RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15622
(217 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 91.0 bits (226), Expect = 2e-21
Identities = 50/134 (37%), Positives = 70/134 (52%), Gaps = 26/134 (19%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVD--LASDLDLELVSDQ 137
A+N P ++D A LR R ++ IYVPLP R E+ ++ LR LA D+DLE +++
Sbjct: 383 AATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEI 442
Query: 138 LEGYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAKCRKT 197
EGYS +DI + R+AA A+R A R R VT DF A+ K + +
Sbjct: 443 TEGYSGADIAALVREAALEALREARR----------------REVTLDDFLDALKKIKPS 486
Query: 198 VTAADIRQFEEWNE 211
VT +EEW E
Sbjct: 487 VT------YEEWKE 494
Score = 74.9 bits (184), Expect = 9e-16
Identities = 34/68 (50%), Positives = 47/68 (69%), Gaps = 1/68 (1%)
Query: 7 RDIIVERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHI-RKPWKGVLMVGPPGTGK 65
R ++ E DV DI +AK+ L+EA+ PL++P F+ + +P KGVL+ GPPGTGK
Sbjct: 230 RGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGK 289
Query: 66 TMLAKAVA 73
T+LAKAVA
Sbjct: 290 TLLAKAVA 297
Score = 49.4 bits (118), Expect = 4e-07
Identities = 34/114 (29%), Positives = 56/114 (49%), Gaps = 13/114 (11%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
GA+N P +D A R R ++ I V LP +GR E+L++ R + L + ++ +
Sbjct: 123 GATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTV 182
Query: 140 GYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAK 193
G S +D+ + ++A A+R R AI + VT+ DFE A+ K
Sbjct: 183 GKSGADLGALAKEA---ALRELRR--------AIDLVGEYIGVTEDDFEEALKK 225
Score = 37.5 bits (87), Expect = 0.003
Identities = 22/38 (57%), Positives = 31/38 (81%), Gaps = 1/38 (2%)
Query: 37 LPLEKPSYFQHI-RKPWKGVLMVGPPGTGKTMLAKAVA 73
LPL++P F+ + +P KGVL+ GPPGTGKT+LA+A+A
Sbjct: 2 LPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA 39
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 87.7 bits (217), Expect = 4e-20
Identities = 45/141 (31%), Positives = 76/141 (53%), Gaps = 3/141 (2%)
Query: 77 NQVHCGASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELV 134
N V A+N P +D A LR R ++ I VP P R+E+ ++ R + LA D+DLE +
Sbjct: 590 NVVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEEL 649
Query: 135 SDQLEGYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRP-VTKADFEMAIAK 193
++ EGY+ +DI VCR+AA A+R +I + +++ LK V F A+ K
Sbjct: 650 AEMTEGYTGADIEAVCREAAMAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKK 709
Query: 194 CRKTVTAADIRQFEEWNEKFG 214
+ +V+ D+ ++E ++
Sbjct: 710 VKPSVSKEDMLRYERLAKELK 730
Score = 76.1 bits (187), Expect = 4e-16
Identities = 37/68 (54%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 7 RDIIVERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGK 65
R+++VE P+V+WSDI + K+ L+EAV PL+ P F+ + +P KGVL+ GPPGTGK
Sbjct: 441 REVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGK 500
Query: 66 TMLAKAVA 73
T+LAKAVA
Sbjct: 501 TLLAKAVA 508
Score = 68.8 bits (168), Expect = 1e-13
Identities = 32/61 (52%), Positives = 44/61 (72%), Gaps = 1/61 (1%)
Query: 14 PDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTMLAKAV 72
P V + DI +AK+ ++E V LP++ P F+H+ +P KGVL+ GPPGTGKT+LAKAV
Sbjct: 173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAV 232
Query: 73 A 73
A
Sbjct: 233 A 233
Score = 67.2 bits (164), Expect = 5e-13
Identities = 38/120 (31%), Positives = 65/120 (54%), Gaps = 4/120 (3%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
GA+N P +D A R R ++ I + +P R+E+L++ R + LA D+DL+ +++
Sbjct: 319 GATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTH 378
Query: 140 GYSASDIVVVCRDAAFMAMRAAIR-GKSVPQIQAIPMAQLKR-PVTKADFEMAIAKCRKT 197
G+ +D+ + ++AA A+R IR GK + + IP LK VT DF A+ +
Sbjct: 379 GFVGADLAALAKEAAMAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKMVEPS 438
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 78.7 bits (195), Expect = 3e-17
Identities = 33/65 (50%), Positives = 47/65 (72%), Gaps = 1/65 (1%)
Query: 10 IVERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTML 68
++E P+V + DI + + ++EAV LPL+KP F+ + +P KGVL+ GPPGTGKT+L
Sbjct: 122 VIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLL 181
Query: 69 AKAVA 73
AKAVA
Sbjct: 182 AKAVA 186
Score = 62.5 bits (153), Expect = 1e-11
Identities = 38/117 (32%), Positives = 59/117 (50%), Gaps = 19/117 (16%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
A+N +D A LR R ++ I VPLP GR E+L++ R+++LA D+DLE +++ E
Sbjct: 275 AATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTE 334
Query: 140 GYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAKCRK 196
G S +D+ +C +A A+R ++ VT DF AI K
Sbjct: 335 GASGADLKAICTEAGMFAIR---DDRTE--------------VTMEDFLKAIEKVMG 374
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 74.6 bits (184), Expect = 1e-15
Identities = 32/63 (50%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 12 ERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTMLAK 70
E+PDV + DI + + ++E V LPL+ P F+ + P KGVL+ GPPGTGKT+LAK
Sbjct: 144 EKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAK 203
Query: 71 AVA 73
AVA
Sbjct: 204 AVA 206
Score = 65.7 bits (161), Expect = 1e-12
Identities = 38/113 (33%), Positives = 60/113 (53%), Gaps = 19/113 (16%)
Query: 83 ASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEG 140
A+N P +D A LR R +++I PLP GR E+L++ R+++LA D+DLEL++ EG
Sbjct: 296 ATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEG 355
Query: 141 YSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAK 193
+S +D+ +C +A A+R + VT DF A+ K
Sbjct: 356 FSGADLKAICTEAGMFAIRE-----------------RRDEVTMEDFLKAVEK 391
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 73.6 bits (181), Expect = 2e-15
Identities = 35/63 (55%), Positives = 44/63 (69%), Gaps = 1/63 (1%)
Query: 12 ERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTMLAK 70
E+PDV +SDI K+ ++EAV LPL P ++ I P +GVL+ GPPGTGKTMLAK
Sbjct: 138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAK 197
Query: 71 AVA 73
AVA
Sbjct: 198 AVA 200
Score = 46.3 bits (110), Expect = 4e-06
Identities = 26/79 (32%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 83 ASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEG 140
A+N +D A LR RL+++I PLP ++ + + I +++L+ ++DLE + E
Sbjct: 290 ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEK 349
Query: 141 YSASDIVVVCRDAAFMAMR 159
SA+DI +C++A A+R
Sbjct: 350 ISAADIAAICQEAGMQAVR 368
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 69.8 bits (171), Expect = 4e-14
Identities = 33/65 (50%), Positives = 46/65 (70%), Gaps = 1/65 (1%)
Query: 10 IVERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTML 68
+ ERP+V + DI + + ++EAV LPL+ P F+ + +P KGVL+ GPPGTGKT+L
Sbjct: 113 VEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLL 172
Query: 69 AKAVA 73
AKAVA
Sbjct: 173 AKAVA 177
Score = 63.7 bits (155), Expect = 6e-12
Identities = 38/114 (33%), Positives = 58/114 (50%), Gaps = 19/114 (16%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
A+N P +D A LR R ++ I VPLP GR E+L++ R++ LA D+DLE ++ E
Sbjct: 266 AATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTE 325
Query: 140 GYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAK 193
G S +D+ +C +A A+R + + VT DF A+ K
Sbjct: 326 GASGADLKAICTEAGMFAIR-----------------EERDYVTMDDFIKAVEK 362
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 62.7 bits (153), Expect = 1e-11
