proteins similar to Mycobacterium
tuberculosis AhpE. AhpE is described as a 1-cys PRX
because of the absence of a resolving cysteine. The
structure and sequence of AhpE, however, show greater
similarity to 2-cys PRXs than 1-cys PRXs. PRXs are
thiol-specific antioxidant (TSA) proteins that confer a
protective role in cells through their peroxidase
activity in which hydrogen peroxide, peroxynitrate, and
organic hydroperoxides are reduced and detoxified using
reducing equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF. The first step of
catalysis is the nucleophilic attack by the peroxidatic
cysteine on the peroxide leading to the formation of a
cysteine sulfenic acid intermediate. The absence of a
resolving cysteine suggests that functional AhpE is
regenerated by an external reductant. The solution
behavior and crystal structure of AhpE show that it
forms dimers and octamers.
Length = 149
Score = 112 bits (283), Expect = 2e-29
Identities = 52/153 (33%), Positives = 80/153 (52%), Gaps = 16/153 (10%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQ-YVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
AP+FE + + + ++LS+++G+ VVL F+PL FT VC E+ A D E F+
Sbjct: 6 KAPDFE---LPDQNGQEVRLSEFRGRKPVVLVFFPLAFTPVCTKELCALRDSLELFEAAG 62
Query: 419 TQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSD--KSMSIARSYGVLNEETGIPYR 476
+V+ S DS FS AW + GL P+LSD +A++YGV +E+ G+ R
Sbjct: 63 AEVLGISVDSPFSLRAW----AEENGLT---FPLLSDFWPHGEVAKAYGVFDEDLGVAER 115
Query: 477 GLFIIDDKQNLRQITINDLPVGRS---VDETLR 506
+F+ID +R ++D R DE L
Sbjct: 116 AVFVIDRDGIIRYAWVSDDGEPRDLPDYDEALD 148
>gnl|CDD|239315 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
comigratory protein (BCP) subfamily; composed of
thioredoxin-dependent thiol peroxidases, widely
expressed in pathogenic bacteria, that protect cells
against toxicity from reactive oxygen species by
reducing and detoxifying hydroperoxides. The protein was
named BCP based on its electrophoretic mobility before
its function was known. BCP shows substrate selectivity
toward fatty acid hydroperoxides rather than hydrogen
peroxide or alkyl hydroperoxides. BCP contains the
peroxidatic cysteine but appears not to possess a
resolving cysteine (some sequences, not all, contain a
second cysteine but its role is still unknown). Unlike
other PRXs, BCP exists as a monomer. The plant homolog
of BCP is PRX Q, which is expressed only in leaves and
is cellularly localized in the chloroplasts and the
guard cells of stomata. Also included in this subfamily
is the fungal nuclear protein, Dot5p (for disrupter of
telomere silencing protein 5), which functions as an
alkyl-hydroperoxide reductase during post-diauxic
growth.
Length = 140
Score = 111 bits (280), Expect = 4e-29
Identities = 47/151 (31%), Positives = 67/151 (44%), Gaps = 14/151 (9%)
Query: 359 KPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
AP+F + + + LS +G+ VVL+FYP D T C E F D EEFK +
Sbjct: 1 DKAPDFTLP---DQDGETVSLSDLRGKPVVLYFYPKDDTPGCTKEACDFRDLYEEFKALG 57
Query: 419 TQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNE---ETGIPY 475
VI S DS SH + K GL P+LSD +A++YGV E +
Sbjct: 58 AVVIGVSPDSVESHAKF----AEKYGLP---FPLLSDPDGKLAKAYGVWGEKKKKYMGIE 110
Query: 476 RGLFIIDDKQNLRQITINDLPVGRSVDETLR 506
R F+ID + ++ + +E L
Sbjct: 111 RSTFLIDPDGKIVKV-WRKVKPKGHAEEVLE 140
>gnl|CDD|106544 PRK13599, PRK13599, putative peroxiredoxin; Provisional.
Length = 215
Score = 109 bits (273), Expect = 2e-27
Identities = 51/145 (35%), Positives = 83/145 (57%), Gaps = 2/145 (1%)
Query: 382 YKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINTQVIACSTDSHFSHLAWCNIPRN 441
Y G++ VLF +P DFT VC TE + F+ +A +FK++NT++I S D FSH+ W ++
Sbjct: 26 YAGKWFVLFSHPADFTPVCTTEFVEFARKANDFKELNTELIGLSVDQVFSHIKWVEWIKD 85
Query: 442 KGGLGDMAIPILSDKSMSIARSYGVLNEETGI-PYRGLFIIDDKQNLRQITINDLPVGRS 500
+ + P+++D ++ G+++ G R +FI+DDK +R I VGR+
Sbjct: 86 NTNI-AIPFPVIADDLGKVSNQLGMIHPGKGTNTVRAVFIVDDKGTIRLIMYYPQEVGRN 144
Query: 501 VDETLRLVQAFQFVAEHGEVCPAGW 525
VDE LR ++A Q ++G P W
Sbjct: 145 VDEILRALKALQTADQYGVALPEKW 169
>gnl|CDD|212658 cd00366, FGGY, FGGY family of carbohydrate kinases. This family is
predominantly composed of glycerol kinase (GK) and
similar carbohydrate kinases including rhamnulokinase
(RhuK), xylulokinase (XK), gluconokinase (GntK),
ribulokinase (RBK), and fuculokinase (FK). These enzymes
catalyze the transfer of a phosphate group, usually from
ATP, to their carbohydrate substrates. The monomer of
FGGY proteins contains two large domains, which are
separated by a deep cleft that forms the active site.
One domain is primarily involved in sugar substrate
binding, and the other is mainly responsible for ATP
binding. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain.
Substrate-induced conformational changes and a divalent
cation may be required for the catalytic activity.
Length = 435
Score = 108 bits (273), Expect = 2e-25
Identities = 60/301 (19%), Positives = 110/301 (36%), Gaps = 43/301 (14%)
Query: 72 DHLKQVKHIESTNDLSFQDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHE 131
+ + I L+ D++ L E V+ NA+ F+ + W+ ++L
Sbjct: 143 EIYSKADKI-----LTVADYLAYRLT--GEFVIDYSNASRTMLFDIQTRDWDPELLE--A 193
Query: 132 PSFPLHLLPKIQPSGTIVGTLTRDW---LGINKDTPINVALGDLQCSVLATLQYHS-DAI 187
P LLP++ P G + G ++ + LG+ TP+ D QC+ L DA
Sbjct: 194 AGIPRELLPEVVPPGEVAGAISAEAAALLGLPPGTPVVAGGHDQQCAALGAGAVDEGDAA 253
Query: 188 VNISTSAQIAFIDE----------------MGASMNGGNCLATFVCTLQNWFKEFGFNVP 231
++ TS I + E G + + L WF++
Sbjct: 254 LSAGTSEVITAVSEPEPATDEGLLCYPAAIPGKYVTEASFFTGG--ALLRWFRDEFGLRE 311
Query: 232 QNQIWAKLINASDPINHITRHHSTLRVTPTLLGDRHVIAESASVTHITIQNLGVTK--LF 289
+ + + L + P G + A+ I LG T+ ++
Sbjct: 312 DGSDYEAAAQEAPNSG---PNG--LLILPHFSGSGTPYWDPAARGAIFGLTLGTTRADIY 366
Query: 290 VALCEGIINNIHDIMNRSVLHRSG--INRIIGIGSCLTRNHILQHYIERIYGLQLIVEQD 347
AL EGI + D ++ L +G I+RI G +R+ + + I+GL + +
Sbjct: 367 RALLEGIAYELRDNLDA--LEAAGIKIDRIRVTGG-GSRSDLWLQILADIFGLPVETPEV 423
Query: 348 Q 348
+
Sbjct: 424 R 424
Score = 46.1 bits (110), Expect = 3e-05
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 7 LGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNCI 66
LG+D+GTTSVK L D L+ S++ + + P PG EQ+ +I L +
Sbjct: 3 LGLDVGTTSVKAVLFDEQGN-ILAEASREYEVSYP-----KPGWVEQDPEEIWQALCEVL 56
Query: 67 LRLPKDH 73
Sbjct: 57 REAAAQA 63
>gnl|CDD|219888 pfam08534, Redoxin, Redoxin. This family of redoxins includes
peroxiredoxin, thioredoxin and glutaredoxin proteins.
Length = 142
Score = 67.7 bits (166), Expect = 1e-13
Identities = 35/143 (24%), Positives = 62/143 (43%), Gaps = 10/143 (6%)
Query: 359 KPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKIN 418
AP+F V K + LS +KG+ VVL F+P F C E ++ +K
Sbjct: 3 DKAPDFTLPDV-ALDGKTVSLSDFKGKKVVLNFWPGAFCPTCSAEHPYLEKLSKLYKAKG 61
Query: 419 TQVIACSTDSH-FSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEETGIPYRG 477
V+A + + F + + K GL P+L+D+ + ++YG+ + G+
Sbjct: 62 VDVVAVNASNDPFFVMNFW----AKEGL---KYPVLADRDGAFTKAYGLTE-DAGLRTPR 113
Query: 478 LFIIDDKQNLRQITINDLPVGRS 500
F+ID+ + + + P S
Sbjct: 114 YFLIDEDGKVVYLEVGPDPGDVS 136
>gnl|CDD|239312 cd03014, PRX_Atyp2cys, Peroxiredoxin (PRX) family, Atypical 2-cys
PRX subfamily; composed of PRXs containing peroxidatic
and resolving cysteines, similar to the homodimeric
thiol specific antioxidant (TSA) protein also known as
TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial
periplasmic peroxidase which differs from other PRXs in
that it shows substrate specificity toward alkyl
hydroperoxides over hydrogen peroxide. As with all other
PRXs, the peroxidatic cysteine (N-terminal) of Tpx is
oxidized into a sulfenic acid intermediate upon reaction
with peroxides. Tpx is able to resolve this intermediate
by forming an intramolecular disulfide bond with a
conserved C-terminal cysteine (the resolving cysteine),
which can then be reduced by thioredoxin. This differs
from the typical 2-cys PRX which resolves the oxidized
cysteine by forming an intermolecular disulfide bond
with the resolving cysteine from the other subunit of
the homodimer. Atypical 2-cys PRX homodimers have a
loop-based interface (A-type for alternate), in contrast
with the B-type interface of typical 2-cys and 1-cys
PRXs.
