RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4311
(190 letters)
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 280 bits (719), Expect = 2e-94
Identities = 127/161 (78%), Positives = 147/161 (91%)
Query: 2 VLADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVID 61
VLADLG ITSALRS+SNATVI+EEVLN+MLKEIC ALLE+DVNIKLV++LREN+++ I+
Sbjct: 1 VLADLGSSITSALRSMSNATVIDEEVLNAMLKEICTALLESDVNIKLVRQLRENIKKAIN 60
Query: 62 FDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKL 121
+EMASGLNKR+MIQ +V+KEL LVDPGV+A P+KGK NVIMFVGLQGSGKTTTCTKL
Sbjct: 61 LEEMASGLNKRKMIQHAVFKELCNLVDPGVEAFTPKKGKQNVIMFVGLQGSGKTTTCTKL 120
Query: 122 AYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGS 162
AY+Y +K +K CLVCADTFRAGA+DQLKQNATKARIPFYGS
Sbjct: 121 AYYYQRKGFKPCLVCADTFRAGAFDQLKQNATKARIPFYGS 161
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 196 bits (501), Expect = 2e-61
Identities = 68/169 (40%), Positives = 98/169 (57%), Gaps = 1/169 (0%)
Query: 2 VLADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVID 61
+ L ++++AL+ L I E+ + L+EI ALLEADVN+K+VK + +++
Sbjct: 1 MFESLSDRLSNALKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERAL 60
Query: 62 FDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKL 121
+E+ GL + VY+EL+KL+ K P VI+ VGLQGSGKTTT KL
Sbjct: 61 GEEVPKGLTPGQQFIKIVYEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKL 120
Query: 122 AYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
A + KK K LV ADT+R A +QLKQ A + +PF+GS K +P+
Sbjct: 121 AKYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEK-DPV 168
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 169 bits (431), Expect = 4e-51
Identities = 73/166 (43%), Positives = 103/166 (62%), Gaps = 4/166 (2%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
LG + AL+ L+ + I+E+ + ++K+I ALL+ADVN+KLVK+L +++++ +E
Sbjct: 1 LGESLRDALKKLAGKSRIDEKTVKEVVKDIQRALLQADVNVKLVKELSKSIKERALEEEP 60
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKG-KPNVIMFVGLQGSGKTTTCTKLAYH 124
GL R + VY+EL+KL+ G + KP IM VGLQGSGKTTT KLA +
Sbjct: 61 PKGLTPREHVIKIVYEELVKLL--GEETEPLVLPLKPQTIMLVGLQGSGKTTTAAKLARY 118
Query: 125 YLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
+ KK K LV ADT+R AYDQLKQ A K +PFYG K + +
Sbjct: 119 FKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNK-DAV 163
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 130 bits (328), Expect = 3e-36
Identities = 59/167 (35%), Positives = 92/167 (55%), Gaps = 4/167 (2%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L ++ + LS I E+ + L+EI ALLEADVN+++VK + V++ E+
Sbjct: 4 LSERLQRIFKKLSGRGTITEKNIKEALREIRLALLEADVNLQVVKDFIKKVKEKALGQEV 63
Query: 66 ASGLNKRRMIQSSVYKELIKLV-DPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYH 124
L+ + V++EL+ ++ + +K P VI+ VGLQGSGKTTTC KLAY+
Sbjct: 64 LKSLSPGQQFIKIVHEELVAILGGENASLNLAKK-PPTVILMVGLQGSGKTTTCGKLAYY 122
Query: 125 YLKKNWKACLVCA-DTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
KK K L+ A D +R A +QLK + +P + KG+ +P+
Sbjct: 123 LKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGVPVFALGKGQ-SPV 168
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 127 bits (321), Expect = 4e-35
Identities = 58/167 (34%), Positives = 86/167 (51%), Gaps = 4/167 (2%)
Query: 6 LGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
L +++SA + L + E + L+E+ ALLEADVN+ +VK V++ E+
Sbjct: 5 LSDRLSSAFKKLRGKGRLTEADIKEALREVRLALLEADVNLPVVKDFIARVKEKAVGQEV 64
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
L + + V EL++++ P VIM VGLQG+GKTTT KLA Y
Sbjct: 65 LKSLTPGQQVIKIVNDELVEILGGENSELNLAAKPPTVIMMVGLQGAGKTTTAGKLAK-Y 123
Query: 126 LKKNW--KACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
LKK K LV AD +R A +QLK + +P + S G+ +P+
Sbjct: 124 LKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGVPVFPSGDGQ-DPV 169
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 118 bits (299), Expect = 7e-34
Identities = 38/66 (57%), Positives = 45/66 (68%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFY 160
PNVI+ VGLQGSGKTTT KLA + K+ K LV ADTFRA A +QLKQ A + +P +
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTFRAAAIEQLKQLAERLGVPVF 60
Query: 161 GSSKGK 166
GS G
Sbjct: 61 GSGTGS 66
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 109 bits (274), Expect = 6e-29
Identities = 45/168 (26%), Positives = 84/168 (50%), Gaps = 8/168 (4%)
Query: 3 LADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDF 62
L+ + ++ L I E++ +L+E+ L+EADV ++ +++ E +R+
Sbjct: 41 LSKTKKNFGKGIKGLFLKK-IKEKLDEDLLEELEELLIEADVGVETAEEIIEELRKREGK 99
Query: 63 DEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQP----QKGKPNVIMFVGLQGSGKTTTC 118
+ + ++ ++ + LI+++ P K P ++ KP VI+FVG+ G GKTTT
Sbjct: 100 KK---KIKDEETVKEALREALIEILRPVDKVDLPLEIPKEKKPFVILFVGVNGVGKTTTI 156
Query: 119 TKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGK 166
KLA + ++ L DTFRA A +QL+ + +P +G
Sbjct: 157 AKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGA 204
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 108 bits (273), Expect = 6e-29
Identities = 45/157 (28%), Positives = 80/157 (50%), Gaps = 8/157 (5%)
Query: 9 KITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASG 68
+ L I+E++L L+E+ L+EADV ++ +++ E +R+ + +
Sbjct: 30 NFGEGINGLFAKKKIDEDLLEE-LEEL---LIEADVGVETTEEIIEELRERVKRKNLKDP 85
Query: 69 LNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKK 128
+ +++ EL ++++P K ++ KP VI+ VG+ G GKTTT KLA+ Y +
Sbjct: 86 EELKELLKE----ELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKTTTIGKLAHKYKAQ 141
Query: 129 NWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKG 165
K L DTFRA A +QL+ + +P +G
Sbjct: 142 GKKVLLAAGDTFRAAAIEQLQVWGERVGVPVIAQKEG 178
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 100 bits (252), Expect = 6e-27
Identities = 30/67 (44%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKN-WKACLVCADTFRAGAYDQLKQNATKARIPF 159
P VI+ VG G GKTTT KLA K K LV ADTFRA A +QLK A +
Sbjct: 1 PGVILLVGPNGVGKTTTIAKLAARLKLKGGKKVLLVAADTFRAAAVEQLKTYAEILGVVP 60
Query: 160 YGSSKGK 166
+G
Sbjct: 61 VAGGEGA 67
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 100 bits (251), Expect = 4e-26
Identities = 39/136 (28%), Positives = 71/136 (52%), Gaps = 8/136 (5%)
Query: 23 INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKE 82
+E+ E+ LLE+DV ++V+K+ E +++ + ++ + +++ + +
Sbjct: 2 DDEDFFE----ELEEILLESDVGYEVVEKIIEALKKELKGKKVKDAELLKEILKEYLKEI 57
Query: 83 LIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRA 142
L + + ++ KPNVI+FVG+ G GKTTT KLA K+ L DTFRA
Sbjct: 58 LKETDLELI----VEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRA 113
Query: 143 GAYDQLKQNATKARIP 158
A +QL++ A + +
Sbjct: 114 AAIEQLEEWAKRLGVD 129
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain.
