RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2881
(302 letters)
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 412 bits (1063), Expect = e-146
Identities = 155/303 (51%), Positives = 220/303 (72%), Gaps = 4/303 (1%)
Query: 2 KINWITRLKESLSKTACN----LKSLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNE 57
K W RLK+ LSKT N + L KKID++L ELE L++ADVG ETT+ ++ E
Sbjct: 13 KEGWFERLKKGLSKTRENFGEGINGLFAKKKIDEDLLEELEELLIEADVGVETTEEIIEE 72
Query: 58 LKKIIYSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIG 117
L++ + K L + E+++ +L L +L+ +EKPL ++ KPFVI++VGVNGVGKTTTIG
Sbjct: 73 LRERVKRKNLKDPEELKELLKEELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKTTTIG 132
Query: 118 KLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIA 177
KLA+ +K + K VLLAA DTFRAAA EQL + G+ VPVI++K+ DPA++AF+AI A
Sbjct: 133 KLAHKYKAQGKKVLLAAGDTFRAAAIEQLQVWGERVGVPVIAQKEGADPASVAFDAIQAA 192
Query: 178 QKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEIFLIIDGNTGQNTLSQI 237
+ + D++I+DT+GRL +++LM ELKKIK+VI+K + P+E+ L++D TGQN LSQ
Sbjct: 193 KARGIDVLIIDTAGRLHNKTNLMEELKKIKRVIKKADPDAPHEVLLVLDATTGQNALSQA 252
Query: 238 KEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGEKIEDLQIFNAVDFVNA 297
K F + + +TG+I+TKLDGT KGG++ AIA + IP+ FIG+GE I+DLQ F+A +FV+A
Sbjct: 253 KAFHEAVGLTGIILTKLDGTAKGGVVFAIADELGIPIKFIGVGEGIDDLQPFDAEEFVDA 312
Query: 298 LLN 300
LL
Sbjct: 313 LLG 315
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 343 bits (882), Expect = e-118
Identities = 153/311 (49%), Positives = 209/311 (67%), Gaps = 12/311 (3%)
Query: 2 KINWITRLKESLSKTACNLKSLIVNK-------KIDKNLYNELESDLLKADVGFETTQFL 54
K W RLK+ LSKT N I K+D++L ELE L++ADVG ET + +
Sbjct: 30 KEGWFERLKQGLSKTKKNFGKGIKGLFLKKIKEKLDEDLLEELEELLIEADVGVETAEEI 89
Query: 55 LNELKK-IIYSKKLFNTEQVRNVLHNLLVNLLKSLEKP----LIFKKCKPFVIMIVGVNG 109
+ EL+K KK+ + E V+ L L+ +L+ ++K I K+ KPFVI+ VGVNG
Sbjct: 90 IEELRKREGKKKKIKDEETVKEALREALIEILRPVDKVDLPLEIPKEKKPFVILFVGVNG 149
Query: 110 VGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAI 169
VGKTTTI KLA Y K++ KSVLLAA DTFRAAA EQL + G+ VPVIS K+ DPAA+
Sbjct: 150 VGKTTTIAKLAKYLKQQGKSVLLAAGDTFRAAAIEQLEVWGERLGVPVISGKEGADPAAV 209
Query: 170 AFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEIFLIIDGNT 229
AF+AI A+ + D+V++DT+GRL + +LM ELKKI +VI+K + P+EI L++D T
Sbjct: 210 AFDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILLVLDATT 269
Query: 230 GQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGEKIEDLQIF 289
GQN LSQ K F++ + + G+I+TKLDGT KGGI+ +IA + IP+ FIG+GE +DL+ F
Sbjct: 270 GQNALSQAKIFNEAVGLDGIILTKLDGTAKGGIILSIAYELGIPIKFIGVGEGYDDLRPF 329
Query: 290 NAVDFVNALLN 300
+A FV+ALL
Sbjct: 330 DAEWFVDALLG 340
>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 = 317 bits (814), Expect = e-109
Identities = 138/272 (50%), Positives = 191/272 (70%)
Query: 28 KIDKNLYNELESDLLKADVGFETTQFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKS 87
K D++ + ELE LL++DVG+E + ++ LKK + KK+ + E ++ +L L +LK
Sbjct: 1 KDDEDFFEELEEILLESDVGYEVVEKIIEALKKELKGKKVKDAELLKEILKEYLKEILKE 60
Query: 88 LEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLL 147
+ LI ++ KP VI+ VGVNGVGKTTTI KLAN KK+ KSVLLAA DTFRAAA EQL
Sbjct: 61 TDLELIVEENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFRAAAIEQLE 120
Query: 148 ILGKYNDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIK 207
K V VI +K+ DPAA+AF+AI A+ +N D+V++DT+GRL + +LM ELKKIK
Sbjct: 121 EWAKRLGVDVIKQKEGADPAAVAFDAIQKAKARNIDVVLIDTAGRLQNKVNLMDELKKIK 180
Query: 208 KVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIA 267
+VI+K + P E+ L++D TGQN L Q K F++ + +TG+I+TKLDGT KGGI+ +IA
Sbjct: 181 RVIKKVDKDAPDEVLLVLDATTGQNALEQAKVFNEAVGLTGIILTKLDGTAKGGIILSIA 240
Query: 268 KKYSIPLYFIGIGEKIEDLQIFNAVDFVNALL 299
+ +P+ FIG+GEKI+DL F+A FV AL
Sbjct: 241 YELKLPIKFIGVGEKIDDLAPFDADWFVEALF 272
>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 = 265 bits (681), Expect = 4e-90
Identities = 105/202 (51%), Positives = 138/202 (68%), Gaps = 6/202 (2%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
P VI++VG+ G GKTTTI KLA Y KK+ K VLL A DTFRAAA EQL L + VPV
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAADTFRAAAIEQLKQLAERLGVPVF 60
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELP 218
+DPAA+AF+A+ A+ +N D+V+VDT+GRL +LM ELKKIK+VI P
Sbjct: 61 GSGTGSDPAAVAFDAVEKAKAENYDVVLVDTAGRLQNDKNLMDELKKIKRVIA------P 114
Query: 219 YEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIG 278
E+ L++D TGQN L+Q K F++ + ITG+I+TKLDG KGG +IA + P+ FIG
Sbjct: 115 DEVLLVLDATTGQNALNQAKAFNEAVGITGVILTKLDGDAKGGAALSIAAETGKPIKFIG 174
Query: 279 IGEKIEDLQIFNAVDFVNALLN 300
+GEKI+DL+ F+ FV+ LL
Sbjct: 175 VGEKIDDLEPFDPERFVSRLLG 196
>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 = 265 bits (680), Expect = 7e-90
Identities = 96/202 (47%), Positives = 133/202 (65%), Gaps = 7/202 (3%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKKR-KKSVLLAACDTFRAAAYEQLLILGKYNDVPV 157
P VI++VG NGVGKTTTI KLA K + K VLL A DTFRAAA EQL + V
Sbjct: 1 PGVILLVGPNGVGKTTTIAKLAARLKLKGGKKVLLVAADTFRAAAVEQLKTYAEILGVVP 60
Query: 158 ISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFEL 217
++ + DP A+A +A+ +A+ + D+V++DT+GRL +LM ELKKIK+VI+
Sbjct: 61 VAGGEGADPVAVAKDAVELAKARGYDVVLIDTAGRLHNDENLMEELKKIKRVIK------ 114
Query: 218 PYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFI 277
P E+ L+ D TGQ+ + Q K F++ L +TG+I+TKLDGT KGG +IA + +P+ FI
Sbjct: 115 PDEVLLVSDATTGQDAVEQAKAFNEALGLTGIILTKLDGTAKGGAALSIAAETGLPIKFI 174
Query: 278 GIGEKIEDLQIFNAVDFVNALL 299
G GEK+ DL+ F+ FV+ LL
Sbjct: 175 GTGEKVPDLEPFDPERFVSRLL 196
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 243 bits (623), Expect = 8e-78
Identities = 114/299 (38%), Positives = 159/299 (53%), Gaps = 17/299 (5%)
Query: 9 LKESLSKTACNLKSLIVNKKIDKNLYNELESD----LLKADVGFETTQFLLNELKKIIY- 63
L + LS LK L +I + E + LL+ADV + + + +K+
Sbjct: 5 LSDRLSNA---LKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERALG 61
Query: 64 ---SKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLA 120
K L +Q +++ LV LL L K P VI++VG+ G GKTTT GKLA
Sbjct: 62 EEVPKGLTPGQQFIKIVYEELVKLLGGENSELNLAKKPPTVILMVGLQGSGKTTTAGKLA 121
Query: 121 NYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIAQKK 180
Y KK+ K VLL A DT+R AA EQL L + VP DP IA A+ A+++
Sbjct: 122 KYLKKKGKKVLLVAADTYRPAAIEQLKQLAEQVGVPFFGSGTEKDPVEIAKAALEKAKEE 181
Query: 181 NTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEF 240
D+VIVDT+GRL LM ELK+IK+VI P E L++D GQ+ ++ K F
Sbjct: 182 GYDVVIVDTAGRLHIDEELMDELKEIKEVIN------PDETLLVVDAMIGQDAVNTAKAF 235
Query: 241 SKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGEKIEDLQIFNAVDFVNALL 299
++ L ITG+I+TKLDG +GG + P+ FIG GEKI+DL+ F+ F + +L
Sbjct: 236 NEALGITGVILTKLDGDARGGAALSARAITGKPIKFIGTGEKIDDLEPFHPDRFASRIL 294
>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 = 228 bits (585), Expect = 9e-76
Identities = 89/179 (49%), Positives = 120/179 (67%), Gaps = 6/179 (3%)
Query: 100 FVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVIS 159
VI++VG+ GVGKTTT KLA Y KK+ K VLL A DT+R AA EQL +LG+ VPV
Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFE 60
Query: 160 EKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPY 219
E + DP +IA AI A+++N D+VIVDT+GRL +LM ELKKIK+V++ P
Sbjct: 61 EGEGKDPVSIAKRAIEHAREENFDVVIVDTAGRLQIDENLMEELKKIKRVVK------PD 114
Query: 220 EIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIG 278
E+ L++D TGQ+ ++Q K F++ L ITG+I+TKLDG +GG +I P+ FIG
Sbjct: 115 EVLLVVDAMTGQDAVNQAKAFNEALGITGVILTKLDGDARGGAALSIRAVTGKPIKFIG 173
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 218 bits (557), Expect = 2e-69
Identities = 113/275 (41%), Positives = 164/275 (59%), Gaps = 20/275 (7%)
Query: 36 ELESDLLKADVGFETTQFLLNELKKIIYSKK---LFNTEQ-VRNVLHNLLVNLLKSLEKP 91
ELE +LL++DV E + +L LK+ + KK + E+ V+N L L+ +L S+
Sbjct: 69 ELELELLESDVALEVAEEILESLKEKLVGKKVKRGEDVEEIVKNALKEALLEVL-SVGDL 127
Query: 92 L-----IFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQL 146
I K KP VI+ VGVNG GKTTTI KLA Y KK SV++AA DTFRA A EQL
Sbjct: 128 FDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGDTFRAGAIEQL 187
Query: 147 LILGKYNDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKI 206
+ V VI K DPAA+A++AI A+ + D+V++DT+GR+ T ++LM ELKKI