Length = 143
Score = 61.1 bits (149), Expect = 3e-11
Identities = 37/136 (27%), Positives = 66/136 (48%), Gaps = 14/136 (10%)
Query: 361 APEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYP-LDFTFVCPTEIIAFSDRAEEFKKINT 419
AP+F +V + L+ + G+ V+ +P +D T VC T+ F+ A + NT
Sbjct: 6 APDFT---LVTSDLSEVSLADFAGKVKVISVFPSID-TPVCATQTKRFNKEAAKLD--NT 59
Query: 420 QVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSD-KSMSIARSYGVLNEETGIPYRGL 478
V+ S D F+ WC G+ ++ LSD + S ++YGVL ++ G+ R +
Sbjct: 60 VVLTISADLPFAQKRWCG----AEGVDNVTT--LSDFRDHSFGKAYGVLIKDLGLLARAV 113
Query: 479 FIIDDKQNLRQITIND 494
F+ID+ + + +
Sbjct: 114 FVIDENGKVIYVELVP 129
>gnl|CDD|220741 pfam10417, 1-cysPrx_C, C-terminal domain of 1-Cys peroxiredoxin.
This is the C-terminal domain of 1-Cys peroxiredoxin
(1-cysPrx), a member of the peroxiredoxin superfamily
which protect cells against membrane oxidation through
glutathione (GSH)-dependent reduction of phospholipid
hydroperoxides to corresponding alcohols. The C-terminal
domain is crucial for providing the extra cysteine
necessary for dimerisation of the whole molecule. Loss
of the enzyme's peroxidase activity is associated with
oxidation of the catalytic cysteine, upstream of this
domain; and glutathionylation, presumably through its
disruption of protein structure, facilitates access for
GSH, resulting in spontaneous reduction of the mixed
disulfide to the sulfhydryl and consequent activation of
the enzyme. The domain is associated with family
AhpC-TSA, pfam00578, which carries the catalytic
cysteine.
Length = 40
Score = 57.2 bits (139), Expect = 6e-11
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 510 AFQFVAEHGEVCPAGWKPGSKTMKADPS----GSQEYFKT 545
A QF +HG V PA WKPG K + P + Y +
Sbjct: 1 ALQFTDKHGVVTPANWKPGDKVIVPPPPTEEEAVKRYLEG 40
>gnl|CDD|223996 COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate
transport and metabolism].
Length = 502
Score = 61.6 bits (150), Expect = 5e-10
Identities = 62/307 (20%), Positives = 105/307 (34%), Gaps = 59/307 (19%)
Query: 72 DHLKQVKHIESTNDLSFQDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRN-H 130
D + I L +D++ L E +A+ G + + W+ ++L
Sbjct: 150 DLFAKAAKI-----LLIKDYLRYRL--TGEFATEISDASGTGLLDIRTRKWDWELLAALG 202
Query: 131 EPSFPLHLLPKIQPSGTIVGTLTRDW---LGINKDTPINVALGDLQCSVLATLQYHSDAI 187
P LLP + G ++GTLT + LG+ TP+ V GD + L +
Sbjct: 203 LP--ERDLLPPVVEPGEVLGTLTPEAAEELGLPAGTPVVVGGGDNAAAALGAGAVDPGDV 260
Query: 188 VNISTSAQIAF---------------------IDE----MGASMNGGNCLATFVCTLQNW 222
ST + MGA+ GG L W
Sbjct: 261 S-SSTGTSGVVRAATDKPLDDPRGSIYTFCLGLPGWFIVMGANNTGGWLLE--------W 311
Query: 223 FKE-FGFNVPQNQIWAKLINASDPINHITRHHSTLRVTPTLLGDRHVIAESASVTHITIQ 281
+E FG ++ + + P I L P L G+R A+ A+
Sbjct: 312 LRELFGLAESYPELLEEALAVPAPAGAI-----GLLFLPYLSGERGPHADPAARGGFVGL 366
Query: 282 NLGVTK--LFVALCEGIINNIHDIMNRSVLHRSG--INRIIGIGSCLTRNHILQHYIERI 337
L T+ L A+ EG+ + D + + G +R+ +G R+ + +
Sbjct: 367 TLPHTRAHLARAVLEGVAFALADGLEA-LEELGGKPPSRVRVVGG-GARSPLWLQILADA 424
Query: 338 YGLQLIV 344
GL ++V
Sbjct: 425 LGLPVVV 431
Score = 51.2 bits (123), Expect = 8e-07
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 5/80 (6%)
Query: 1 MSSQVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVS 60
M + VLGIDIGTTSVK L D + E +++ + + P PG EQ+ ++
Sbjct: 1 MMMKYVLGIDIGTTSVKAVLFDEDGGEVVATARFENPVSTPQ-----PGWAEQDPDELWQ 55
Query: 61 TLHNCILRLPKDHLKQVKHI 80
+ + +L ++ I
Sbjct: 56 AILEALRQLLEESKIDPDAI 75
>gnl|CDD|224988 COG2077, Tpx, Peroxiredoxin [Posttranslational modification,
protein turnover, chaperones].
Length = 158
Score = 50.8 bits (122), Expect = 2e-07
Identities = 36/140 (25%), Positives = 65/140 (46%), Gaps = 17/140 (12%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYP-LDFTFVCPTEIIAFSDRAEEFKKIN 418
AP+F +V ++ L+ + G+ V+ +P +D T VC T++ F++ A + N
Sbjct: 23 KAPDFT---LVGKDLNDVSLADFAGKKKVISVFPSID-TPVCATQVRKFNEEAAKLG--N 76
Query: 419 TQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSD-KSMSIARSYGVLNEE---TGIP 474
T V+ S D F+ +C G G + LSD + + +YGVL E G+
Sbjct: 77 TVVLCISMDLPFAQKRFC------GAEGIENVITLSDFRDRAFGENYGVLINEGPLAGLL 130
Query: 475 YRGLFIIDDKQNLRQITIND 494
R +F++D+ + +
Sbjct: 131 ARAVFVLDENGKVTYSELVP 150
>gnl|CDD|212659 cd07770, FGGY_GntK, Gluconate kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of a group of gluconate kinases (GntK, also
known as gluconokinase; EC 2.7.1.12) encoded by the gntK
gene, which catalyzes the ATP-dependent phosphorylation
of D-gluconate and produce 6-phospho-D-gluconate and
ADP. The presence of Mg2+ might be required for
catalytic activity. The prototypical member of this
subfamily is GntK from Lactobacillus acidophilus. Unlike
Escherichia coli GntK, which belongs to the superfamily
of P-loop containing nucleoside triphosphate hydrolases,
members in this subfamily are homologous to glycerol
kinase, xylulose kinase, and rhamnulokinase from
Escherichia coli. They have been classified as members
of the FGGY family of carbohydrate kinases, which
contain two large domains separated by a deep cleft that
forms the active site. This model spans both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Some uncharacterized homologous sequences are also
included in this subfamily. The Lactobacillus gnt operon
contains a single gntK gene. The gnt operons of some
bacteria, such as Corynebacterium glutamicum, have two
gntK genes. For example, the C. glutamicum gnt operon
has both a gluconate kinase gntV gene (also known as
gntK) and a second hypothetical gntK gene (also known as
gntK2). Both gluconate kinases encoded by these genes
belong to this family, however the protein encoded by C.
glutamicum gntV is not included in this model as it is
truncated in the C-terminal domain.
Length = 440
Score = 49.1 bits (118), Expect = 4e-06
Identities = 48/255 (18%), Positives = 81/255 (31%), Gaps = 62/255 (24%)
Query: 86 LSFQDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILR--NHEPSFPLHLLPKIQ 143
+S +++++ L E V+ A+ G N W+E+ L LP++
Sbjct: 152 VSIKEYVLYRLFG--ELVVDYSIASGTGLLNIHTLDWDEEALEIAGISEE----QLPELV 205
Query: 144 PSGTIVGTLTRDW---LGINKDTPINVALGDLQCSVL---ATLQYHSDAIVNISTSAQI- 196
P+ + L + LG+ +DTP + D S L A A + I TS I
Sbjct: 206 PTTEQLRGLKAERAPKLGLPEDTPFVLGASDGALSNLGVGAVDP--GVAAITIGTSGAIR 263
Query: 197 AFIDEM---------------------GASMNGGNCLATFVCTLQNWF-KEFGFNVPQNQ 234
+D+ GA NGG L W + +
Sbjct: 264 VVLDQPVTDPPGRLFCYRLDKGRWVLGGAVNNGGIVL--------RWLRDTL-ALPEEEE 314
Query: 235 IWAKLINASDPINHITRHH---STLRVTPTLLGDRHVIAESASVTHITIQNLGVTKLFVA 291
I+ D + + R P L G+R + F+
Sbjct: 315 AEELGIDPYDGLTRGLEFLPAGAGERFPPWLSGERAPLWGL---------TRAARGSFIG 365
Query: 292 LC--EGIINNIHDIM 304
L EG+ + + I+
Sbjct: 366 LAAMEGVAHRLRAIL 380
Score = 41.8 bits (99), Expect = 7e-04
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
+LG+DIGTTS K L D + R ++ SK P GA EQ+ +I +
Sbjct: 1 YILGVDIGTTSTKAVLFDEDGR-IVAGVSK----RYPLETPP-DGAAEQDPDEIFDAVLE 54
Query: 65 CILRLPK 71
+ +
Sbjct: 55 ILDEVVA 61
>gnl|CDD|181857 PRK09437, bcp, thioredoxin-dependent thiol peroxidase; Reviewed.
Length = 154
Score = 46.1 bits (110), Expect = 6e-06
Identities = 37/142 (26%), Positives = 60/142 (42%), Gaps = 26/142 (18%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCPTEIIAFSDRAEEFKKINT 419
AP+F + + + L+ ++GQ V+++FYP T C + D +E KK
Sbjct: 9 IAPKFSLP---DQDGEQVSLTDFQGQRVLVYFYPKAMTPGCTVQACGLRDNMDELKKAGV 65
Query: 420 QVIACSTD-----SHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEET--G 472
V+ STD S F+ K L +LSD+ +A +GV E+ G
Sbjct: 66 VVLGISTDKPEKLSRFA---------EKELLN---FTLLSDEDHQVAEQFGVWGEKKFMG 113
Query: 473 IPYRGL----FIIDDKQNLRQI 490
Y G+ F+ID + +
Sbjct: 114 KTYDGIHRISFLIDADGKIEHV 135
>gnl|CDD|179055 PRK00522, tpx, lipid hydroperoxide peroxidase; Provisional.