Identities = 34/63 (53%), Positives = 43/63 (68%), Gaps = 2/63 (3%)
Query: 12 ERPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHI-RKPWKGVLMVGPPGTGKTMLAK 70
E+P V + D+A +AK+ L E V L+ PS F + K KGVL+VGPPGTGKT+LAK
Sbjct: 48 EKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAK 106
Query: 71 AVA 73
AVA
Sbjct: 107 AVA 109
Score = 55.4 bits (134), Expect = 3e-09
Identities = 28/79 (35%), Positives = 49/79 (62%), Gaps = 2/79 (2%)
Query: 83 ASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEG 140
A+N P +D A LR R ++++ V LP GR+E+L++ + LA D+DL+ V+ + G
Sbjct: 199 ATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPG 258
Query: 141 YSASDIVVVCRDAAFMAMR 159
+S +D+ + +AA +A R
Sbjct: 259 FSGADLANLLNEAALLAAR 277
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 62.8 bits (153), Expect = 1e-11
Identities = 30/70 (42%), Positives = 45/70 (64%), Gaps = 1/70 (1%)
Query: 5 IKRDIIVERPDVQWSDIANQVKAKKLLQEAVILPLEKPS-YFQHIRKPWKGVLMVGPPGT 63
++ ++ E PDV ++DI + +++AV LP P Y ++ KP KGVL+ GPPG
Sbjct: 168 VEDLVLEEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGC 227
Query: 64 GKTMLAKAVA 73
GKT++AKAVA
Sbjct: 228 GKTLIAKAVA 237
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 61.6 bits (150), Expect = 3e-11
Identities = 30/60 (50%), Positives = 40/60 (66%), Gaps = 2/60 (3%)
Query: 15 DVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHI-RKPWKGVLMVGPPGTGKTMLAKAVA 73
+ + DIA +AK+ +E V L+KP F + K KGVL+VGPPGTGKT+LAKA+A
Sbjct: 179 GITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIA 237
Score = 45.0 bits (107), Expect = 1e-05
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 2/83 (2%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
A+N +D A LR R +++I V LP GR ++L++ R L+ D+ LEL++ +
Sbjct: 326 AATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTP 385
Query: 140 GYSASDIVVVCRDAAFMAMRAAI 162
G+S +D+ + +AA + R
Sbjct: 386 GFSGADLANLLNEAAILTARRKK 408
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 60.2 bits (146), Expect = 8e-11
Identities = 31/65 (47%), Positives = 43/65 (66%), Gaps = 2/65 (3%)
Query: 11 VER-PDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTML 68
V++ P ++DI + + ++EAV LPL P + I KP KGV++ GPPGTGKT+L
Sbjct: 174 VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLL 233
Query: 69 AKAVA 73
AKAVA
Sbjct: 234 AKAVA 238
Score = 37.1 bits (86), Expect = 0.005
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 83 ASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEG 140
A+N ++D A +R R++++I P P ++ + + ++ LA D+DLE +
Sbjct: 328 ATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDE 387
Query: 141 YSASDIVVVCRDAAFMAMR 159
S +DI +C +A +A+R
Sbjct: 388 LSGADIKAICTEAGLLALR 406
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 53.1 bits (127), Expect = 2e-08
Identities = 28/84 (33%), Positives = 50/84 (59%), Gaps = 2/84 (2%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
A+N P +D A LR R ++++ V LP GR+++L++ +R+V LA D+D +++
Sbjct: 295 AATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTP 354
Query: 140 GYSASDIVVVCRDAAFMAMRAAIR 163
G+S +D+ + +AA A R R
Sbjct: 355 GFSGADLANLVNEAALFAARGNKR 378
Score = 51.6 bits (123), Expect = 1e-07
Identities = 31/57 (54%), Positives = 41/57 (71%), Gaps = 2/57 (3%)
Query: 18 WSDIANQVKAKKLLQEAVILPLEKPSYFQHIR-KPWKGVLMVGPPGTGKTMLAKAVA 73
++D+A +AK+ + E V L +PS FQ + K KGVLMVGPPGTGKT+LAKA+A
Sbjct: 151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA 206
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 53.1 bits (128), Expect = 3e-08
Identities = 30/59 (50%), Positives = 42/59 (71%), Gaps = 2/59 (3%)
Query: 16 VQWSDIANQVKAKKLLQEAVILPLEKPSYFQHI-RKPWKGVLMVGPPGTGKTMLAKAVA 73
V ++D+A +AK+ L E ++ L+ P +Q + K KGVL+VGPPGTGKT+LAKAVA
Sbjct: 147 VTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVA 204
Score = 45.0 bits (107), Expect = 1e-05
Identities = 27/80 (33%), Positives = 48/80 (60%), Gaps = 2/80 (2%)
Query: 82 GASNFPWNIDDAFLR--RLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLE 139
A+N P +D A LR R +++I V LP GR+++L++ + LA D+DL+ ++
Sbjct: 293 AATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTP 352
Query: 140 GYSASDIVVVCRDAAFMAMR 159
G+S +D+ + +AA +A R
Sbjct: 353 GFSGADLANLLNEAALLAAR 372
>gnl|CDD|204202 pfam09336, Vps4_C, Vps4 C terminal oligomerisation domain. This
domain is found at the C terminal of ATPase proteins
involved in vacuolar sorting. It forms an alpha helix
structure and is required for oligomerisation.
Length = 62
Score = 46.1 bits (110), Expect = 2e-07
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 171 QAIPMAQLKRP-VTKADFEMAIAKCRKTVTAADIRQFEEWNEKFG 214
I +L P +T DF A+A + TV+ D+ + EE+ +FG
Sbjct: 18 MDIEEDKLLEPPLTMKDFIKALATTKPTVSKDDLEKHEEFTNEFG 62
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 47.5 bits (113), Expect = 2e-06
Identities = 27/65 (41%), Positives = 36/65 (55%), Gaps = 9/65 (13%)
Query: 12 ERPDVQWSDIANQVKAKKLLQEAVILP-LEKPSYFQHIRKPW--KGVLMVGPPGTGKTML 68
D+ D+ Q +AK+ + +I+ LE P F W K VL GPPGTGKTM+
Sbjct: 114 IISDITLDDVIGQEEAKR--KCRLIMEYLENPERF----GDWAPKNVLFYGPPGTGKTMM 167
Query: 69 AKAVA 73
AKA+A
Sbjct: 168 AKALA 172
Score = 39.0 bits (91), Expect = 0.001
Identities = 32/115 (27%), Positives = 48/115 (41%), Gaps = 16/115 (13%)
Query: 82 GASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEGY 141
A+N P +D A R E+ I LP+ R E+L ++ L D DL ++ + +G
Sbjct: 259 AATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGM 318
Query: 142 SASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRPVTKADFEMAIAKCRK 196
S DI A +AI A+ + V + D E A+ K RK
Sbjct: 319 SGRDIKEKVLKTALH--------------RAI--AEDREKVEREDIEKALKKERK 357
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 45.3 bits (108), Expect = 2e-06
Identities = 15/19 (78%), Positives = 17/19 (89%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+ GPPGTGKT LAKAVA
Sbjct: 1 LLLYGPPGTGKTTLAKAVA 19
Score = 34.1 bits (79), Expect = 0.016
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 82 GASNFPWNIDDAFLR-RLEKRIYVPL 106
A+N P +D A LR R ++ I PL
Sbjct: 106 AATNRPDKLDPALLRGRFDRIIEFPL 131
>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 = 45.2 bits (107), Expect = 2e-06
Identities = 15/25 (60%), Positives = 19/25 (76%)
Query: 49 RKPWKGVLMVGPPGTGKTMLAKAVA 73
P K +L+ GPPGTGKT LA+A+A
Sbjct: 16 LPPPKNLLLYGPPGTGKTTLARAIA 40
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 42.9 bits (102), Expect = 3e-05
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 20/57 (35%)
Query: 18 WSDIANQVKAKKLLQEAVILPLEKPSYFQHIRKPWKG---VLMVGPPGTGKTMLAKA 71
+D+ Q +AK+ L+ A G +LM+GPPG+GKTMLAK
Sbjct: 2 LADVKGQEQAKRALEIAAA-----------------GGHNLLMIGPPGSGKTMLAKR 41
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 41.4 bits (98), Expect = 2e-04
Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 8/55 (14%)
Query: 19 SDIANQVKAKKLLQEAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
SD+ KAK+ L+E + L+ KP K +L+ GPPG GKT LA A+A
Sbjct: 14 SDVVGNEKAKEQLREWIESWLKG--------KPKKALLLYGPPGVGKTSLAHALA 60
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 41.1 bits (97), Expect = 2e-04
Identities = 14/19 (73%), Positives = 18/19 (94%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
V+M+G PGTGK+MLAKA+A
Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 40.4 bits (95), Expect = 3e-04