Sbjct: 188 EEHAERLGVKVIKHKYGADPAAVAYDAIEHAKARGIDVVLIDTAGRMHTDANLMDELKKI 247
Query: 207 KKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAI 266
+V + P + + D G + + Q +EF++ + I G+I+TK+D KGG AA+
Sbjct: 248 VRVTK------PDLVIFVGDALAGNDAVEQAREFNEAVGIDGVILTKVDADAKGG--AAL 299
Query: 267 AKKYSI--PLYFIGIGEKIEDLQIFNAVDFVNALL 299
+ Y I P+ F+G+G+ +DL F+ FV+ LL
Sbjct: 300 SIAYVIGKPILFLGVGQGYDDLIPFDPDWFVDKLL 334
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 211 bits (541), Expect = 9e-66
Identities = 115/300 (38%), Positives = 165/300 (55%), Gaps = 22/300 (7%)
Query: 9 LKESLSKTACNLKSLIVNKKIDKNLYNELESD----LLKADVGFETTQFLLNELKKIIYS 64
L ESL LK L +ID+ E+ D LL+ADV + + L +K+
Sbjct: 1 LGESLRDA---LKKLAGKSRIDEKTVKEVVKDIQRALLQADVNVKLVKELSKSIKERALE 57
Query: 65 KK----LFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLA 120
++ L E V +++ LV LL E + KP IM+VG+ G GKTTT KLA
Sbjct: 58 EEPPKGLTPREHVIKIVYEELVKLLGE-ETEPLVLPLKPQTIMLVGLQGSGKTTTAAKLA 116
Query: 121 NYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIAQKK 180
YFKK+ V L A DT+R AAY+QL L + VP + D IA + + K
Sbjct: 117 RYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEG--LEKFK 174
Query: 181 NTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEF 240
D++IVDT+GR + + L+ E+K+IK+ ++ P E+ L+ID GQ +Q K F
Sbjct: 175 KADVIIVDTAGRHALEEDLIEEMKEIKEAVK------PDEVLLVIDATIGQQAKNQAKAF 228
Query: 241 SKILRITGLIITKLDGTTKGG-ILAAIAKKYSIPLYFIGIGEKIEDLQIFNAVDFVNALL 299
+ + I G+IITKLDGT KGG L+A+A+ + P+ FIG GEKI+DL+ F+ F++ LL
Sbjct: 229 HEAVGIGGIIITKLDGTAKGGGALSAVAETGA-PIKFIGTGEKIDDLERFDPDRFISRLL 287
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 210 bits (537), Expect = 4e-65
Identities = 107/258 (41%), Positives = 148/258 (57%), Gaps = 15/258 (5%)
Query: 41 LLKADVGFETTQFLLNELK-KII---YSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKK 96
LL+ADV + + +K K + K L +QV ++++ LV +L L
Sbjct: 38 LLEADVNLPVVKDFIARVKEKAVGQEVLKSLTPGQQVIKIVNDELVEILGGENSELNLAA 97
Query: 97 CKPFVIMIVGVNGVGKTTTIGKLANYFKKR-KKSVLLAACDTFRAAAYEQLLILGKYNDV 155
P VIM+VG+ G GKTTT GKLA Y KK+ KK VLL A D +R AA EQL LG+ V
Sbjct: 98 KPPTVIMMVGLQGAGKTTTAGKLAKYLKKKKKKKVLLVAADVYRPAAIEQLKTLGEQIGV 157
Query: 156 PVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIF 215
PV DP IA A+ A++ D+VIVDT+GRL LM ELK IK +
Sbjct: 158 PVFPSGDGQDPVDIAKAALEEAKENGYDVVIVDTAGRLHIDEELMDELKAIKAAVN---- 213
Query: 216 ELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYS--IP 273
P EI L++D TGQ+ ++ K F++ L +TG+I+TKLDG +GG AA++ + P
Sbjct: 214 --PDEILLVVDAMTGQDAVNTAKAFNEALGLTGVILTKLDGDARGG--AALSIRAVTGKP 269
Query: 274 LYFIGIGEKIEDLQIFNA 291
+ FIG GEK++DL+ F+
Sbjct: 270 IKFIGTGEKLDDLEPFHP 287
>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 = 205 bits (525), Expect = 1e-63
Identities = 101/256 (39%), Positives = 151/256 (58%), Gaps = 11/256 (4%)
Query: 41 LLKADVGFETTQFLLNELKKIIYSKKLFNT----EQVRNVLHNLLVNLLKSLEKPLIFKK 96
LL+ADV + + + ++K+ +++ + +Q ++H LV +L L K
Sbjct: 37 LLEADVNLQVVKDFIKKVKEKALGQEVLKSLSPGQQFIKIVHEELVAILGGENASLNLAK 96
Query: 97 CKPFVIMIVGVNGVGKTTTIGKLANYFKKR-KKSVLLAACDTFRAAAYEQLLILGKYNDV 155
P VI++VG+ G GKTTT GKLA Y KK+ K VLL ACD +R AA EQL +LG+ V
Sbjct: 97 KPPTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLYRPAAIEQLKVLGQQVGV 156
Query: 156 PVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIF 215
PV + K P IA A+ A++ D+VIVDT+GRL LM EL IK+++
Sbjct: 157 PVFALGKGQSPVEIARRALEYAKENGFDVVIVDTAGRLQIDEELMEELAAIKEILN---- 212
Query: 216 ELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLY 275
P EI L++D TGQ+ ++ K F++ L +TG+++TKLDG +GG ++ P+
Sbjct: 213 --PDEILLVVDAMTGQDAVNTAKTFNERLGLTGVVLTKLDGDARGGAALSVRSVTGKPIK 270
Query: 276 FIGIGEKIEDLQIFNA 291
FIG+GEKI+DL+ F+
Sbjct: 271 FIGVGEKIDDLEPFHP 286
>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 = 175 bits (445), Expect = 8e-52
Identities = 95/283 (33%), Positives = 152/283 (53%), Gaps = 12/283 (4%)
Query: 22 SLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNELKKIIYSKKLFNTEQVRNVLHNL- 80
+ ++++++ + E+ + LL++DV + + L +KK I +++ + R ++ +
Sbjct: 19 ATVIDEEVLNAMLKEICTALLESDVNIKLVRQLRENIKKAINLEEMASGLNKRKMIQHAV 78
Query: 81 ---LVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDT 137
L NL+ + KK K VIM VG+ G GKTTT KLA Y++++ L DT
Sbjct: 79 FKELCNLVDPGVEAFTPKKGKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADT 138
Query: 138 FRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQS 197
FRA A++QL +P +DP IA + +K+N DI+IVDTSGR +
Sbjct: 139 FRAGAFDQLKQNATKARIPFYGSYTESDPVKIASEGVEKFKKENFDIIIVDTSGRHKQED 198
Query: 198 HLMRELKKIKKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGT 257
L E+ ++ + I+ P I ++DG+ GQ +Q K F + + +IITKLDG
Sbjct: 199 SLFEEMLQVAEAIQ------PDNIIFVMDGSIGQAAEAQAKAFKDSVDVGSVIITKLDGH 252
Query: 258 TK-GGILAAIAKKYSIPLYFIGIGEKIEDLQIFNAVDFVNALL 299
K GG L+A+A S P+ FIG GE I+D +IF F++ LL
Sbjct: 253 AKGGGALSAVAATKS-PIIFIGTGEHIDDFEIFKTQPFISKLL 294
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 106 bits (268), Expect = 2e-26
Identities = 75/270 (27%), Positives = 133/270 (49%), Gaps = 25/270 (9%)
Query: 36 ELESDLLKADVGFETTQFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFK 95
EL L ++ + E + LL L + + ++ L LL N++ + ++ +
Sbjct: 165 ELYKRLKRSGLSPEIAEKLLKLLLEHMPPRE----RTAWRYLLELLANMIPVRVEDILKQ 220
Query: 96 KCKPFVIMIVGVNGVGKTTTIGKLANYFKKR--KKSVLLAACDTFRAAAYEQLLILGKYN 153
V+ +VG GVGKTTT+ KLA + KK V L DT+R A EQL K
Sbjct: 221 GG---VVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIM 277
Query: 154 DVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKK 213
+PV + A + Q ++ D++++DT+GR R ++++K +IE
Sbjct: 278 GIPVEVVYDPKELAKA------LEQLRDCDVILIDTAGR---SQRDKRLIEELKALIEFS 328
Query: 214 IFELPYEIFLIIDGNTGQNTLSQI-KEFSKILRITGLIITKLDGTTK-GGILAAIAKKYS 271
P +++L++ T L I K FS++ + GLI TKLD T+ G IL ++ +
Sbjct: 329 --GEPIDVYLVLSATTKYEDLKDIYKHFSRL-PLDGLIFTKLDETSSLGSIL-SLLIESG 384
Query: 272 IPLYFIGIGEKI-EDLQIFNAVDFVNALLN 300
+P+ ++ G+++ +D+++ N + V LL
Sbjct: 385 LPISYLTNGQRVPDDIKVANPEELVRLLLG 414
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 101 bits (254), Expect = 2e-24
Identities = 74/250 (29%), Positives = 124/250 (49%), Gaps = 24/250 (9%)
Query: 52 QFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVG 111
+ L L+ I K + E +R L LL SL + LI ++ + VI +VG GVG
Sbjct: 159 ELLRAGLELEILDMKDESYEDLR-YFSEKLRKLLLSLIENLIVEQKR--VIALVGPTGVG 215
Query: 112 KTTTIGKLANYFK--KRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAI 169
KTTT+ KLA + K+KK V + DT+R A EQL VP+
Sbjct: 216 KTTTLAKLAARYVMLKKKKKVAIITTDTYRIGAVEQLKTYADIMGVPLE--------VVY 267
Query: 170 AFNAINIA--QKKNTDIVIVDTSGRLSTQSHLMRE-LKKIKKVIEKKIFELPYEIFLIID 226
+ + A ++ D+++VDT+GR S +E ++++K++I+ E++L++
Sbjct: 268 SPKELAEAIEALRDCDVILVDTAGR----SQYDKEKIEELKELID---VSHSIEVYLVLS 320
Query: 227 GNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGEKI-ED 285
T L +I + + I GLI TKLD TT G L ++ + +P+ ++ G+++ ED
Sbjct: 321 ATTKYEDLKEIIKQFSLFPIDGLIFTKLDETTSLGNLFSLMYETRLPVSYVTNGQRVPED 380
Query: 286 LQIFNAVDFV 295
+ + N V
Sbjct: 381 IVVANPDYLV 390
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 84.5 bits (209), Expect = 4e-18
Identities = 61/215 (28%), Positives = 98/215 (45%), Gaps = 37/215 (17%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKR--KKSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
V+ +VG GVGKTTT KLA R + L D+FR A EQL I G+ VPV
Sbjct: 187 VLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVH 246
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSG------RLSTQSHLMRELKKIKKVIEK 212
+ K D A + F +A + +V++DT G +S Q ++ + +
Sbjct: 247 AVK---DAADLRF---ALAALGDKHLVLIDTVGMSQRDRNVSEQIAMLCGVGR------- 293
Query: 213 KIFELPYEIFLIIDGNTGQNTLSQIKEFSKILR------ITGLIITKLDGTTKGGILAAI 266
P L+++ + +TL+ E R + G IITKLD T G
Sbjct: 294 -----PVRRLLLLNAASHGDTLN---EVVHAYRHGAGEDVDGCIITKLDEATHLGPALDT 345
Query: 267 AKKYSIPLYFIGIGEKI-EDLQIFNAVDFVN-ALL 299
++ +P++++ G+K+ E L++ A + V+ A
Sbjct: 346 VIRHRLPVHYVSTGQKVPEHLELAQADELVDRAFA 380
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 76.6 bits (189), Expect = 4e-16
Identities = 52/159 (32%), Positives = 77/159 (48%), Gaps = 17/159 (10%)
Query: 36 ELESDLLKADVGFETTQFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKSL-EKPLIF 94
+L LL+A V E + LL +L + + E L L +L E+ I