Length = 173
Score = 95.3 bits (238), Expect = 4e-25
Identities = 30/65 (46%), Positives = 39/65 (60%)
Query: 102 NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYG 161
VI+ VGLQG GKTTT KLA + KK K LV ADT+R A +QL+ + +P +
Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFE 60
Query: 162 SSKGK 166
+GK
Sbjct: 61 EGEGK 65
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 98.5 bits (246), Expect = 6e-25
Identities = 45/151 (29%), Positives = 89/151 (58%), Gaps = 4/151 (2%)
Query: 19 NATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSS 78
T I E+ + +L+E+ LLE+DV +++ +++ E++++ + ++ G + +++++
Sbjct: 54 KITEIKEKDIEDLLEELELELLESDVALEVAEEILESLKEKLVGKKVKRGEDVEEIVKNA 113
Query: 79 VYKELIKLVDPG----VKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACL 134
+ + L++++ G + KGKP VI+FVG+ G+GKTTT KLAY+ K + +
Sbjct: 114 LKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVI 173
Query: 135 VCADTFRAGAYDQLKQNATKARIPFYGSSKG 165
DTFRAGA +QL+++A + + G
Sbjct: 174 AAGDTFRAGAIEQLEEHAERLGVKVIKHKYG 204
>gnl|CDD|214941 smart00963, SRP54_N, SRP54-type protein, helical bundle domain.
This entry represents the N-terminal helical bundle
domain of the 54 kDa SRP54 component, a GTP-binding
protein that interacts with the signal sequence when it
emerges from the ribosome. SRP54 of the signal
recognition particle has a three-domain structure: an
N-terminal helical bundle domain, a GTPase domain, and
the M-domain that binds the 7s RNA and also binds the
signal sequence. The extreme C-terminal region is
glycine-rich and lower in complexity and poorly
conserved between species.
Length = 77
Score = 68.3 bits (168), Expect = 1e-15
Identities = 23/78 (29%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 10 ITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGL 69
++ AL L + E+ +L+E+ ALLEADV +++VK++ E V++ E+ GL
Sbjct: 1 LSKALGKLLGELFLTEKDDEELLEELEEALLEADVGVEVVKEIIERVKEKAKG-EVLKGL 59
Query: 70 NKRRMIQSSVYKELIKLV 87
++ ++ + +EL+K++
Sbjct: 60 TPKQEVKKILKEELVKIL 77
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 69.2 bits (170), Expect = 4e-14
Identities = 41/162 (25%), Positives = 70/162 (43%), Gaps = 17/162 (10%)
Query: 3 LADLGRKITSALRSLSN---ATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQV 59
L +L ++ L++L + + E + E+ L + ++ ++ +KL + + +
Sbjct: 132 LDELRDELKE-LKNLLEDQLSGLRQVERIPPEFAELYKRLKRSGLSPEIAEKLLKLLLEH 190
Query: 60 IDFDEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCT 119
+ + R + + L ++ V+ Q G V+ VG G GKTTT
Sbjct: 191 MP--------PRERTAWRYLLELLANMIPVRVEDILKQGG---VVALVGPTGVGKTTTLA 239
Query: 120 KLAYHY--LKKNWKACLVCADTFRAGAYDQLKQNATKARIPF 159
KLA Y L K L+ DT+R GA +QLK A IP
Sbjct: 240 KLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPV 281
>gnl|CDD|217266 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain.
Length = 77
Score = 63.8 bits (156), Expect = 4e-14
Identities = 19/81 (23%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 6 LGRKITSALRSLSNA---TVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDF 62
L ++ L + E+ ++ +L+E+ ALLEADV ++ +K+ E +++++
Sbjct: 1 LKEGLSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEADVGVETTEKIIERLKELVG- 59
Query: 63 DEMASGLNKRRMIQSSVYKEL 83
GL+ I+ ++ +EL
Sbjct: 60 ---RKGLSDPEEIKKALKEEL 77
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 64.7 bits (158), Expect = 9e-13
Identities = 43/157 (27%), Positives = 70/157 (44%), Gaps = 15/157 (9%)
Query: 8 RKITSALRSLSNATV--INEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEM 65
RK SALR L + + + + ++ LLEA V+ +L ++L E + + +D ++
Sbjct: 111 RKELSALRELLERLLAGLALQRRDPEGAKLLERLLEAGVSEELARELLEKLPEDLDAEDA 170
Query: 66 ASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
R ++ ++ L + + VI VG G GKTTT KLA +
Sbjct: 171 ------WRWLREALEGMLPVKPEEDPILERGG-----VIALVGPTGVGKTTTLAKLAARF 219
Query: 126 L--KKNWKACLVCADTFRAGAYDQLKQNATKARIPFY 160
+ K L+ DT+R GA +QLK A +P
Sbjct: 220 VLEHGKKKVALITTDTYRIGAVEQLKTYAEILGVPVK 256
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 58.9 bits (143), Expect = 1e-10
Identities = 41/159 (25%), Positives = 64/159 (40%), Gaps = 16/159 (10%)
Query: 3 LADLGRKITSALRSLSNATVINEEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDF 62
+A++ R +R L + EI + +N L L
Sbjct: 119 IAEMMRDEKVPIRELEEIPPEFVALYKQ---EIQSPTRLNLINELLRAGLEL-------- 167
Query: 63 DEMASGLNKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLA 122
E+ ++ ++L KL+ ++ ++ + VI VG G GKTTT KLA
Sbjct: 168 -EILDMKDESYEDLRYFSEKLRKLLLSLIENLIVEQKR--VIALVGPTGVGKTTTLAKLA 224
Query: 123 YHY--LKKNWKACLVCADTFRAGAYDQLKQNATKARIPF 159
Y LKK K ++ DT+R GA +QLK A +P
Sbjct: 225 ARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPL 263
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 55.0 bits (132), Expect = 3e-09
Identities = 42/131 (32%), Positives = 60/131 (45%), Gaps = 21/131 (16%)
Query: 46 IKLVKKL-RENVRQVIDFDEMASGLNKR--------------RMIQSSVYKELIKLVDPG 90
+L ++L RE + Q +EMAS L +R R + +E + VD
Sbjct: 158 QRLGERLVREGMSQSY-VEEMASKLEERLSPVDQGRNHNVTERAVT--YLEERVS-VDSD 213
Query: 91 VKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY-LKKNWKACLVCADTFRAGAYDQLK 149
+ + K + V+ FVG GSGKTT+ KLA Y L L D +R A +QLK
Sbjct: 214 LFSGTG-KNQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQLK 272
Query: 150 QNATKARIPFY 160
+ A +PFY
Sbjct: 273 RYADTMGMPFY 283
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 50.1 bits (119), Expect = 4e-08
Identities = 16/69 (23%), Positives = 20/69 (28%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPF 159
VI+ VG GSGKTT LA + + DQL +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 160 YGSSKGKRN 168
R
Sbjct: 61 GSGELRLRL 69
>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 407
Score = 50.1 bits (119), Expect = 1e-07
Identities = 40/150 (26%), Positives = 66/150 (44%), Gaps = 26/150 (17%)
Query: 25 EEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDF---------------DEMASGL 69
EE L++M E+ A +N +L K+RE Q DF D M +G
Sbjct: 116 EEELSAMRLELAA------LNRELAVKMREEREQNSDFVKFLKGRGISDTYVADFMQAGR 169
Query: 70 NKRRMIQSSVYKELIKLVDPGVKAHQPQKGKPN-----VIMFVGLQGSGKTTTCTKLAYH 124
+ + ++++ ++ P + + + +I +G G GKTTT KL +
Sbjct: 170 KQFKQVETAHLDDITDWFVPYLSGKLAVEDSFDLSNHRIISLIGQTGVGKTTTLVKLGWQ 229
Query: 125 YLKKNWKACLVCADTFRAGAYDQLKQNATK 154
LK+N + DTFR+GA +Q + A K
Sbjct: 230 LLKQNRTVGFITTDTFRSGAVEQFQGYADK 259
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 43.1 bits (101), Expect = 4e-05
Identities = 21/48 (43%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNW--KACLVCADTFRAGAYDQL 148
VI VG G+GKTTT KLA + ++ LV DT R G +QL
Sbjct: 352 VIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQL 399