Identities = 14/21 (66%), Positives = 18/21 (85%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+G+L+VGPPGTGKT LA +A
Sbjct: 66 RGILIVGPPGTGKTALAMGIA 86
>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 = 38.9 bits (90), Expect = 4e-04
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 51 PWKGVLMVGPPGTGKTMLAKAVAIVYNQVHCGAS--NFPWNIDDAFLRRLEKRIYVPLPS 108
P + +L+VGPPG+GKT LA+A+A G + +++ + L + S
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 109 SSGRQELLRLI 119
SG L +
Sbjct: 61 GSGELRLRLAL 71
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 38.2 bits (89), Expect = 0.002
Identities = 13/19 (68%), Positives = 17/19 (89%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+ GPPG GKT+LA+A+A
Sbjct: 46 VLLEGPPGVGKTLLARALA 64
Score = 27.0 bits (60), Expect = 8.8
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 3/44 (6%)
Query: 89 NIDDAFLRRLEKRIYVPLPSSSGRQELLRLILRQVDLASDLDLE 132
+ +A L R RIYV P S +E R+IL +V +LDLE
Sbjct: 171 PLPEALLDRFLLRIYVDYPDS---EEEERIILARVGGVDELDLE 211
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 36.5 bits (85), Expect = 0.002
Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 25/76 (32%)
Query: 53 KGVLMV-GPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKR--IYVPLPSS 109
G+ ++ G G+GKT L + R+L R +YV PS
Sbjct: 4 AGIGVLTGESGSGKTTLLR----------------------RLARQLPNRRVVYVEAPSL 41
Query: 110 SGRQELLRLILRQVDL 125
++LLR ILR + L
Sbjct: 42 GTPKDLLRKILRALGL 57
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 36.5 bits (85), Expect = 0.002
Identities = 30/109 (27%), Positives = 40/109 (36%), Gaps = 26/109 (23%)
Query: 54 GVLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQ 113
GVL+VGPPGTGK+ LA+ +A SN P YV L + +
Sbjct: 1 GVLLVGPPGTGKSELAERLAAAL-------SNRPVF-------------YVQLTRDTTEE 40
Query: 114 ELLRLILRQVDLASDLDLELVSDQLEGYSASDIVVVCRDAAFMAMRAAI 162
+L AS +D LV EG + D A +
Sbjct: 41 DLKGRRNIDPGGASWVDGPLVRAAREGE------IAVLDEINRANPDVL 83
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49
(TIP49) was originally identified as a TBP-binding
protein, and two related proteins are encoded by
individual genes, tip49a and b. Although the function
of this gene family has not been elucidated, they are
supposed to play a critical role in nuclear events
because they interact with various kinds of nuclear
factors and have DNA helicase activities.TIP49a has
been suggested to act as an autoantigen in some
patients with autoimmune diseases.
Length = 395
Score = 37.3 bits (87), Expect = 0.004
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+ VL+ GPPGTGKT LA A++
Sbjct: 51 RAVLIAGPPGTGKTALAIAIS 71
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 34.9 bits (81), Expect = 0.011
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
L +GP G GKT LAKA+A
Sbjct: 6 FLFLGPTGVGKTELAKALA 24
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 34.5 bits (79), Expect = 0.016
Identities = 20/78 (25%), Positives = 29/78 (37%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQE 114
VL+ GP GTGKT L + + N AF + L + + L +
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAELL 86
Query: 115 LLRLILRQVDLASDLDLE 132
LLR L A ++
Sbjct: 87 LLREALLAALGAELIEGL 104
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 35.6 bits (83), Expect = 0.016
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 54 GVLMVGPPGTGKTMLAKAVAIVYN 77
G+L+ G PG GK+ A+A+A Y
Sbjct: 259 GILIAGAPGAGKSTFAQALAEFYA 282
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 34.1 bits (79), Expect = 0.017
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+ G PG KT+LA+ +A
Sbjct: 2 VLLEGVPGLAKTLLARTLA 20
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.3 bits (82), Expect = 0.018
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 53 KGVLMVGPPGTGKTMLAK 70
+L+VGPPGTGKTMLA
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 35.2 bits (82), Expect = 0.023
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 46 QHIRKPWKGVLM--VGPPGTGKTMLAKAVA 73
Q + K KG ++ VGPPG GKT L K++A
Sbjct: 342 QKLTKKLKGPILCLVGPPGVGKTSLGKSIA 371
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 34.8 bits (80), Expect = 0.027
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 56 LMVGPPGTGKTMLAKAVAIVY 76
L GPPGTGKT +A+ VA +Y
Sbjct: 316 LFAGPPGTGKTTIARVVAKIY 336
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 34.4 bits (79), Expect = 0.036
Identities = 13/21 (61%), Positives = 18/21 (85%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+ VL++G PG GK+MLAKA+A
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 34.0 bits (79), Expect = 0.049
Identities = 10/19 (52%), Positives = 17/19 (89%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L++GP G+GKT+LA+ +A
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 33.9 bits (79), Expect = 0.053
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 59 GPPGTGKTMLAKAVA 73
GPPGTGKT LA+ +A
Sbjct: 43 GPPGTGKTTLARIIA 57
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 33.8 bits (78), Expect = 0.057
Identities = 12/21 (57%), Positives = 18/21 (85%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+G+L+VG GTGK++ AKA+A
Sbjct: 260 RGLLLVGIQGTGKSLTAKAIA 280
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 33.9 bits (78), Expect = 0.058
Identities = 20/108 (18%), Positives = 39/108 (36%), Gaps = 24/108 (22%)
Query: 1 MKRLIKRDIIVERP--------DVQWSDIANQVKAKKLLQEAVILPLE----------KP 42
++LI D I +P ++ +A + A++ L
Sbjct: 12 FRKLIDSDPIYYKPYKLGVAYKNLSAYGVAADSDYQPTFPNALLKILTRGFRKLKKFRDT 71
Query: 43 SYFQHIR------KPWKGVLMVGPPGTGKTMLAKAVAIVYNQVHCGAS 84
F ++ KP + +++G PG+G + L K +A + H G
Sbjct: 72 KTFDILKPMDGLIKPGELTVVLGRPGSGCSTLLKTIASNTDGFHIGVE 119
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 33.7 bits (77), Expect = 0.061
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 55 VLMVGPPGTGKTMLAK 70
+L+ GPPG+GKTMLA
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 33.3 bits (77), Expect = 0.064
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+ GPPG GKT LA +A
Sbjct: 55 VLLFGPPGLGKTTLAHIIA 73
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 33.2 bits (77), Expect = 0.069
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+ GPPG GKT LA +A
Sbjct: 54 VLLYGPPGLGKTTLANIIA 72
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 33.3 bits (77), Expect = 0.069
Identities = 10/19 (52%), Positives = 17/19 (89%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L++GP G+GKT+LA+ +A
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 33.4 bits (76), Expect = 0.081
Identities = 12/15 (80%), Positives = 15/15 (100%)
Query: 55 VLMVGPPGTGKTMLA 69
+L++GPPGTGKTMLA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 33.1 bits (76), Expect = 0.085
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 9/57 (15%)
Query: 55 VLMVGPPGTGKTMLAKAVA---IVYNQVHCGASNFPWNIDDAFLRRL----EKRIYV 104
V GP TGKT LA+A+A +Y V+ NFP+N D + L E + V
Sbjct: 116 VWFYGPASTGKTNLAQAIAHAVPLYGCVNWTNENFPFN--DCPNKLLIWWEEGLMTV 170
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 33.1 bits (76), Expect = 0.086
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 53 KGVLMVGPPGTGKTMLAKAVAIVYN 77
+G+L+ G PG GK+ A+A+A Y
Sbjct: 264 EGILIAGAPGAGKSTFAQALAEFYA 288
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic
protein and predicted ATPase that is induced by
phosphate starvation.