Sbjct: 139 KLLERLLEAGVSEELARELLEKLPE------DLDAEDAWRWLREALEGMLPVKPEEDPIL 192
Query: 95 KKCKPFVIMIVGVNGVGKTTTIGKLANYF--KKRKKSVLLAACDTFRAAAYEQLLILGKY 152
++ VI +VG GVGKTTT+ KLA F + KK V L DT+R A EQL +
Sbjct: 193 ER--GGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTYRIGAVEQLKTYAEI 250
Query: 153 NDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSG 191
VPV K DP + A + + ++ D++++DT+G
Sbjct: 251 LGVPV---KVARDPKEL---AEALDRLRDKDLILIDTAG 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 = 63.9 bits (155), Expect = 1e-12
Identities = 26/128 (20%), Positives = 43/128 (33%), Gaps = 6/128 (4%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPV 157
VI+IVG G GKTT LA V+ + +QLL + V
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLL------LIIV 54
Query: 158 ISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFEL 217
+K A+ +A+K D++I+D L L + + +
Sbjct: 55 GGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSE 114
Query: 218 PYEIFLII 225
++
Sbjct: 115 KNLTVILT 122
>gnl|CDD|173185 PRK14722, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 374
Score = 67.1 bits (163), Expect = 1e-12
Identities = 51/197 (25%), Positives = 95/197 (48%), Gaps = 25/197 (12%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKR--KKSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
V ++G GVGKTTT KLA R V L D++R +EQL I GK VPV
Sbjct: 139 VFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVH 198
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELP 218
+ K D + +A+ +N +V++DT G + ++ + + P
Sbjct: 199 AVKDGGDLQ------LALAELRNKHMVLIDTIGMSQRDRTVSDQIAMLHGA------DTP 246
Query: 219 YEIFLIIDGNTGQNTLSQIKEFSK---------ILRITGLIITKLD-GTTKGGILAAIAK 268
+ L+++ + +TL+++ + + + + G I+TKLD + GG+L + +
Sbjct: 247 VQRLLLLNATSHGDTLNEVVQAYRSAAGQPKAALPDLAGCILTKLDEASNLGGVLDTVIR 306
Query: 269 KYSIPLYFIGIGEKIED 285
Y +P++++ G+K+ +
Sbjct: 307 -YKLPVHYVSTGQKVPE 322
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 67.3 bits (164), Expect = 2e-12
Identities = 50/205 (24%), Positives = 94/205 (45%), Gaps = 30/205 (14%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRK--KSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
VI +VG G GKTTTI KLA F + + V L DT R EQL G+ + V
Sbjct: 352 VIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVH 411
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSG------RLSTQSHLMRELKKIKKVIEK 212
+ + + ++ +V++DT+G L+ Q + +R +++ +
Sbjct: 412 EADSAESLLDL------LERLRDYKLVLIDTAGMGQRDRALAAQLNWLRAARQVTSL--- 462
Query: 213 KIFELPYEIFLIIDGNTGQNTLSQ-IKEFSKILRITGLIITKLDGTTKGGILAAIAKKYS 271
L++ N + L + ++ F+ + G+++TKLD T + G ++ +
Sbjct: 463 ----------LVLPANAHFSDLDEVVRRFAHA-KPQGVVLTKLDETGRFGSALSVVVDHQ 511
Query: 272 IPLYFIGIGEKI-EDLQIFNAVDFV 295
+P+ ++ G+++ +DL NA V
Sbjct: 512 MPITWVTDGQRVPDDLHRANAASLV 536
>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 407
Score = 64.0 bits (155), Expect = 2e-11
Identities = 50/185 (27%), Positives = 87/185 (47%), Gaps = 9/185 (4%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISE 160
+I ++G GVGKTTT+ KL K+ ++V DTFR+ A EQ DV +I
Sbjct: 208 IISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSGAVEQFQGYADKLDVELIVA 267
Query: 161 KKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYE 220
T PA + + D +++DT GR + E+ V+ +
Sbjct: 268 ---TSPAELEEAVQYMTYVNCVDHILIDTVGRNYLAEESVSEISAYTDVVHPDL-----T 319
Query: 221 IFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIG 280
F G + ++ + + ++I I G IITK+D TT+ G L + ++ ++P+ ++ G
Sbjct: 320 CFTFSSGMKSADVMTILPKLAEI-PIDGFIITKMDETTRIGDLYTVMQETNLPVLYMTDG 378
Query: 281 EKIED 285
+ I +
Sbjct: 379 QNITE 383
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 62.3 bits (152), Expect = 6e-11
Identities = 60/208 (28%), Positives = 98/208 (47%), Gaps = 43/208 (20%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRK--KSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
V ++G GVGKTTT KLA R V L D++R +EQL I GK VPV
Sbjct: 258 VFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIGGHEQLRIYGKILGVPVH 317
Query: 159 SEKKITDPA--AIAFNAINIAQKKNTDIVIVDTSG------RLSTQ----SHLMRELKKI 206
+ K D A +A + + +N IV++DT G +S Q +K++
Sbjct: 318 AVK---DAADLRLALSEL-----RNKHIVLIDTIGMSQRDRMVSEQIAMLHGAGAPVKRL 369
Query: 207 KKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLD-GTTKGGIL-A 264
L+++ + +TL+++ + + + G I+TKLD + GG L
Sbjct: 370 ----------------LLLNATSHGDTLNEVVQAYRGPGLAGCILTKLDEAASLGGALDV 413
Query: 265 AIAKKYSIPLYFIGIGEKI-EDLQIFNA 291
I +Y +PL+++ G+++ EDL + N
Sbjct: 414 VI--RYKLPLHYVSNGQRVPEDLHLANK 439
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 60.0 bits (145), Expect = 3e-10
Identities = 55/193 (28%), Positives = 90/193 (46%), Gaps = 15/193 (7%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRK--KSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
V ++G GVGKTTT KLA R V L D++R +EQL I GK V V
Sbjct: 193 VYALIGPTGVGKTTTTAKLAARAVIRHGADKVALLTTDSYRIGGHEQLRIYGKLLGVSVR 252
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELP 218
S K I D + + + + +V++DT G +S + ++ E + ++ L
Sbjct: 253 SIKDIADL------QLMLHELRGKHMVLIDTVG-MSQRDQMLAEQIAMLSQCGTQVKHL- 304
Query: 219 YEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIG 278
L+++ + +TL ++ + I G IITK+D GI + + L+++
Sbjct: 305 ----LLLNATSSGDTLDEVISAYQGHGIHGCIITKVDEAASLGIALDAVIRRKLVLHYVT 360
Query: 279 IGEKI-EDLQIFN 290
G+K+ EDL N
Sbjct: 361 NGQKVPEDLHEAN 373
>gnl|CDD|75717 PRK06731, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 270
Score = 58.6 bits (141), Expect = 5e-10
Identities = 49/183 (26%), Positives = 82/183 (44%), Gaps = 9/183 (4%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEK 161
I ++G GVGKTTT+ K+A F +KK+V D R +QL K VI+
Sbjct: 78 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA-- 135
Query: 162 KITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEI 221
+ D AA+ ++ D +++DT+G+ S + E+ + +E P I
Sbjct: 136 -VRDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVE------PDYI 188
Query: 222 FLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGE 281
L + + + +I K + I G++ TK D T G L I S P+ + G+
Sbjct: 189 CLTLSASMKSKDMIEIITNFKDIHIDGIVFTKFDETASSGELLKIPAVSSAPIVLMTDGQ 248
Query: 282 KIE 284
++
Sbjct: 249 DVK 251
>gnl|CDD|183360 PRK11889, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 436
Score = 57.8 bits (139), Expect = 2e-09
Identities = 49/183 (26%), Positives = 82/183 (44%), Gaps = 9/183 (4%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEK 161
I ++G GVGKTTT+ K+A F +KK+V D R +QL K VI+
Sbjct: 244 IALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIA-- 301
Query: 162 KITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYEI 221
+ D AA+ ++ D +++DT+G+ S + E+ + +E P I
Sbjct: 302 -VRDEAAMTRALTYFKEEARVDYILIDTAGKNYRASETVEEMIETMGQVE------PDYI 354
Query: 222 FLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSIPLYFIGIGE 281
L + + + +I K + I G++ TK D T G L I S P+ + G+
Sbjct: 355 CLTLSASMKSKDMIEIITNFKDIHIDGIVFTKFDETASSGELLKIPAVSSAPIVLMTDGQ 414
Query: 282 KIE 284
++
Sbjct: 415 DVK 417
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 52.2 bits (125), Expect = 1e-07
Identities = 47/177 (26%), Positives = 78/177 (44%), Gaps = 16/177 (9%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYF----KKRKKSVLLAACDTFRAAAYEQLLILGKYN 153
K V ++VG GVGKTTTI KLA + + ++ + D +R A +Q+ G
Sbjct: 173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIM 232
Query: 154 DVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKK 213
+PV + + D I Q K+ D+V+VDT G+ + E+K++ +
Sbjct: 233 GIPVKAIESFKDLKE------EITQSKDFDLVLVDTIGKSPKDFMKLAEMKELLNACGRD 286
Query: 214 IFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTK-GGILAAIAKK 269
E L + T + + +I +I TKLD TT G +++ I +
Sbjct: 287 A-----EFHLAVSSTTKTSDVKEIFHQFSPFSYKTVIFTKLDETTCVGNLISLIYEM 338
>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 = 47.5 bits (114), Expect = 2e-07
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 20 LKSLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNELK---KIIYSKKLFNTEQVRNV 76
L L + +K D+ L ELE LL+ADVG E + ++ +K K K L ++V+ +
Sbjct: 9 LGELFLTEKDDEELLEELEEALLEADVGVEVVKEIIERVKEKAKGEVLKGLTPKQEVKKI 68
Query: 77 LHNLLVNLL 85
L LV +L
Sbjct: 69 LKEELVKIL 77
>gnl|CDD|217266 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain.