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 40.5 bits (95), Expect = 5e-05
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
VI+ G G GKTT LA K+ + L+
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 42.5 bits (100), Expect = 6e-05
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 2/49 (4%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNW--KACLVCADTFRAGAYDQLK 149
V+ VG G GKTTT KLA + + + L+ D+FR GA +QL+
Sbjct: 187 VLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLR 235
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 40.0 bits (94), Expect = 2e-04
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYD 146
+I+ VGL GSGK+T +L + A ++ +DT R
Sbjct: 1 LILMVGLPGSGKSTFARRLL-----RELGAVVLSSDTLRKRLRG 39
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 37.0 bits (86), Expect = 0.001
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
+++ VG + SGKTT KL + ++ ++ +V
Sbjct: 2 IVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVV 34
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 35.3 bits (81), Expect = 0.004
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHY 125
+I+ G GSGK+T KLA
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKL 23
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 35.4 bits (82), Expect = 0.006
Identities = 10/36 (27%), Positives = 16/36 (44%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
++ VG + SGKTT KL + ++ V
Sbjct: 1 MMKILGIVGYKNSGKTTLIEKLVRKLKARGYRVATV 36
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 35.7 bits (82), Expect = 0.010
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNW--KACLVCADTFRAGAYDQLK 149
+ V +G G GKTTT KLA + ++ K L+ D++R G ++QL+
Sbjct: 190 QGGVYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLR 241
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 35.6 bits (82), Expect = 0.011
Identities = 33/132 (25%), Positives = 56/132 (42%), Gaps = 16/132 (12%)
Query: 25 EEVLNSMLKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVY---K 81
EE+ + + +I L E D + +K + E +++ + L+ ++ SV
Sbjct: 104 EEINHPTILKIEDILRENDFSESYIKDINEFIKKEFSLSD----LDDYDKVRDSVIIYIA 159
Query: 82 ELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY----LKKNWKACLVCA 137
+ IK + K V + VG G GKTTT KLA Y K+ ++
Sbjct: 160 KTIKCSGSII-----DNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITI 214
Query: 138 DTFRAGAYDQLK 149
D +R GA Q++
Sbjct: 215 DNYRIGAKKQIQ 226
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 34.6 bits (80), Expect = 0.026
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 107 VGLQGSGKTTTCTKLAYHYLKKNW--KACLVCADTFRAGAYDQLK 149
+G G GKTTT KLA + ++ K L+ D++R G ++QL+
Sbjct: 262 MGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLR 306
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 33.6 bits (78), Expect = 0.026
Identities = 15/40 (37%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCA-DTFR 141
+I G GSGKTT LA K V A + FR
Sbjct: 2 IITISGPPGSGKTTVARLLAEKL---GLK--HVSAGEIFR 36
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the form
of molybdenum cofactor (Moco) which is associated with
the metabolism of nitrogen, carbon and sulfur by redox
active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe and
mog. The mob locus contains mobA and mobB genes. MobB
catalyzes the attachment of the guanine dinucleotide to
molybdopterin.
Length = 159
Score = 33.8 bits (78), Expect = 0.026
Identities = 14/27 (51%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLK 127
VI FVG GSGKTT KL L
Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLI-PALS 26
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 34.3 bits (79), Expect = 0.028
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 4/66 (6%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSS 163
++ VG GSGK+T LA L + ++ D G Y L + I S
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARG--GRVIVID--PKGEYSGLARALGGEVIDLGPGS 59
Query: 164 KGKRNP 169
NP
Sbjct: 60 GISLNP 65
>gnl|CDD|223506 COG0429, COG0429, Predicted hydrolase of the alpha/beta-hydrolase
fold [General function prediction only].
Length = 345
Score = 33.9 bits (78), Expect = 0.037
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 5/70 (7%)
Query: 71 KRRMIQSSVYKELIKLVDPGVK-----AHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
RR + + +E ++ D G KP V++F GL+GS + L
Sbjct: 41 FRRKPKVAYTRERLETPDGGFIDLDWSEDPRAAKKPLVVLFHGLEGSSNSPYARGLMRAL 100
Query: 126 LKKNWKACLV 135
++ W +
Sbjct: 101 SRRGWLVVVF 110
>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). This protein,
adenylylsulfate kinase, is often found as a fusion
protein with sulfate adenylyltransferase. Important
residue (active site in E.coli) is residue 100 of the
seed alignment [Central intermediary metabolism, Sulfur
metabolism].
Length = 184
Score = 33.2 bits (76), Expect = 0.046
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 92 KAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQL 148
+A +G VI GL GSGK+T L K ++ ++ D R G L
Sbjct: 11 QALNGHRG--VVIWLTGLSGSGKSTIANALEKKLESKGYRVYVLDGDNVRHGLNKDL 65
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 32.6 bits (74), Expect = 0.060
Identities = 11/51 (21%), Positives = 20/51 (39%)
Query: 95 QPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAY 145
+ + G P ++ G G+GKT+ +L L K + A +
Sbjct: 18 RARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQ 68
>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 374
Score = 33.2 bits (75), Expect = 0.066
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKK--NWKACLVCADTFRAGAYDQLKQNATKARIPFY 160
V +G G GKTTT KLA + + K L+ D++R G ++QL+ +P +
Sbjct: 139 VFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVH 198
Query: 161 GSSKG 165
G
Sbjct: 199 AVKDG 203
>gnl|CDD|226691 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 32.9 bits (75), Expect = 0.075
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 84 IKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKN 129
+ L+ Q +G+P ++ G QGSGK+T + K
Sbjct: 34 LPLLAKIAPWAQE-RGRPLIVGISGPQGSGKSTLSALIVRLLAAKG 78
>gnl|CDD|238997 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a
conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase activity
by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its DNA
binding sites. Increasing the fraction of ParA-ADP in
the cell inhibits cell division, suggesting that this
simple nucleotide switch may regulate cytokinesis. ParA
shares sequence similarity to a conserved and widespread
family of ATPases which includes the repA protein of the
repABC operon in R. etli Sym plasmid. This operon is
involved in the plasmid replication and partition.