Length = 205
Score = 32.4 bits (75), Expect = 0.12
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
V +GP GTGKT LA A A+
Sbjct: 22 VFGIGPAGTGKTYLAVAAAV 41
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 32.8 bits (75), Expect = 0.13
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 25 VKAKKLLQEAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
+ + L+ A+ L P G L+ G GT K+ LA+A+A
Sbjct: 19 IVGQDPLKLALGLNAVDPQI--------GGALIAGEKGTAKSTLARALA 59
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.9 bits (73), Expect = 0.18
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 54 GVLMVGPPGTGKTMLAKAVA 73
G+L+ G GTGKT LA +A
Sbjct: 116 GLLLWGSVGTGKTYLAACIA 135
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 32.3 bits (74), Expect = 0.18
Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 46 QHIRKPWKGVLM--VGPPGTGKTMLAKAVA 73
Q +R KG ++ VGPPG GKT L K++A
Sbjct: 339 QKLRGKMKGPILCLVGPPGVGKTSLGKSIA 368
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 32.2 bits (74), Expect = 0.18
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 59 GPPGTGKTMLAKAVA 73
GPPGTGKT LA+ +A
Sbjct: 55 GPPGTGKTTLARLIA 69
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 30.3 bits (69), Expect = 0.21
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+ + GPPG GK+ LAK +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLA 19
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 31.4 bits (72), Expect = 0.22
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+++ G P TGKT L +A+A
Sbjct: 2 IVITGGPSTGKTTLLEALA 20
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 31.5 bits (72), Expect = 0.23
Identities = 14/22 (63%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 49 RKPWKGVLMVGPPGTGKTMLAK 70
K K VL+ GPPG GKT LAK
Sbjct: 1 TKNIK-VLIYGPPGIGKTSLAK 21
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 31.1 bits (71), Expect = 0.25
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 54 GVLMVGPPGTGKTMLAKAVAI 74
+L++GPPG GKT LA A+
Sbjct: 49 NLLLLGPPGVGKTHLACALGH 69
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 31.3 bits (72), Expect = 0.27
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+ GPPG GKT LA +A
Sbjct: 53 VLLYGPPGLGKTTLANIIA 71
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form (CCALD),
the milder adult form, adrenomyeloneuropathy (AMN), and
variants without neurologic involvement (i.e.
asymptomatic).
Length = 166
Score = 30.6 bits (70), Expect = 0.31
Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 20/88 (22%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPS------ 108
+L+ GP GTGK+ L +A+A ++ G P D FL + R Y+PL +
Sbjct: 30 LLITGPSGTGKSSLFRALAGLW-PWGSGRIGMPEGEDLLFLPQ---RPYLPLGTLREQLI 85
Query: 109 -------SSGRQELL---RLILRQVDLA 126
S G Q+ L RL+L +
Sbjct: 86 YPWDDVLSGGEQQRLAFARLLLHKPKFV 113
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 31.4 bits (71), Expect = 0.33
Identities = 23/67 (34%), Positives = 31/67 (46%), Gaps = 20/67 (29%)
Query: 45 FQHIRKPWKG---VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWN-------IDDAF 94
F + +P G V+MVG PG GKT +A+ + F WN I A+
Sbjct: 205 FSAVPQPMMGSLIVIMVGLPGRGKTYVARQI----------QRYFQWNGLQSRIFIHQAY 254
Query: 95 LRRLEKR 101
RRLE+R
Sbjct: 255 RRRLERR 261
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 30.7 bits (70), Expect = 0.35
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 53 KGVLMVGPPGTGKTMLAKAV 72
VL+ G PG GKT LA+A+
Sbjct: 13 VAVLLGGQPGAGKTELARAL 32
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 31.3 bits (71), Expect = 0.41
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 24 QVKAKKLLQEAV------ILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
Q +AKK+L AV + + + +L++GP G+GKT+LA+ +A
Sbjct: 82 QEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLA 137
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.6 bits (69), Expect = 0.44
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
V+ +GPPGTGKT LA + I
Sbjct: 101 VVFLGPPGTGKTHLAIGLGI 120
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 30.4 bits (69), Expect = 0.45
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
V++ G G+GKT L + +A
Sbjct: 3 VILQGEAGSGKTTLLQKIA 21
>gnl|CDD|184146 PRK13565, PRK13565, anthranilate synthase component I; Provisional.
Length = 490
Score = 31.0 bits (71), Expect = 0.48
Identities = 10/40 (25%), Positives = 17/40 (42%)
Query: 166 SVPQIQAIPMAQLKRPVTKADFEMAIAKCRKTVTAADIRQ 205
+ P A + TK D+ A+ K ++ + A D Q
Sbjct: 200 APPVTSASSRTEFVSEFTKEDYLAAVRKAKEYIAAGDCMQ 239
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 30.9 bits (70), Expect = 0.48
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 13 RPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAV 72
RP +S++ Q KKL+ A L S+ + GP GTGKT +A+ +
Sbjct: 9 RPK-TFSEVVGQDHVKKLIINA--LKKNSISH---------AYIFAGPRGTGKTTVARIL 56
Query: 73 A 73
A
Sbjct: 57 A 57
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 30.0 bits (69), Expect = 0.51
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 VLMVGPPGTGKTMLAKAV 72
VL+ G GTGK + A+A+
Sbjct: 25 VLITGESGTGKELFARAI 42
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.6 bits (70), Expect = 0.51
Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 21/84 (25%)
Query: 55 VLMVGPPGTGKTMLAK---------AVAIVYNQVHCGASNFPWNIDD---AFLRRLEKRI 102
VL+ GPPGTGKT K AV +VY ++C ID A + +++
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINC-------QIDRTRYAIFSEIARQL 110
Query: 103 YVPLPSSSG--RQELLRLILRQVD 124
+ P SSG EL I +D
Sbjct: 111 FGHPPPSSGLSFDELFDKIAEYLD 134
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 30.8 bits (70), Expect = 0.55
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 59 GPPGTGKTMLAKAVA-------IVYNQVHCGASNFPWNIDDAFLRR 97
GPPG GKT LA+ +A N V G + +D A R
Sbjct: 59 GPPGVGKTTLARIIANHTRAHFSSLNAVLAGVKDLRAEVDRAKERL 104
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 30.7 bits (70), Expect = 0.58
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
V +GP GTGKT LA A A+
Sbjct: 146 VFGIGPAGTGKTYLAVAKAV 165
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 30.6 bits (70), Expect = 0.59
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 7/69 (10%)
Query: 118 LILRQVDLASDLDLELVSDQLEGYSASDIVVVCRDAAFMAMRAAIRGK---SVPQIQAI- 173
+L Q +L + +L+ D+L SD + A MA AIR ++ ++ A+
Sbjct: 526 ALLGQQELEELI-RDLL-DELAEEGDSDTLKERELLATMACHGAIRAGRRLTLEEMNALL 583
Query: 174 -PMAQLKRP 181
+ + P
Sbjct: 584 RQLEATENP 592
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 30.4 bits (69), Expect = 0.62
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 56 LMVGPPGTGKTMLAKAVA 73
L+V PP GKT+L + +A
Sbjct: 137 LIVAPPRAGKTVLLQQIA 154
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 29.2 bits (65), Expect = 0.67
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+ GPPG+GK+ LAK +A
Sbjct: 2 ILITGPPGSGKSTLAKKLA 20
>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 = 29.7 bits (68), Expect = 0.76
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
+ + G GTGKT+L +A
Sbjct: 18 IGIFGGSGTGKTVLLGMIAR 37
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 30.3 bits (69), Expect = 0.78
Identities = 16/26 (61%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 49 RKPWKGV-LMVGPPGTGKTMLAKAVA 73
RKP GV L+VGP G GKT A A+A
Sbjct: 593 RKP-LGVFLLVGPSGVGKTETALALA 617
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 30.2 bits (68), Expect = 0.82
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 11/47 (23%)
Query: 50 KPWKGVLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLR 96
+P L +GP G GKT L KA+A NF ++ DDA +R
Sbjct: 596 RPIGSFLFLGPTGVGKTELCKALA-----------NFMFDSDDAMVR 631
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 30.1 bits (68), Expect = 0.83
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 53 KGVLMVGPPGTGKTMLAKAVAI 74
+ ++++GPPG GKT LA A+
Sbjct: 106 ENLVLLGPPGVGKTHLAIAIGN 127
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 30.1 bits (69), Expect = 0.83
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 56 LMVGPPGTGKTMLAKAVA--IVYN 77
L+V PP GKT+L + +A I N
Sbjct: 173 LIVAPPKAGKTVLLQNIANSITTN 196
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.6 bits (67), Expect = 0.88
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+L++GPPG GK+ LAK +A
Sbjct: 1 MRILILGPPGAGKSTLAKKLA 21
>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 = 29.2 bits (66), Expect = 0.89
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+LMVG PG+GK+ A+ +
Sbjct: 2 ILMVGLPGSGKSTFARRLL 20
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 30.0 bits (68), Expect = 0.94
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+ GPPG GKT LA +A
Sbjct: 33 LLLYGPPGLGKTTLAHIIA 51
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 29.9 bits (68), Expect = 0.99
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 44 YFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
+ ++ K + +L G GTGKT L+ +A
Sbjct: 175 FIENFDKNNENLLFYGNTGTGKTFLSNCIA 204
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 29.6 bits (67), Expect = 1.0
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 56 LMVGPPGTGKTMLAKAVA--IVYNQ 78
L+V PP GKT L +++A I N
Sbjct: 20 LIVAPPKAGKTTLLQSIANAITKNH 44
>gnl|CDD|233914 TIGR02538, type_IV_pilB, type IV-A pilus assembly ATPase PilB.