Length = 77
Score = 47.2 bits (113), Expect = 3e-07
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 9 LKESLSKTACNL----KSLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNELKKIIYS 64
LKE LSKT L K L + +K L ELE LL+ADVG ETT+ ++ LK+++
Sbjct: 1 LKEGLSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEADVGVETTEKIIERLKELVGR 60
Query: 65 KKLFNTEQVRNVLHNLL 81
K L + E+++ L L
Sbjct: 61 KGLSDPEEIKKALKEEL 77
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 50.3 bits (120), Expect = 5e-07
Identities = 47/191 (24%), Positives = 82/191 (42%), Gaps = 25/191 (13%)
Query: 101 VIMIVGVNGVGKTTTIGKL-ANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVIS 159
V+ VG G GKTT+I KL A YF KSV L D +R AA EQL
Sbjct: 225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIAAIEQL------------- 271
Query: 160 EKKITDPAAIAFNAI-NIAQKKNT------DIVIVDTSGRLSTQSHLMRELKKIKKVIEK 212
K+ D + F + +I + K T +++++DT+G + ++ +
Sbjct: 272 -KRYADTMGMPFYPVKDIKKFKETLARDGSELILIDTAGYSHRNLEQLERMQSFYSCFGE 330
Query: 213 KIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKYSI 272
K E L++ + + + + + L +++TKLD G +A YS
Sbjct: 331 KD---SVENLLVLSSTSSYHHTLTVLKAYESLNYRRILLTKLDEADFLGSFLELADTYSK 387
Query: 273 PLYFIGIGEKI 283
++ +G+++
Sbjct: 388 SFTYLSVGQEV 398
>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 = 42.0 bits (99), Expect = 2e-05
Identities = 17/33 (51%), Positives = 19/33 (57%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLA 133
VI++ G GVGKTT LA KR K VLL
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>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 = 37.6 bits (88), Expect = 0.003
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 100 FVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
I+ G++G GKTT I LA + R V+L
Sbjct: 1 MFIVFEGIDGAGKTTLIELLAERLEARGYEVVL 33
>gnl|CDD|234188 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein YhjQ.
Members of this family are the YhjQ protein, found
immediately upsteam of bacterial cellulose synthase
(bcs) genes in a broad range of bacteria, including both
copies of the bcs locus in Klebsiella pneumoniae. In
several species it is seen clearly as part of the bcs
operon. It is identified as a probable component of the
bacterial cellulose metabolic process not only by gene
location, but also by partial phylogenetic profiling, or
Haft-Selengut algorithm (PMID:16930487), based on a
bacterial cellulose biosynthesis genome property
profile. Cellulose plays an important role in biofilm
formation and structural integrity in some bacteria.
Mutants in yhjQ in Escherichia coli, show altered
morphology an growth, but the function of YhjQ has not
yet been determined [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 246
Score = 36.6 bits (85), Expect = 0.009
Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 101 VIMIVGV-NGVGKTTTIGKLANYFKKRKKSVLLAACD 136
VI IV V GVGKTT LA+ K + VL D
Sbjct: 3 VIAIVSVRGGVGKTTLTANLASALKLLGEPVLAIDLD 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 = 34.1 bits (79), Expect = 0.019
Identities = 16/36 (44%), Positives = 18/36 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
I I G GVGKTT LA Y ++ K VL D
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDAD 36
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 33.1 bits (76), Expect = 0.023
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAY 143
+ ++ G G GKT T + +SVL+ A RAA
Sbjct: 12 LFVVDGGPGTGKTATAAAIIARLLAAGRSVLVVAPTG-RAARR 53
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 33.9 bits (78), Expect = 0.030
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 100 FVIMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
++++VG GKTT I KL NY K+R V
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGYRV 31
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 34.6 bits (80), Expect = 0.051
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
VI I GV G GK+T I L ++R V + A D
Sbjct: 50 NAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVD 88
>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 = 33.1 bits (76), Expect = 0.060
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAY 143
+I++VG+ G GK+T +L + +V+L++ DT R
Sbjct: 1 LILMVGLPGSGKSTFARRLL----RELGAVVLSS-DTLRKRLR 38
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems.
Length = 148
Score = 33.4 bits (77), Expect = 0.061
Identities = 16/36 (44%), Positives = 19/36 (52%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
VI I GV G GK+T I L + R K V + A D
Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKRVAVLAID 36
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 33.8 bits (78), Expect = 0.067
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
K I+I G++G GKTT L ++R V+L
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVL 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 = 33.8 bits (78), Expect = 0.070
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
+I IVG GKTT + LA +K K VL+
Sbjct: 1 IISIVG--AGGKTTLMFALARELRKEGKPVLV 30
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 33.3 bits (77), Expect = 0.075
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKL 119
V+++ GV GVGKTT + K
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKA 22
>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 = 31.8 bits (73), Expect = 0.094
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 109 GVGKTTTIGKLANYFKKRKKSVLL 132
GVGKTTT LA +R K VLL
Sbjct: 10 GVGKTTTAVNLAAALARRGKRVLL 33
>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
reductase, iron-sulfur ATP-binding protein. The BchL
peptide (ChlL in chloroplast and cyanobacteria) is an
ATP-binding iron-sulfur protein of the dark form
protochlorophyllide reductase, an enzyme similar to
nitrogenase. This subunit resembles the nitrogenase NifH
subunit [Biosynthesis of cofactors, prosthetic groups,
and carriers, Chlorophyll and bacteriochlorphyll].
Length = 268
Score = 33.2 bits (76), Expect = 0.11
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
++ + G G+GK+TT L+ F K K VL CD
Sbjct: 2 ILAVYGKGGIGKSTTSSNLSVAFAKLGKRVLQIGCD 37
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 33.5 bits (77), Expect = 0.12
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 7/85 (8%)
Query: 42 LKADVGFETTQFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIF----KKC 97
+ D+ + + ELKK +L +++R V LL + K + +K
Sbjct: 29 VDPDLAYSIAIEIQEELKK--EGIRLVTKDEIREVYQKLLEKGDPEVAKRYLLWRRIRKM 86
Query: 98 K-PFVIMIVGVNGVGKTTTIGKLAN 121
K P +I+I G +GVGK+T G+LA
Sbjct: 87 KRPLIILIGGASGVGKSTIAGELAR 111
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 33.1 bits (76), Expect = 0.12
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 86 KSLEKPLIFK---KCKPFVIMIVGVNGVGKTTTIGKLANYFKKRK 127
K L P++ + + P V+++VG GVGK+T I L + K+
Sbjct: 23 KKLHVPVVDRTPEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQN 67
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 32.5 bits (74), Expect = 0.12
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
+I++ G G GKTT +LA + V+ +
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIE 36
>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 = 33.1 bits (76), Expect = 0.13
Identities = 27/110 (24%), Positives = 40/110 (36%), Gaps = 17/110 (15%)
Query: 104 IVGVNGVGKTTTIGKLANYFKKRKKSV----LLAACDTFRAAAYEQLLILGKYNDVPVIS 159
+VG G GKTT +G L+ +SV L A + A + L DV
Sbjct: 1 VVGPAGSGKTTFVGALSEILPLLGRSVYVVNLDPAAENLPYEADIDIRELITVADV---M 57
Query: 160 EKKITDP-----AAIAFNAINIAQ-----KKNTDIVIVDTSGRLSTQSHL 199
E P A+ F I + + D + DT G++ +H
Sbjct: 58 EDDGLGPNGALTVAMDFLRITLDWLLEELEYEDDYYLFDTPGQIELFTHW 107
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.9 bits (72), Expect = 0.13
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYF 123
+I+I G G GK+T KLA
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKL 23
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 33.6 bits (77), Expect = 0.13
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 16/61 (26%)
Query: 71 EQVRNVLHNLLVN-----------LLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKL 119
+Q+R + LL+ LL+S+ +P +P ++I GV+GVGK+ L
Sbjct: 221 DQLRRKVEALLLEEAGEEVARRYRLLRSIRRPP-----RPLHVLIGGVSGVGKSVLASAL 275
Query: 120 A 120
A
Sbjct: 276 A 276
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 32.5 bits (75), Expect = 0.17
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
I I G++G GK+T I L +++ + V+
Sbjct: 6 ITIEGIDGAGKSTQIELLKELLEQQGRDVVF 36
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 32.7 bits (75), Expect = 0.17
Identities = 24/101 (23%), Positives = 42/101 (41%), Gaps = 7/101 (6%)
Query: 24 IVNKKIDKNLYNELESDLLKADVGFETTQFLLNELKKIIY---SKKLFNTEQVRNVLHNL 80
IV +K + N+ +DL +V + ++ E +K +++R L L
Sbjct: 58 IVKEKPKLLVLNK--ADLAPKEVTKKWKKYFKKEEGIKPIFVSAKSRQGGKKIRKALEKL 115
Query: 81 LVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLAN 121
+K L K K + + +VG VGK+T I +L
Sbjct: 116 SEEKIKRL-KKKGLLK-RKIRVGVVGYPNVGKSTLINRLLG 154
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 33.1 bits (76), Expect = 0.18
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 93 IFKKCKPF---VIMIVGVNGVGKTTTIGKLANYF 123
I + +PF + I+G GK+T + KLAN F
Sbjct: 210 IPTEVRPFFVRTVAILGGESSGKSTLVNKLANIF 243
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 32.3 bits (74), Expect = 0.19
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 81 LVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTF-- 138
L + +L +P + I G+ GKTT +LA KKR + V+ A+ D F
Sbjct: 10 LAEHILTLNLT------RPLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFHN 63
Query: 139 -RAAAYEQ 145
R Y +
Sbjct: 64 PRVIRYRR 71
>gnl|CDD|238989 cd02032, Bchl_like, This family of proteins contains bchL and chlL.
Protochlorophyllide reductase catalyzes the reductive
formation of chlorophyllide from protochlorophyllide
during biosynthesis of chlorophylls and
bacteriochlorophylls. Three genes, bchL, bchN and bchB,
are involved in light-independent protochlorophyllide
reduction in bacteriochlorophyll biosynthesis. In
cyanobacteria, algae, and gymnosperms, three similar
genes, chlL, chlN and chlB are involved in
protochlorophyllide reduction during chlorophylls
biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit
significant sequence similarity to the nifH, nifD and
nifK subunits of nitrogenase, respectively. Nitrogenase
catalyzes the reductive formation of ammonia from
dinitrogen.
Length = 267
Score = 32.7 bits (75), Expect = 0.20
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
V+ + G G+GK+TT L+ KR K VL CD
Sbjct: 2 VLAVYGKGGIGKSTTSSNLSVALAKRGKKVLQIGCD 37
>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 = 31.8 bits (73), Expect = 0.22
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
VI VG +G GKTT + KL R V
Sbjct: 1 MKVIGFVGYSGSGKTTLLEKLIPALSARGLRV 32
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 32.2 bits (74), Expect = 0.23
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
V+ + G G+GK+TT L+ F K K VL CD
Sbjct: 4 VLAVYGKGGIGKSTTSSNLSAAFAKLGKKVLQIGCD 39
>gnl|CDD|238990 cd02033, BchX, Chlorophyllide reductase converts chlorophylls into
bacteriochlorophylls by reducing the chlorin B-ring.
This family contains the X subunit of this three-subunit
enzyme. Sequence and structure similarity between bchX,
protochlorophyllide reductase L subunit (bchL and chlL)
and nitrogenase Fe protein (nifH gene) suggest their
functional similarity. Members of the BchX family serve
as the unique electron donors to their respective
catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase
component 1). Mechanistically, they hydrolyze ATP and
transfer electrons through a Fe4-S4 cluster.