Length = 104
Score = 31.4 bits (72), Expect = 0.082
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 111 GSGKTTTCTKLAYHYLKKNWKACLVCAD 138
G GKTTT LA ++ + L+ D
Sbjct: 10 GVGKTTTAVNLAAALARRGKRVLLIDLD 37
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 31.7 bits (72), Expect = 0.13
Identities = 14/84 (16%), Positives = 25/84 (29%), Gaps = 9/84 (10%)
Query: 76 QSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
Q + L + + + P ++ G G+GKTT +A + +
Sbjct: 3 QEEAIEALREAL---------ELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYL 53
Query: 136 CADTFRAGAYDQLKQNATKARIPF 159
A G R+ F
Sbjct: 54 NASDLLEGLVVAELFGHFLVRLLF 77
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 31.3 bits (71), Expect = 0.13
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 104 IMFVGLQGSGKTTTCTKLA 122
I+ G GSGKTT +LA
Sbjct: 1 ILITGTPGSGKTTLAKELA 19
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 31.7 bits (72), Expect = 0.14
Identities = 16/63 (25%), Positives = 22/63 (34%)
Query: 111 GSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKARIPFYGSSKGKRNPI 170
G+GKTT T LA K LV D + + + IP K R +
Sbjct: 11 GAGKTTVATNLASWLHADGHKVLLVDLDPQGSSTDWAEAREEGEPLIPVVRMGKSIRADL 70
Query: 171 HNM 173
+
Sbjct: 71 PKV 73
>gnl|CDD|183360 PRK11889, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 436
Score = 32.0 bits (72), Expect = 0.17
Identities = 16/48 (33%), Positives = 22/48 (45%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQN 151
I +G G GKTTT K+A+ + K + D R G QL+
Sbjct: 244 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDY 291
>gnl|CDD|75717 PRK06731, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 270
Score = 31.6 bits (71), Expect = 0.19
Identities = 16/46 (34%), Positives = 22/46 (47%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLK 149
I +G G GKTTT K+A+ + K + D R G QL+
Sbjct: 78 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQ 123
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 30.7 bits (70), Expect = 0.29
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHY 125
I+ +G GSGK T +LA Y
Sbjct: 1 RILLLGPPGSGKGTQAERLAKKY 23
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 30.7 bits (70), Expect = 0.32
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
K I+ G+ G+GKTT L ++ K L
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLT 37
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 30.4 bits (69), Expect = 0.33
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHY 125
V++ G QGSGK+T KL +
Sbjct: 54 VLILQGAQGSGKSTFLKKLGGEW 76
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.9 bits (65), Expect = 0.35
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 111 GSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAY 145
G+GKT T + L ++ LV A T RA
Sbjct: 20 GTGKTATAAAIIARLLAAG-RSVLVVAPTGRAARR 53
>gnl|CDD|176685 cd07264, Glo_EDI_BRP_like_15, This conserved domain belongs to a
superfamily including the bleomycin resistance protein,
glyoxalase I, and type I ring-cleaving dioxygenases.
This protein family belongs to a conserved domain
superfamily that is found in a variety of structurally
related metalloproteins, including the bleomycin
resistance protein, glyoxalase I, and type I
ring-cleaving dioxygenases. A bound metal ion is
required for protein activities for the members of this
superfamily. A variety of metal ions have been found in
the catalytic centers of these proteins including
Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein
superfamily contains members with or without domain
swapping.
Length = 125
Score = 29.9 bits (68), Expect = 0.40
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 54 ENVRQVIDFDEMASGLNKRRMIQSSVYKEL 83
E+V + ++F E A G +R + +S Y EL
Sbjct: 9 EDVEKTLEFYERAFGFERRFLHESGDYGEL 38
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 30.3 bits (69), Expect = 0.43
Identities = 13/36 (36%), Positives = 15/36 (41%), Gaps = 1/36 (2%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
K VI F GL GSGK+T L L +
Sbjct: 22 KGAVIWFTGLSGSGKSTIANAL-EEKLFAKGYHVYL 56
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 29.7 bits (67), Expect = 0.47
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLK 127
IMF+G G GKTT L +
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEIL 26
>gnl|CDD|179661 PRK03846, PRK03846, adenylylsulfate kinase; Provisional.
Length = 198
Score = 30.3 bits (69), Expect = 0.49
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 95 QPQKG-KPNVIMFVGLQGSGKTT 116
+ G K V+ F GL GSGK+T
Sbjct: 17 EQLHGHKGVVLWFTGLSGSGKST 39
>gnl|CDD|178512 PLN02924, PLN02924, thymidylate kinase.
Length = 220
Score = 30.1 bits (68), Expect = 0.50
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 96 PQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACL 134
+ + +I+ GL SGK+T C KL A L
Sbjct: 11 SVESRGALIVLEGLDRSGKSTQCAKLVSFLKGLGVAAEL 49
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 30.4 bits (69), Expect = 0.51
Identities = 17/41 (41%), Positives = 22/41 (53%)
Query: 98 KGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
GK V+M VG SGK+T T LA L + K ++ AD
Sbjct: 70 AGKVGVVMVVGPVDSGKSTLTTYLANKLLARGRKVAIIDAD 110
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.0 bits (68), Expect = 0.53
Identities = 20/41 (48%), Positives = 21/41 (51%), Gaps = 8/41 (19%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHY-LKKNWKACLVCA-DTFR 141
VI GL GSGKTT +LA H LK LV A FR
Sbjct: 2 VITISGLPGSGKTTVARELAEHLGLK------LVSAGTIFR 36
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 30.4 bits (69), Expect = 0.65
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 96 PQKGKPNVIMFVGLQGSGKTTTCTKL 121
P KP +I+ GL G+GKTT +
Sbjct: 24 PSSPKP-IILIGGLNGAGKTTLLDAI 48
>gnl|CDD|237731 PRK14494, PRK14494, putative molybdopterin-guanine dinucleotide
biosynthesis protein MobB/FeS domain-containing protein
protein; Provisional.
Length = 229
Score = 29.9 bits (68), Expect = 0.68
Identities = 8/33 (24%), Positives = 16/33 (48%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
I +G + SGKTT K+ + ++ ++
Sbjct: 3 AIGVIGFKDSGKTTLIEKILKNLKERGYRVATA 35
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 29.6 bits (67), Expect = 0.69
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 97 QKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTF 140
+ K +I G GSGKTT +L+ K ++ D +
Sbjct: 4 KPEKVIIIGIAGGSGSGKTTVAKELSEQL--GVEKVVVISLDDY 45
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK) catalyzes
the phosphorylation of adenosine 5'-phosphosulfate to
form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The
end-product PAPS is a biologically "activated" sulfate
form important for the assimilation of inorganic
sulfate.