Length = 167
Score = 45.7 bits (109), Expect = 1e-05
Identities = 39/128 (30%), Positives = 61/128 (47%), Gaps = 19/128 (14%)
Query: 361 APEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYP-LDFTFVCPTEIIAFSDRAEEFKKINT 419
AP+F +V ++ L+ + G+ VL +P +D T VC T + F+ A E NT
Sbjct: 24 APDF---TLVANDLSDVSLADFAGKRKVLNIFPSID-TGVCATSVRKFNQEAAELD--NT 77
Query: 420 QVIACSTDSHFSHLAWCNIPRNKGGLG-DMAIPILSD-KSMSIARSYGVLNEE---TGIP 474
V+ S D F+ +C G G + I LSD + S ++YGV E G+
Sbjct: 78 VVLCISADLPFAQKRFC------GAEGLENVIT-LSDFRDHSFGKAYGVAIAEGPLKGLL 130
Query: 475 YRGLFIID 482
R +F++D
Sbjct: 131 ARAVFVLD 138
>gnl|CDD|198374 cd07808, FGGY_D-XK_EcXK-like, Escherichia coli xylulokinase-like
D-xylulose kinases; a subgroup of the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial D-xylulose kinases (XK, also known
as xylulokinase; EC 2.7.1.17), which catalyze the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. D-xylulose has been used as a source of carbon
and energy by a variety of microorganisms. Some
uncharacterized sequences are also included in this
subgroup. The prototypical member of this CD is
Escherichia coli xylulokinase (EcXK), which exists as a
dimer. Each monomer consists of two large domains
separated by an open cleft that forms an active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The presence of Mg2+ or Mn2+
is required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 482
Score = 46.7 bits (112), Expect = 2e-05
Identities = 52/246 (21%), Positives = 90/246 (36%), Gaps = 53/246 (21%)
Query: 109 AASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDW---LGINKDTPI 165
A+ + W++++L +LP++ S + GTLT + LG+ TP+
Sbjct: 174 ASGTLLLDVAKRDWSDELLDALG--IDRAILPELYESSEVTGTLTAEAAAELGLPAGTPV 231
Query: 166 NVALGDLQCSVLATLQYHS-DAIVNISTSAQI-AFIDE---------------------- 201
GD + DA V++ TS + A D
Sbjct: 232 VAGGGDNAAGAVGNGVVRPGDAFVSLGTSGVVFAVSDSPAPDPEGRVHTFCHAVPGRWYL 291
Query: 202 MGASMNGGNCLATFVCTLQNWFKE-FGFNVPQNQIWAKLINASDPINHITRHHSTLRVTP 260
MG +++ G L WF++ FG + ++ P + L P
Sbjct: 292 MGVTLSAGGSL--------KWFRDTFGPDDSYEEL-LAEAEQVPPGSE------GLLFLP 336
Query: 261 TLLGDR--HVIAE-SASVTHITIQNLGVTKLFVALCEGIINNIHDIMNRSVLHRSG--IN 315
L G+R H + +T+ + L A+ EG+ ++ D + +L G I+
Sbjct: 337 YLSGERTPHNDPNARGAFIGLTLSH-TRAHLTRAVLEGVAFSLRDSLE--ILRELGVPID 393
Query: 316 RIIGIG 321
RII IG
Sbjct: 394 RIIAIG 399
Score = 42.5 bits (101), Expect = 4e-04
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 11/80 (13%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQN----VRKIVS 60
LGID+GT+ VK L+D + ++S S + + P PG EQ+ +
Sbjct: 1 YYLGIDLGTSGVKALLVDEDGE-VVASASAEYPLSQP-----KPGWSEQDPEDWWEATKA 54
Query: 61 TLHNCILRLPKDHLKQVKHI 80
+ + + +V+ I
Sbjct: 55 AIRELLAKSGIA-GGEVRGI 73
>gnl|CDD|198349 cd07771, FGGY_RhuK, L-rhamnulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial L-rhamnulose kinases
(RhuK, also known as rhamnulokinase; EC 2.7.1.5), which
are encoded by the rhaB gene and catalyze the
ATP-dependent phosphorylation of L-rhamnulose to produce
L-rhamnulose-1-phosphate and ADP. Some uncharacterized
homologous sequences are also included in this
subfamily. The prototypical member of this subfamily is
Escherichia coli RhuK, which exists as a monomer
composed of two large domains. The ATP binding site is
located in the cleft between the two domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of divalent Mg2+ or Mn2+
is required for catalysis. Although an intramolecular
disulfide bridge is present in Rhuk, disulfide formation
is not important to the regulation of RhuK enzymatic
activity. Members of this subfamily belong to the FGGY
family of carbohydrate kinases.
Length = 440
Score = 45.2 bits (108), Expect = 6e-05
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 5/75 (6%)
Query: 108 NAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDW--LGINKDTP- 164
NA++ + + W+ ++L + P L P + GT++G L + KD P
Sbjct: 172 NASTTQLLDPRTRDWDTELLE--KLGIPEELFPPLVEPGTVLGPLKPEVAEELGGKDIPV 229
Query: 165 INVALGDLQCSVLAT 179
I VA D +V A
Sbjct: 230 IAVASHDTASAVAAV 244
>gnl|CDD|198352 cd07774, FGGY_1, uncharacterized subgroup; belongs to the FGGY
family of carbohydrate kinases. This subfamily is
composed of uncharacterized carbohydrate kinases. They
are sequence homologous to bacterial glycerol kinase and
have been classified as members of the FGGY family of
carbohydrate kinases. The monomers of FGGY proteins
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 430
Score = 45.1 bits (107), Expect = 7e-05
Identities = 30/118 (25%), Positives = 52/118 (44%), Gaps = 9/118 (7%)
Query: 86 LSFQDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPS-FPLHLLPKIQP 144
L D+I+ L PV A+ F+ + W+E++L E P LP++ P
Sbjct: 150 LHIPDYILFRLT--GRPVTDFTLASRTLLFDIRAREWSEELL---EMFGIPPDALPELVP 204
Query: 145 SGTIVGTLTRD---WLGINKDTPINVALGDLQCSVLATLQYHSDAIVNISTSAQIAFI 199
SGTI+G +++D LG++ TP+ + D A I++ +A+
Sbjct: 205 SGTIIGEVSKDAAESLGLSTGTPVVLGGHDHPVGSYAAGVIDPGDILDSMGTAEALLA 262
Score = 32.0 bits (73), Expect = 0.83
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 7 LGIDIGTTSVKVCLID 22
GID+GTT+ KV + D
Sbjct: 3 CGIDVGTTNTKVVVFD 18
>gnl|CDD|198376 cd07810, FGGY_D-XK_2, D-xylulose kinases, subgroup 2; members of
the FGGY family of carbohydrate kinases. This subgroup
is predominantly composed of bacterial D-xylulose
kinases (XK, also known as xylulokinase; EC 2.7.1.17).
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. EcXK exists as a dimer. Each monomer consists
of two large domains separated by an open cleft that
forms an active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 490
Score = 45.1 bits (107), Expect = 7e-05
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 7/78 (8%)
Query: 7 LGIDIGTTSVKVCLIDANTREELSSESK-DTQANIPSAHDSNPGAHEQNVRKIVSTLHNC 65
LG DIG++S+K L+DA T + L+S S + + I S PG EQ+
Sbjct: 3 LGYDIGSSSIKAALVDAETGKSLASVSYPEQEMEILSPQ---PGWAEQDPEIWWDYTCAA 59
Query: 66 ILRL---PKDHLKQVKHI 80
+L K+ L ++ I
Sbjct: 60 TKQLINQGKEDLSNIQAI 77
>gnl|CDD|198372 cd07804, FGGY_XK_like_1, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
bacterial and archaeal xylulose kinases-like proteins
with similarity to bacterial D-xylulose kinases (XK,
also known as xylulokinase; EC 2.7.1.17), which catalyze
the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 492
Score = 44.5 bits (106), Expect = 1e-04
Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 8/115 (6%)
Query: 89 QDFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTI 148
+IV L E + + +A+ G ++ + W+E++L P LLPK+ G I
Sbjct: 157 NSYIVYKLTG--ELAVDHSSASGSGLYDIRKGEWSEELLDLLGI--PEDLLPKLVRPGDI 212
Query: 149 VGTLTRDW---LGINKDTPINVALGDLQCSVLAT-LQYHSDAIVNISTSAQIAFI 199
VGT+T + G+ TP+ D + L + DA+ + TS I +
Sbjct: 213 VGTVTEEAAEETGLPAGTPVVAGGADAAAAALGAGVVEPGDAMEMLGTSGVIIVV 267
Score = 40.3 bits (95), Expect = 0.003
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNV----RKIVST 61
+LGIDIGT+S K L D + E L+ S++ + + P PG EQ+ +
Sbjct: 2 LLGIDIGTSSTKAVLFDLD-GEVLAQASREYELSTPQ-----PGWAEQDPEVWWDAVCEI 55
Query: 62 LHNCI 66
+ +
Sbjct: 56 IRELV 60
>gnl|CDD|233354 TIGR01312, XylB, D-xylulose kinase. This model describes
D-xylulose kinases, a subfamily of the FGGY family of
carbohydrate kinases. The member from Klebsiella
pneumoniae, designated DalK (see PMID:9324246), was
annotated erroneously in GenBank as D-arabinitol kinase
but is authentic D-xylulose kinase. D-xylulose kinase
(XylB) generally is found with xylose isomerase (XylA)
and acts in xylose utilization [Energy metabolism,
Sugars].
Length = 481
Score = 42.7 bits (101), Expect = 4e-04
Identities = 66/321 (20%), Positives = 120/321 (37%), Gaps = 63/321 (19%)
Query: 90 DFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIV 149
D++ L E V +A+ G+F+ W++++L P LP++ S
Sbjct: 156 DYLRYRLTG--EYVTEYSDASGTGWFDVAKRAWSKELL--DALDLPESQLPELIESSEKA 211
Query: 150 GTLT---RDWLGINKDTPINVALGDLQCSVLATLQYHS-DAIVNISTSAQI-AFIDE--- 201
GT+ LG++ P+ GD + T DA++++ TS + A D+
Sbjct: 212 GTVRPEVAARLGLSAGVPVAAGGGDNAAGAIGTGTVDPGDAMMSLGTSGVVYAVTDKPLP 271
Query: 202 -------------------MGASMNGGNCLATFVCTLQNWFKEFGFNVPQNQIWAKLINA 242
MG +++ + L WF+E + +L
Sbjct: 272 DPAGAVHGFCHALPGGWLPMGVTLSATSSL--------EWFRELFGKEDVEAL-NELAEQ 322
Query: 243 SDPINHITRHHSTLRVTPTLLGDR--HVIAESASVTHITIQNLGVTKLFVALCEGIINNI 300
S P + P L G+R H+ ++ N L A+ EG+ +
Sbjct: 323 SPPGAE------GVTFLPYLNGERTPHLDPQARGSFIGLTHNTTRADLTRAVLEGVTFAL 376
Query: 301 HDIMNRSVLHRSGIN----RIIGIGSCLTRNHILQHYIERIYGLQLIV-EQDQ-----AM 350
D ++ + GI R+IG G+ ++ + + I+G + V E ++ A
Sbjct: 377 RDSLD-ILREAGGIPIQSIRLIGGGA---KSPAWRQMLADIFGTPVDVPEGEEGPALGAA 432
Query: 351 RDASYAL-EKPAPEFEGQAVV 370
A++AL EK +AVV
Sbjct: 433 ILAAWALGEKDLAALCSEAVV 453
Score = 35.0 bits (81), Expect = 0.11
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 7 LGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNCI 66
LGID+GT+ VK L+D E ++S A PG EQ+ I
Sbjct: 1 LGIDLGTSGVKALLVDEQ-GEVIAS----GSAPHTVISPH-PGWSEQDPEDWWDATEEAI 54
Query: 67 LRLPKDHLKQVKHIE 81
L + + + I+
Sbjct: 55 KELLEQASEMGQDIK 69
>gnl|CDD|215880 pfam00370, FGGY_N, FGGY family of carbohydrate kinases, N-terminal
domain. This domain adopts a ribonuclease H-like fold
and is structurally related to the C-terminal domain.