Length = 329
Score = 32.6 bits (74), Expect = 0.24
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 87 SLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
+LE P K +I I G G+GK+ T+ L+ ++ K VLL CD
Sbjct: 19 TLEIPTAPPTKKTQIIAIYGKGGIGKSFTLANLSYMMAQQGKRVLLIGCD 68
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 32.2 bits (74), Expect = 0.31
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 12/64 (18%)
Query: 63 YSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFV-----IMIVGVNGVGKTTTIG 117
KKL RN L + NL K + +FK + + I+G NGVGKTT +
Sbjct: 311 QDKKLH-----RNALE--VENLTKGFDNGPLFKNLNLLLEAGERLAIIGENGVGKTTLLR 363
Query: 118 KLAN 121
L
Sbjct: 364 TLVG 367
>gnl|CDD|221912 pfam13086, AAA_11, AAA 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 = 220
Score = 31.9 bits (73), Expect = 0.31
Identities = 29/141 (20%), Positives = 53/141 (37%), Gaps = 18/141 (12%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYF--KKRKKSVLL-----AACDTFRAAAYEQLLILG 150
+ +I G G GKTTTI ++ K VL+ +A D +L
Sbjct: 16 SSDITLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAVDNIL------ERLLE 69
Query: 151 KYNDVPVI---SEKKITDPAAIAFNAINIAQKKNTDIV--IVDTSGRLSTQSHLMRELKK 205
+ + ++ S + + ++ + + K ++ I L +S L RE +K
Sbjct: 70 QKFGLKIVRIGSPAREIHEDVLQYSLEYLLEAKFEQLLKRIRKLKSLLEEKSKLKRERRK 129
Query: 206 IKKVIEKKIFELPYEIFLIID 226
++ I+K EL I
Sbjct: 130 LRSEIKKLKKELERLRKSIRK 150
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 31.3 bits (71), Expect = 0.36
Identities = 28/141 (19%), Positives = 55/141 (39%), Gaps = 22/141 (15%)
Query: 95 KKCKPF---VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGK 151
++ +PF + I+G GK+T + KLAN F Y + +
Sbjct: 1 REVRPFFVKTVAILGGESSGKSTLVNKLANIFNTTSAWE------------YGREYVFEH 48
Query: 152 YNDVPVISEKKITDPAAIA---FNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKK 208
+ +D A IA + A + + +DT L+TQ+ + +
Sbjct: 49 LGGD---EALQYSDYAKIALGQAAYEDAAVRYANKVAFIDTDF-LTTQAFCKKYEGREHP 104
Query: 209 VIEKKIFELPYEIFLIIDGNT 229
++ I E +++ L+++ NT
Sbjct: 105 FLQALIAEYRFDLTLLLEPNT 125
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 32.2 bits (74), Expect = 0.36
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 103 MIVGVNGVGKTTT---IGKLANY 122
M+ GV GVGKTTT + + NY
Sbjct: 50 MLTGVRGVGKTTTARILARALNY 72
>gnl|CDD|213904 TIGR04291, arsen_driv_ArsA, arsenical pump-driving ATPase. The
broader family (TIGR00345) to which the current family
belongs consists of transport-energizing ATPases,
including to TRC40/GET3 family involved in
post-translational insertion of protein C-terminal
transmembrane anchors into membranes from the cyotosolic
face. This family, however, is restricted to ATPases
that energize pumps that export arsenite (or
antimonite).
Length = 566
Score = 32.0 bits (73), Expect = 0.38
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPV--I 158
+IM +G GVGKTT +A + V L D AA+ + + G N++ V I
Sbjct: 323 LIMTMGKGGVGKTTVAAAIAVRLANKGLDVHLTTSD---PAAHLSVTLTGSLNNLQVSRI 379
Query: 159 SEKKITD 165
K+ T+
Sbjct: 380 DPKQETE 386
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 31.3 bits (71), Expect = 0.48
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
G G+GK+TT+ +A + K VL+ CD
Sbjct: 4 FCFYGKGGIGKSTTVCNIAAALAESGKKVLVVGCD 38
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 30.9 bits (71), Expect = 0.52
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
++ I+G NG GK+T + LA K +LL D
Sbjct: 27 IVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKD 62
>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 = 31.1 bits (71), Expect = 0.59
Identities = 14/32 (43%), Positives = 15/32 (46%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
VI G GVGKTT A + K VLL
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLL 32
>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 = 29.8 bits (68), Expect = 0.63
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 2/55 (3%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKY 152
+I+I G VGKTT + + +++L D R L +L ++
Sbjct: 1 NNKIIVITGPRQVGKTTLLLQFLKELL--SENILYINLDDPRFLRLALLDLLEEF 53
>gnl|CDD|220813 pfam10567, Nab6_mRNP_bdg, RNA-recognition motif. This conserved
domain is found in fungal proteins and appears to be
involved in RNA-processing. It binds to poly-adenylated
RNA, interacts genetically with mRNA 3'-end processing
factors, copurifies with the nuclear cap-binding protein
Cbp20p, and is found in complexes containing other
translation factors, such as EIF4G.
Length = 309
Score = 31.0 bits (70), Expect = 0.72
Identities = 18/73 (24%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 5 WITRLKESLSKTACNLKSLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNELKK--II 62
WI+ L E+ +LK I+++ +++ E ++K+D ++ FL N K I+
Sbjct: 121 WISELLEA------SLKMNIISRGATRSIAVEFADPVVKSDFIWDKLPFLDNSGNKRYIL 174
Query: 63 YSKKLFNTEQVRN 75
S + N ++ R
Sbjct: 175 ESVDIINADERRK 187
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139) is
part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules.
Length = 222
Score = 30.5 bits (70), Expect = 0.79
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYE 144
++ ++G NG GKTT + + R S+ D +E
Sbjct: 28 IVALLGRNGAGKTTLLKTIMGLLPPRSGSIRFDGRDITGLPPHE 71
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 30.1 bits (69), Expect = 0.92
Identities = 11/32 (34%), Positives = 15/32 (46%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLA 133
I I G +G GKT +G +A K V +
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNAKADVVEVYVL 49
>gnl|CDD|215977 pfam00532, Peripla_BP_1, Periplasmic binding proteins and sugar
binding domain of LacI family. This family includes the
periplasmic binding proteins, and the LacI family
transcriptional regulators. The periplasmic binding
proteins are the primary receptors for chemotaxis and
transport of many sugar based solutes. The LacI family
of proteins consist of transcriptional regulators
related to the lac repressor. In this case, generally
the sugar binding domain binds a sugar which changes the
DNA binding activity of the repressor domain
(pfam00356).
Length = 281
Score = 30.6 bits (69), Expect = 0.95
Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 3/74 (4%)
Query: 205 KIKKVIEKKIFELPYEIFLIIDGNTGQNTLSQIKEFSKILRITGLIITKLDGTTKGGILA 264
+ K I K + +++FL+ G+ + I G+IIT G +
Sbjct: 18 DLVKGITKAAKDHGFDVFLLAVGDGEDTLTNAIDLL-LASGADGIIITTPA--PSGDDIT 74
Query: 265 AIAKKYSIPLYFIG 278
A A+ Y IP+
Sbjct: 75 AKAEGYGIPVIAAD 88
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 31.0 bits (70), Expect = 0.95
Identities = 40/177 (22%), Positives = 78/177 (44%), Gaps = 24/177 (13%)
Query: 124 KKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIAQKKNTD 183
K+RK V + FRA Y++ I+ + P++ + D I F +++ Q+ D
Sbjct: 202 KRRKVPVTI----LFRAMDYQKQDIIKMF--YPLVKVRYENDKYLIPFASLDANQRMEFD 255
Query: 184 IVIVDTSGRLSTQSHLMRELKKIKKVIEKKI--FELPYEIFL-------IIDGNTGQ-NT 233
+ D G++ + +KIK++ E + E P +I L ++ G +
Sbjct: 256 LK--DPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGKEVLLDM 313
Query: 234 LSQIKEFSKILRITGLIITK--LDGTTKGGILAAIAKKYSI---PLYFIGIGEKIED 285
L+Q+ + +K+ +I L + + + G A+I +S L + EKI+D
Sbjct: 314 LTQLDK-NKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKLLKQTEKIDD 369
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 30.7 bits (70), Expect = 1.0
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVL 131
VI+I G G+GK+T + ++A KR VL
Sbjct: 84 VILIGGDPGIGKSTLLLQVAARLAKRGGKVL 114
>gnl|CDD|236354 PRK08942, PRK08942, D,D-heptose 1,7-bisphosphate phosphatase;
Validated.
Length = 181
Score = 29.8 bits (68), Expect = 1.0
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 259 KGGILAAIAKKYSIPL---YFIGIGEKIEDLQIFNAVDFVNAL 298
K G+L +IA++ +I L +G + + DLQ A L
Sbjct: 105 KPGMLLSIAERLNIDLAGSPMVG--DSLRDLQAAAAAGVTPVL 145
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as twitching
motility.
Length = 198
Score = 30.0 bits (68), Expect = 1.0
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
+++ G G GK+TT+ + +Y K K +L
Sbjct: 4 VLVTGPTGSGKSTTLAAMIDYINKNKTHHIL 34
>gnl|CDD|238993 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer.