Length = 149
Score = 29.4 bits (67), Expect = 0.70
Identities = 15/42 (35%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCA-DTFRAG 143
VI GL GSGK+T L L + + V D R G
Sbjct: 1 VIWLTGLSGSGKSTIARAL-EEKLFQRGRPVYVLDGDNVRHG 41
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 29.1 bits (66), Expect = 0.70
Identities = 11/27 (40%), Positives = 12/27 (44%), Gaps = 3/27 (11%)
Query: 104 IMFVGLQGSGKTTTCTKL---AYHYLK 127
IM +G G GKTT L Y K
Sbjct: 4 IMLIGRSGCGKTTLTQALNGEELKYKK 30
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It has
been suggested that torsins play a role in effectively
managing protein folding and that possible breakdown in
a neuroprotective mechanism that is, in part, mediated
by torsins may be responsible for the neuronal
dysfunction associated with dystonia.
Length = 127
Score = 29.2 bits (66), Expect = 0.71
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 84 IKLVDPGVKAH--QPQKGKPNVIMFVGLQGSGK 114
+LV VK H P+ KP V+ F G G+GK
Sbjct: 34 KQLVVRSVKGHWENPKPRKPLVLSFHGWTGTGK 66
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 29.9 bits (68), Expect = 0.83
Identities = 14/24 (58%), Positives = 14/24 (58%), Gaps = 3/24 (12%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYL 126
V F G GSGKTTT LA YL
Sbjct: 109 VTNFKG--GSGKTTTAAHLA-QYL 129
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 29.9 bits (67), Expect = 0.97
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 88 DPGVKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
G + QKGK V++ +G GSGK+ LA H+
Sbjct: 9 GAGEEGSPKQKGKAKVVVVMGPTGSGKSKLAVDLASHF 46
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.3 bits (64), Expect = 1.0
Identities = 11/36 (30%), Positives = 12/36 (33%), Gaps = 1/36 (2%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADT 139
+ V GSGKT T L K K L
Sbjct: 21 GLIVMATGSGKTLTAAALIARLAKGK-KKVLFVVPR 55
>gnl|CDD|129606 TIGR00515, accD, acetyl-CoA carboxylase, carboxyl transferase, beta
subunit. The enzyme acetyl-CoA carboxylase contains a
biotin carboxyl carrier protein or domain, a biotin
carboxylase, and a carboxyl transferase. This model
represents the beta chain of the carboxyl transferase
for cases in which the architecture of the protein is as
in E. coli, in which the carboxyltransferase portion
consists of two non-identical subnits, alpha and beta
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 285
Score = 29.4 bits (66), Expect = 1.0
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 114 KTTTCTKLAYHY-LKKNWKACLVCADTFRAGAYDQLKQ 150
K C ++ Y L++N + C C R A ++++
Sbjct: 28 KCPKCGQVLYTKELERNLEVCPKCDHHMRMDARERIES 65
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 29.4 bits (66), Expect = 1.1
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFR 141
+I+ GL G GK+T +LA +KN ++ D R
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIR 39
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 29.5 bits (67), Expect = 1.1
Identities = 13/25 (52%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 93 AHQPQKG-KPNVIMFVGLQGSGKTT 116
A +KG KP + F GL GSGK+T
Sbjct: 451 ARAARKGQKPATVWFTGLSGSGKST 475
>gnl|CDD|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 447
Score = 29.4 bits (67), Expect = 1.3
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 106 FVGLQGS-GKTTTCTKLAYHYLKKNWKACLVC 136
+G+ GS GKTTT T L LK + L+
Sbjct: 110 IIGITGSNGKTTT-TTLIGEMLKAGGQHALLA 140
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de novo
or salvage biosynthesis of thymidine triphosphate (TTP).
Length = 200
Score = 28.8 bits (65), Expect = 1.3
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKN 129
I+F G+ G+GKTT LA L+
Sbjct: 3 IVFEGIDGAGKTTLIELLA-ERLEAR 27
>gnl|CDD|238682 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 767
Score = 29.4 bits (66), Expect = 1.4
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 104 IMFVGLQGSGKTTTCTKLAYH 124
I+F+G G+GKTT+C +
Sbjct: 89 IIFLGRSGAGKTTSCKHALEY 109
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 1.4
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHY 125
I+ +G G GKTT +L
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDE 29
>gnl|CDD|130724 TIGR01663, PNK-3'Pase, polynucleotide 5'-kinase 3'-phosphatase.
This model represents the metazoan
5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is
believed to be involved in repair of oxidative DNA
damage. Removal of 3' phosphates is essential for the
further processing of the break by DNA polymerases. The
central phosphatase domain is a member of the IIIA
subfamily (TIGR01662) of the haloacid dehalogenase (HAD)
superfamily of aspartate-nucleophile hydrolases. As is
common in this superfamily, the enzyme is magnesium
dependent. A difference between this enzyme and other
HAD-superfamily phosphatases is in the third conserved
catalytic motif which usually contains two conserved
aspartate residues believed to be involved in binding
the magnesium ion. Here, the second aspartate is
replaced by a conserved arginine residue which may
indicate an interaction with the phosphate backbone of
the substrate. Very close relatives of this domain are
also found separate from the N- and C-terminal domains
seen here, as in the 3'-phosphatase found in plants. The
larger family of these domains is described by
TIGR01664. Outside of the phosphatase domain is a P-loop
ATP-binding motif associated with the kinase activity.
The entry for the mouse homolog, GP|7108591, appears to
be missing a large piece of sequence corresponding to
the first conserved catalytic motif of the phosphatase
domain as well as the conserved threonine of the second
motif. Either this is a sequencing artifact or this may
represent a pseudo- or non-functional gene. Note that
the EC number for the kinase function is: 2.7.1.78.
Length = 526
Score = 29.2 bits (65), Expect = 1.5
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 8/48 (16%)
Query: 101 PNVIMFVGLQGSGKTTTCTKL----AYHYLKKN----WKACLVCADTF 140
+++ VG G+GK+ C K Y ++ + + CL +
Sbjct: 369 CEMVIAVGFPGAGKSHFCKKFFQPAGYKHVNADTLGSTQNCLTACERA 416
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.2 bits (64), Expect = 1.6
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 98 KGKPNVIMFVGLQGSGKTTTCTKLA 122
PN++ +G G+GK+T LA
Sbjct: 2 LKGPNIV-LIGFMGAGKSTIGRLLA 25
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 28.1 bits (63), Expect = 1.6
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWK 131
V+ VG + SGKTT +L + ++
Sbjct: 1 VLQIVGPKNSGKTTLIERLVKALKARGYR 29
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 28.4 bits (64), Expect = 1.7
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLK 127
+ + G G+GK+T LA
Sbjct: 35 LTLLAGAPGTGKSTLALDLAAAVAT 59
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 28.3 bits (64), Expect = 1.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 104 IMFVGLQGSGKTTTCTKLA 122
I+ +GL G+GKTT KL
Sbjct: 2 ILMLGLDGAGKTTILYKLK 20
>gnl|CDD|178608 PLN03046, PLN03046, D-glycerate 3-kinase; Provisional.