This model describes a protein of type IV pilus
biogenesis designated PilB in Pseudomonas aeruginosa but
PilF in Neisseria gonorrhoeae; the more common usage,
reflected here, is PilB. This protein is an ATPase
involved in protein export for pilin assembly and is
closely related to GspE (TIGR02533) of type II
secretion, also called the main terminal branch of the
general secretion pathway. Note that type IV pilus
systems are often divided into type IV-A and IV-B, with
the latter group including bundle-forming pilus,
mannose-sensitive hemagglutinin, etc. Members of this
family are found in type IV-A systems [Cell envelope,
Surface structures, Protein fate, Protein and peptide
secretion and trafficking].
Length = 564
Score = 30.0 bits (68), Expect = 1.0
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 38 PLEKPSYFQHIRKPWKGVLMVGPPGTGKT 66
P +K + + I KP VL+ GP G+GKT
Sbjct: 302 PDQKALFLEAIHKPQGMVLVTGPTGSGKT 330
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.0 bits (68), Expect = 1.2
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 46 QHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
++ +P L GP G GKT L KA+A
Sbjct: 533 KNPNRPIASFLFSGPTGVGKTELTKALA 560
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.4 bits (66), Expect = 1.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 52 WKGVLMVGPPGTGKTMLAKAVA 73
W L++GPP GKT L + +A
Sbjct: 137 WLNTLIIGPPQVGKTTLLRDIA 158
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. This RNA
helicase, the transcription termination factor Rho,
occurs in nearly all bacteria but is missing from the
Cyanobacteria, the Mollicutes (Mycoplasmas), and various
Lactobacillales including Streptococcus. It is also
missing, of course, from the Archaea, which also lack
Nus factors. Members of this family from Micrococcus
luteus, Mycobacterium tuberculosis, and related species
have a related but highly variable long, highly charged
insert near the amino end. Members of this family differ
in the specificity of RNA binding [Transcription,
Transcription factors].
Length = 415
Score = 29.7 bits (67), Expect = 1.2
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 56 LMVGPPGTGKTMLAK--AVAIVYNQVHC 81
L+V PP GKT+L + A AI N
Sbjct: 172 LIVAPPKAGKTVLLQKIAQAITRNHPEV 199
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 29.1 bits (66), Expect = 1.2
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHC 81
+L++GPPG+GK A+ +A Y H
Sbjct: 2 ILLLGPPGSGKGTQAERLAKKYGLPHI 28
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 29.5 bits (67), Expect = 1.2
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 43 SYFQHIRKPWKGVLMV-GPPGTGKTMLAKAVA 73
S + I + ++ G PGTGK+ L K +
Sbjct: 20 SLYDSIIDGANRIFILKGGPGTGKSTLMKKIG 51
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 29.9 bits (67), Expect = 1.2
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 41 KPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
KP + P +G+L++G GTG++ L K +A
Sbjct: 1619 KPFSLRLALSPSRGILVIGSIGTGRSYLVKYLA 1651
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 29.9 bits (68), Expect = 1.2
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 49 RKPWKGVLMVGPPGTGKTMLAKAVA 73
+P L +GP G GKT LAKA+A
Sbjct: 518 NRPIGSFLFLGPTGVGKTELAKALA 542
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 29.8 bits (67), Expect = 1.3
Identities = 13/26 (50%), Positives = 18/26 (69%)
Query: 48 IRKPWKGVLMVGPPGTGKTMLAKAVA 73
I KP + L++GPP +GKT L A+A
Sbjct: 187 IIKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU,
while the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop
ATP-binding motif. Cys-287 of E. coli (position 308 in
the seed alignment), studied in MEDLINE:98389714, is
Ser in other members of the seed alignment [Protein
fate, Protein folding and stabilization].
Length = 441
Score = 29.4 bits (66), Expect = 1.4
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 21 IANQVKAKKLLQEAVI-----LPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
I Q +AKK + A+ L + + P K +LM+GP G GKT +A+ +A
Sbjct: 14 IIGQDEAKKSVAIALRNRYRRSQLPEE--LKDEVTP-KNILMIGPTGVGKTEIARRLA 68
>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 = 28.6 bits (64), Expect = 1.5
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+ GP G+GKT LA +A
Sbjct: 2 ILVFGPTGSGKTTLALQLA 20
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.9 bits (65), Expect = 1.6
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
+ VL+ G PG+GK+ LA+ +A
Sbjct: 2 RLVLVGGLPGSGKSTLARGLA 22
>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 = 28.7 bits (65), Expect = 1.6
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQ 78
++ GP GTGKT KA +
Sbjct: 21 AVVQGPAGTGKTTSLKAAREAWEA 44
>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 = 28.9 bits (66), Expect = 1.7
Identities = 10/17 (58%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 55 VLMVGPPGTGKTM-LAK 70
+L+VGP G GKT +AK
Sbjct: 4 ILLVGPNGVGKTTTIAK 20
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 28.6 bits (65), Expect = 1.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 59 GPPGTGKTMLAKAVAIVYN 77
GPPG+GKT +A+ +A
Sbjct: 7 GPPGSGKTTVARLLAEKLG 25
>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 = 28.4 bits (64), Expect = 1.8
Identities = 30/104 (28%), Positives = 41/104 (39%), Gaps = 29/104 (27%)
Query: 55 VLMVGPPGTGKTMLAKAVA---------IVYNQVHCGASNFPWNIDDAFLRRLEKRIYVP 105
V +VGP G+GK+ L +A+A I+ + +I L L +RI
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGK---------DIAKLPLEELRRRIGY- 77
Query: 106 LPSSSG----RQELLRLILRQVDLA------SDLDLELVSDQLE 139
+P SG R L R +L DL S LD LE
Sbjct: 78 VPQLSGGQRQRVALARALLLNPDLLLLDEPTSGLDPASRERLLE 121
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.9 bits (65), Expect = 1.9
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCG 82
++++GP G GKT L A+A+ Y V G
Sbjct: 105 IVLLGPSGVGKTHL--AIALGYEAVRAG 130
>gnl|CDD|224080 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 29.2 bits (66), Expect = 1.9
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 56 LMVGPPGTGKTMLAK--AVAIVYNQVHC 81
L+V PP GKT L + A AI N C
Sbjct: 177 LIVAPPKAGKTTLLQNIANAITTNHPEC 204
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 29.0 bits (65), Expect = 2.0
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 53 KGVLMVGPPGTGKTMLAKAVAIVYNQVH 80
K V++ G PGTGKT + +A+ + ++
Sbjct: 339 KVVILTGGPGTGKTTITRAIIELAEELG 366
>gnl|CDD|223996 COG1070, XylB, Sugar (pentulose and hexulose) kinases [Carbohydrate
transport and metabolism].
Length = 502
Score = 28.9 bits (65), Expect = 2.1
Identities = 18/65 (27%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 106 LPSSSGRQELLRLILRQVDLASDLDLELVSDQLEGYSASDIVVV---CRDAAFMAMRAAI 162
L R L R +L V A LE + + L G S + VV R ++ + A
Sbjct: 366 LTLPHTRAHLARAVLEGVAFALADGLEALEE-LGGKPPSRVRVVGGGARSPLWLQILADA 424
Query: 163 RGKSV 167
G V
Sbjct: 425 LGLPV 429
>gnl|CDD|188169 TIGR01829, AcAcCoA_reduct, acetoacetyl-CoA reductase. This model
represent acetoacetyl-CoA reductase, a member of the
family short-chain-alcohol dehydrogenases. Note that,
despite the precision implied by the enzyme name, the
reaction of EC 1.1.1.36 is defined more generally as
(R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH.
Members of this family may act in the biosynthesis of
poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and
related poly-beta-hydroxyalkanoates. Note that the
member of this family from Azospirillum brasilense,
designated NodG, appears to lack acetoacetyl-CoA
reductase activity and to act instead in the production
of nodulation factor. This family is downgraded to
subfamily for this NodG. Other proteins designated NodG,
as from Rhizobium, belong to related but distinct
protein families.