Length = 245
Score = 41.5 bits (98), Expect = 5e-04
Identities = 22/73 (30%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 108 NAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDW---LGINKDTP 164
+A+ FN K W+E++L P LLP + S I GTL + G+++ P
Sbjct: 174 DASGTMMFNIKTLEWDEELL--AILGIPPDLLPPLVESSEIYGTLNPEHAALFGLDEGIP 231
Query: 165 INVALGDLQCSVL 177
+ GD Q + L
Sbjct: 232 VVGGGGDNQAAAL 244
Score = 40.4 bits (95), Expect = 0.001
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
VLGID GTTS K + + + ++S S P PG EQ+ +I L
Sbjct: 1 YVLGIDCGTTSTKAIVFNKQGK-VVASASAPYALISPK-----PGWAEQDPEEIWQALAQ 54
Query: 65 CILRLPKDH---LKQVKHIESTN 84
I ++ + KQ+K I +
Sbjct: 55 AIRKILQQSGISPKQIKGIGISG 77
>gnl|CDD|198347 cd07769, FGGY_GK, Glycerol kinases; a subfamily of the FGGY family
of carbohydrate kinases. This subfamily includes
glycerol kinases (GK; EC 2.7.1.30) and glycerol
kinase-like proteins from all three kingdoms of living
organisms. Glycerol is an important intermediate of
energy metabolism and it plays fundamental roles in
several vital physiological processes. GKs are involved
in the entry of external glycerol into cellular
metabolism. They catalyze the rate-limiting step in
glycerol metabolism by transferring a phosphate from ATP
to glycerol thus producing glycerol 3-phosphate (G3P) in
the cytoplasm. Human GK deficiency, called
hyperglycerolemia, is an X-linked recessive trait
associated with psychomotor retardation, osteoporosis,
spasticity, esotropia, and bone fractures. Under
different conditions, GKs from different species may
exist in different oligomeric states. The monomer of GKs
is composed of two large domains separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain. The high affinity ATP binding site of GKs is
created only by a substrate-induced conformational
change. Based on sequence similarity, some GK-like
proteins from metazoa, which have lost their GK
enzymatic activity, are also included in this CD.
Members in this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 484
Score = 41.8 bits (99), Expect = 7e-04
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 108 NAASWGYFNCKLST--WNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDWLGINKDTPI 165
NA+ N L T W+E++L P LP+I+ S + G L + PI
Sbjct: 181 NASRTMLMN--LHTLQWDEELLELF--GIPSECLPEIRSSSEVYGYTNEGGLL-GEGIPI 235
Query: 166 NVALGDLQ 173
LGD Q
Sbjct: 236 AGCLGDQQ 243
Score = 32.6 bits (75), Expect = 0.64
Identities = 16/62 (25%), Positives = 26/62 (41%), Gaps = 6/62 (9%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
+L ID GTTS + + D + S + + Q PG E + +I + +
Sbjct: 1 YILAIDQGTTSTRFIIFDRDGEVVSSHQVEHEQ------IYPQPGWVEHDPEEIWANVVQ 54
Query: 65 CI 66
CI
Sbjct: 55 CI 56
>gnl|CDD|198369 cd07798, FGGY_AI-2K_like, Autoinducer-2 kinase-like proteins;
belongs to the FGGY family of carbohydrate kinases.
This subgroup consists of uncharacterized hypothetical
bacterial proteins with similarity to bacterial
autoinducer-2 (AI-2) kinases, which catalyzes the
phosphorylation of intracellular AI-2 to phospho-AI-2,
leading to the inactivation of lsrR, the repressor of
the lsr operon. Members of this subgroup belong to the
FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 437
Score = 41.4 bits (97), Expect = 8e-04
Identities = 20/96 (20%), Positives = 44/96 (45%), Gaps = 5/96 (5%)
Query: 109 AASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTR---DWLGINKDTPI 165
A F+ + W+E++ + +LP++ +GT +G + + D LG+++D +
Sbjct: 171 ACETLLFDVESKEWSERLCGIF--GISMDILPELVRAGTSLGKIKKEMADELGLSEDAEV 228
Query: 166 NVALGDLQCSVLATLQYHSDAIVNISTSAQIAFIDE 201
GD Q ++ + D ++ T+ I I +
Sbjct: 229 IAGGGDTQLALKSVGAGVGDIVIVSGTTTPITKITD 264
>gnl|CDD|239264 cd02966, TlpA_like_family, TlpA-like family; composed of TlpA,
ResA, DsbE and similar proteins. TlpA, ResA and DsbE are
bacterial protein disulfide reductases with important
roles in cytochrome maturation. They are
membrane-anchored proteins with a soluble TRX domain
containing a CXXC motif located in the periplasm. The
TRX domains of this family contain an insert,
approximately 25 residues in length, which correspond to
an extra alpha helix and a beta strand when compared
with TRX. TlpA catalyzes an essential reaction in the
biogenesis of cytochrome aa3, while ResA and DsbE are
essential proteins in cytochrome c maturation. Also
included in this family are proteins containing a
TlpA-like TRX domain with domain architectures similar
to E. coli DipZ protein, and the N-terminal TRX domain
of PilB protein from Neisseria which acts as a disulfide
reductase that can recylce methionine sulfoxide
reductases.
Length = 116
Score = 38.8 bits (91), Expect = 0.001
Identities = 31/125 (24%), Positives = 50/125 (40%), Gaps = 26/125 (20%)
Query: 373 QFKNIKLSQYKGQYVVLFFY-----PLDFTFVCPTEIIAFSDRAEEFKKINTQVIACSTD 427
K + LS KG+ V++ F+ P C E+ A+E+K +V+ + D
Sbjct: 8 DGKPVSLSDLKGKVVLVNFWASWCPP------CRAEMPELEALAKEYKDDGVEVVGVNVD 61
Query: 428 SHFSHLAWCNIPRNKGGLGDMAI--PILSDKSMSIARSYGVLNEETGIPYRGLFIIDDKQ 485
+ K L I P+L D +A++YGV G+P F+ID
Sbjct: 62 DD-------DPAAVKAFLKKYGITFPVLLDPDGELAKAYGV----RGLPT--TFLIDRDG 108
Query: 486 NLRQI 490
+R
Sbjct: 109 RIRAR 113
>gnl|CDD|239268 cd02970, PRX_like2, Peroxiredoxin (PRX)-like 2 family; hypothetical
proteins that show sequence similarity to PRXs. Members
of this group contain a CXXC motif, similar to TRX. The
second cysteine in the motif corresponds to the
peroxidatic cysteine of PRX, however, these proteins do
not contain the other two residues of the catalytic
triad of PRX. PRXs confer a protective antioxidant role
in cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF. TRXs alter the
redox state of target proteins by catalyzing the
reduction of their disulfide bonds via the CXXC motif
using reducing equivalents derived from either NADPH or
ferredoxins.
Length = 149
Score = 39.3 bits (92), Expect = 0.001
Identities = 25/160 (15%), Positives = 45/160 (28%), Gaps = 48/160 (30%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFVCP---TEIIAFSDRAEEFKK 416
AP+FE + VV+ FY F CP + A S E
Sbjct: 1 TAPDFELPDAGGETV--TLSALLGEGPVVVVFYR---GFGCPFCREYLRALSKLLPELDA 55
Query: 417 INTQVIACSTDS-----HFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEET 471
+ +++A +S F + P+ +D + R+ G++
Sbjct: 56 LGVELVAVGPESPEKLEAFDKGKFLP------------FPVYADPDRKLYRALGLVRSLP 103
Query: 472 -----------------------GIPYRGLFIIDDKQNLR 488
G+ G+F+I +
Sbjct: 104 WSNTPRALWKNAAIGFRGNDEGDGLQLPGVFVIGPDGTIL 143
>gnl|CDD|198353 cd07775, FGGY_AI-2K, Autoinducer-2 kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial autoinducer-2 (AI-2) kinases and
similar proteins. AI-2 is a small chemical
quorum-sensing signal involved in interspecies
communication in bacteria. Cytoplasmic autoinducer-2
kinase, encoded by the lsrK gene from Salmonella
enterica serovar Typhimurium lsr (luxS regulated)
operon, is the prototypical member of this subfamily.
AI-2 kinase catalyzes the phosphorylation of
intracellular AI-2 to phospho-AI-2, which leads to the
inactivation of lsrR, the repressor of the lsr operon.
Members of this family are homologs of glycerol
kinase-like proteins and belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 452
Score = 40.5 bits (95), Expect = 0.002
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 11/98 (11%)
Query: 87 SFQDFIVAMLCDL--QEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQP 144
D+I+ L + EP NA + G F+ K W+ ++L + P +
Sbjct: 157 MISDWILYKLSGVLAVEP----SNAGTTGLFDLKTRDWSPEMLD--IVGLRDDIFPPVVE 210
Query: 145 SGTIVGTLTRDW---LGINKDTPINVALGDLQCSVLAT 179
+GT++GT+T + G+ TP+ GD+Q L
Sbjct: 211 TGTVIGTVTNEAASETGLAAGTPVVAGGGDVQLGALGL 248
>gnl|CDD|240348 PTZ00294, PTZ00294, glycerol kinase-like protein; Provisional.