Length = 460
Score = 28.7 bits (64), Expect = 1.7
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 3/66 (4%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLK---QNATKARI 157
P VI F QG GKTT L Y + K+ + D F A Q + +N A +
Sbjct: 212 PLVIGFSAPQGCGKTTLVFALDYLFRVTGRKSATLSIDDFYLTAEGQAELRERNPGNALL 271
Query: 158 PFYGSS 163
G++
Sbjct: 272 ELRGNA 277
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 28.2 bits (64), Expect = 1.8
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 108 GLQGSGKTTTCTKLAYHY 125
G GSGK+T LA
Sbjct: 6 GPAGSGKSTVAKLLAKKL 23
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 27.6 bits (62), Expect = 1.9
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 2/38 (5%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
+ + G GSGKTT +LA N + V A
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLARQL--PNRRVVYVEAP 39
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 27.6 bits (62), Expect = 2.1
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
I G G GKTT LA + +K + AD
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDAD 36
>gnl|CDD|234135 TIGR03172, TIGR03172, probable selenium-dependent hydroxylase
accessory protein YqeC. This uncharacterized protein
family includes YqeC from Escherichia coli. A
phylogenetic profiling analysis shows correlation with
SelD, the selenium donor protein, even in species where
SelD contributes to neither selenocysteine nor
selenouridine biosynthesis. Instead, this family, and
families TIGR03309 and TIGR03310 appear to mark
selenium-dependent molybdenum hydroxylase maturation
systems [Unknown function, General].
Length = 210
Score = 28.0 bits (63), Expect = 2.2
Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADT 139
+I VG GKTT LA K+ LV T
Sbjct: 1 IISIVG--AGGKTTLMFALARELRKEGKP-VLVTTTT 34
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 28.0 bits (63), Expect = 2.3
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 103 VIMFVGLQGSGKTTTCTKLA 122
V+M G+ GSGK+T LA
Sbjct: 3 VVM--GVSGSGKSTVGKALA 20
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 28.2 bits (63), Expect = 2.3
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 102 NVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNA 152
+V++ G G+GKT + Y ++ V + + L +NA
Sbjct: 24 SVVLITGPPGTGKTIFALQFLYEGAREGEPVLYV---STEESPEE-LLENA 70
>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
Length = 175
Score = 27.7 bits (62), Expect = 2.6
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 103 VIMFVGLQGSGKTTTCTKLA 122
+ F GL G+GKTT LA
Sbjct: 6 TVWFTGLSGAGKTTIARALA 25
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 28.3 bits (64), Expect = 2.6
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 104 IMFVGLQGSGKTTTCTKL 121
I+ VG G+GKT +L
Sbjct: 18 ILIVGTTGTGKTQALREL 35
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 28.4 bits (64), Expect = 2.6
Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 10/78 (12%)
Query: 49 VKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKEL---IKLVDPGVKAHQPQKGKPN-VI 104
V KL E+ ++ + + L KR + Q + + I+ G+ +P
Sbjct: 471 VAKLLEDEKEKLLN--LERRLKKRVIGQDEAVEAVSDAIRRARAGLGD----PNRPIGSF 524
Query: 105 MFVGLQGSGKTTTCTKLA 122
+F+G G GKT LA
Sbjct: 525 LFLGPTGVGKTELAKALA 542
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 28.1 bits (63), Expect = 2.9
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFR 141
+I+ VG+ GSGK+T A + KN KA V D R
Sbjct: 1 MMKIILTVGVPGSGKST----WAREFAAKNPKAVNVNRDDLR 38
>gnl|CDD|216631 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyze amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well as
the plasmid partitioning proteins of the MinD/ParA
family.
Length = 217
Score = 27.8 bits (62), Expect = 2.9
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 111 GSGKTTTCTKLAYHYLKKNWKACLVCADT 139
G GKTT LA K+ ++ L+ D
Sbjct: 9 GVGKTTLAANLARALAKRGYRVLLIDLDP 37
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 27.9 bits (62), Expect = 3.1
Identities = 20/89 (22%), Positives = 28/89 (31%), Gaps = 7/89 (7%)
Query: 100 KPNVIMFVGLQG-SGKTTTCTKLAYHY-LKKNWKACLVCAD-----TFRAGAYDQLKQNA 152
+I +G GKTTT LA + K L+ D T G L+ +
Sbjct: 1 MMKIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRPDLEGDL 60
Query: 153 TKARIPFYGSSKGKRNPIHNMGLSLIPTY 181
+ GL LIP+
Sbjct: 61 YNLLSGLKERPDILDYTVVIEGLDLIPSN 89
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 27.2 bits (61), Expect = 3.4
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 100 KPNVIMFVGLQGSGKTT 116
+ I F GL GSGK+T
Sbjct: 1 RGCTIWFTGLSGSGKST 17
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 27.5 bits (62), Expect = 3.7
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKL 121
V++ G+ G GKTT K
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKA 22
>gnl|CDD|184430 PRK13975, PRK13975, thymidylate kinase; Provisional.
Length = 196
Score = 27.4 bits (61), Expect = 3.7
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNW 130
I+F G+ GSGKTT LA L W
Sbjct: 5 IVFEGIDGSGKTTQAKLLA-EKLNAFW 30
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 27.2 bits (61), Expect = 3.9
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 104 IMFVGLQGSGKTTTCTKLA 122
++ VGL G+GK+T +LA
Sbjct: 13 VVLVGLMGAGKSTVGRRLA 31
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 26.9 bits (60), Expect = 3.9
Identities = 9/30 (30%), Positives = 10/30 (33%), Gaps = 1/30 (3%)
Query: 111 GSGKTTTCTK-LAYHYLKKNWKACLVCADT 139
GSGKT + LV A T
Sbjct: 10 GSGKTLAALLPILELLDSLKGGQVLVLAPT 39
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.2 bits (61), Expect = 4.0
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 104 IMFVGLQGSGKTTTCTKLA 122
I+ +G G+GK+T KLA
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 27.8 bits (62), Expect = 4.0
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAYHYLKKNWK 131
PN+I G G+GKTT+ LA+ L N+K
Sbjct: 35 PNLI-LSGPPGTGKTTSILALAHELLGPNYK 64
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 27.5 bits (62), Expect = 4.0
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 105 MFV---GLQGSGKTTTCTKLAYHYLKKN 129
MF+ G+ G+GK+T L ++
Sbjct: 4 MFITIEGIDGAGKSTQIELLKELLEQQG 31
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 28.0 bits (63), Expect = 4.1
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 99 GKPN-VIMFVGLQGSGKTTTCTKLA 122
KP V + VG G GKT T LA
Sbjct: 593 RKPLGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|237728 PRK14490, PRK14490, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MobA;
Provisional.
Length = 369
Score = 27.7 bits (62), Expect = 4.3
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 101 PNVIMFVGLQGSGKTTTCTKL 121
P I F G GSGKTT T L
Sbjct: 5 PFEIAFCGYSGSGKTTLITAL 25
>gnl|CDD|217946 pfam04183, IucA_IucC, IucA / IucC family. IucA and IucC catalyze
discrete steps in biosynthesis of the siderophore
aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine
and citrate. This family represents the N-terminal
region. The C-terminal region appears to be related to
iron transporter proteins.