Length = 179
Score = 29.9 bits (68), Expect = 1.1
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 101 VIMIV-GVNGVGKTTTIGKLANYFKKRKKSVLL 132
VI++ G GVGKTTT L + V+L
Sbjct: 1 VIVVTSGKGGVGKTTTTANLGTALAQLGYKVVL 33
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 30.1 bits (68), Expect = 1.1
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
+I+I G+ G GK+TT L + + V
Sbjct: 5 LIIIEGLPGFGKSTTAKMLNDILSQNGIEV 34
>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 = 29.4 bits (66), Expect = 1.2
Identities = 10/47 (21%), Positives = 15/47 (31%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLI 148
+++ G G GKTT +AN + L L
Sbjct: 22 LLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELF 68
>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 = 1.2
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 15/89 (16%)
Query: 101 VIMIVGVNGVGKTTTIG--KLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
+I+I G+NG GKTT + +LA Y K+ A C +YEQ L
Sbjct: 30 IILIGGLNGAGKTTLLDAIQLALYGKR-------ALCSGRGNKSYEQYLRGLINRQ---- 78
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIV 187
T+PA+I + K + +V
Sbjct: 79 --AGKTNPASITLTFSVVEGGKRHEYTLV 105
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 30.1 bits (68), Expect = 1.3
Identities = 33/149 (22%), Positives = 61/149 (40%), Gaps = 21/149 (14%)
Query: 69 NTEQVRNVLHNLLV-------NLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLAN 121
N++ + NVL LL +L+ L + +K +P ++++G G GK++ I L
Sbjct: 3 NSDSLNNVLKGLLGLPSLLSERILEQLRMLQLTEK-EPVNVLLMGATGAGKSSLINAL-- 59
Query: 122 YFKKRKKSVLLAACDT-----FRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINI 176
F+ K V T R + + L+L D P + + K D A +
Sbjct: 60 -FQGEVKEVSKVGVGTDITTRLRLSYDGENLVLW---DTPGLGDGKDKD-AEHRQLYRDY 114
Query: 177 AQKKNTDIVIVDTSGR-LSTQSHLMRELK 204
K + + ++ R L T +R++
Sbjct: 115 LPKLDLVLWLIKADDRALGTDEDFLRDVI 143
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 30.1 bits (68), Expect = 1.3
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAA 142
+ ++G NG GKTT + +A V + DT R +
Sbjct: 30 ITGLLGENGAGKTTLLRMIATLLIPDSGKVTIDGVDTVRDPS 71
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 29.7 bits (67), Expect = 1.3
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 82 VNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLA 120
+ + LE+ L F+ + I G NG GK+T + +A
Sbjct: 23 LPAFRHLEERLEFR---APITFITGENGSGKSTLLEAIA 58
>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 = 29.7 bits (67), Expect = 1.4
Identities = 21/68 (30%), Positives = 25/68 (36%), Gaps = 4/68 (5%)
Query: 109 GVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAA 168
GVGKTT LA KR VLL D LGK +V + + A
Sbjct: 9 GVGKTTLAANLARALAKRGYRVLLIDLDP----QANNSSYLGKVEEVLPEGLEIVDAQAL 64
Query: 169 IAFNAINI 176
A A +
Sbjct: 65 QAIAAAIV 72
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 29.3 bits (66), Expect = 1.4
Identities = 23/119 (19%), Positives = 39/119 (32%), Gaps = 12/119 (10%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVI 158
I+IVG VGK+T L N K S+ T R + GK ++
Sbjct: 1 EIKIVIVGDPNVGKST----LLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLL 56
Query: 159 SEKKITDPAAIAFNAINIAQKKNTDIVIVDTSG---RLSTQSHLMRELKKIKKVIEKKI 214
++AI + + + L + L ++ K+I E +
Sbjct: 57 DT-----AGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGV 110
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 272
Score = 30.0 bits (68), Expect = 1.4
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
I I G G+GK+TT + + K VL+ CD
Sbjct: 2 KIAIYGKGGIGKSTTTQNTSAALAEMGKKVLIVGCD 37
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 30.3 bits (68), Expect = 1.5
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 2/68 (2%)
Query: 69 NTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKK 128
+ L+ NL LEK +F K +M+VG + GKT+ L +Y K K
Sbjct: 71 YVSDTTPM--PLIFNLHFFLEKRRMFNYEKGPTVMVVGGSQNGKTSFCFTLISYALKLGK 128
Query: 129 SVLLAACD 136
L D
Sbjct: 129 KPLFTNLD 136
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 30.5 bits (68), Expect = 1.5
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKK 125
PF++ +VG G GK+T I L F K
Sbjct: 69 PFIVAVVGPPGTGKSTLIRSLVRRFTK 95
>gnl|CDD|236133 PRK07933, PRK07933, thymidylate kinase; Validated.
Length = 213
Score = 29.6 bits (67), Expect = 1.5
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
I I GV+G GK T L + R +SV
Sbjct: 3 IAIEGVDGAGKRTLTEALRAALEARGRSV 31
>gnl|CDD|215427 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 29.7 bits (67), Expect = 1.6
Identities = 15/50 (30%), Positives = 20/50 (40%)
Query: 96 KCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQ 145
+ P VI I G GKTT + L F + + D F A +Q
Sbjct: 97 EIPPLVIGISAPQGCGKTTLVFALVYLFNATGRRAASLSIDDFYLTAADQ 146
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 29.6 bits (67), Expect = 1.6
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
+ I GV G GK+T I L ++R V + A D
Sbjct: 31 RVGITGVPGAGKSTLIEALGMELRRRGHRVAVLAVD 66
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 30.2 bits (68), Expect = 1.7
Identities = 28/105 (26%), Positives = 43/105 (40%), Gaps = 11/105 (10%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISE 160
V M+ G G GKTT I +A K+ LLAA T +AA + N+ +
Sbjct: 336 VSMLTGGPGTGKTTAIKAIARLIKEGDGDQLLAA-PTGKAA--------KRLNESTGLEA 386
Query: 161 KKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKK 205
+ I + N + + D++I+D + L T L L
Sbjct: 387 RTIHRLLGLWEKTGNNEEPLDGDLLIIDEASMLDTS--LAFGLLS 429
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and
metabolism].
Length = 189
Score = 29.3 bits (66), Expect = 1.7
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 99 PFVIMIVGVNGVGKTT 114
V++I GV GVGKTT
Sbjct: 4 RKVVVITGVPGVGKTT 19
>gnl|CDD|222258 pfam13604, AAA_30, AAA 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. There is a Walker A and
Walker B.
Length = 195
Score = 29.5 bits (67), Expect = 1.8
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAA 134
V ++ G G GKTT++ ++ V+ A
Sbjct: 20 VAVVQGPAGTGKTTSLKAAREAWEAAGYRVIGLA 53
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 29.8 bits (68), Expect = 1.9
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
++I G G GKTTT+ K+ ++ V
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEELEEIAVKV 86
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.5 bits (67), Expect = 2.0
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFR 139
+ I+G NG GK+T + LA K + VLL D
Sbjct: 30 ITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIAS 68
>gnl|CDD|213233 cd03266, ABC_NatA_sodium_exporter, ATP-binding cassette domain of
the Na+ transporter. NatA is the ATPase component of a
bacterial ABC-type Na+ transport system called NatAB,
which catalyzes ATP-dependent electrogenic Na+ extrusion
without mechanically coupled proton or K+ uptake. NatB
possess six putative membrane spanning regions at its
C-terminus. In B. subtilis, NatAB is inducible by agents
such as ethanol and protonophores, which lower the
proton-motive force across the membrane. The closest
sequence similarity to NatA is exhibited by DrrA of the
two-component daunorubicin- and doxorubicin-efflux
system. Hence, the functional NatAB is presumably
assembled with two copies of a single ATP-binding
protein and a single integral membrane protein.
Length = 218
Score = 29.3 bits (66), Expect = 2.0
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAA 142
V ++G NG GKTTT+ LA + + D + A
Sbjct: 33 VTGLLGPNGAGKTTTLRMLAGLLEPDAGFATVDGFDVVKEPA 74
>gnl|CDD|214851 smart00846, Gp_dh_N, Glyceraldehyde 3-phosphate dehydrogenase, NAD
binding domain. GAPDH is a tetrameric NAD-binding
enzyme involved in glycolysis and glyconeogenesis.
N-terminal domain is a Rossmann NAD(P) binding fold.
Length = 149
Score = 28.7 bits (65), Expect = 2.1
Identities = 26/110 (23%), Positives = 44/110 (40%), Gaps = 23/110 (20%)
Query: 104 IVGVNGVGKTTTIGKLANYFKKRKKSV--LLAACDTFRAAAYEQLLILGKYNDVPVISEK 161
+V +N + + L Y SV + L++ GK + V +E+
Sbjct: 27 VVAINDLTDPEYLAYLLKY-----DSVHGRFPGTVEVEG---DGLVVNGKA--IKVFAER 76
Query: 162 KITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKK-IKKVI 210
DPA + + + + DIV V+ +G +T+ LK KKVI
Sbjct: 77 ---DPANLPWGELGV------DIV-VECTGGFTTREKASAHLKAGAKKVI 116
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.4 bits (66), Expect = 2.3
Identities = 32/144 (22%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 93 IFKKCKPFVIMIVGVNG---VGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLIL 149
I ++ +PF + V + G GK+T + KLA F S A Y + +
Sbjct: 153 IPREVRPFFVKTVAILGGESTGKSTLVNKLAAVF--NTTSA------WEYAREYVEEKLG 204
Query: 150 G----KYNDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKK 205
G +Y+D I+ + I+ A + I +DT ++TQ + +
Sbjct: 205 GDEALQYSDYAQIALGQQ--------RYIDYAVRHAHKIAFIDTDF-ITTQVFAKQYEGR 255
Query: 206 IKKVIEKKIFELPYEIFLIIDGNT 229
++ I E P+++ L++ NT
Sbjct: 256 EHPFLDSDIAEYPFDLTLLLKPNT 279
>gnl|CDD|235498 PRK05541, PRK05541, adenylylsulfate kinase; Provisional.
Length = 176
Score = 28.9 bits (65), Expect = 2.5
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFR 139
+VI I G+ G GKTT L K + +V+ D R
Sbjct: 6 NGYVIWITGLAGSGKTTIAKALYERLKLKYSNVIYLDGDELR 47
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of RNase
L inhibitor. The ABC ATPase RNase L inhibitor (RLI) is
a key enzyme in ribosomal biogenesis, formation of
translation preinitiation complexes, and assembly of HIV
capsids. RLI's are not transport proteins, and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains, which
are arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity more than 48%. The high degree of evolutionary
conservation suggests that RLI performs a central role
in archaeal and eukaryotic physiology.
Length = 177
Score = 28.7 bits (64), Expect = 2.5
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
VI IVG NG GKTT + LA
Sbjct: 27 VIGIVGPNGTGKTTAVKILA 46
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 29.1 bits (66), Expect = 2.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 109 GVGKTTTIGKLANYFKKRKKSVLL 132
GVGK+ + +AN K+ S L
Sbjct: 166 GVGKSYLLAAIANELAKKGVSSTL 189
>gnl|CDD|222130 pfam13439, Glyco_transf_4, Glycosyltransferase Family 4.
Length = 171
Score = 28.5 bits (64), Expect = 2.6
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 3/69 (4%)
Query: 119 LANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEKKITDPAAIAFNAINIAQ 178
LA +R V + A + + VP +S K+ A F + +
Sbjct: 21 LARALARRGHEVTVVA---PELGRPLEEELGVILVSVPGLSFKRALRSPAFVFALRRLLK 77
Query: 179 KKNTDIVIV 187
K+ D+V
Sbjct: 78 KERFDLVHS 86
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 28.6 bits (65), Expect = 2.6
Identities = 21/78 (26%), Positives = 29/78 (37%), Gaps = 7/78 (8%)
Query: 49 ETTQFLLNELKKIIYSKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCK-----PFVIM 103
T+ L K N + + V L+ K L K K K P M
Sbjct: 62 AKTKKWLKYFKSQGEPVLFVNAKNGKGVKK--LLKKAKKLLKENEKLKAKGLLPRPLRAM 119
Query: 104 IVGVNGVGKTTTIGKLAN 121
+VG+ VGK+T I +L
Sbjct: 120 VVGIPNVGKSTLINRLRG 137
>gnl|CDD|239034 cd02117, NifH_like, This family contains the NifH (iron protein) of
nitrogenase, L subunit (BchL/ChlL) of the
protochlorophyllide reductase and the BchX subunit of
the Chlorophyllide reductase. Members of this family use
energey from ATP hydrolysis and transfer electrons
through a Fe4-S4 cluster to other subunit for reduction
of substrate.