Length = 504
Score = 39.6 bits (93), Expect = 0.004
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 108 NAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDWLGINKDTPINV 167
NA+ N K W+E++L ++ P LP+I+ S GT++ + + + + PI
Sbjct: 186 NASRTFLMNIKTLKWDEELL--NKFGIPKETLPEIKSSSENFGTISGEAVPLLEGVPITG 243
Query: 168 ALGDLQCSVL 177
+GD Q +++
Sbjct: 244 CIGDQQAALI 253
Score = 33.8 bits (78), Expect = 0.26
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 6/62 (9%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
+ ID GTTS + + D S + Q +PG E + +I+ ++
Sbjct: 3 YIGSIDQGTTSTRFIIFDEKGNVVSSHQIPHEQ------ITPHPGWLEHDPEEILRNVYK 56
Query: 65 CI 66
C+
Sbjct: 57 CM 58
>gnl|CDD|212666 cd07802, FGGY_L-XK, L-xylulose kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial L-xylulose kinases (L-XK, also
known as L-xylulokinase; EC 2.7.1.53), which catalyze
the ATP-dependent phosphorylation of L-xylulose to
produce L-xylulose 5-phosphate and ADP. The presence of
Mg2+ might be required for catalytic activity. Some
uncharacterized sequences are also included in this
subfamily. L-XKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 447
Score = 39.1 bits (92), Expect = 0.005
Identities = 21/97 (21%), Positives = 31/97 (31%), Gaps = 7/97 (7%)
Query: 136 LHLLPKIQPSGTIVGTLTR---DWLGINKDTPINVALGDLQCSVLATLQYHSDAIVNI-- 190
LLP I S IVGTLT G+ TP+ L D+ L + + +I
Sbjct: 202 RDLLPPIVDSADIVGTLTAEAAALTGLPAGTPVVGGLFDVVACALGSGLVDEGDLCSIAG 261
Query: 191 STSAQIAFIDEMGASMNGGNCLATFVCTLQNWFKEFG 227
+ S D+ + + E
Sbjct: 262 TWSINEVLSDD--PVPEAEPFGYSLYLPPGYYLVEES 296
Score = 36.4 bits (85), Expect = 0.033
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQN 54
+LGID GTT K L D + R E++ S+ P PG EQ+
Sbjct: 2 LLGIDAGTTVTKAVLFDLDGR-EIAVASRRNPTLTP-----QPGYVEQD 44
>gnl|CDD|198371 cd07803, FGGY_D-XK, D-xylulose kinases; a subgroup of the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of bacterial D-xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. Some uncharacterized
sequences are also included in this subfamily. The
prototypical member of this subfamily is Escherichia
coli xylulokinase (EcXK), which exists as a dimer. Each
monomer consists of two large domains separated by an
open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. XKs do not have any known allosteric
regulators, and they may have weak but significant
activity in the absence of substrate. The presence of
Mg2+ or Mn2+ is required for catalytic activity. Members
of this subfamily belong to the FGGY family of
carbohydrate kinases.
Length = 482
Score = 38.9 bits (91), Expect = 0.006
Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 6/98 (6%)
Query: 108 NAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDW---LGINKDTP 164
+A+ F+ W++ + P LLP + I G +T + G+ TP
Sbjct: 173 DASGTLLFDAASREWSDDLCA--LYGIPEDLLPPLHEPSEIAGAVTPEAARKTGLKAGTP 230
Query: 165 INVALGDLQCSVLATLQYH-SDAIVNISTSAQIAFIDE 201
+ GD + L A +++ TS +A + E
Sbjct: 231 VVAGAGDNAAAALGAGVVDPGQASLSLGTSGVVAVVSE 268
Score = 34.3 bits (79), Expect = 0.18
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 6 VLGIDIGTTSVKVCLIDA 23
+GIDIGT+SVK L++
Sbjct: 2 YIGIDIGTSSVKASLVNL 19
>gnl|CDD|198373 cd07805, FGGY_XK_like_2, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
proteins with similarity to bacterial D-Xylulose
kinases (XK, also known as xylulokinase; EC 2.7.1.17),
which catalyze the rate-limiting step in the
ATP-dependent phosphorylation of D-xylulose to produce
D-xylulose 5-phosphate (X5P) and ADP. The presence of
Mg2+ or Mn2+ is required for catalytic activity. D-XK
exists as a dimer with an active site that lies at the
interface between the N- and C-terminal domains. This
model includes both the N-terminal domain, which adopts
a ribonuclease H-like fold, and the structurally
related C-terminal domain. Members of this subgroup
belong to the FGGY family of carbohydrate kinases.
Length = 514
Score = 38.8 bits (91), Expect = 0.007
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQN 54
VL ID+GT+ VK L+ ++S ++ + + G EQ+
Sbjct: 2 VLAIDLGTSGVKAALVSP-DGRLVASATEAYETHYL-----PGGGAEQD 44
Score = 38.4 bits (90), Expect = 0.008
Identities = 26/118 (22%), Positives = 49/118 (41%), Gaps = 18/118 (15%)
Query: 90 DFIVAMLCDLQEPVMSNQNAASWGYFNCKLS--TWNEQILR--NHEPSFPLHLLPKIQPS 145
D++ L +A+ + + W+E++L + LP++ PS
Sbjct: 167 DYLNLRLTG--RFATDPDDASLTWLTDNRDGRIRWSEELLAAAGIDRE----KLPELVPS 220
Query: 146 GTIVGTLTRD---WLGINKDTPINVALGDLQCSVL---ATLQYHSDAIVNISTSAQIA 197
+VGT+ + LG+ + TP+ GD + + A DA + + TS+ IA
Sbjct: 221 TDVVGTVLPEAARELGLPEGTPVVAGGGDASAAAVGAGAVADG--DAHLYLGTSSWIA 276
>gnl|CDD|212662 cd07779, FGGY_ygcE_like, uncharacterized ygcE-like proteins. This
subfamily consists of uncharacterized hypothetical
bacterial proteins with similarity to Escherichia coli
sugar kinase ygcE , whose functional roles are not yet
clear. Escherichia coli ygcE is recognized by this
model, but is not present in the alignment as it
contains a deletion relative to other members of the
group. These proteins belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 488
Score = 38.8 bits (91), Expect = 0.007
Identities = 36/148 (24%), Positives = 57/148 (38%), Gaps = 20/148 (13%)
Query: 101 EPVMSNQNAASWGYFNCKLSTW-NEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDW--- 156
V S + + F+ K W ++ L+ LP++ P G ++GT+T +
Sbjct: 168 RFVDSVASQVGYIPFDYKKRRWAKKEDLKWQGFPIEPEQLPELVPPGKLIGTITAEAAEA 227
Query: 157 LGINKDTPINVALGDLQCSVL---------ATLQYHSDAIVNISTSAQIA---FIDEMGA 204
G+ + TP+ D C L A L + A VN ++S F A
Sbjct: 228 TGLPEGTPVIAGGSDKACETLGAGALEPGIACLSLGTTATVNGTSSRYFEPDRFFPAYPA 287
Query: 205 SMNGGNCLATFVCT---LQNWFK-EFGF 228
+ GG + L +WFK EFG
Sbjct: 288 VIPGGYNPEIEIFRGYWLVSWFKEEFGQ 315
Score = 36.5 bits (85), Expect = 0.033
Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 5/69 (7%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
VL ID GT SV+ L D + L ++ Q I + PG EQ+ L
Sbjct: 1 YVLAIDCGTQSVRALLFDR--QGNLVAKG---QVPIEPYYSPKPGWAEQDPDYYWQALCE 55
Query: 65 CILRLPKDH 73
L +
Sbjct: 56 ACRELWEQI 64
>gnl|CDD|198375 cd07809, FGGY_D-XK_1, D-xylulose kinases, subgroup 1; members of
the FGGY family of carbohydrate kinases. This subgroup
is composed of D-xylulose kinases (XK, also known as
xylulokinase; EC 2.7.1.17) from bacteria and eukaryota.
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. Some uncharacterized sequences are also
included in this subfamily. EcXK exists as a dimer.
Each monomer consists of two large domains separated by
an open cleft that forms an active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. The presence of Mg2+ or Mn2+ might
be required for catalytic activity. Members of this
subgroup belong to the FGGY family of carbohydrate
kinases.
Length = 487
Score = 38.1 bits (89), Expect = 0.011
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHD---SNPGAHEQNVRKIVSTL 62
LG+D GT S KV ++DA T E L+ S + H+ + G EQ + + L
Sbjct: 2 YLGVDCGTQSTKVIVLDAETGEVLAEGS--------APHELISGSNGRREQQPQWWIDAL 53
Query: 63 HNCI---LRLPKDHLKQVKHI 80
L K+V+ I
Sbjct: 54 VEAFRQALADAGIDPKEVRAI 74
Score = 31.1 bits (71), Expect = 1.5
Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 101 EPVMSNQNAASWGYFNCKLSTWNEQILRNHEPS-FPLHLLPKIQPSGTIVGTL---TRDW 156
V +A+ GYF+ + W+E++L +P+ LP + GT+ +
Sbjct: 169 RYVTEYGDASGTGYFDVRTREWSEEVLDAIDPALDLADALPTLLSPDEPAGTVRPEAAEA 228
Query: 157 LGINKDTPINVALGD 171
LG++ D + GD
Sbjct: 229 LGLSGDVLVASGGGD 243
>gnl|CDD|223995 COG1069, AraB, Ribulose kinase [Energy production and
conversion].
Length = 544
Score = 37.3 bits (87), Expect = 0.018
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 4 QVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLH 63
V+G+D+GT S + + D T L+ + P EQ+ R +
Sbjct: 3 AYVIGVDVGTGSARAGVFDCQTGTLLARAVRP----YPMWQPG-SNLAEQHSRDYWEAVC 57
Query: 64 NCI 66
+
Sbjct: 58 AAV 60
>gnl|CDD|233353 TIGR01311, glycerol_kin, glycerol kinase. This model describes
glycerol kinase, a member of the FGGY family of
carbohydrate kinases [Energy metabolism, Other].
Length = 493
Score = 37.2 bits (87), Expect = 0.023
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 4/71 (5%)
Query: 108 NAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDWLGINKDTPINV 167
NA+ FN W++++L P +LP+++ S + G LG + PI
Sbjct: 182 NASRTMLFNIHTLDWDDELLE--LFGIPREILPEVRSSSEVYGYTDPGLLG--AEIPITG 237
Query: 168 ALGDLQCSVLA 178
LGD Q ++
Sbjct: 238 VLGDQQAALFG 248
>gnl|CDD|224851 COG1940, NagC, Transcriptional regulator/sugar kinase
[Transcription / Carbohydrate transport and
metabolism].
Length = 314
Score = 36.7 bits (85), Expect = 0.025
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 1 MSSQVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAH 44
+ VLGIDIG T +KV L+D + E L E T P
Sbjct: 3 PEAMTVLGIDIGGTKIKVALVDLDG-EILLRERIPTPTPDPEEA 45
>gnl|CDD|198358 cd07781, FGGY_RBK, Ribulokinases; belongs to the FGGY family of
carbohydrate kinases. This subgroup is predominantly
composed of bacterial ribulokinases (RBK) which
catalyze the MgATP-dependent phosphorylation of L(or
D)-ribulose to produce L(or D)-ribulose 5-phosphate and
ADP. RBK also phosphorylates a variety of other sugar
substrates including ribitol and arabitol. The reason
why L-RBK can phosphorylate so many different
substrates is not yet clear. The presence of Mg2+ is
required for catalytic activity. This group belongs to
the FGGY family of carbohydrate kinases, the monomers
of which contain two large domains, which are separated
by a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 498
Score = 36.4 bits (85), Expect = 0.036
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSE 32
+G+D GT SV+ L+D T EL+S
Sbjct: 3 AIGLDFGTLSVRALLVDTETGAELASA 29
Score = 36.1 bits (84), Expect = 0.050
Identities = 22/105 (20%), Positives = 37/105 (35%), Gaps = 22/105 (20%)
Query: 90 DFIVAMLCDLQEP--VMSNQNAA--------SWGYFNCKLSTWNEQILRNHEPSFPL--- 136
D+I A L +P + ++ AA WG +++ L +P
Sbjct: 180 DWIPAQLTGTTDPKKLKRSRCAAGHKAMWHEEWGGLP------SDEFLSALDPKLAGVRD 233
Query: 137 HLLPKIQPSGTIVGTLTRDW---LGINKDTPINVALGDLQCSVLA 178
L I SG G L+ +W LG+ + + V D +
Sbjct: 234 KLSGPIYTSGEKAGGLSPEWAARLGLPEGIAVAVGAFDAHMGAVG 278
>gnl|CDD|198362 cd07789, FGGY_CsGK_like, Cellulomonas sp. glycerol kinase-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a small group of
bacterial glycerol kinases (GK) with similarity to
Cellulomonas sp. glycerol kinase (CsGK). CsGK might
exist as a dimer. Its monomer is composed of two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. The regulation
of the catalytic activity of this group has not yet been
examined. Members in this subgroup belong to the FGGY
family of carbohydrate kinases.