Length = 241
Score = 27.2 bits (61), Expect = 4.4
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 9 KITSALRSLSNATVINEEVLNSMLKEICAA 38
+ T+++R+LS + L+ L+ + A
Sbjct: 152 RNTNSVRTLSPKELARGPALSRWLQSLLAQ 181
>gnl|CDD|224719 COG1806, COG1806, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 273
Score = 27.6 bits (62), Expect = 4.4
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLK 127
++ VG+ + KT T LA +K
Sbjct: 147 VILVGVSRTSKTPTSLYLALQGIK 170
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 27.7 bits (61), Expect = 4.5
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 72 RRMIQSSVYKELIKLVDPGVKAHQPQKGKPNVIMFVGLQGSGKTTT----CTKLAYHY 125
RR + +++K+ I VD +KA + K +++ G G GK+TT +L
Sbjct: 16 RRRDELAIHKKKIAEVDHWLKAVFLESNKQLILLLTGPSGCGKSTTVKVLSKELGIEI 73
>gnl|CDD|232811 TIGR00073, hypB, hydrogenase accessory protein HypB. A GTP
hydrolase for assembly of nickel metallocenter of
hydrogenase. A similar protein, ureG, is an accessory
protein for urease, which also uses nickel. hits scoring
75 and above are safe as orthologs. [SS 1/05/04 I
changed the role_ID and process GO from protein folding
to to protein modification, since a protein folding role
has not been established, but HypB is implicated in
insertion of nickel into the large subunit of NiFe
hydrogenases.] [Protein fate, Protein modification and
repair].
Length = 208
Score = 27.4 bits (61), Expect = 4.6
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLKQNATKA 155
V+ F+ GSGKTT KL LK K ++ D ++L++ A
Sbjct: 24 VLNFMSSPGSGKTTLIEKLI-DNLKDEVKIAVIEGDVITKFDAERLRKYGAPA 75
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 27.3 bits (61), Expect = 4.7
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 101 PNVIMFVGLQGSGKTTTCTKLAY 123
P V+ +G SGKT TKL
Sbjct: 1 PTVL-LLGPSDSGKTALFTKLTT 22
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 26.8 bits (60), Expect = 4.9
Identities = 8/30 (26%), Positives = 13/30 (43%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKN 129
+I+ G + GKTT + L +N
Sbjct: 1 NNKIIVITGPRQVGKTTLLLQFLKELLSEN 30
>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands.
Length = 271
Score = 27.4 bits (61), Expect = 5.2
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYH 124
+I+ G GKTT + A
Sbjct: 32 LIILTAGTGVGKTTFLREYALD 53
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 27.0 bits (61), Expect = 5.3
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 18/48 (37%)
Query: 111 GSGKTTTCTKLA----YHYLKKNWKACLVCADT---FRAGAYDQLKQN 151
GSGK T LA +HYL DT +RA A L+
Sbjct: 14 GSGKGTVAKILAKKLGFHYL-----------DTGAMYRAVALAALRHG 50
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 27.0 bits (60), Expect = 5.4
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 93 AHQPQKGKPNVIM-FVGLQGSGKTTTCTKLAYHYLKKNWKACLVCAD 138
A +KG NVI G G GK+T LA + + L+ AD
Sbjct: 49 AKVLRKGVKNVIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDAD 95
>gnl|CDD|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 27.4 bits (62), Expect = 5.5
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 20/60 (33%)
Query: 89 PGVKAH-QPQKGKP-NV------IMF----------VGLQGS-GKTTTCTKLAYHYLKKN 129
PG++ H P +GKP NV ++F V + G+ GKTTT T+L H LK +
Sbjct: 447 PGLRMHLAPSEGKPRNVGEAIVDMLFPEGDDGRIPIVAVTGTNGKTTT-TRLIAHILKLS 505
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 27.3 bits (61), Expect = 6.0
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 91 VKAHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHY 125
++A P+ G +VI G+ G+GK+T L
Sbjct: 41 LRALYPRTGNAHVIGITGVPGAGKSTLIEALGREL 75
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 27.0 bits (60), Expect = 6.5
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 96 PQKGKPNVIMFVGLQGSGKTTTCTKL 121
G P ++ VG G+GKTT KL
Sbjct: 200 TTTGAPPLLGVVGYSGTGKTTLLEKL 225
>gnl|CDD|238992 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence.
Length = 217
Score = 26.8 bits (60), Expect = 6.5
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 103 VIMFVGLQGSGKTTTCTKLAY 123
VI F G G GKTT A
Sbjct: 1 VIFFTGKGGVGKTTIAAATAV 21
>gnl|CDD|233266 TIGR01087, murD, UDP-N-acetylmuramoylalanine--D-glutamate ligase.
[Cell envelope, Biosynthesis and degradation of murein
sacculus and peptidoglycan].
Length = 433
Score = 26.9 bits (60), Expect = 6.8
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 106 FVGLQGS-GKTTTCTKLAYHYLKKN 129
V + G+ GKTTT T L YH LK
Sbjct: 104 VVAITGTNGKTTT-TSLLYHLLKAA 127
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 26.5 bits (59), Expect = 7.2
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 99 GKPNVIMFVGLQGSGKTTTCTKLAYHYLK 127
K I+F+GL +GKTT H LK
Sbjct: 17 KKEAKIVFLGLDNAGKTTL-----LHMLK 40
>gnl|CDD|225891 COG3355, COG3355, Predicted transcriptional regulator
[Transcription].
Length = 126
Score = 26.1 bits (58), Expect = 7.3
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 8/52 (15%)
Query: 40 LEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLVDPGV 91
L+ +V L+++ + DE+A LN+ R S+VY+ L L++ G+
Sbjct: 28 LDVEVYKALLEENGP-----LTVDELAEILNRSR---STVYRSLQNLLEAGL 71
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is a
important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 26.4 bits (59), Expect = 7.5
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 104 IMFVGLQGSGKTTTCTKLA 122
I+ +G+ G+GKTT LA
Sbjct: 2 IVLIGMMGAGKTTVGRLLA 20
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo and
salvage pathways of DTTP synthesis. Catalytic activity:
ATP + thymidine 5'-phosphate = ADP + thymidine
5'-diphosphate [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 26.6 bits (59), Expect = 7.5
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKA 132
I+ G+ G+GKTT L + +
Sbjct: 6 IVIEGIDGAGKTTQANLLKKLLQENGYDV 34
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase is
also found in Gram-positive bacteria, archaea, and the
roundworm C. elegans. It may have a more general, but
still unknown function. Mutations have also been found
that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase activity
of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein interactions].
Length = 300
Score = 26.7 bits (59), Expect = 7.6
Identities = 15/72 (20%), Positives = 28/72 (38%), Gaps = 10/72 (13%)
Query: 83 LIKLVD-PGVKAHQ------PQKGKPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
I LV+ +A + P G + + G G+GK+T L ++ + ++
Sbjct: 9 AITLVENRHPEAKELLDRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRRGLRVAVI 68
Query: 136 CAD---TFRAGA 144
D F G+
Sbjct: 69 AVDPSSPFTGGS 80
>gnl|CDD|227254 COG4917, EutP, Ethanolamine utilization protein [Amino acid
transport and metabolism].
Length = 148
Score = 26.4 bits (58), Expect = 7.7
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLK 127
I FVG G GKTT L +
Sbjct: 4 IAFVGQVGCGKTTLFQSLYGNDTL 27
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 26.9 bits (60), Expect = 7.7
Identities = 10/38 (26%), Positives = 20/38 (52%)
Query: 104 IMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFR 141
I+ GL SGK+T +LA + +K + ++ ++
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDESLG 39
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 26.8 bits (60), Expect = 7.8
Identities = 12/33 (36%), Positives = 12/33 (36%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLV 135
I G G GKTT L L K LV
Sbjct: 2 KIAITGKGGVGKTTIAALLLKRLLSKGGYNVLV 34
>gnl|CDD|238279 cd00501, Peptidase_C15, Pyroglutamyl peptidase (PGP) type I, also
known as pyrrolidone carboxyl peptidase (pcp) type I:
Enzymes responsible for cleaving pyroglutamate (pGlu)
from the N-terminal end of specialized proteins. The
N-terminal pGlu protects these proteins from proteolysis
by other proteases until the pGlu is removed by a PGP.