Length = 212
Score = 28.7 bits (65), Expect = 2.7
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
I I G G+GK+TT L+ + K VL CD
Sbjct: 2 QIAIYGKGGIGKSTTSQNLSAALAEMGKKVLQVGCD 37
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 29.0 bits (66), Expect = 2.8
Identities = 10/44 (22%), Positives = 20/44 (45%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYE 144
++ ++G NG GKTT + + + R ++ D +E
Sbjct: 31 IVALLGRNGAGKTTLLKTIMGLVRPRSGRIIFDGEDITGLPPHE 74
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 29.3 bits (66), Expect = 2.8
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
I+I G G GK+ I KL + ++R ++
Sbjct: 179 ILIHGTTGSGKSVAIRKLLRWIRQRGDRAII 209
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 28.3 bits (64), Expect = 2.9
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
I I G GVGKTT + K+ K V
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVKV 30
>gnl|CDD|226691 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 29.1 bits (65), Expect = 2.9
Identities = 14/72 (19%), Positives = 28/72 (38%), Gaps = 3/72 (4%)
Query: 85 LKSLEK--PLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKR-KKSVLLAACDTFRAA 141
L L K P ++ +P ++ I G G GK+T + + + + D
Sbjct: 34 LPLLAKIAPWAQERGRPLIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLDDLYLT 93
Query: 142 AYEQLLILGKYN 153
++L + + N
Sbjct: 94 HADRLRLARQVN 105
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 179
Score = 28.4 bits (64), Expect = 3.1
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSV 130
I I G GVGKTT + K+A +++ V
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKV 36
>gnl|CDD|184429 PRK13973, PRK13973, thymidylate kinase; Provisional.
Length = 213
Score = 28.8 bits (65), Expect = 3.3
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 106 GVNGVGKTTTIGKLANYFKKRKKSVLL 132
G G GK+T I LA + VL+
Sbjct: 10 GGEGAGKSTQIRLLAERLRAAGYDVLV 36
>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 = 29.1 bits (66), Expect = 3.3
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKK 128
I+IVG G GKT + +L + + R
Sbjct: 18 ILIVGTTGTGKTQALRELLDQIRARGD 44
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases are
sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and tend
to undergo disruption to form pseudogenes. A unique
feature of all eukaryotic and certain bacterial KAP
NTPases is the presence of two or four transmembrane
helices inserted into the P-loop NTPase domain. These
transmembrane helices anchor KAP NTPases in the membrane
such that the P-loop domain is located on the
intracellular side.
Length = 301
Score = 28.9 bits (65), Expect = 3.3
Identities = 24/149 (16%), Positives = 48/149 (32%), Gaps = 20/149 (13%)
Query: 99 PFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLL---------IL 149
FVI + G G GKT+ + L + K+ + + D + + + + L
Sbjct: 20 GFVIGLYGAWGSGKTSFLNLLEDELKEFPEEFHIVYFDPWLFSGQDDAVASLLAALADAL 79
Query: 150 GKYNDVPVISEKKITDPAAIAFN---------AINIAQKKNTDIVIVDTSGRLSTQSHLM 200
+ A+ +A V + LS +
Sbjct: 80 EEEYSALATKLLIGKKLLALVIGAKIGGNFGVGTALALTGLVASVEGKSLKLLSIEPLKK 139
Query: 201 R--ELKKIKKVIEKKIFELPYEIFLIIDG 227
E+++++ I + +L I +IID
Sbjct: 140 LQTEIEELRTDIASTLDDLQKRIVVIIDD 168
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 28.4 bits (64), Expect = 3.5
Identities = 14/46 (30%), Positives = 18/46 (39%)
Query: 94 FKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFR 139
K K VI G++G GK+T L + V L D R
Sbjct: 18 LKGQKGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNVR 63
>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 = 28.6 bits (64), Expect = 3.5
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
+ I G G GK+T + L ++R V + A D
Sbjct: 36 RVGITGTPGAGKSTLLEALGMELRRRGLRVAVIAVD 71
>gnl|CDD|217208 pfam02734, Dak2, DAK2 domain. This domain is the predicted
phosphatase domain of the dihydroxyacetone kinase
family.
Length = 174
Score = 28.3 bits (64), Expect = 3.6
Identities = 20/86 (23%), Positives = 30/86 (34%), Gaps = 23/86 (26%)
Query: 226 DGNTGQN---TLSQIKEFSKILRITGLIITKLDGTTKGGILAAIAKKY-------SIPLY 275
DG+ G N + + + L+ G +L AIA S PLY
Sbjct: 4 DGDHGTNMARGFEAVLKA----------LDALEDADIGEVLKAIAMALLSGAGGTSGPLY 53
Query: 276 ---FIGIGEKIEDLQIFNAVDFVNAL 298
F G + ++ +A D AL
Sbjct: 54 GQFFRGAAKALKGKDELDAEDLAAAL 79
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 28.5 bits (64), Expect = 3.8
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
V+ I+G NG GK+T + L+ V L
Sbjct: 29 VLAILGPNGAGKSTLLKALSGELSPDSGEVTL 60
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 28.4 bits (64), Expect = 3.8
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 101 VIMIVGVNGVGKTTTIG-KLANYFKKRKKSVLLAACD 136
I I G GVGKTT L K +VL+ D
Sbjct: 2 KIAITGKGGVGKTTIAALLLKRLLSKGGYNVLVVDAD 38
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 28.5 bits (64), Expect = 4.0
Identities = 13/20 (65%), Positives = 15/20 (75%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
VI I+G NG+GKTT I LA
Sbjct: 27 VIGILGPNGIGKTTFIKMLA 46
>gnl|CDD|213230 cd03263, ABC_subfamily_A, ATP-binding cassette domain of the lipid
transporters, subfamily A. The ABCA subfamily mediates
the transport of a variety of lipid compounds. Mutations
of members of ABCA subfamily are associated with human
genetic diseases, such as, familial high-density
lipoprotein (HDL) deficiency, neonatal surfactant
deficiency, degenerative retinopathies, and congenital
keratinization disorders. The ABCA1 protein is involved
in disorders of cholesterol transport and high-density
lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein
transports vitamin A derivatives in the outer segments
of photoreceptor cells, and therefore, performs a
crucial step in the visual cycle. The ABCA genes are not
present in yeast. However, evolutionary studies of ABCA
genes indicate that they arose as transporters that
subsequently duplicated and that certain sets of ABCA
genes were lost in different eukaryotic lineages.
Length = 220
Score = 28.2 bits (64), Expect = 4.1
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 101 VIMIVGVNGVGKTTTIGKLAN 121
+ ++G NG GKTTT+ L
Sbjct: 30 IFGLLGHNGAGKTTTLKMLTG 50
>gnl|CDD|216936 pfam02223, Thymidylate_kin, Thymidylate kinase.
Length = 186
Score = 28.0 bits (63), Expect = 4.1
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 104 IVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
I G++G GKTT L K++ V+L
Sbjct: 1 IEGLDGAGKTTQAELLKERLKEQGIKVVL 29
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 28.8 bits (65), Expect = 4.2
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
VI I+G NG+GKTT + LA
Sbjct: 369 VIGILGPNGIGKTTFVKLLA 388
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 28.0 bits (63), Expect = 4.2
Identities = 26/127 (20%), Positives = 45/127 (35%), Gaps = 21/127 (16%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISE 160
V+ I G +G GKTT KL+N + ++ + D + G Y D
Sbjct: 1 VVGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYVPRKTPRDEDGNY-DFES--- 56
Query: 161 KKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIFELPYE 220
I D + N ++ K ++ I D + K + +LP
Sbjct: 57 --ILDLDLLNKNLHDLLNGKEVELPIYD---------------FRTGKRRGYRKLKLPPS 99
Query: 221 IFLIIDG 227
+I++G
Sbjct: 100 GVVILEG 106
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 28.6 bits (65), Expect = 4.3
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
VI IVG NG+GKTT LA
Sbjct: 367 VIGIVGPNGIGKTTFAKLLA 386
Score = 28.2 bits (64), Expect = 6.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
V I+G NG+GKTT + L+
Sbjct: 101 VTGILGPNGIGKTTAVKILS 120
>gnl|CDD|215408 PLN02763, PLN02763, hydrolase, hydrolyzing O-glycosyl compounds.
Length = 978
Score = 28.7 bits (64), Expect = 4.4
Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 208 KVIEKKIFELPYEIFLIIDGNTG-----QNTLSQIKEFSKILRITGLIITKLDGTTKGG 261
KV+E+ + + E L ++G+ G +S K+ K+++I+ I+ + G GG
Sbjct: 806 KVVERDLEQAGGEESLGLEGDIGGGLVLAREISIPKDSPKVVKISSSIVARSVGAGSGG 864
>gnl|CDD|237066 PRK12338, PRK12338, hypothetical protein; Provisional.
Length = 319
Score = 28.6 bits (64), Expect = 4.5
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLAN 121
KP+VI+I +G+GK+T +LA
Sbjct: 3 KPYVILIGSASGIGKSTIASELAR 26
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 28.3 bits (63), Expect = 4.5
Identities = 26/131 (19%), Positives = 44/131 (33%), Gaps = 7/131 (5%)
Query: 98 KPFVIMIVGVNG-VGKTTTIGKLANYF-KKRKKSVLLAACDTFRAAAYEQLLILGKYNDV 155
+I + G VGKTTT LA K+ K VLL D + LG D+
Sbjct: 1 MMKIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSL----TSWLGLRPDL 56
Query: 156 PVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRLSTQSHLMRELKKIKKVIEKKIF 215
++ + D++ + + L K++
Sbjct: 57 EGDLYNLLSGLKERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPV 116
Query: 216 ELPYEIFLIID 226
+ Y+ ++IID
Sbjct: 117 KDDYD-YIIID 126
>gnl|CDD|224267 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 28.4 bits (64), Expect = 4.6
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
I I G G+GK+TT LA + K VL+ CD
Sbjct: 4 IAIYGKGGIGKSTTSQNLAAALAELGKKVLIVGCD 38
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 28.5 bits (64), Expect = 4.6
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRK 127
MI+G G GKTT I +L + R
Sbjct: 45 TMIIGTTGTGKTTQIRELLASIRARG 70
>gnl|CDD|234321 TIGR03708, poly_P_AMP_trns, polyphosphate:AMP phosphotransferase.
Members of this protein family contain a domain
duplication. The characterized member from Acinetobacter
johnsonii is polyphosphate:AMP phosphotransferase (PAP),
which can transfer the terminal phosphate from poly(P)
to AMP, yielding ADP. In the opposite direction, this
enzyme can synthesize poly(P). Each domain of this
protein family is homologous to polyphosphate kinase, an
enzyme that can run in the forward direction to extend a
polyphosphate chain with a new terminal phosphate from
ATP, or in reverse to make ATP (or GTP) from ADP (or
GDP) [Central intermediary metabolism, Phosphorus
compounds].
Length = 493
Score = 28.5 bits (64), Expect = 4.6
Identities = 14/42 (33%), Positives = 20/42 (47%)
Query: 85 LKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKR 126
L L+ L+ P +I+I G +G GK TI L + R
Sbjct: 26 LLDLQYELLESAGFPVIILIEGWDGAGKGETINLLNEWMDPR 67
>gnl|CDD|238995 cd02038, FleN-like, FleN is a member of the Fer4_NifH superfamily.
It shares the common function as an ATPase, with the
ATP-binding domain at the N-terminus. In Pseudomonas
aeruginosa, FleN gene is involved in regulating the
number of flagella and chemotactic motility by
influencing FleQ activity.