Length = 242
Score = 28.5 bits (64), Expect = 2.1
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 11/42 (26%)
Query: 140 GYSASDIVVVCRDAAFMAMRAAIRGKSVPQIQAIPMAQLKRP 181
GY A+D+V MAMR + V Q IP+ +L RP
Sbjct: 181 GYIATDMV--------MAMREDVLNSIVAQ---IPVGRLGRP 211
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including 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 = 202
Score = 28.4 bits (64), Expect = 2.1
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 50 KPWKGVLMVGPPGTGKTMLAKAVA 73
KP + VL++G PG+G + L KA+A
Sbjct: 31 KPGEMVLVLGRPGSGCSTLLKALA 54
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 28.4 bits (64), Expect = 2.2
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
V + GPPG GK+ LA+ +
Sbjct: 36 VGIAGPPGAGKSTLAEFLE 54
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 26.9 bits (60), Expect = 2.3
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 46 QHIRKPWKGVLMVGPPGTGKTMLAKAVA 73
+ ++ G PGTGKT A A+
Sbjct: 4 EAAASGRSLFVVDGGPGTGKTATAAAII 31
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 29.0 bits (65), Expect = 2.3
Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 7 RDIIVERPDVQWSDIAN-QVKAKKLLQEAVILPLEKPSYFQHI------RKPWKGVLMVG 59
+ + + I + K +K E +L L + + Q + + +L++G
Sbjct: 171 LEEVPLASQ-RSKRIFDLNTKGEKRFDEEFLLELTQSADDQDALPGLEALEKYAKLLILG 229
Query: 60 PPGTGKTMLAKAVAIVYNQ 78
PG+GKT + +A+ Q
Sbjct: 230 APGSGKTTFLQRLALWLAQ 248
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 28.8 bits (65), Expect = 2.3
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 50 KPWKGVLMVGPPGTGKTMLAKAVA 73
KP L VGP G GKT LAK +A
Sbjct: 481 KPVGSFLFVGPTGVGKTELAKQLA 504
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 28.8 bits (65), Expect = 2.4
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+ G G GKT L +A+A
Sbjct: 422 LLITGESGAGKTSLLRALA 440
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 28.2 bits (63), Expect = 2.5
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 59 GPPGTGKTMLAKAVAIVYNQVHCGA 83
GPPG+GKT +AK +A + A
Sbjct: 7 GPPGSGKTTVAKILAEKLSLKLISA 31
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 28.8 bits (65), Expect = 2.5
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 2/18 (11%)
Query: 51 PWKGVLMVGPPGTGKTML 68
PW L++GPPG+GKT L
Sbjct: 112 PW--YLVIGPPGSGKTTL 127
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 28.5 bits (63), Expect = 2.6
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
K +++ GPPG GKT +A+ +A
Sbjct: 195 KNIILQGPPGVGKTFVARRLA 215
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 28.6 bits (64), Expect = 2.7
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 13/60 (21%)
Query: 13 RPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAV 72
RP +S+I Q +A K L V P + QHI ++ GPPG GKT A+
Sbjct: 149 RPR-AFSEIVGQERAIKALLAKVASP-----FPQHI-------ILYGPPGVGKTTAARLA 195
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 28.4 bits (64), Expect = 2.7
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 56 LMVGPPGTGKTMLAKAV 72
L PGTGKT +AKA+
Sbjct: 47 LHSPSPGTGKTTVAKAL 63
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 28.6 bits (64), Expect = 2.8
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 56 LMVGPPGTGKTMLAKAVAIVYNQVH 80
L GP GTGKT +AK A N H
Sbjct: 44 LFSGPRGTGKTSVAKIFANALNCSH 68
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 28.0 bits (63), Expect = 2.8
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 56 LMVGPPGTGKTMLAKAVA 73
L GP G GK +LA A+A
Sbjct: 18 LFAGPEGVGKELLALALA 35
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 28.4 bits (64), Expect = 2.8
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 55 VLMVGPPGTGKTMLAKAV 72
V + G GTGKT + K V
Sbjct: 43 VFIYGKTGTGKTAVTKYV 60
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.4 bits (61), Expect = 2.9
Identities = 24/126 (19%), Positives = 47/126 (37%), Gaps = 16/126 (12%)
Query: 55 VLMVGPPGTGKTMLAKAVA----IVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSS 110
+L+ G PG+GKT LAK +A V + + +D+ ++
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLA-KENGLVLELDEEITDESKRLDE------D 53
Query: 111 GRQELLRLILRQVDLASDLDLELVSDQLEGYSASD-----IVVVCRDAAFMAMRAAIRGK 165
+LL + + ++ ++ + ++ L VV+ D + R RG
Sbjct: 54 KLAKLLDKLEKIIEELAEGENVIIDGHLAELELERFKDLVFVVLRADPEELLERLKKRGY 113
Query: 166 SVPQIQ 171
S +I
Sbjct: 114 SEEKIS 119
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 27.9 bits (63), Expect = 2.9
Identities = 6/17 (35%), Positives = 11/17 (64%)
Query: 57 MVGPPGTGKTMLAKAVA 73
++G G GKT + + +A
Sbjct: 4 LIGMMGAGKTTVGRLLA 20
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 28.3 bits (64), Expect = 3.1
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL+VG PGT K+ L K VA
Sbjct: 60 VLLVGDPGTAKSQLLKYVA 78
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 27.6 bits (62), Expect = 3.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
L+ G PGTGK+ LA +A
Sbjct: 36 TLLAGAPGTGKSTLALDLAA 55
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 28.3 bits (64), Expect = 3.1
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 56 LMVGPPGTGKTMLAKAVAI 74
L GPPGTGKT A A+A
Sbjct: 42 LFAGPPGTGKTTAALALAR 60
>gnl|CDD|200445 cd11289, gelsolin_S2_like, Gelsolin sub-domain 2-like domain found
in gelsolin, severin, villin, and related proteins.
Gelsolin repeats occur in gelsolin, severin, villin,
advillin, villidin, supervillin, flightless, quail,
fragmin, and other proteins, usually in several copies.
They co-occur with villin headpiece domains,
leucine-rich repeats, and several other domains. These
gelsolin-related actin binding proteins (GRABPs) play
regulatory roles in the assembly and disassembly of
actin filaments; they are involved in F-actin capping,
uncapping, severing, or the nucleation of actin
filaments. Severing of actin filaments is Ca2+
dependent. Villins are also linked to generating bundles
of F-actin with uniform filament polarity, which is most
likely mediated by their extra villin headpiece domain.
Many family members have also adopted functions in the
nucleus, including the regulation of transcription.
Supervillin, gelsolin, and flightless I are involved in
intracellular signaling via nuclear hormone receptors.
The gelsolin-like domain is distantly related to the
actin depolymerizing domains found in cofilin and
similar proteins.
Length = 92
Score = 26.8 bits (60), Expect = 3.1
Identities = 14/52 (26%), Positives = 20/52 (38%), Gaps = 6/52 (11%)
Query: 78 QVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQELLRLILRQVDLASDL 129
+V S+ N D F+ L IY S S R E + + LA +
Sbjct: 17 EVELSWSSL--NSGDVFILDLGSTIYQWNGSKSNRFE----KAKAMQLAQGI 62
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 28.2 bits (63), Expect = 3.3
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+L+VGP G+GK+ L K +A
Sbjct: 4 MLIVGPSGSGKSTLLKLLA 22
>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 = 28.3 bits (63), Expect = 3.5
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 44 YFQHIRKPW-----KGVLMVGPPGTGKTMLAKAVAIVYN 77
+++HI + K V ++G TGK+ L +A V+N
Sbjct: 149 HWKHIPREVRPFFVKTVAILGGESTGKSTLVNKLAAVFN 187
>gnl|CDD|185049 PRK15093, PRK15093, antimicrobial peptide ABC transporter
ATP-binding protein; Provisional.
Length = 330
Score = 28.2 bits (63), Expect = 3.5
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 15/52 (28%)
Query: 57 MVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNI-------DDAFLRRLEKR 101
+VG G+GK+++AKA+ CG + W + DD L RL R
Sbjct: 38 LVGESGSGKSLIAKAI--------CGVTKDNWRVTADRMRFDDIDLLRLSPR 81
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 28.4 bits (64), Expect = 3.5
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 53 KGVLMVGPPGTGKTMLAKAVA 73
K +LM+GP G GKT +A+ +A
Sbjct: 51 KNILMIGPTGVGKTEIARRLA 71
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea.