PGPs are cysteine proteases with a Cys-His-Glu/Asp
catalytic triad. Type I PGPs are found in a wide variety
of prokaryotes and eukaryotes. It is not clear whether
the functional form is a monomer, a homodimer, or a
homotetramer.
Length = 194
Score = 26.5 bits (59), Expect = 7.9
Identities = 14/63 (22%), Positives = 26/63 (41%), Gaps = 3/63 (4%)
Query: 64 EMASGLNKRRMIQSSVYKELIKLVDPGVKA---HQPQKGKPNVIMFVGLQGSGKTTTCTK 120
E L K + + V + +V ++ KP++++ VGL G T T +
Sbjct: 21 EAVKELPKLILGGAEVVGLELPVVFQKAVEVLPELIEEHKPDLVIHVGLAGGRSTITIER 80
Query: 121 LAY 123
+A
Sbjct: 81 VAI 83
>gnl|CDD|161774 TIGR00224, pckA, phosphoenolpyruvate carboxykinase (ATP). Involved
in the gluconeogenesis pathway. It converts oxaloacetic
acid to phosphoenolpyruvate using ATP. Enzyme is a
monomer. The reaction is also catalysed by
phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32)
using GTP instead of ATP, described in PROSITE:PDOC00421
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 532
Score = 26.8 bits (59), Expect = 7.9
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 93 AHQPQKGKPNVIMFVGLQGSGKTTTCT 119
A+ +KG +V +F GL G+GKTT T
Sbjct: 227 ANVGEKG--DVALFFGLSGTGKTTLST 251
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 26.4 bits (59), Expect = 8.0
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 93 AHQPQKGKPNVIMFVGLQGSGKTTTCTKL 121
A K I+ +GL +GKTT KL
Sbjct: 6 AKLFGWNKEMRILILGLDNAGKTTILYKL 34
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 261
Score = 26.7 bits (59), Expect = 8.1
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFR 141
+I+ G GSGKTT +LA ++ W+ + D R
Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLR 41
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 26.2 bits (58), Expect = 8.2
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 102 NVIMFVGLQGSGKTTTCTKL 121
++ GL SGKT+ T L
Sbjct: 4 PAVIIAGLCDSGKTSLFTLL 23
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 26.6 bits (59), Expect = 8.2
Identities = 11/34 (32%), Positives = 13/34 (38%)
Query: 106 FVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADT 139
VG GSGKTT L+ +V D
Sbjct: 1 VVGPAGSGKTTFVGALSEILPLLGRSVYVVNLDP 34
>gnl|CDD|215427 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 26.6 bits (59), Expect = 8.3
Identities = 27/105 (25%), Positives = 37/105 (35%), Gaps = 25/105 (23%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKLAYHYLKKNWKACLVCADTFRAGAYDQLK---QNATKAR 156
P VI QG GKTT L Y + +A + D F A DQ K N A
Sbjct: 99 PPLVIGISAPQGCGKTTLVFALVYLFNATGRRAASLSIDDFYLTAADQAKLAEANPGNAL 158
Query: 157 IPFYGSSKGKRNPIHNMGLS-----------------LIPTYEKS 184
+ G++ H++ L +P Y+KS
Sbjct: 159 LELRGNAGS-----HDLALGVETLEALRKLNKEGSKMKVPRYDKS 198
>gnl|CDD|224553 COG1638, DctP, TRAP-type C4-dicarboxylate transport system,
periplasmic component [Carbohydrate transport and
metabolism].
Length = 332
Score = 26.8 bits (60), Expect = 8.4
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 17/86 (19%)
Query: 17 LSNATVINEEVLNSMLKEICAALLEA-------------DVNIKLVKKLRENVRQVIDFD 63
L A ++++ +S+ +E LLEA ++ +L++KL+E +V++ D
Sbjct: 236 LPLAVLVSKAFWDSLPEEDQTILLEAAKEAAEEQRKLVEELEDELLEKLKEAGVEVVEPD 295
Query: 64 EMASGLNKRRMIQSSVYKELIKLVDP 89
R + VY E K
Sbjct: 296 AAE---AFREAAK-PVYDEFAKKAGE 317
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 26.3 bits (58), Expect = 8.7
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 97 QKGKPNVIMFVGLQGSGKTTTCTKLA 122
+ K V++F+G G+GK T +LA
Sbjct: 2 TQTKNKVVIFLGPPGAGKGTQAERLA 27
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 26.6 bits (59), Expect = 8.7
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 100 KPNVIMFVGLQGSGKTTTCTKL 121
+I+ GL G GK+TT L
Sbjct: 2 MTKLIIIEGLPGFGKSTTAKML 23
>gnl|CDD|238683 cd01387, MYSc_type_XV, Myosin motor domain, type XV myosins. In
vertebrates, myosin XV appears to be expressed in
sensory tissue and play a role in hearing. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Myosins are
actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 677
Score = 26.8 bits (59), Expect = 9.0
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 93 AHQPQKGKPNVIMFVGLQGSGKTTTCTKLAYHYL 126
A + ++ G GSGKT TKL YL
Sbjct: 79 AKMLDAKQNQCVIISGESGSGKTEA-TKLILRYL 111
>gnl|CDD|201213 pfam00406, ADK, Adenylate kinase.
Length = 186
Score = 26.1 bits (58), Expect = 9.2
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 106 FVGLQGSGKTTTCTKLAYHY 125
+G G+GK T ++ Y
Sbjct: 1 LLGPPGAGKGTQAERIVQKY 20
>gnl|CDD|130427 TIGR01360, aden_kin_iso1, adenylate kinase, isozyme 1 subfamily.
Members of this family are adenylate kinase, EC 2.7.4.3.
This clade is found only in eukaryotes and includes
human adenylate kinase isozyme 1 (myokinase). Within the
adenylate kinase superfamily, this set appears
specifically closely related to a subfamily of
eukaryotic UMP-CMP kinases (TIGR01359), rather than to
the large clade of bacterial, archaeal, and eukaryotic
adenylate kinase family members in TIGR01351.
Length = 188
Score = 26.3 bits (58), Expect = 9.5
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 103 VIMFVGLQGSGKTTTCTKLAYHY 125
+I VG GSGK T C K+ Y
Sbjct: 5 IIFIVGGPGSGKGTQCEKIVEKY 27
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 26.7 bits (59), Expect = 9.8
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 32 LKEICAALLEADVNIKLVKKLRENVRQVIDFDEMASGLNKRRMIQSSVYKELIKLV 87
LKE+ +L E N KL K LR V F G +R +I+ + + LIK++
Sbjct: 274 LKELADSLEENPTNEKLKKALRGGVA----FHHAGLGRTERVLIEDAFREGLIKVI 325
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
0.319 0.133 0.387
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,434,751
Number of extensions: 854007
Number of successful extensions: 1491
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1465
Number of HSP's successfully gapped: 179
Length of query: 190
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 99
Effective length of database: 6,901,388
Effective search space: 683237412
Effective search space used: 683237412
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: 56 (25.2 bits)