Length = 495
Score = 36.3 bits (84), Expect = 0.044
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 121 TWNEQILRNHEPSFPLHLLPKIQPSGTIVGTLTRDWLGINKDTPINVALGDLQCS 175
W+ ++L P +LP+I+PS + GT+ GI PI LGD Q +
Sbjct: 197 DWDPELLAAF--GIPRSMLPEIRPSSEVYGTVRGR--GILAGVPIAGVLGDQQAA 247
>gnl|CDD|239267 cd02969, PRX_like1, Peroxiredoxin (PRX)-like 1 family; hypothetical
proteins that show sequence similarity to PRXs. Members
of this group contain a conserved cysteine that aligns
to the first cysteine in the CXXC motif of TRX. This
does not correspond to the peroxidatic cysteine found in
PRXs, which aligns to the second cysteine in the CXXC
motif of TRX. In addition, these proteins do not contain
the other two conserved residues of the catalytic triad
of PRX. PRXs confer a protective antioxidant role in
cells through their peroxidase activity in which
hydrogen peroxide, peroxynitrate, and organic
hydroperoxides are reduced and detoxified using reducing
equivalents derived from either thioredoxin,
glutathione, trypanothione and AhpF.
Length = 171
Score = 34.5 bits (80), Expect = 0.058
Identities = 31/161 (19%), Positives = 57/161 (35%), Gaps = 44/161 (27%)
Query: 360 PAPEFEGQAVVNGQFKNIKLSQYKGQ-YVVLFFYPLDFTFVCP------TEIIAFSDRAE 412
PAP+F + L+ + +V+ F CP + A+
Sbjct: 3 PAPDFSLPDTDGKTYS---LADFADGKALVVMF----ICNHCPYVKAIEDRLNRL---AK 52
Query: 413 EFKKINTQVIACSTDSHFSH--------LAWCNIPRNKGGLGDMAIPILSDKSMSIARSY 464
E+ V+A +++ ++ A + G P L D++ +A++Y
Sbjct: 53 EYGAKGVAVVAINSNDIEAYPEDSPENMKAKA---KEHG----YPFPYLLDETQEVAKAY 105
Query: 465 G--------VLNEETGIPYRGLFIIDD--KQNLRQITINDL 495
G + + + + YRG IDD N +T DL
Sbjct: 106 GAACTPDFFLFDPDGKLVYRGR--IDDSRPGNDPPVTGRDL 144
>gnl|CDD|182034 PRK09698, PRK09698, D-allose kinase; Provisional.
Length = 302
Score = 35.3 bits (82), Expect = 0.064
Identities = 17/37 (45%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 1 MSSQVVLGIDIGTTSVKVCLIDANTREELSSESKDTQ 37
VVLGID+G T ++ CL+DA E L E K T
Sbjct: 1 KQKNVVLGIDMGGTHIRFCLVDAE-GEILHCEKKRTA 36
>gnl|CDD|212657 cd00012, NBD_sugar-kinase_HSP70_actin, Nucleotide-Binding Domain
of the sugar kinase/HSP70/actin superfamily. This
superfamily includes the actin family, the HSP70 family
of molecular chaperones and nucleotide exchange
factors, the ROK (repressor, ORF, kinase) family, the
hexokinase family, the FGGY family (which includes
glycerol kinase and similar carbohydrate kinases such
as rhamnulokinase and xylulokinase), the
exopolyphosphatase/guanosine pentaphosphate
phosphohydrolase/nucleoside triphosphate
diphosphohydrolase family, propionate kinase/acetate
kinase family, glycerol dehydratase reactivase,
2-hydroxyglutaryl-CoA dehydratase component A,
N-acetylglucosamine kinase, butyrate kinase 2,
Escherichia coli YeaZ and similar glycoproteases, the
cell shape-determining protein MreB, the plasmid DNA
segregation factor ParM, cell cycle proteins FtsA, Pili
assembly protein PilM, ethanolamine utilization protein
EutJ, and similar proteins. The nucleotide-binding site
residues are conserved; the nucleotide sits in a deep
cleft formed between the two lobes of the
nucleotide-binding domain (NBD). Substrate binding to
superfamily members is associated with closure of this
catalytic site cleft. The functional activities of
several members of the superfamily, including
hexokinases, actin, and HSP70s, are modulated by
allosteric effectors, which may act on the cleft
closure.
Length = 185
Score = 33.7 bits (77), Expect = 0.12
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 7 LGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLH 63
LGIDIG+TS K + D E L E T P ++ E+ +R+++
Sbjct: 1 LGIDIGSTSTKAGVAD-LDGEILPEEIVPTPVGRPG-AVTDLDELEEALRELLKEAL 55
>gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional.
Length = 520
Score = 34.6 bits (80), Expect = 0.12
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 11/89 (12%)
Query: 90 DFIVAMLCD-LQ-EPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGT 147
D+I ML L +P NA + G + W+ +L +LP ++ +GT
Sbjct: 163 DWIAYMLSGELAVDP----SNAGTTGLLDLVTRDWDPALLE--MAGLRADILPPVKETGT 216
Query: 148 IVGTLTRD---WLGINKDTPINVALGDLQ 173
++G +T G+ TP+ + GD+Q
Sbjct: 217 VLGHVTAKAAAETGLRAGTPVVMGGGDVQ 245
>gnl|CDD|212664 cd07792, FGGY_GK1-3_metazoa, Metazoan glycerol kinase 1 and
3-like proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
group of metazoan glycerol kinases (GKs), coded by X
chromosome-linked GK genes, and glycerol kinase
(GK)-like proteins, coded by autosomal testis-specific
GK-like genes (GK-like genes, GK1 and GK3). Sequence
comparison shows that metazoan GKs and GK-like proteins
in this family are closely related to the bacterial
GKs, which catalyze the Mg-ATP dependent
phosphorylation of glycerol to yield glycerol
3-phosphate (G3P). The metazoan GKs do have GK
enzymatic activity. However, the GK-like metazoan
proteins do not exhibit GK activity and their
biological functions are not yet clear. Some of them
lack important functional residues involved in the
binding of ADP and Mg2+, which may result in the loss
of GK catalytic function. Others that have conserved
catalytic residues have lost their GK activity as well;
the reason remains unclear. It has been suggested the
conserved catalytic residues might facilitate them
performing a distinct function. GKs belong to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a
deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 504
Score = 34.6 bits (80), Expect = 0.13
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 9 IDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNCI 66
ID GT+S + + +A T E LSS + + P G EQ+ ++I+++++ CI
Sbjct: 6 IDQGTSSTRFLVFNAKTAELLSSHQVEIKQIFP-----KEGWVEQDPKEILNSVYECI 58
>gnl|CDD|223628 COG0554, GlpK, Glycerol kinase [Energy production and conversion].
Length = 499
Score = 34.1 bits (79), Expect = 0.17
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 91 FIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQILRNHEPSFPLHLLPKIQPSGTIVG 150
+++ L + V NA+ FN W++++L P +LP+++PS I G
Sbjct: 169 WLIWKLTGGKVHVTDYSNASRTMLFNIHSLEWDDELLE--LLGIPRSMLPEVRPSSEIYG 226
Query: 151 TLTRDWLGINKDTPINVALGDLQCS 175
+LG + PI GD Q +
Sbjct: 227 VTGIGFLG--AEVPITGVAGDQQAA 249
>gnl|CDD|179545 PRK03147, PRK03147, thiol-disulfide oxidoreductase; Provisional.
Length = 173
Score = 33.1 bits (76), Expect = 0.17
Identities = 33/131 (25%), Positives = 56/131 (42%), Gaps = 20/131 (15%)
Query: 354 SYALEKPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTFV--CPTEIIAFSDRA 411
+ K AP F + + + K I+L KG+ V L F+ T+ C E+ ++
Sbjct: 34 KVQVGKEAPNF---VLTDLEGKKIELKDLKGKGVFLNFWG---TWCKPCEKEMPYMNELY 87
Query: 412 EEFKKINTQVIACSTDSHFSHLAWCNIPRNKGGLGDMAIPILSDKSMSIARSYGVLNEET 471
++K+ ++IA + D + LA N G + P+ DK + +YGV
Sbjct: 88 PKYKEKGVEIIAVNVDE--TELAVKNFVNRYG----LTFPVAIDKGRQVIDAYGV----- 136
Query: 472 GIPYRGLFIID 482
P F+ID
Sbjct: 137 -GPLPTTFLID 146
>gnl|CDD|240089 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2.
DHOD catalyzes the oxidation of (S)-dihydroorotate to
orotate. This is the fourth step and the only redox
reaction in the de novo biosynthesis of UMP, the
precursor of all pyrimidine nucleotides. DHOD requires
FMN as co-factor. DHOD divides into class 1 and class 2
based on their amino acid sequences, their cellular
location and their natural electron acceptor used to
reoxidize the flavin group. Members of class 1 are
cytosolic enzymes and multimers, while class 2 enzymes
are membrane associated, monomeric and use respiratory
quinones as their physiological electron acceptors.
Length = 327
Score = 34.0 bits (79), Expect = 0.17
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 157 LGINKDTPINVALGDLQCSVLATLQYHSDAIV-NIS 191
+G NKDTP+ A+ D V L ++D +V N+S
Sbjct: 135 IGKNKDTPLEDAVEDYVIGV-RKLGPYADYLVVNVS 169
>gnl|CDD|235221 PRK04123, PRK04123, ribulokinase; Provisional.