Length = 139
Score = 27.5 bits (62), Expect = 4.8
Identities = 13/28 (46%), Positives = 13/28 (46%)
Query: 109 GVGKTTTIGKLANYFKKRKKSVLLAACD 136
GVGKT LA K K VLL D
Sbjct: 10 GVGKTNISANLALALAKLGKRVLLLDAD 37
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 27.9 bits (62), Expect = 4.9
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 103 MIVGV----NGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAA 142
I+ V G GKTT LA++ VLL D ++
Sbjct: 1 KIIAVLNQKGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSST 44
>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 = 27.6 bits (62), Expect = 5.3
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 101 VIMIVGVNGVGKTTTIGKLA 120
+I+++GV+G GK+T LA
Sbjct: 1 IIVVMGVSGSGKSTVGKALA 20
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 28.2 bits (64), Expect = 5.3
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLAN 121
+P MIVG+ VGK+T I +LA
Sbjct: 117 RPIRAMIVGIPNVGKSTLINRLAG 140
>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 = 27.6 bits (62), Expect = 5.4
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 98 KPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFR 139
+ I G++G GK+T L + SV + D R
Sbjct: 1 RGCTIWFTGLSGSGKSTIANALERKLFAQGISVYVLDGDNVR 42
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 28.2 bits (63), Expect = 5.8
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 101 VIMIV-GVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
VI + G GVGK+T LA + K VLL D
Sbjct: 59 VIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDAD 95
>gnl|CDD|118909 pfam10388, YkuI_C, EAL-domain associated signalling protein
domain. In Bacillus species this highly conserved
region of the YkuI protein lies immediately downstream
of the EAL (diguanylate cyclase/phosphodiesterase
domain 2) pfam00563 domain so that together they form a
monomer which dimerises for its enzymatic action. The
region contains three alpha helices and five beta
strands and is the C-terminal half of the structure.
Length = 166
Score = 27.7 bits (62), Expect = 5.9
Identities = 16/54 (29%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 37 LESDLLKADVGFETTQFLLNELKKIIYSKKLFN-TEQVRNVLHNLLVNLLKSLE 89
+E D+LK + E QF+ +E KK+ + + E+++ LH L L K+ +
Sbjct: 2 IERDVLKERLKKEFHQFITHEKKKL---EAQYQLAEKLQKRLHQALSELKKAAD 52
>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 = 27.4 bits (61), Expect = 5.9
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKS 129
IM +G G GKTT L KK+
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEILYKKT 30
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 27.9 bits (63), Expect = 6.0
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 100 FVIMIVGVNGVGKTTTI 116
F IM+VG +G+GK+T I
Sbjct: 5 FNIMVVGESGLGKSTFI 21
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 28.1 bits (63), Expect = 6.1
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 22/69 (31%)
Query: 145 QLLILGKYNDVPVISEKKITDPAAIAFNAINIAQKKNTDIVIVDTSGRL--------STQ 196
QLL LG +P I +A N ++IA+K+N I I S RL ST+
Sbjct: 107 QLLELG----IPCI----------VALNMLDIAEKQNIRIDIDALSARLGCPVIPLVSTR 152
Query: 197 SHLMRELKK 205
+ LK
Sbjct: 153 GRGIEALKL 161
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.8 bits (60), Expect = 6.1
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 3/48 (6%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLIL 149
+IV G GKT T L K KK VL R EQ L++
Sbjct: 21 GLIVMATGSGKTLTAAALIARLAKGKKKVLFVV---PRKDLLEQALVI 65
>gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 450
Score = 28.0 bits (63), Expect = 6.2
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 89 EKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLA 133
E L ++ K ++ I G NG KTTT L FK + L+A
Sbjct: 98 EVELAYRFSKAPIVAITGTNG--KTTTTTLLGEIFKNAGRKTLVA 140
>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 = 27.3 bits (61), Expect = 6.2
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
V+ IVG GKTT I +L K R V
Sbjct: 1 VLQIVGPKNSGKTTLIERLVKALKARGYRVAT 32
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 27.8 bits (63), Expect = 6.3
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
V+ I+G NG GK+T + L+ V L
Sbjct: 30 VVAILGPNGAGKSTLLRALSGELSPDSGEVRLNGRP 65
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid transport,
and lantibiotic immunity. In bacteria and archaea, these
transporters usually include an ATP-binding protein and
one or two integral membrane proteins. Eukaryotic
systems of the ABCA subfamily display ABC domains that
are quite similar to this family. The ATP-binding domain
shows the highest similarity between all members of the
ABC transporter family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 27.4 bits (62), Expect = 6.4
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 104 IVGVNGVGKTTTI 116
++G NG GKTT I
Sbjct: 31 LLGPNGAGKTTLI 43
>gnl|CDD|133404 cd04777, HTH_MerR-like_sg1, Helix-Turn-Helix DNA binding domain
of putative transcription regulators from the MerR
superfamily. Putative helix-turn-helix (HTH) MerR-like
transcription regulators (subgroup 1), N-terminal
domain. Based on sequence similarity, these proteins
are predicted to function as transcription regulators
that mediate responses to stress in eubacteria. They
belong to the MerR superfamily of transcription
regulators that promote transcription of various stress
regulons by reconfiguring the operator sequence located
between the -35 and -10 promoter elements. A typical
MerR regulator is comprised of two distinct domains
that harbor the regulatory (effector-binding) site and
the active (DNA-binding) site. Their N-terminal domains
are homologous and contain a DNA-binding winged HTH
motif, while the C-terminal domains are often
dissimilar and bind specific coactivator molecules such
as metal ions, drugs, and organic substrates.
Length = 107
Score = 26.6 bits (59), Expect = 6.5
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 2/77 (2%)
Query: 19 NLKSLIVNKKIDKNLYNELESDLLKADVGFETTQFLLNELKKIIYSKKL--FNTEQVRNV 76
+L LI KK + ++E D L+ + + F L E++KI K+L T + ++
Sbjct: 22 DLGLLIPEKKGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKRLTKSRTHEDQDY 81
Query: 77 LHNLLVNLLKSLEKPLI 93
+ L N LEK +
Sbjct: 82 YKSFLKNKKDELEKEIE 98
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 28.1 bits (63), Expect = 6.6
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 14/69 (20%)
Query: 71 EQVRNVLHNLLVNL-LKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLANYFKKRKKS 129
Q L N NL L EK + I+G +G GK+T + LA + ++ S
Sbjct: 348 GQQTKALKNF--NLTLAQGEK-----------VAILGRSGSGKSTLLQLLAGAWDPQQGS 394
Query: 130 VLLAACDTF 138
+ L +
Sbjct: 395 ITLNGVEIA 403
>gnl|CDD|183173 PRK11519, PRK11519, tyrosine kinase; Provisional.
Length = 719
Score = 28.2 bits (63), Expect = 6.8
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 79 NLLVNLLKSLEKPLIFK--KCKPFVIMIVGVN-GVGKTTTIGKLANYFKKRKKSVLLAAC 135
+L + ++SL L F + + V+M+ GV+ +GKT LA + K VLL C
Sbjct: 504 DLAIEAIRSLRTSLHFAMMQAQNNVLMMTGVSPSIGKTFVCANLAAVISQTNKRVLLIDC 563
Query: 136 DTFRAAAYEQL 146
D + +E L
Sbjct: 564 DMRKGYTHELL 574
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 27.3 bits (61), Expect = 7.3
Identities = 26/128 (20%), Positives = 48/128 (37%), Gaps = 32/128 (25%)
Query: 5 WITRLKESLSKTACNLKSLIV--NKKIDKNLYNELESDLLKADVGFETTQFLLNELKKII 62
+TR ++ K LI+ NK +DL+ +V + + +E ++
Sbjct: 25 ELTRSRKLERMALELGKKLIIVLNK-----------ADLVPREVLEKWKEVFESEGLPVV 73
Query: 63 Y--SKKLFNTEQVRNVLHNLLVNLLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLA 120
Y +++ T +R + L KP ++ +VG VGK++ I
Sbjct: 74 YVSARERLGTRILRRTIKELA-------------IDGKPVIVGVVGYPKVGKSSII---- 116
Query: 121 NYFKKRKK 128
N K R
Sbjct: 117 NALKGRHS 124
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.0 bits (63), Expect = 7.6
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 102 IMIVGVNGVGKTTTIGKLAN 121
I IVG NG GK+T + LA
Sbjct: 351 IAIVGPNGAGKSTLLKLLAG 370
>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
Length = 273
Score = 27.7 bits (61), Expect = 7.8
Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 5/90 (5%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACDTFRAAAYEQLLILGKYNDVPVISEK 161
I I G G+GK+TT L +LL CD A ++LG N V+
Sbjct: 4 IAIYGKGGIGKSTTTQNLTAALSTMGNKILLVGCD---PKADSTRMLLGGLNQKTVLDTL 60
Query: 162 KITDPAAIAFNAINIAQKKNTDIVIVDTSG 191
+ + + + Q DI V++ G
Sbjct: 61 RSEGDEGVDLDV--VMQPGFGDIKCVESGG 88
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 27.2 bits (61), Expect = 7.9
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 101 VIMIVGVNGVGKTTTI 116
++ +VG NG GK+T +
Sbjct: 27 IVALVGPNGSGKSTLL 42
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 26.9 bits (60), Expect = 8.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKR 126
+ ++ G +G GKTT + +LA R
Sbjct: 6 IGVLTGESGSGKTTLLRRLARQLPNR 31
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 27.7 bits (62), Expect = 8.4
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 102 IMIVGVNGVGKTTTIGKLANYFKKRKKSVLL 132
I++ G G GK+TT+ + +Y K K ++
Sbjct: 125 ILVTGPTGSGKSTTLASMIDYINKNKAYHII 155
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 27.5 bits (61), Expect = 8.8
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 84 LLKSLEKPLIFKKCKPFVIMIVGVNGVGKTTTIGKLAN 121
+++ LE P F P ++ G G GKT LAN
Sbjct: 136 IMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALAN 173
>gnl|CDD|233686 TIGR02016, BchX, chlorophyllide reductase iron protein subunit X.
This model represents the X subunit of the three-subunit
enzyme, (bacterio)chlorophyllide reductase. This enzyme
is responsible for the reduction of the chlorin B-ring
and is closely related to the protochlorophyllide
reductase complex which reduces the D-ring. Both of
these complexes in turn are homologous to nitrogenase.
This subunit is homologous to the nitrogenase component
II, or "iron" protein [Energy metabolism,
Photosynthesis].
Length = 296
Score = 27.5 bits (61), Expect = 8.9
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 101 VIMIVGVNGVGKTTTIGKLANYFKKRKKSVLLAACD 136
+I I G G GK+ T L++ + K VL CD
Sbjct: 2 IIAIYGKGGSGKSFTTTNLSHMMAEMGKRVLQLGCD 37
>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 = 26.8 bits (60), Expect = 9.6
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 102 IMIVGVNGVGKTTTIGKLANYF 123
I+++G++G GKTT + KL
Sbjct: 2 ILMLGLDGAGKTTILYKLKLGE 23
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 0.138 0.376
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: 15,469,440
Number of extensions: 1559859
Number of successful extensions: 2869
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2813
Number of HSP's successfully gapped: 288
Length of query: 302
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 206
Effective length of database: 6,679,618
Effective search space: 1376001308
Effective search space used: 1376001308
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: 59 (26.4 bits)