Length = 187
Score = 27.7 bits (62), Expect = 3.9
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 55 VLMVGPPGTGKTMLA 69
L+ G PGTGKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 27.8 bits (62), Expect = 3.9
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
V + GP GTGKT LA VA
Sbjct: 24 VHLRGPAGTGKTTLAMHVA 42
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 27.8 bits (62), Expect = 3.9
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
VL+ GPPGTGKT+ A
Sbjct: 26 VLITGPPGTGKTIFALQFLY 45
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 27.5 bits (62), Expect = 4.0
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 59 GPPGTGKTMLAKAVA 73
GP G+GK+ +AK +A
Sbjct: 6 GPAGSGKSTVAKLLA 20
>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 = 27.7 bits (62), Expect = 4.0
Identities = 15/60 (25%), Positives = 22/60 (36%), Gaps = 17/60 (28%)
Query: 33 EAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKT-MLAKAVAIVYNQVH------CGASN 85
EA+ L L+ GPPGTGKT + + + + + C SN
Sbjct: 8 EAIKKALSSSDIT----------LIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSN 57
>gnl|CDD|234254 TIGR03552, F420_cofC, 2-phospho-L-lactate guanylyltransferase.
Members of this protein family are the CofC enzyme of
coenzyme F420 biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Other].
Length = 195
Score = 27.6 bits (62), Expect = 4.3
Identities = 15/50 (30%), Positives = 20/50 (40%), Gaps = 11/50 (22%)
Query: 105 PLPSSSGRQELLRLILRQVDLASDLDLELVSDQLEGYSASDIVVVCRDAA 154
P+ S R+EL +LR V L G A ++VV D A
Sbjct: 18 PVLSPEEREELALAMLRD-----------VITALRGAGAGAVLVVSPDPA 56
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 27.6 bits (61), Expect = 4.4
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
+L+ GPPG GK+ LA A+ +
Sbjct: 109 LLLFGPPGGGKSHLAAAIGL 128
>gnl|CDD|147898 pfam05989, Chordopox_A35R, Chordopoxvirus A35R protein. This
family consists of several Chordopoxvirus sequences
homologous to the Vaccinia virus A35R protein. The
function of this family is unknown.
Length = 176
Score = 27.3 bits (61), Expect = 4.4
Identities = 13/37 (35%), Positives = 16/37 (43%)
Query: 75 VYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSG 111
VYN G +F N D FL L K+ L +G
Sbjct: 131 VYNLYEKGDYHFIINPSDNFLMFLSKKSNFCLTDGNG 167
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 27.6 bits (62), Expect = 4.4
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 57 MVGPPGTGKTMLAKAVA 73
++G G GK+ + +A+A
Sbjct: 7 LIGFMGAGKSTIGRALA 23
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 27.7 bits (62), Expect = 4.5
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 55 VLMVGPPGTGKTMLAKAVAI 74
V + G GTGKT+LA A +
Sbjct: 248 VSLGGKAGTGKTLLALAAGL 267
>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 = 27.2 bits (61), Expect = 4.7
Identities = 7/19 (36%), Positives = 15/19 (78%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
++++G G+GK+ + KA+A
Sbjct: 2 IVVMGVSGSGKSTVGKALA 20
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 28.0 bits (62), Expect = 4.8
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 57 MVGPPGTGKTMLAKAVA 73
+VGPPG GKT L +++A
Sbjct: 354 LVGPPGVGKTSLGQSIA 370
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 28.2 bits (62), Expect = 4.8
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 18/82 (21%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQE 114
V +VGPPGTGK+ L +++ + + ID+ I P+ SG+
Sbjct: 72 VAVVGPPGTGKSTLIRSLVRRFTK---------QTIDE---------IRGPITVVSGKTR 113
Query: 115 LLRLILRQVDLASDLDLELVSD 136
+ + DL +D+ ++D
Sbjct: 114 RITFLECPSDLHQMIDVAKIAD 135
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter
reaction uses inorganic phosphate as substrate and
produces pyrophosphate. Phosphoenolpyruvate
carboxykinase (PEPCK) and the C-terminal catalytic
domain of HprK/P are structurally similar with
conserved active site residues suggesting these two
phosphotransferases have related functions. The HprK/P
N-terminal domain is structurally similar to the
N-terminal domains of the MurE and MurF amino acid
ligases.
Length = 149
Score = 27.2 bits (61), Expect = 4.9
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 53 KGVLMVGPPGTGKTMLA 69
GVL+ GP G GK+ LA
Sbjct: 15 IGVLITGPSGIGKSELA 31
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 27.7 bits (62), Expect = 4.9
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
VL++G GTGK + A+ +
Sbjct: 104 VLIIGETGTGKELFARLIH 122
>gnl|CDD|233026 TIGR00564, trpE_most, anthranilate synthase component I,
non-proteobacterial lineages. This enzyme resembles
some other chorismate-binding enzymes, including
para-aminobenzoate synthase (pabB) and isochorismate
synthase. There is a fairly deep split between two sets,
seen in the pattern of gaps as well as in amino acid
sequence differences. Archaeal enzymes have been
excluded from this model (and are now found in
TIGR01820) as have a clade of enzymes which constitute a
TrpE paralog which may have PabB activity (TIGR01824).
This allows the B. subtilus paralog which has been shown
to have PabB activity to score below trusted to this
model. This model contains sequences from gram-positive
bacteria, certain proteobacteria, cyanobacteria, plants,
fungi and assorted other bacteria.A second family of
TrpE enzymes is modelled by TIGR00565. The breaking of
the TrpE family into these diverse models allows for the
separation of the models for the related enzyme, PabB
[Amino acid biosynthesis, Aromatic amino acid family].
Length = 454
Score = 27.7 bits (62), Expect = 5.2
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 152 DAAFMAMRAAIRGKSVPQIQAIPMAQL--KRPVTKADFEMAIAKCRKTVTAADIRQ 205
DA A+ A ++ +P++ A L K ++E +AK ++ + A DI Q
Sbjct: 158 DARLEALVADLQDPLLPEVPVPYPAALSFTSNYEKEEYEANVAKAKEYIKAGDIFQ 213
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 27.7 bits (62), Expect = 5.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLMVGPPGTGKTMLAKAVA 73
+++ GP GTGKT K V
Sbjct: 45 IIIYGPTGTGKTATVKFVM 63
>gnl|CDD|236769 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR;
Provisional.