Length = 548
Score = 34.4 bits (80), Expect = 0.17
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 4 QVVLGIDIGTTSVKVCLIDANTREELSSESKD 35
V+G+D GT SV+ L+D T EEL++ +
Sbjct: 3 AYVIGLDFGTDSVRALLVDCATGEELATAVVE 34
Score = 34.1 bits (79), Expect = 0.20
Identities = 21/94 (22%), Positives = 38/94 (40%), Gaps = 19/94 (20%)
Query: 90 DFIVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNEQI--------LRNHEPSFPLHLLPK 141
D++VA+L +P ++ + G+ K + W+E +P L K
Sbjct: 182 DWVVALLTGTTDPQDIVRSRCAAGH---K-ALWHESWGGLPSADFFDALDPLLARGLRDK 237
Query: 142 ----IQPSGTIVGTLTRDW---LGINKDTPINVA 168
+G GTLT +W LG+ + ++V
Sbjct: 238 LFTETWTAGEPAGTLTAEWAQRLGLPEGVAVSVG 271
>gnl|CDD|198367 cd07795, FGGY_ScGut1p_like, Saccharomyces cerevisiae Gut1p and
related proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
small group of fungal glycerol kinases (GK), including
Saccharomyces cerevisiae Gut1p/YHL032Cp, which
phosphorylates glycerol to glycerol-3-phosphate in the
cytosol. Glycerol utilization has been considered as
the sole source of carbon and energy in S. cerevisiae,
and is mediated by glycerol kinase and glycerol
3-phosphate dehydrogenase, which is encoded by the GUT2
gene. Members in this family show high similarity to
their prokaryotic and eukaryotic homologs. GKs belong
to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 496
Score = 34.0 bits (78), Expect = 0.23
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 9 IDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNCI 66
ID GTTS + L + + + S + + +Q +PG HE + +IVS++ CI
Sbjct: 7 IDQGTTSTRFILFNRDGQPVASHQIEFSQIY------PHPGWHEHDPEEIVSSVVQCI 58
>gnl|CDD|198360 cd07783, FGGY_CarbK-RPE_like, Carbohydrate kinase and
ribulose-phosphate 3-epimerase fusion proteins-like;
belongs to the FGGY family of carbohydrate kinases.
This subgroup is composed of uncharacterized proteins
with similarity to carbohydrate kinases. Some members
are carbohydrate kinase and ribulose-phosphate
3-epimerase fusion proteins. Carbohydrate kinases
catalyze the ATP-dependent phosphorylation of their
carbohydrate substrate to produce phosphorylated sugar
and ADP. The presence of Mg2+ is required for catalytic
activity. This subgroup shows high homology to
characterized ribulokinases and belongs to the FGGY
family of carbohydrate kinases, the monomers of which
contain two large domains, which are separated by a
deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 484
Score = 33.1 bits (76), Expect = 0.39
Identities = 18/50 (36%), Positives = 21/50 (42%), Gaps = 6/50 (12%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQN 54
VLGID GT SV+ L D R S+ + PG EQN
Sbjct: 2 YVLGIDGGTESVRAGLFDTTGRPLGSAAAP------YGTTHPRPGWAEQN 45
>gnl|CDD|212663 cd07782, FGGY_YpCarbK_like, Yersinia Pseudotuberculosis
carbohydrate kinase-like subgroup; belongs to the FGGY
family of carbohydrate kinases. This subgroup is
composed of the uncharacterized Yersinia
Pseudotuberculosis carbohydrate kinase that has been
named glyerol/xylulose kinase and similar
uncharacterized proteins from bacteria and eukaryota.
Carbohydrate kinases catalyze the ATP-dependent
phosphorylation of their carbohydrate substrate to
produce phosphorylated sugar and ADP. The presence of
Mg2+ is required for catalytic activity. This subgroup
shows high homology to characterized ribulokinases and
belongs to the FGGY family of carbohydrate kinases, the
monomers of which contain two large domains, which are
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain.
Length = 536
Score = 32.9 bits (76), Expect = 0.44
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 4 QVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKI 58
+ +G+D+GT S + L DA R L+ + Q P P EQ+ I
Sbjct: 1 KYYIGVDVGTGSARAGLFDAKGR-LLARAVRPIQIWHPQ-----PDFVEQSSDDI 49
>gnl|CDD|233356 TIGR01315, 5C_CHO_kinase, FGGY-family pentulose kinase. This
model represents a subfamily of the FGGY family of
carbohydrate kinases. This subfamily is closely related
to a set of ribulose kinases, and many members are
designated ribitol kinase. However, the member from
Klebsiella pneumoniae, from a ribitol catabolism
operon, accepts D-ribulose and to a lesser extent
D-arabinitol and ribitol (PMID:9639934 and JW Lengeler,
personal communication); its annotation in GenBank as
ribitol kinase is imprecise and may have affected
public annotation of related proteins.
Length = 541
Score = 32.6 bits (74), Expect = 0.63
Identities = 16/61 (26%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNC 65
+G+D+GT S + C+ID+ L+ +++ + PS G Q+ I + NC
Sbjct: 2 YIGVDVGTGSARACIIDSTGD-ILALAAQNIKTWTPS-----SGLEGQSSVYIWQAICNC 55
Query: 66 I 66
+
Sbjct: 56 V 56
>gnl|CDD|130381 TIGR01314, gntK_FGGY, gluconate kinase, FGGY type. Gluconate is
derived from glucose in two steps. This model describes
one form of gluconate kinase, belonging to the FGGY
family of carbohydrate kinases. Gluconate kinase
phosphoryates gluconate for entry into the
Entner-Douderoff pathway [Energy metabolism, Sugars].
Length = 505
Score = 32.2 bits (73), Expect = 0.70
Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 13/90 (14%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHNC 65
++G+DIGTTS K L + N + S P + G E+N +I +
Sbjct: 2 MIGVDIGTTSTKAVLFEENGKIVAKS-----SIGYP-LYTPASGMAEENPEEIFEAVLVT 55
Query: 66 ILRLPKDHLKQVKHIESTNDLSFQDFIVAM 95
I + + E +++ F F M
Sbjct: 56 IREVSINL-------EDEDEILFVSFSTQM 78
>gnl|CDD|198346 cd07768, FGGY_RBK_like, Ribulokinase-like carbohydrate kinases; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is composed of ribulokinases (RBKs) and
similar proteins from bacteria and eukaryota. RBKs
catalyze the MgATP-dependent phosphorylation of a
variety of sugar substrates including L- and/or
D-ribulose. Members of this subfamily contain two large
domains separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain. Members of this
subfamily belong to the FGGY family of carbohydrate
kinases.
Length = 465
Score = 31.7 bits (72), Expect = 1.1
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 5 VVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLHN 64
V+G+D+GT SV+ + D N R EL+S S P G EQ+ +
Sbjct: 2 YVIGVDVGTESVRAGVFDLNGR-ELASAS----RPYPVPVPYGAGWAEQDPEDWWPAVRT 56
>gnl|CDD|224910 COG1999, COG1999, Uncharacterized protein SCO1/SenC/PrrC, involved
in biogenesis of respiratory and photosynthetic systems
[General function prediction only].
Length = 207
Score = 30.8 bits (70), Expect = 1.5
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 346 QDQAMRDASYALEKPAPEFEGQAVVNGQFKNIKLSQYKGQYVVLFFYPLDFTF---VCPT 402
+ A +FE + + K L KG+ ++FF +T VCPT
Sbjct: 32 DKGDRFNLDAAAVYIGGDFE---LTDQDGKPFTLKDLKGKPSLVFF---GYTHCPDVCPT 85
Query: 403 E 403
Sbjct: 86 T 86
>gnl|CDD|239266 cd02968, SCO, SCO (an acronym for Synthesis of Cytochrome c
Oxidase) family; composed of proteins similar to Sco1, a
membrane-anchored protein possessing a soluble domain
with a TRX fold. Members of this family are required for
the proper assembly of cytochrome c oxidase (COX). They
contain a metal binding motif, typically CXXXC, which is
located in a flexible loop. COX, the terminal enzyme in
the respiratory chain, is imbedded in the inner
mitochondrial membrane of all eukaryotes and in the
plasma membrane of some prokaryotes. It is composed of
two subunits, COX I and COX II. It has been proposed
that Sco1 specifically delivers copper to the CuA site,
a dinuclear copper center, of the COX II subunit.
Mutations in human Sco1 and Sco2 cause fatal infantile
hepatoencephalomyopathy and cardioencephalomyopathy,
respectively. Both disorders are associated with severe
COX deficiency in affected tissues. More recently, it
has been argued that the redox sensitivity of the copper
binding properties of Sco1 implies that it participates
in signaling events rather than functioning as a
chaperone that transfers copper to COX II.
Length = 142
Score = 29.9 bits (68), Expect = 1.7
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 379 LSQYKGQYVVLFFYPLDFTF---VCPTEIIAFS---DRAEEFKKINTQVIACSTD 427
LS KG+ V+++F +T VCPT + + + + QV+ S D
Sbjct: 17 LSDLKGKPVLVYFG---YTHCPDVCPTTLANLAQALKQLGADGGDDVQVVFISVD 68
>gnl|CDD|232891 TIGR00238, TIGR00238, KamA family protein. This model represents
essentially the whole of E. coli YjeK and of some of its
apparent orthologs. YodO in Bacillus subtilis, a family
member which is longer protein by an additional 100
residues, is characterized as a lysine 2,3-aminomutase
with iron, sulphide and pyridoxal 5'-phosphate groups.
The homolog MJ0634 from M. jannaschii is preceded by
nearly 200 C-terminal residues. This family shows
similarity to molybdenum cofactor biosynthesis protein
MoaA and related proteins. Note that the E. coli homolog
was expressed in E. coli and purified and found not to
display display lysine 2,3-aminomutase activity. Active
site residues are found in 100 residue extension in B.
subtilis. Name changed to KamA family protein [Energy
metabolism, Electron transport].
Length = 331
Score = 30.6 bits (69), Expect = 2.2
Identities = 22/93 (23%), Positives = 37/93 (39%), Gaps = 11/93 (11%)
Query: 233 NQIWAKLINASDPINHITR---HHSTLRVTPTLLGDR--HVIAESAS----VTHITIQNL 283
+ L+ + I H+ R V P + D ++A VTHI N
Sbjct: 175 DHELEWLLKRLEEIPHLVRLRIGTRLPVVIPQRITDELCELLASFELQLMLVTHINHCN- 233
Query: 284 GVTKLFVALCEGIINNIHDIMNRSVLHRSGINR 316
+T+ F + + ++N+SVL R G+N
Sbjct: 234 EITEEFAEAMKKLRTVNVTLLNQSVLLR-GVND 265
>gnl|CDD|234882 PRK00976, PRK00976, hypothetical protein; Provisional.
Length = 326
Score = 29.9 bits (68), Expect = 3.2
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 5 VVLGIDIGTTSVKVCLIDAN-------TREELSSESK 34
+ +GID GTT ++ +I+ R E S K
Sbjct: 2 MFVGIDHGTTGIRFAIIEGGKKSIFKLPRTEAKSMEK 38
>gnl|CDD|223520 COG0443, DnaK, Molecular chaperone [Posttranslational modification,
protein turnover, chaperones].
Length = 579
Score = 30.4 bits (69), Expect = 3.2
Identities = 20/105 (19%), Positives = 37/105 (35%), Gaps = 15/105 (14%)
Query: 2 SSQVVLGIDIGTT--SVKVCLIDANTREELSSESKDTQANIPS--AHDSNPG--AHEQNV 55
+++ +GID+GTT V V + ++E + PS A N +
Sbjct: 3 TAKKAIGIDLGTTNSVVAVMRGGGLPKVIENAEGERL---TPSVVAFSKNGEVLVGQAAK 59
Query: 56 RKIVSTLHNCI-----LRLPKDHLKQVKHIESTNDLSFQDFIVAM 95
R+ V N I + ++ + ++ I AM
Sbjct: 60 RQAVDNPENTIFSIKRKIGRGSNGLKISVEVDGKKYTPEE-ISAM 103
>gnl|CDD|198366 cd07794, FGGY_GK_like_proteobact, Proteobacterial glycerol
kinase-like proteins; belongs to the FGGY family of
carbohydrate kinases. This subgroup corresponds to a
small group of proteobacterial glycerol kinase
(GK)-like proteins, including the glycerol kinase from
Pseudomonas aeruginosa. Most bacteria, such as
Escherichia coli, take up glycerol passively by
facilitated diffusion. In contrast, P. aeruginosa may
also utilize a binding protein-dependent active
transport system to mediate glycerol transportation.
The glycerol kinase subsequently phosphorylates the
intracellular glycerol to glycerol 3-phosphate (G3P).
GKs belong to the FGGY family of carbohydrate kinases,
the monomers of which contain two large domains, which
are separated by a deep cleft that forms the active
site. This model includes both the N-terminal domain,
which adopts a ribonuclease H-like fold, and the
structurally related C-terminal domain.
Length = 470
Score = 29.8 bits (67), Expect = 4.1
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 6/63 (9%)
Query: 4 QVVLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQNVRKIVSTLH 63
+ ID GTTS +V + + + + + Q H NPG E + ++++ L
Sbjct: 1 MRIAAIDQGTTSTRVLVAGEDGKAFILLALRHKQ------HYPNPGWVEHDPLELLANLR 54
Query: 64 NCI 66
C+
Sbjct: 55 ACL 57
>gnl|CDD|212665 cd07793, FGGY_GK5_metazoa, metazoan glycerol kinase 5-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup corresponds to a group of
metazoan putative glycerol kinases (GK), which may be
coded by the GK-like gene, GK5. Sequence comparison
shows members of this group are homologs of bacterial
GKs, and they retain all functionally important
residues. However, GK-like proteins in this family do
not have detectable GK activity. The reason remains
unclear. It has been suggested tha the conserved
catalytic residues might facilitate them performing a
distinct function. GKs belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 504
Score = 30.0 bits (68), Expect = 4.2
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 6 VLGIDIGTTSVKVCLIDANTREELSSESKDTQANIPSAHDSNPGAHEQN 54
VL +D+GTT+++ + D SS K + P PG E +
Sbjct: 2 VLALDVGTTTIRCFIYDRQAEVVGSSYDK-IELLYPE-----PGYVEID 44
>gnl|CDD|239646 cd03674, Nudix_Hydrolase_1, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity. They also
contain a highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, U=I, L or V), which forms a structural
motif that functions as a metal binding and catalytic
site. Substrates of nudix hydrolases include intact and
oxidatively damaged nucleoside triphosphates,
dinucleoside polyphosphates, nucleotide-sugars and
dinucleotide enzymes. These substrates are metabolites
or cell signaling molecules that require regulation
during different stages of the cell cycle or during
periods of stress. In general, the role of the nudix
hydrolase is to sanitize the nucleotide pools and to
maintain cell viability, thereby serving as surveillance
& "house-cleaning" enzymes. Substrate specificity is
used to define families within the superfamily.
Differences in substrate specificity are determined by
the N-terminal extension or by residues in variable loop
regions. Mechanistically, substrate hydrolysis occurs by
a nucleophilic substitution reaction, with variation in
the numbers and roles of divalent cations required.
Length = 138
Score = 28.5 bits (64), Expect = 5.0
Identities = 19/54 (35%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 469 EETGIPYRGLFIIDDKQNLRQITINDLPVGRSVDETLRLVQAFQFVAEHGEVCP 522
EETGI GL + +L I D R V L L F VA +V P
Sbjct: 51 EETGIELLGLRPLSVLVDLDVHPI-DGHPKRGVPGHLHLDLRFLAVAPADDVAP 103
>gnl|CDD|198350 cd07772, FGGY_NaCK_like, Novosphingobium aromaticivorans
carbohydrate kinase-like proteins; belongs to the FGGY
family of carbohydrate kinases. This subfamily is
predominantly composed of uncharacterized bacterial
proteins with similarity to carbohydrate kinase from
Novosphingobium aromaticivorans (NaCK). These proteins
may catalyze the transfer of a phosphate group from ATP
to their carbohydrate substrates. They belong to the
FGGY family of carbohydrate kinases, the monomers of
which contain two large domains, which are separated by
a deep cleft that forms the active site. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain.
Length = 419
Score = 29.6 bits (67), Expect = 5.1
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 5 VVLGIDIGTTSVKVCLIDANTRE 27
VV IDIG T+ K+ L DA+ RE
Sbjct: 1 VVAVIDIGKTNAKLFLFDADGRE 23
>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 29.4 bits (67), Expect = 5.2
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 157 LGINKDTPINVALGDLQCSVLATLQYHSDAI-VNIS 191
+G NKDTP+ A+ D L L ++D VNIS
Sbjct: 144 IGKNKDTPLEDAVDDY-LICLEKLYPYADYFTVNIS 178
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 28.9 bits (65), Expect = 5.5
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 5/61 (8%)
Query: 453 LSDKSMSIARSYGVLNEETGIPYRGLFIIDDKQNLRQIT-INDLPVGRSVDETLRLVQAF 511
+ R GVL E G+ R + ++NL+ +N L L +
Sbjct: 66 TVRDPSFVRRKIGVLFGERGLYAR----LTARENLKYFARLNGLSRKEIKARIAELSKRL 121
Query: 512 Q 512
Q
Sbjct: 122 Q 122
>gnl|CDD|198361 cd07786, FGGY_EcGK_like, Escherichia coli glycerol kinase-like
proteins; belongs to the FGGY family of carbohydrate
kinases. This subgroup is composed of mostly bacterial
and archaeal glycerol kinases (GK), including the well
characterized proteins from Escherichia coli (EcGK),
Thermococcus kodakaraensis (TkGK), and Enterococcus
casseliflavus (EnGK). GKs contain two large domains
separated by a deep cleft that forms the active site.
This model includes both the N-terminal domain, which
adopts a ribonuclease H-like fold, and the structurally
related C-terminal domain. The high affinity ATP binding
site of EcGK is created only by a substrate-induced
conformational change, which is initiated by
protein-protein interactions through complex formation
with enzyme IIAGlc (also known as IIIGlc), the
glucose-specific phosphocarrier protein of the
phosphotransferase system (PTS). EcGK exists in a
dimer-tetramer equilibrium. IIAGlc binds to both EcGK
dimer and tetramer, and inhibits the uptake and
subsequent metabolism of glycerol and maltose. Another
well-known allosteric regulator of EcGK is fructose
1,6-bisphosphate (FBP), which binds to the EcGK tetramer
and plays an essential role in the stabilization of the
inactive tetrameric form. EcGK requires Mg2+ for its
enzymatic activity. Members in this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 486
Score = 29.4 bits (67), Expect = 6.0
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 135 PLHLLPKIQPSGTIVGTLTRDWLGINKDTPINVALGDLQ 173
P +LP+++PS + G D LG + PI GD Q
Sbjct: 206 PASMLPEVKPSSEVFGYTDPDLLG--AEIPIAGIAGDQQ 242
>gnl|CDD|235315 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
Length = 903
Score = 29.1 bits (66), Expect = 7.7
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 425 STDSHFSHLAWCNIPRNKGGLG--DMAIPILSDKSMSIARSYG 465
++HF W NI R + LG D A IL ++ ARS
Sbjct: 684 FANNHFLQGQWRNIARAQILLGQFDEAEIIL-EELNENARSLR 725
>gnl|CDD|216750 pfam01869, BcrAD_BadFG, BadF/BadG/BcrA/BcrD ATPase family. This
family includes the BadF and BadG proteins that are two
subunits of Benzoyl-CoA reductase, that may be involved
in ATP hydrolysis. The family also includes an activase
subunit from the enzyme 2-hydroxyglutaryl-CoA
dehydratase. An uncharacterized protein from Aquifex
aeolicus contains two copies of this region suggesting
that the family may structurally dimerise. This family
appears to be related to pfam00370.
Length = 257
Score = 28.5 bits (64), Expect = 7.9
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 8 GIDIGTTSVKVCLIDANTREELSSESKDTQANIPSA 43
GID G+T K L+D + E+ + ANI S
Sbjct: 1 GIDGGSTKTKAVLMDED--GEVLGRAISGSANIESV 34
>gnl|CDD|222728 pfam14390, DUF4420, Domain of unknown function (DUF4420). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria and archaea.
Proteins in this family are typically between 310 and
334 amino acids in length.
Length = 305
Score = 28.4 bits (64), Expect = 9.3
Identities = 10/40 (25%), Positives = 22/40 (55%)
Query: 278 ITIQNLGVTKLFVALCEGIINNIHDIMNRSVLHRSGINRI 317
+++Q+ + ++F LCE +I I D + L + + R+
Sbjct: 79 LSLQDSDLEEVFATLCEDLIERIEDAEDPRDLLSAVVERL 118
>gnl|CDD|198356 cd07778, FGGY_L-RBK_like, L-ribulokinase-like proteins; a
subfamily of the FGGY family of carbohydrate kinases.
This subfamily is composed of a group of putative
bacterial L-ribulokinases (RBK; EC 2.7.1.16) and
similar proteins. L-RBK catalyzes the MgATP-dependent
phosphorylation of a variety of sugar substrates.
Members of this subfamily belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 466
Score = 28.8 bits (65), Expect = 9.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 4 QVVLGIDIGTTSVKVCLIDAN 24
+ LGI+ G+T +K LID +
Sbjct: 5 KTALGIEFGSTRIKAVLIDDD 25
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 28.6 bits (65), Expect = 9.6
Identities = 11/55 (20%), Positives = 22/55 (40%), Gaps = 2/55 (3%)
Query: 92 IVAMLCDLQEPVMSNQNAASWGYFNCKLSTWNE--QILRNHEPSFPLHLLPKIQP 144
+ L +PV+ + + N + TW++ Q L H + L +I+
Sbjct: 478 LFRALAIYLKPVLPELAERAEAFLNLEELTWDDAQQPLAGHPINKFKILFTRIED 532
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
0.320 0.135 0.406
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,292,900
Number of extensions: 2634856
Number of successful extensions: 2137
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2086
Number of HSP's successfully gapped: 117
Length of query: 547
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 445
Effective length of database: 6,413,494
Effective search space: 2854004830
Effective search space used: 2854004830
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 (21.8 bits)
S2: 61 (27.3 bits)