Length = 520
Score = 27.7 bits (62), Expect = 5.7
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 56 LMVGPPGTGKTMLAKAV 72
L+ G GTGK +LA A
Sbjct: 231 LITGDTGTGKDLLAYAC 247
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 27.6 bits (62), Expect = 6.2
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 49 RKPWKGVLMVGPPGTGKTMLAKAVA 73
+P L +GP G GKT LAKA+A
Sbjct: 592 NRPIGSFLFLGPTGVGKTELAKALA 616
>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 = 27.3 bits (61), Expect = 6.2
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 55 VLMVGPPGTGKTMLAKA 71
V++VGPPG GK+ L ++
Sbjct: 42 VVVVGPPGVGKSTLIRS 58
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 27.2 bits (61), Expect = 6.3
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 55 VLMVGPPGTGKTMLAK 70
VL+ G PGTGKT+
Sbjct: 22 VLITGGPGTGKTIFGL 37
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 27.1 bits (60), Expect = 6.3
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 54 GVLMVGPPGTGKTMLAKAVAIVYNQVHCGASN-FPWNIDDA 93
++ +GPPG+GK +AK ++ N H + F NI ++
Sbjct: 2 KLVFLGPPGSGKGTIAKILSNELNYYHISTGDLFRENILNS 42
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 27.6 bits (61), Expect = 7.0
Identities = 16/61 (26%), Positives = 22/61 (36%), Gaps = 14/61 (22%)
Query: 18 WSDIANQVKAKKLLQEAVILPLE----------KPSYFQHIRKPWKGVLMVGPPGTGKTM 67
IA +L E V+L E S+ + + GPPG+GK M
Sbjct: 1454 NGSIA----GFELRGERVMLRKEVVIPTSDTGFVDSFSNEALNTLRSYIYCGPPGSGKEM 1509
Query: 68 L 68
L
Sbjct: 1510 L 1510
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 27.4 bits (61), Expect = 7.0
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 7 RDIIVERPDVQWSDIANQVKAKKLLQEAVIL--PLEKPSYFQHI---RKPWKGVLMVGPP 61
+++ E P+V+ + + E V P +KP + I +P + V +VGP
Sbjct: 306 FELLDEEPEVEDPPDPLKDTIGSIEFENVSFSYPGKKPVL-KDISFSIEPGEKVAIVGPS 364
Query: 62 GTGKTMLAK 70
G+GK+ L K
Sbjct: 365 GSGKSTLIK 373
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 27.3 bits (61), Expect = 7.2
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 4/51 (7%)
Query: 22 ANQVKA-KKLLQEAVILPLEKPSYFQHIRK---PWKGVLMVGPPGTGKTML 68
A +L E V + + + P +G+ + G G GKTML
Sbjct: 31 PAAAAALDRLYDELVAPRSARKALGWLFGRDHGPVRGLYLWGGVGRGKTML 81
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.7 bits (59), Expect = 7.5
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 40 EKPSYFQ-----HIRKPWKGVLMVGPPGTGKTMLA 69
E +Q + + V++ P G+GKT+ A
Sbjct: 7 EPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAA 41
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 26.8 bits (60), Expect = 7.5
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 57 MVGPPGTGKTMLA 69
+ G G+GKT L
Sbjct: 24 IFGEFGSGKTQLC 36
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 26.8 bits (60), Expect = 7.9
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 57 MVGPPGTGKTMLA 69
+ G G+GKT L
Sbjct: 24 IFGEFGSGKTQLC 36
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 26.9 bits (60), Expect = 8.0
Identities = 21/84 (25%), Positives = 34/84 (40%), Gaps = 16/84 (19%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQE 114
V +VG G GKT LAK +YN DD+ + +V + +
Sbjct: 22 VGIVGMGGVGKTTLAKQ---IYN-------------DDSVGGHFDSVAWVVVSKTYTEFR 65
Query: 115 LLRLILRQVDLASDLDLELVSDQL 138
L + IL+++ L +E +L
Sbjct: 66 LQKDILQELGLDDSDWVEKNESEL 89
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 27.0 bits (60), Expect = 8.1
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 13/60 (21%)
Query: 13 RPDVQWSDIANQVKAKKLLQEAVILPLEKPSYFQHIRKPWKGVLMVGPPGTGKTMLAKAV 72
RP + +I Q + K L+ A+ P P QH V++ GPPG GKT A+ V
Sbjct: 60 RPK-SFDEIIGQEEGIKALKAALCGP--NP---QH-------VIIYGPPGVGKTAAARLV 106
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 26.9 bits (60), Expect = 8.2
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 54 GVLMVGPPGTGKTMLA 69
GVL+ GP G GK+ LA
Sbjct: 147 GVLITGPSGAGKSELA 162
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 26.5 bits (59), Expect = 8.4
Identities = 20/99 (20%), Positives = 37/99 (37%), Gaps = 18/99 (18%)
Query: 59 GPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQELLRL 118
G PG+GKT +A+ +A A R + + + L +E R
Sbjct: 7 GLPGSGKTTVARELAEHLGLKLVSAGT--------IFREMARERGMSL------EEFSRY 52
Query: 119 ILRQVDLASDLDLELVSDQLEGYSASDIVVVCRDAAFMA 157
+ ++D E+ Q E ++V+ R A ++
Sbjct: 53 ----AEEDPEIDKEIDRRQKELAKEGNVVLEGRLAGWIV 87
>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 = 26.5 bits (59), Expect = 8.6
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 20/87 (22%)
Query: 55 VLMVGPPGTGKTMLAKAVA-IVYNQVHCGASNFPWNIDDAFLRRLEKRIYVPLPSSSGRQ 113
V + GP G+GKT AK ++ + ++DD ++ R R +
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGP---VVISLDDYYVPRKTPR---DEDGNY--- 52
Query: 114 ELLRLILRQVDLASDLDLELVSDQLEG 140
D S LDL+L++ L
Sbjct: 53 ----------DFESILDLDLLNKNLHD 69
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 26.5 bits (59), Expect = 8.9
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 55 VLMVGPPGTGKTMLAKAVAIV-YNQVHCG 82
+ + G PG GKT + K + + Y +
Sbjct: 3 IAITGTPGVGKTTVCKLLRELGYKVIELN 31
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 27.1 bits (60), Expect = 8.9
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 59 GPPGTGKTMLAKAVAIVYN 77
GP G GKT +AK A N
Sbjct: 45 GPRGIGKTSIAKIFAKAIN 63
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 27.0 bits (60), Expect = 9.2
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 48 IRKPWKG--VLMVGPPGTGKTMLAKAVA 73
IR+P + VL+ G G GK++LA A+A
Sbjct: 249 IRRPPRPLHVLIGGVSGVGKSVLASALA 276
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 26.8 bits (59), Expect = 9.3
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 55 VLMVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWN--IDDAFLRR-LEKRIYVPLPSSSG 111
V++VG GTGK++L + N P+N A L+ LEK PL +G
Sbjct: 36 VMLVGNAGTGKSVLVGDKLASLDPDAYLVKNVPFNYYTTSAMLQAVLEK----PLEKKAG 91
Query: 112 R 112
R
Sbjct: 92 R 92
>gnl|CDD|107248 cd01391, Periplasmic_Binding_Protein_Type_1, Type 1 periplasmic
binding fold superfamily. Type 1 periplasmic binding
fold superfamily. This model and hierarchy represent the
ligand binding domains of the LacI family of
transcriptional regulators, periplasmic binding proteins
of the ABC-type transport systems, the family C
G-protein couples receptors (GPCRs), membrane bound
guanylyl cyclases including the family of natriuretic
peptide receptors (NPRs), and the N-terminal
leucine/isoleucine/valine- binding protein (LIVBP)-like
domains of the ionotropic glutamate receptors (iGluRs).
In LacI-like transcriptional regulator and the bacterial
periplasmic binding proteins the ligands are
monosaccharides including lactose, ribose, fructose,
xylose, arabinose, galactose/glucose, and other sugars,
with a few exceptions. Periplasmic sugar binding
proteins are one of the components of ABC transporters
and are involved in the active transport of
water-soluble ligands. The LacI family of proteins
consists of transcriptional regulators related to the
lac repressor. In this case, the sugar binding domain
binds a sugar which changes the DNA binding activity of
the repressor domain. The periplasmic binding proteins
are the primary receptors for chemotaxis and transport
of many sugar based solutes. The core structures of
periplasmic binding proteins are classified into two
types, and they differ in number and order of beta
strands: type 1 has six beta strands, while type 2 has
five beta strands per sub-domain. These two structural
folds are thought to be distantly related via a common
ancestor. Notably, while the N-terminal LIVBP-like
domain of iGluRs belongs to the type 1
periplasmic-binding fold protein superfamily, the
glutamate-binding domain of the iGluR is structurally
similar to the type 2 periplasmic-binding fold.
Length = 269
Score = 26.8 bits (59), Expect = 9.4
Identities = 15/87 (17%), Positives = 30/87 (34%), Gaps = 15/87 (17%)
Query: 92 DAFLRRLEKRIYV----PLPSSSGRQELLRLILRQ----------VDLASDLDLELVSDQ 137
+ + KR+ + R E + L++ DL ++ + +
Sbjct: 117 EYLAEKGWKRVALIYGDDGAYGRERLEGFKAALKKAGIEVVAIEYGDLDTEKGFQALLQL 176
Query: 138 LEGYSASDIVVVCRDA-AFMAMRAAIR 163
L+ D + C D A A++AA
Sbjct: 177 LKAAPKPDAIFACNDEMAAGALKAARE 203
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair, Transport and binding proteins,
Other].
Length = 708
Score = 27.0 bits (60), Expect = 9.6
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 57 MVGPPGTGKTMLAKAVAIVYNQVHCGASNFPWNIDDAFLRRLEKRI-YVP 105
+VG G+GK+ LAK + + +++ D L + I Y+P
Sbjct: 505 IVGMSGSGKSTLAKLLVGFFQARSGEILLNGFSLKDIDRHTLRQFINYLP 554
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 26.8 bits (60), Expect = 9.7
Identities = 12/21 (57%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 56 LMVGPPGTGKT----MLAKAV 72
L GP GTGKT + AKAV
Sbjct: 42 LFSGPRGTGKTSAAKIFAKAV 62
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 26.4 bits (59), Expect = 9.9
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 50 KPWKGVLMVGPPGTGKTMLAKAVA 73
+P + + ++GP G+GK+ LA+ +
Sbjct: 26 EPGESLAIIGPSGSGKSTLARLIL 49
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
0.322 0.135 0.398
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,517,395
Number of extensions: 1112478
Number of successful extensions: 1996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1973
Number of HSP's successfully gapped: 261
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.4 bits)